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Zhang L, Dai W, Rong S, Schwaneberg U, Xu G, Ni Y. Engineering diaryl alcohol dehydrogenase KpADH reveals importance of retaining hydration shell in organic solvent tolerance. Protein Sci 2024; 33:e4933. [PMID: 38501647 PMCID: PMC10949390 DOI: 10.1002/pro.4933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/27/2024] [Accepted: 02/01/2024] [Indexed: 03/20/2024]
Abstract
Alcohol dehydrogenases (ADHs) are synthetically important biocatalysts for the asymmetric synthesis of chiral alcohols. The catalytic performance of ADHs in the presence of organic solvents is often important since most prochiral ketones are highly hydrophobic. Here, the organic solvent tolerance of KpADH from Kluyveromyces polyspora was semi-rationally evolved. Using tolerant variants obtained, meticulous experiments and computational studies were conducted to explore properties including stability, activity and kinetics in the presence of various organic solvents. Compared with WT, variant V231D exhibited 1.9-fold improvement in ethanol tolerance, while S237G showed a 6-fold increase in catalytic efficiency, a higherT 50 15 $$ {\mathrm{T}}_{50}^{15} $$ , as well as 15% higher tolerance in 7.5% (v/v) ethanol. Based on 3 × 100 ns MD simulations, the increased tolerance of V231D and S237G against ethanol may be ascribed to their enhanced ability in retaining water molecules and repelling ethanol molecules. Moreover, 6.3-fold decreased KM value of V231D toward hydrophilic ketone substrate confirmed its capability of retaining hydration shell. Our results suggest that retaining hydration shell surrounding KpADH is critical for its tolerance to organic solvents, as well as catalytic performance. This study provides useful guidance for engineering organic solvent tolerance of KpADH and other ADHs.
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Affiliation(s)
- Lu Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of EducationSchool of Biotechnology, Jiangnan UniversityWuxiChina
| | - Wei Dai
- Key Laboratory of Industrial Biotechnology, Ministry of EducationSchool of Biotechnology, Jiangnan UniversityWuxiChina
| | - Shuo Rong
- Key Laboratory of Industrial Biotechnology, Ministry of EducationSchool of Biotechnology, Jiangnan UniversityWuxiChina
| | | | - Guochao Xu
- Key Laboratory of Industrial Biotechnology, Ministry of EducationSchool of Biotechnology, Jiangnan UniversityWuxiChina
| | - Ye Ni
- Key Laboratory of Industrial Biotechnology, Ministry of EducationSchool of Biotechnology, Jiangnan UniversityWuxiChina
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2
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Dai C, Cao HX, Tian JX, Gao YC, Liu HT, Xu SY, Wang YJ, Zheng YG. Structural-guided design to improve the catalytic performance of aldo-keto reductase KdAKR. Biotechnol Bioeng 2023; 120:3543-3556. [PMID: 37641876 DOI: 10.1002/bit.28535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 08/07/2023] [Accepted: 08/13/2023] [Indexed: 08/31/2023]
Abstract
Aldo-keto reductases (AKRs) are important biocatalysts that can be used to synthesize chiral pharmaceutical alcohols. In this study, the catalytic activity and stereoselectivity of a NADPH-dependent AKR from Kluyveromyces dobzhanskii (KdAKR) toward t-butyl 6-chloro (5S)-hydroxy-3-oxohexanoate ((5S)-CHOH) were improved by mutating its residues in the loop regions around the substrate-binding pocket. And the thermostability of KdAKR was improved by a consensus sequence method targeted on the flexible regions. The best mutant M6 (Y28A/L58I/I63L/G223P/Y296W/W297H) exhibited a 67-fold higher catalytic efficiency compared to the wild-type (WT) KdAKR, and improved R-selectivity toward (5S)-CHOH (dep value from 47.6% to >99.5%). Moreover, M6 exhibited a 6.3-fold increase in half-life (t1/2 ) at 40°C compared to WT. Under the optimal conditions, M6 completely converted 200 g/L (5S)-CHOH to diastereomeric pure t-butyl 6-chloro-(3R, 5S)-dihydroxyhexanoate ((3R, 5S)-CDHH) within 8.0 h, with a space-time yield of 300.7 g/L/day. Our results deepen the understandings of the structure-function relationship of AKRs, providing a certain guidance for the modification of other AKRs.
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Affiliation(s)
- Chen Dai
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Hai-Xing Cao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Jia-Xin Tian
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Yan-Chi Gao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Hua-Tao Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Shen-Yuan Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Ya-Jun Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, People's Republic of China
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Sardauna AE, Abdulrasheed M, Nzila A, Musa MM. Biocatalytic asymmetric reduction of prochiral bulky-bulky ketones. MOLECULAR CATALYSIS 2023. [DOI: 10.1016/j.mcat.2023.113099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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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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Kozaeva E, Mol V, Nikel PI, Nielsen AT. High-throughput colorimetric assays optimized for detection of ketones and aldehydes produced by microbial cell factories. Microb Biotechnol 2022; 15:2426-2438. [PMID: 35689383 PMCID: PMC9437884 DOI: 10.1111/1751-7915.14097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/19/2022] [Indexed: 11/29/2022] Open
Abstract
Randomized strain and pathway engineering are critical to improving microbial cell factory performance, calling for the development of high‐throughput screening and selection systems. To facilitate this effort, we have developed two 96‐well plate format colorimetric assays for reliable quantification of various ketones and aldehydes from culture supernatants, based on either a vanillin‐acetone reaction or the 2,4‐dinitrophenylhydrazine (2,4‐DNPH) reagent. The vanillin‐acetone assay enabled accurate and selective measurement of acetone titers up to 2 g l−1 in a minimal culture medium. The 2,4‐DNPH‐based assay can be used for a wide range of aldehydes and ketones, shown here through the optimization of conditions for 15 different compounds. Both assays were implemented to improve acetone production from different substrates by an engineered Escherichia coli strain. The fast and user‐friendly colorimetric assays proposed here open the potential for iterative rounds of (automated) strain and pathway engineering and screening, facilitating the efforts towards further boosting production titers of industrially relevant ketones and aldehydes.
