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Tenberg V, Sadeghi M, Schultheis A, Joshi M, Stein M, Lorenz H. Aqueous solution and solid-state behaviour of l-homophenylalanine: experiment, modelling, and DFT calculations. RSC Adv 2024; 14:10580-10589. [PMID: 38567323 PMCID: PMC10985536 DOI: 10.1039/d4ra01897d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
In the present study, the solid-state and aqueous solubility behaviour of l-homophenylalanine (l-Hpa) is explored. Different characterization techniques such as TG, DSC, temperature-resolved PXRD, and hot-stage microscopy were used to investigate basic thermal solid-state characteristics. Solubilities of l-Hpa in water were determined as a function of temperature and pH. Moreover, a thermodynamic model based on perturbation theory (PC-SAFT) is applied to represent the data. In addition, aqueous density data of l-Hpa were measured in a broader temperature range. To model the solubility data as a function of pH, pKa values are needed, which were accessed by employing density functional theory (DFT) calculations. The solid-state investigation did not show a simple melting process of l-Hpa, but a complete decomposition of the prevalent initial solid phase at elevated temperatures approximately above 520 K. This system exhibited extraordinarily low solubilities for an amino acid at all investigated temperatures. While the solubility does not differ from its isoelectric-point value over a wide pH range, it dramatically increases as the pH falls below 2.5 and rises above 9.5. The PC-SAFT model was able to calculate the solubilities as a function of pH and predict the density values.
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Affiliation(s)
- Vico Tenberg
- Physical and Chemical Foundations of Process Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems Magdeburg Germany +49 391 6110 321
| | - Masoud Sadeghi
- Physical and Chemical Foundations of Process Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems Magdeburg Germany +49 391 6110 321
| | - Axel Schultheis
- Physical and Chemical Foundations of Process Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems Magdeburg Germany +49 391 6110 321
| | - Meenakshi Joshi
- Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems Magdeburg Germany
| | - Matthias Stein
- Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems Magdeburg Germany
| | - Heike Lorenz
- Physical and Chemical Foundations of Process Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems Magdeburg Germany +49 391 6110 321
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2
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Bird AR, Molloy JC, Hall EAH. Biocatalytic synthesis of 2'-deoxynucleotide 5'-triphosphates from bacterial genomic DNA: Proof of principle. Biotechnol Bioeng 2023; 120:1531-1544. [PMID: 36919278 PMCID: PMC10952841 DOI: 10.1002/bit.28374] [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: 12/02/2022] [Revised: 02/25/2023] [Accepted: 03/05/2023] [Indexed: 03/16/2023]
Abstract
2'-deoxynucleoside 5'-triphosphates (dNTPs) are the building blocks of DNA and are key reagents which are incorporated by polymerase enzymes during nucleic acid amplification techniques, such as polymerase chain reaction (PCR). These techniques are of high importance, not only in molecular biology research, but also in molecular diagnostics. dNTPs are generally produced by a bottom-up technique which relies on synthesis or isolation of purified small molecules like deoxynucleosides. However, the disproportionately high cost of dNTPs in low- and middle-income countries (LMICs) and the requirement for cold chain storage during international shipping makes an adequate supply of these molecules challenging. To reduce supply chain dependency and promote domestic manufacturing in LMICs, a unique top-down biocatalytic synthesis method is described to produce dNTPs. Readily available bacterial genomic DNA provides a crude source material to generate dNTPs and is extracted directly from Escherichia coli (step 1). Nuclease enzymes are then used to digest the genomic DNA creating monophosphorylated deoxynucleotides (dNMPs) (step 2). Design and recombinant production and characterization of E. coli nucleotide kinases is presented to further phosphorylate the monophosphorylated products to generate dNTPs (step 3). Direct use of the in-house produced dNTPs in nucleic acid amplification is shown (step 4) and their successful use as reagents in the application of PCR, thereby providing proof of principle for the future development of recombinant nucleases and design of a recombinant solid-state bioreactor for on-demand dNTP production.
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Affiliation(s)
- Anna R. Bird
- Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeUK
| | - Jennifer C. Molloy
- Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeUK
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3
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Wu T, Wang Y, Zhang N, Yin