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Affiliation(s)
- Ekaterina Kozaeva
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Viviënne Mol
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
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6
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Zheng T, Zhang Q, Peng Z, Li D, Wu X, Liu Y, Li P, Zhang J, Du G. Metabolite-based cell sorting workflow for identifying microbes producing carbonyls in tobacco leaves. Appl Microbiol Biotechnol 2022; 106:4199-4209. [PMID: 35599257 DOI: 10.1007/s00253-022-11982-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 05/10/2022] [Accepted: 05/13/2022] [Indexed: 11/29/2022]
Abstract
Carbonyl compounds represented by aldehydes and ketones make an important contribution to the flavor of tobacco. Since most carbonyl compounds are produced by microbes during tobacco fermentation, identifying their producers is important to improve the quality of tobacco. Here, we created an efficient workflow that combines metabolite labeling with fluorescence-activated cell sorting (ML-FACS), 16S rRNA gene sequencing, and microbial culture to identify the microbes that produce aldehydes or ketones in fermented cigar tobacco leaves (FCTL). Microbes were labeled with a specific fluorescent dye (cyanine5 hydrazide) and separated by flow cytometry. Subsequently, the sorted microbes were identified and cultured under laboratory conditions. Four genera, Acinetobacter, Sphingomonas, Solibacillus, and Lysinibacillus, were identified as the main carbonyl compound-producing microbes in FCTL. In addition, these microorganisms could produce flavor-related aldehydes and ketones in a simple synthetic medium, such as benzaldehyde, phenylacetaldehyde, 4-hydroxy-3-ethoxy-benzaldehyde, and 3,5,5-trimethyl-2-cyclohexene-1-one. On the whole, this research has developed a new method to quickly isolate and identify microorganisms that produce aldehydes or ketones from complex microbial communities. ML-FACS would also be used to identify other compound-producing microorganisms in other systems. KEY POINTS: • An approach was developed to identify target microbes in complex communities. • Microbes that produce aldehyde/ketone flavor compounds in fermented cigar tobacco leaves were identified. • Functional microbes that produce aldehyde/ketone flavor compounds from the native environment were captured in pure cultures.
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Affiliation(s)
- Tianfei Zheng
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Qianying Zhang
- Cigar Fermentation Technology Key Laboratory of China Tobacco, China Tobacco Sichuan Industrial Co., Ltd, Chengdu, 610000, China
| | - Zheng Peng
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Dongliang Li
- Cigar Fermentation Technology Key Laboratory of China Tobacco, China Tobacco Sichuan Industrial Co., Ltd, Chengdu, 610000, China
| | - Xinying Wu
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Yi Liu
- Cigar Fermentation Technology Key Laboratory of China Tobacco, China Tobacco Sichuan Industrial Co., Ltd, Chengdu, 610000, China
| | - Pinhe Li
- Cigar Fermentation Technology Key Laboratory of China Tobacco, China Tobacco Sichuan Industrial Co., Ltd, Chengdu, 610000, China
| | - Juan Zhang
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
| | - Guocheng Du
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
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Zhang J, Zhou J, Xu G, Ni Y. Stereodivergent evolution of KpADH for the asymmetric reduction of diaryl ketones with para-substituents. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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8
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Zhu HQ, Hu WY, Tang XL, Zheng RC, Zheng YG. High-throughput assay of tyrosine phenol-lyase activity using a cascade of enzymatic reactions. Anal Biochem 2022; 640:114547. [PMID: 35026146 DOI: 10.1016/j.ab.2022.114547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 12/14/2021] [Accepted: 01/05/2022] [Indexed: 01/17/2023]
Abstract
Tyrosine phenol-lyase (TPL) exhibits great potential in industrial biosynthesis of l-tyrosine and its derivates. To uncover and screen TPLs with excellent catalytic properties, there is unmet demand for development of facile and reliable screening system for TPL. Here we presented a novel assay format for the detection of TPL activity based on catechol 2,3-dioxygenase (C23O)-catalyzed reaction. Catechol released from TPL-catalyzed cleavage of 3,4-dihydroxy-l-phenylalanine (l-DOPA) was further oxidized by C23O to form 2-hydroxymuconate semialdehyde, which could be readily detected by spectrophotometric measurements at 375 nm. The assay achieved a unique balance between the ease of operation and superiority of analytical performances including linearity, sensitivity and accuracy. In addition, this assay enabled real-time monitoring of TPL activity with high efficiency and reliability. As C23O is highly specific towards catechol, a non-natural product of microorganism, the assay was therefore accessible to both crude cell extracts and the whole-cell system without elaborate purification steps of enzymes, which could greatly expedite discovery and engineering of TPLs. This study provided fundamental principle for high-throughput screening of other enzymes consuming or producing catechol derivatives.
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Affiliation(s)
- Hang-Qin Zhu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Wen-Ye Hu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Xiao-Ling Tang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Ren-Chao Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
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Musa MM. Alcohol Dehydrogenases with anti-Prelog Stereopreference in Synthesis of Enantiopure Alcohols. Chemistry 2022; 11:e202100251. [PMID: 35191611 PMCID: PMC8973272 DOI: 10.1002/open.202100251] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 02/03/2022] [Indexed: 01/03/2023]
Abstract
Biocatalytic production of both enantiomers of optically active alcohols with high enantiopurities is of great interest in industry. Alcohol dehydrogenases (ADHs) represent an important class of enzymes that could be used as catalysts to produce optically active alcohols from their corresponding prochiral ketones. This review covers examples of the synthesis of optically active alcohols using ADHs that exhibit anti‐Prelog stereopreference. Both wild‐type and engineered ADHs that exhibit anti‐Prelog stereopreference are highlighted.
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Affiliation(s)
- Musa M Musa
- Department of Chemistry Interdisciplinary Research Center for Refining and Advanced Chemicals, King Fahd University of Petroleum and Minerals, Dhahran, 31261, Saudi Arabia
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10
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Semi-Rational Design of Proteus mirabilis l-Amino Acid Deaminase for Expanding Its Substrate Specificity in α-Keto Acid Synthesis from l-Amino Acids. Catalysts 2022. [DOI: 10.3390/catal12020175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
l-amino acid deaminases (LAADs) are flavoenzymes that catalyze the stereospecific oxidative deamination of l-amino acids into α-keto acids, which are widely used in the pharmaceutical, food, chemical, and cosmetic industries. However, the substrate specificity of available LAADs is limited, and most substrates are concentrated on several bulky or basic l-amino acids. In this study, we employed a LAAD from Proteus mirabilis (PmiLAAD) and broadened its substrate specificity using a semi-rational design strategy. Molecular docking and alanine scanning identified F96, Q278, and E417 as key residues around the substrate-binding pocket of PmiLAAD. Site-directed saturation mutagenesis identified E417 as the key site for substrate specificity expansion. Expansion of the substrate channel with mutations of E417 (E417L, E417A) improved activity toward the bulky substrate l-Trp, and mutation of E417 to basic amino acids (E417K, E417H, E417R) enhanced the universal activity toward various l-amino acid substrates. The variant PmiLAADE417K showed remarkable catalytic activity improvement on seven substrates (l-Ala, l-Asp, l-Ile, l-Leu, l-Phe, l-Trp, and l-Val). The catalytic efficiency improvement obtained by E417 mutation may be attributed to the expansion of the entrance channel and its electrostatic interactions. These PmiLAAD variants with a broadened substrate spectrum can extend the application potential of LAADs.
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11
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Ni ZF, Xu P, Zong MH, Lou WY. Structure-guided protein engineering of ammonia lyase for efficient synthesis of sterically bulky unnatural amino acids. BIORESOUR BIOPROCESS 2021; 8:103. [PMID: 38650190 PMCID: PMC10992142 DOI: 10.1186/s40643-021-00456-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/08/2021] [Indexed: 11/10/2022] Open
Abstract
Enzymatic asymmetric amination addition is seen as a promising approach for synthesizing amine derivatives, especially unnatural amino acids, which are valuable precursors to fine chemicals and drugs. Despite the broad substrate spectrum of methylaspartate lyase (MAL), some bulky substrates, such as caffeic acid, cannot be effectively accepted. Herein, we report a group of variants structurally derived from Escherichia coli O157:H7 MAL (EcMAL). A combined mutagenesis strategy was used to simultaneously redesign the key residues of the entrance tunnel and binding pocket to explore the possibility of accepting bulky substrates with potential application to chiral drug synthesis. Libraries of residues capable of lining the active center of EcMAL were then constructed and screened by an effective activity solid-phase color screening method using tyrosinase as a cascade catalyst system. Activity assays and molecular dynamics studies of the resultant variants showed that the substrate specificity of EcMAL was modified by adjusting the polarity of the binding pocket and the degree of flexibility of the entrance tunnel. Compared to M3, the optimal variant M8 was obtained with a 15-fold increase in catalytic activity. This structure-based protein engineering of EcMAL can be used to open new application directions or to develop practical multi-enzymatic processes for the production of various useful compounds.
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Affiliation(s)
- Zi-Fu Ni
- Laboratory of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, No. 381 Wushan Road, Guangzhou, 510640, Guangdong, China
| | - Pei Xu
- Laboratory of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, No. 381 Wushan Road, Guangzhou, 510640, Guangdong, China
| | - Min-Hua Zong
- Laboratory of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, No. 381 Wushan Road, Guangzhou, 510640, Guangdong, China
| | - Wen-Yong Lou
- Laboratory of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, No. 381 Wushan Road, Guangzhou, 510640, Guangdong, China.
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12
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An efficient chitosan-based naphthalimide-modified fluorescent sensor for rapid detection of 2,4-dinitrophenylhydrazine and its applications in environmental analysis. Eur Polym J 2021. [DOI: 10.1016/j.eurpolymj.2021.110705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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13
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Zhou F, Mu X, Nie Y, Xu Y. Enhanced catalytic efficiency and coenzyme affinity of leucine dehydrogenase by comprehensive screening strategy for L-tert-leucine synthesis. Appl Microbiol Biotechnol 2021; 105:3625-3634. [PMID: 33929595 DOI: 10.1007/s00253-021-11323-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/25/2021] [Accepted: 04/26/2021] [Indexed: 11/25/2022]
Abstract
L-tert-leucine (L-Tle) is widely used as vital chiral intermediate for pharmaceuticals and as chiral auxiliarie for organocatalysis. L-Tle is generally prepared via the asymmetric reduction of trimethylpyruvate (TMP) catalyzed by NAD+-dependent leucine dehydrogenase (LeuDH). To improve the catalytic efficiency and coenzyme affinity of LeuDH from Bacillus cereus, mutation libraries constructed by error-prone PCR and iterative saturation mutation were screened by two kinds of high-throughput methods. Compared with the wild type, the affinity of the selected mutant E24V/E116V for TMP and NADH increased by 7.7- and 2.8-fold, respectively. And the kcat/Km of E24V/E116V on TMP was 5.4-fold higher than that of the wild type. A coupled reaction comprising LeuDH with glucose dehydrogenase of Bacillus amyloliquefaciens resulted in substrate inhibition at high TMP concentrations (0.5 M), which was overcome by batch-feeding of the TMP substrate. The total turnover number and specific space-time conversion of 0.57 M substrate increased to 11,400 and 22.8 mmol·h-1·L-1·g-1, respectively. KEY POINTS: • The constructed new high-throughput screening strategy takes into account the two indicators of catalytic efficiency and coenzyme affinity. • A more efficient leucine dehydrogenase (LeuDH) mutant (E24V/E116V) was identified. • E24V/E116V has potential for the industrial synthesis of L-tert-leucine.
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Affiliation(s)
- Feng Zhou
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Xiaoqing Mu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China. .,Suqian Industrial Technology Research Institute of Jiangnan University, Suqian, 223814, China.
| | - Yao Nie
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China. .,Suqian Industrial Technology Research Institute of Jiangnan University, Suqian, 223814, China.
| | - Yan Xu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
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14
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Li Z, Yang H, Liu J, Huang Z, Chen F. Application of Ketoreductase in Asymmetric Synthesis of Pharmaceuticals and Bioactive Molecules: An Update (2018-2020). CHEM REC 2021; 21:1611-1630. [PMID: 33835705 DOI: 10.1002/tcr.202100062] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/01/2021] [Accepted: 04/01/2021] [Indexed: 02/05/2023]
Abstract
With the rapid development of genomic DNA sequencing, recombinant DNA expression, and protein engineering, biocatalysis has been increasingly and widely adopted in the synthesis of pharmaceuticals, bioactive molecules, fine chemicals, and agrochemicals. In this review, we have summarized the most recent advances achieved (2018-2020) in the research area of ketoreductase (KRED)-catalyzed asymmetric synthesis of chiral secondary alcohol intermediates to pharmaceuticals and bioactive molecules. In the first part, synthesis of chiral alcohols with one stereocenter through the bioreduction of four different ketone classes, namely acyclic aliphatic ketones, benzyl or phenylethyl ketones, cyclic aliphatic ketones, and aryl ketones, is discussed. In the second part, KRED-catalyzed dynamic reductive kinetic resolution and reductive desymmetrization are presented for the synthesis of chiral alcohols with two contiguous stereocenters.
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Affiliation(s)
- Zhining Li
- Department of Chemistry, Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai Engineering Research Center of Industrial Asymmetric Catalysis of Chiral Drugs, 220 Handan Road, Shanghai, 200433, P. R. China
| | - Haidi Yang
- Department of Chemistry, Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai Engineering Research Center of Industrial Asymmetric Catalysis of Chiral Drugs, 220 Handan Road, Shanghai, 200433, P. R. China
| | - Jinyao Liu
- Department of Chemistry, Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai Engineering Research Center of Industrial Asymmetric Catalysis of Chiral Drugs, 220 Handan Road, Shanghai, 200433, P. R. China
| | - Zedu Huang
- Department of Chemistry, Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai Engineering Research Center of Industrial Asymmetric Catalysis of Chiral Drugs, 220 Handan Road, Shanghai, 200433, P. R. China
| | - Fener Chen
- Department of Chemistry, Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai Engineering Research Center of Industrial Asymmetric Catalysis of Chiral Drugs, 220 Handan Road, Shanghai, 200433, P. R. China
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15
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Zhou J, Wu Y, Zhang Q, Xu G, Ni Y. Co-immobilized Alcohol Dehydrogenase and Glucose Dehydrogenase with Resin Extraction for Continuous Production of Chiral Diaryl Alcohol. Appl Biochem Biotechnol 2021; 193:2742-2758. [PMID: 33826065 DOI: 10.1007/s12010-021-03561-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
Ni2+-functionalized porous ceramic/agarose composite beads (Ni-NTA Cerose) can be used as carrier materials to immobilize enzymes harboring a metal affinity tag. Here, a 6×His-tag fusion alcohol dehydrogenase Mu-S5 and glucose dehydrogenase from Bacillus megaterium (BmGDH) were co-immobilized on Ni-NTA Cerose to construct a packed bed reactor (PBR) for the continuous synthesis of the chiral intermediate (S)-(4-chlorophenyl)-(pyridin-2-yl) methanol ((S)-CPMA) NADPH recycling, and in situ product adsorption was achieved simultaneously by assembling a D101 macroporous resin column after the PBR. Using an optimum enzyme activity ratio of 2:1 (Mu-S5: BmGDH) and hydroxypropyl-β-cyclodextrin as co-solvent, a space-time yield of 1560 g/(L·d) could be achieved in the first three days at a flow rate of 5 mL/min and substrate concentration of 10 mM. With simplified selective adsorption and extraction procedures, (S)-CPMA was obtained in 84% isolated yield.
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Affiliation(s)
- Jieyu Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Yanfei Wu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Qingye Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Guochao Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Ye Ni
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
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16
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Chen J, Zhu R, Zhou J, Yang T, Zhang X, Xu M, Rao Z. Efficient single whole-cell biotransformation for L-2-aminobutyric acid production through engineering of leucine dehydrogenase combined with expression regulation. BIORESOURCE TECHNOLOGY 2021; 326:124665. [PMID: 33540211 DOI: 10.1016/j.biortech.2021.124665] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 06/12/2023]
Abstract
Leucine dehydrogenase (LDH) is widely used in the preparation of L-2-aminobutyric acid (L-2-ABA), however its wide application is limited by 2-ketobutyric acid (2-OBA) inhibition. Firstly, a novel high-throughput screening method of LDH was established, specific enzyme activity and 2-OBA tolerance of Lys72Ala mutant were 33.3% higher than those of the wild type. Subsequently, we constructed a single cell comprised of ivlA, EsldhK72A, fdh and optimized expression through fine-tuning RBS intensity, so that the yield of E. coli BL21/pET28a-R3ivlA-EsldhK72A-fdh was 2.6 times higher than that of the original strain. As a result, 150 g L-threonine was transformed to 121 g L-2-ABA in 5 L fermenter with 95% molar conversion rate, and a productivity of 5.04 g·L-1·h-1, which is the highest productivity of L-2-ABA currently reported by single-cell biotransformation. In summary, our research provided a green synthesis for L-2-ABA, which has potential for industrial production of drug precursors.
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Affiliation(s)
- Jiajie Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China
| | - Rongshuai Zhu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China
| | - Junping Zhou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China
| | - Taowei Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China.
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17
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Wu Y, Zhou J, Ni J, Zhu C, Sun Z, Xu G, Ni Y. Engineering an Alcohol Dehydrogenase from
Kluyveromyces polyspora
for Efficient Synthesis of Ibrutinib Intermediate. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202001313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yanfei Wu
- Key laboratory of industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University, Wuxi 214122 Jiangsu People's Republic of China
| | - Jieyu Zhou
- Key laboratory of industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University, Wuxi 214122 Jiangsu People's Republic of China
| | - Jie Ni
- Warshel Institute for Computational Biology, School of Life and Health Science Chinese University of Hong Kong Shenzhen), Shenzhen 518172 People's Republic of China
| | - Cheng Zhu
- Key laboratory of industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University, Wuxi 214122 Jiangsu People's Republic of China
| | - Zewen Sun
- Key laboratory of industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University, Wuxi 214122 Jiangsu People's Republic of China
| | - Guochao Xu
- Key laboratory of industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University, Wuxi 214122 Jiangsu People's Republic of China
| | - Ye Ni
- Key laboratory of industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University, Wuxi 214122 Jiangsu People's Republic of China
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18
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Gong L, Xu G, Cao X, Han R, Dong J, Ni Y. High-Throughput Screening Method for Directed Evolution and Characterization of Aldol Activity of D-Threonine Aldolase. Appl Biochem Biotechnol 2020; 193:417-429. [PMID: 33015743 DOI: 10.1007/s12010-020-03447-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/29/2020] [Indexed: 11/28/2022]
Abstract
A rapid and reliable method for the determination of aldol condensation activity of threonine aldolases (TAs) toward aldehydes and glycine was developed. This 2,4-dinitrophenylhydrazine (DNPH) method has high sensitivity and low background disturbance and can be spectrophotometrically measured for high-throughput screening and characterization of TAs. For 4-methylsulfonyl benzaldehyde (MSB), the maximum absorbance peak was observed at around 485 nm. Site-directed saturation mutagenesis libraries of D-threonine aldolase from Alcaligenes xylosoxidans CGMCC 1.4257 (AxDTA) was constructed and screened with this DNPH method for increased aldol activity toward MSB. Two beneficial variants AxDTAD321C and AxDTAN101G were identified. Substrate specificity of AxDTA and variants toward nineteen aldehydes with different substituents was facilely characterized employing this DNPH method. Furthermore, AxDTA variants displayed enhanced catalytic performance and selectivity in aldol reaction. Consequently, our study provides a rapid screening and characterization method for TAs with potential applications in preparation of chiral β-hydroxy-α-amino acids.
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Affiliation(s)
- Lei Gong
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Guochao Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
| | - Xudong Cao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Ruizhi Han
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Jinjun Dong
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Ye Ni
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
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19
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Zhou J, Xu G, Ni Y. Stereochemistry in Asymmetric Reduction of Bulky–Bulky Ketones by Alcohol Dehydrogenases. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02646] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jieyu Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 Jiangsu, China
| | - Guochao Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 Jiangsu, China
| | - Ye Ni
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 Jiangsu, China
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20
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Mei Z, Zhang K, Qu G, Li JK, Liu B, Ma JA, Tu R, Sun Z. High-Throughput Fluorescence Assay for Ketone Detection and Its Applications in Enzyme Mining and Protein Engineering. ACS OMEGA 2020; 5:13588-13594. [PMID: 32566823 PMCID: PMC7301380 DOI: 10.1021/acsomega.0c00245] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 05/21/2020] [Indexed: 06/11/2023]
Abstract
Ketones are of great importance as building blocks in synthetic organic chemistry and biocatalysis. Most ketones cannot easily be quantitatively assayed due to the lack of visible photometric properties. Effective high-throughput assay (HTA) development is therefore necessary for ketone determination. Inspired by previous works of an aldehyde assay based on 2-amino benzamidoxime derivatives, we developed a colorimetric method for rapid a HTA of structurally diverse ketones by using para-methoxy-2-amino benzamidoxime (PMA). This PMA-based method is characterized by high sensitivity manner (μM) with low background, as checked by gas chromatography (GC). It can be used for quantitatively monitoring ketones by fluorescence screening in microtiter plates. Furthermore, this HTA method was employed in mining alcohol dehydrogenases (ADHs), and in directed evolution aimed at enhancing ADH activity in the catalytic transformation of alcohols to ketones. This work provides a general tool for ketone detection in biocatalyst development.
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Affiliation(s)
- Zelong Mei
- College
of Biotechnology, Tianjin University of
Science and Technology, Tianjin 300457, China
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport
Economic Area, Tianjin 300308, China
| | - Kun Zhang
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport
Economic Area, Tianjin 300308, China
| | - Ge Qu
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport
Economic Area, Tianjin 300308, China
| | - Jun-Kuan Li
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport
Economic Area, Tianjin 300308, China
- Department
of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences,
and Tianjin Collaborative Innovation Center of Chemical Science and
Engineering, Tianjin University, Tianjin 300072, China
| | - Baoyan Liu
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport
Economic Area, Tianjin 300308, China
| | - Jun-An Ma
- Department
of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences,
and Tianjin Collaborative Innovation Center of Chemical Science and
Engineering, Tianjin University, Tianjin 300072, China
| | - Ran Tu
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport
Economic Area, Tianjin 300308, China
| | - Zhoutong Sun
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport
Economic Area, Tianjin 300308, China
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21
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Nakano Y, Black MJ, Meichan AJ, Sandoval BA, Chung MM, Biegasiewicz KF, Zhu T, Hyster TK. Photoenzymatic Hydrogenation of Heteroaromatic Olefins Using 'Ene'-Reductases with Photoredox Catalysts. Angew Chem Int Ed Engl 2020; 59:10484-10488. [PMID: 32181943 DOI: 10.1002/anie.202003125] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Indexed: 12/20/2022]
Abstract
Flavin-dependent 'ene'-reductases (EREDs) are highly selective catalysts for the asymmetric reduction of activated alkenes. This function is, however, limited to enones, enoates, and nitroalkenes using the native hydride transfer mechanism. Here we demonstrate that EREDs can reduce vinyl pyridines when irradiated with visible light in the presence of a photoredox catalyst. Experimental evidence suggests the reaction proceeds via a radical mechanism where the vinyl pyridine is reduced to the corresponding neutral benzylic radical in solution. DFT calculations reveal this radical to be "dynamically stable", suggesting it is sufficiently long-lived to diffuse into the enzyme active site for stereoselective hydrogen atom transfer. This reduction mechanism is distinct from the native one, highlighting the opportunity to expand the synthetic capabilities of existing enzyme platforms by exploiting new mechanistic models.
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Affiliation(s)
- Yuji Nakano
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.,Present address: Monash Institute of Pharmaceutical Science, Monash University, Parkville, Victoria, 3052, Australia
| | - Michael J Black
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Andrew J Meichan
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | | | - Megan M Chung
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Kyle F Biegasiewicz
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.,Present address: School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Tianyu Zhu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Todd K Hyster
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
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22
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Nakano Y, Black MJ, Meichan AJ, Sandoval BA, Chung MM, Biegasiewicz KF, Zhu T, Hyster TK. Photoenzymatic Hydrogenation of Heteroaromatic Olefins Using ‘Ene’‐Reductases with Photoredox Catalysts. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003125] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Yuji Nakano
- Department of Chemistry Princeton University Princeton NJ 08544 USA
- Present address: Monash Institute of Pharmaceutical Science Monash University Parkville Victoria 3052 Australia
| | - Michael J. Black
- Department of Chemistry Princeton University Princeton NJ 08544 USA
| | | | | | - Megan M. Chung
- Department of Chemistry Princeton University Princeton NJ 08544 USA
| | - Kyle F. Biegasiewicz
- Department of Chemistry Princeton University Princeton NJ 08544 USA
- Present address: School of Molecular Sciences Arizona State University Tempe AZ 85287 USA
| | - Tianyu Zhu
- Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena CA 91125 USA
| | - Todd K. Hyster
- Department of Chemistry Princeton University Princeton NJ 08544 USA
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23
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Molecular switch manipulating Prelog priority of an alcohol dehydrogenase toward bulky-bulky ketones. MOLECULAR CATALYSIS 2020. [DOI: 10.1016/j.mcat.2019.110741] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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24
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Wen P, Wu D, Zheng P, Chen P, Liu S, Fu Y. Highly Efficient Biosynthesis of Heliotropin by Engineered Escherichia coli Coexpressing Trans-Anethole Oxygenase and Formate Dehydrogenase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:14121-14128. [PMID: 31775508 DOI: 10.1021/acs.jafc.9b05382] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Heliotropin, a compound with important roles in the spice and fragrance industries and broad application prospects, is mainly produced through chemical methods. Here, we established a novel process for the synthesis of heliotropin by Escherichia coli whole cells through biotransformation of isosafrole. Directed evolution and high-throughput screening based on 2,4-dinitrophenylhydrazine were used to improve the activity of trans-anethole oxygenase toward isosafrole, and a mutant (TAO3G2) was obtained that had a high ability to oxidize isosafrole. Formate dehydrogenase (FDH) and TAO3G2 were coexpressed in E. coli, significantly increasing the catalytic efficiency by regenerating more NADH to promote isosafrole oxidation. Furthermore, after optimizing the molar ratio of isosafrole to the auxiliary substrate, the final concentration of heliotropin was increased from 9.15 to 19.45 g/L, and the maximum yield and space-time yield reached 96.02% and 3.89 g/L/h, respectively. These results suggest that the biosynthesis of heliotropin should have excellent industrial application value.
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Affiliation(s)
- Peng Wen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi 214122 , China
| | - Dan Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi 214122 , China
| | - Pu Zheng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi 214122 , China
| | - Pengcheng Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi 214122 , China
| | - Siqin Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi 214122 , China
| | - Yin Fu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi 214122 , China
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25
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Li Z, Wang Z, Wang Y, Wu X, Lu H, Huang Z, Chen F. Substituent Position‐Controlled Stereoselectivity in Enzymatic Reduction of Diaryl‐ and Aryl(heteroaryl)methanones. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201801543] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Zhining Li
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of ChemistryFudan University 220 Handan Road Shanghai 200433 People's Republic of China
- Shanghai Engineering Research Center of Industrial Asymmetric Catalysis of Chiral Drugs 220 Handan Road Shanghai 200433 People's Republic of China
| | - Zexu Wang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of ChemistryFudan University 220 Handan Road Shanghai 200433 People's Republic of China
- Shanghai Engineering Research Center of Industrial Asymmetric Catalysis of Chiral Drugs 220 Handan Road Shanghai 200433 People's Republic of China
| | - Yuhan Wang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of ChemistryFudan University 220 Handan Road Shanghai 200433 People's Republic of China
| | - Xiaofan Wu
- College of Chemical EngineeringFuzhou University 2 Xueyuan Road Fuzhou 350100 People's Republic of China
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan University 2005 Songhu Road Shanghai 200438 People's Republic of China
- Shanghai Engineering Research Center of Industrial Microorganisms 2005 Songhu Road Shanghai 200438 People's Republic of China
| | - Zedu Huang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of ChemistryFudan University 220 Handan Road Shanghai 200433 People's Republic of China
- Shanghai Engineering Research Center of Industrial Asymmetric Catalysis of Chiral Drugs 220 Handan Road Shanghai 200433 People's Republic of China
| | - Fener Chen
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of ChemistryFudan University 220 Handan Road Shanghai 200433 People's Republic of China
- Shanghai Engineering Research Center of Industrial Asymmetric Catalysis of Chiral Drugs 220 Handan Road Shanghai 200433 People's Republic of China
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26
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Zhou J, Wang Y, Xu G, Wu L, Han R, Schwaneberg U, Rao Y, Zhao YL, Zhou J, Ni Y. Structural Insight into Enantioselective Inversion of an Alcohol Dehydrogenase Reveals a "Polar Gate" in Stereorecognition of Diaryl Ketones. J Am Chem Soc 2018; 140:12645-12654. [PMID: 30247889 DOI: 10.1021/jacs.8b08640] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Diaryl ketones are important building blocks for synthesizing pharmaceuticals and are generally regarded as "difficult-to-reduce" ketones due to the large steric hindrance of their two bulky aromatic side chains. Alcohol dehydrogenase from Kluyveromyces polyspora ( KpADH) has been identified as a robust biocatalyst due to its high conversion of diaryl ketone substrate (4-chlorophenyl)(pyridine-2-yl)ketone (CPMK) with a moderate R-selectivity of 82% ee. To modulate the stereoselectivity of KpADH, a "polarity scanning" strategy was proposed, in which six key residues inside and at the entrance of the substrate binding pocket were identified. After iterative combinatorial mutagenesis, variants Mu-R2 and Mu-S5 with enhanced (99.2% ee, R) and inverted (97.8% ee, S) stereoselectivity were obtained. The crystal structures of KpADH and two mutants in complex with NADPH were resolved to elucidate the evolution of enantioselective inversion. Based on MD simulation, Mu-R2-CPMKProR and Mu-S5-CPMKProS were more favorable in the formation of prereaction states. Interestingly, a quadrilateral plane formed by α-carbons of four residues (N136, V161, C237, and G214) was identified at the entrance of the substrate binding pocket of Mu-S5; this plane acts as a "polar gate" for substrates. Due to the discrepancy in charge characteristics between chlorophenyl and pyridine substituents, the pro- S orientation of CPMK is defined when it passes through the "polar gate" in Mu-S5, whereas the similar plane in wild-type is blocked by several aromatic residues. Our result paves the way for engineering stereocomplementary ADH toward bulky diaryl ketones and provides structural insight into the mechanism of stereoselective inversion.
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Affiliation(s)
- Jieyu Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , 214122 Jiangsu , China
| | - Yue Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , 214122 Jiangsu , China
| | - Guochao Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , 214122 Jiangsu , China
| | - Lian Wu
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis , Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , Shanghai 200032 , China
| | - Ruizhi Han
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , 214122 Jiangsu , China
| | - Ulrich Schwaneberg
- Institute of Biotechnology , RWTH Aachen University , Worringerweg 3 , 52074 Aachen , Germany
| | - Yijian Rao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , 214122 Jiangsu , China
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Jiahai Zhou
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis , Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , Shanghai 200032 , China
| | - Ye Ni
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , 214122 Jiangsu , China
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27
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Xu GC, Wang Y, Tang MH, Zhou JY, Zhao J, Han RZ, Ni Y. Hydroclassified Combinatorial Saturation Mutagenesis: Reshaping Substrate Binding Pockets of KpADH for Enantioselective Reduction of Bulky–Bulky Ketones. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02286] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Guo-Chao Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Yue Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Ming-Hui Tang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Jie-Yu Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Jing Zhao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Rui-Zhi Han
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Ye Ni
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
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Abstract
Collagen is the dominant protein of the extracellular matrix. Its distinguishing feature is a three-stranded helix of great tensile strength. (2 S,4 R)-4-Hydroxyproline residues are essential for the stability of this triple helix. These residues arise from the post-translational modification of (2 S)-proline residues by collagen prolyl 4-hydroxylases (CP4Hs), which are members of the Fe(II)- and α-ketoglutarate (AKG)-dependent dioxygenase family. Here, we provide a framework for the inhibition of CP4Hs as the basis for treating fibrotic diseases and cancer metastasis. We begin with a summary of the structure and enzymatic reaction mechanism of CP4Hs. Then, we review the metal ions, metal chelators, mimetics of AKG and collagen strands, and natural products that are known to inhibit CP4Hs. Our focus is on inhibitors with potential utility in the clinic. We conclude with a prospectus for more effective inhibitors.
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Affiliation(s)
| | - Ronald T Raines
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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Biosynthesis of miglitol intermediate 6-( N-hydroxyethyl)-amino-6-deoxy-α-l-sorbofuranose by an improved d-sorbitol dehydrogenase from Gluconobacter oxydans. 3 Biotech 2018; 8:231. [PMID: 29719773 DOI: 10.1007/s13205-018-1251-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/23/2018] [Indexed: 01/03/2023] Open
Abstract
Adaptable exploitation of the catalytic potential of membrane-bound d-sorbitol dehydrogenase (mSLDH) from Gluconobacter oxydans is desperately needed in the industrial-scale production of miglitol. In the present study, a carbonyl group-dependent colorimetric quantification method was developed for the assay of miglitol key intermediate 6-(N-hydroxyethyl)-amino-6-deoxy-α-l-sorbofuranose (6NSL), and a high-throughput screening process of positive mutants was processed. Combined with several rounds of ultraviolet irradiation mutagenesis and screening procedure, a positive mutant strain G. oxydans ZJB16009 was obtained with significant increase in mSLDH catalytic activity by 1.5-fold, which exhibited an extremely accelerated uptake rate of d-sorbitol, and the fermentation time was significantly shortened from 22 to 11 h. In a 5-L biotransformation system, 60 g/L substrate N-2-hydroxyethyl glucamine (NHEG) was catalyzed by the resting cells of the mutant strain within 36 h and accumulated 53.6 g/L 6NSL, showing a 33.6% increase in the product yield. Therefore, it was indicated that the established high-throughput screening method could provide a highly efficient platform for the breading of G. oxydans strain for the industrial biosynthesis of miglitol intermediate 6NSL.
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Wang Y, Dai W, Liu Y, Zhang Z, Zhou J, Xu G, Ni Y. Fine tuning the enantioselectivity and substrate specificity of alcohol dehydrogenase from Kluyveromyces polysporus by single residue at 237. CATAL COMMUN 2018. [DOI: 10.1016/j.catcom.2018.01.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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He YC, Jiang CX, Chong GG, Di JH, Wu YF, Wang BQ, Xue XX, Ma CL. Chemical-enzymatic conversion of corncob-derived xylose to furfuralcohol by the tandem catalysis with SO 42-/SnO 2-kaoline and E. coli CCZU-T15 cells in toluene-water media. BIORESOURCE TECHNOLOGY 2017; 245:841-849. [PMID: 28926917 DOI: 10.1016/j.biortech.2017.08.219] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 08/29/2017] [Accepted: 08/31/2017] [Indexed: 05/14/2023]
Abstract
One-pot synthesis of furfuralcohol from corncob-derived xylose was attempted by the tandem catalysis with solid acid SO42-/SnO2-kaoline and recombination Escherichia coli CCZU-T15 whole-cells in the toluene-water media. Using SO42-/SnO2-kaoline (3.5wt%) as catalyst, the furfural yield of 74.3% was obtained from corncob-derived xylose in the toluene-water (1:2, v:v) containing 10mM OP-10 at 170°C for 30min. After furfural liquor was mixed with corncob-hydrolysate from the enzymatic hydrolysis of oxalic acid-pretreated corncob residue, furfural (50.5mM) could be completely biotransformed to furfuralcohol with Escherichia coli CCZU-T15 whole-cells harboring an NADH-dependent reductase (ClCR) in the toluene-water (1:3, v:v) containing 12.5mM OP-10 and 1.6mM glucose/mM furfural at 30°C and pH 6.5. Furfuralcohol was obtained at 13.0% yield based on starting material corncob (100% furfuralcohol yield for bioreduction of furfural step). Clearly, this one-pot synthesis of furfuralcohol strategy shows high potential application for the effective utilization of corncob.
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Affiliation(s)
- Yu-Cai He
- Platform of Bioethanol, Laboratory of Biochemical Engineering, College of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, China; Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China; Key Laboratory of Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China.
| | - Chun-Xia Jiang
- Platform of Bioethanol, Laboratory of Biochemical Engineering, College of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, China
| | - Gang-Gang Chong
- Platform of Bioethanol, Laboratory of Biochemical Engineering, College of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, China
| | - Jun-Hua Di
- Platform of Bioethanol, Laboratory of Biochemical Engineering, College of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, China
| | - Yan-Fei Wu
- Platform of Bioethanol, Laboratory of Biochemical Engineering, College of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, China
| | - Bing-Qian Wang
- Platform of Bioethanol, Laboratory of Biochemical Engineering, College of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, China
| | - Xin-Xia Xue
- Platform of Bioethanol, Laboratory of Biochemical Engineering, College of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, China
| | - Cui-Luan Ma
- Platform of Bioethanol, Laboratory of Biochemical Engineering, College of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, China; Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
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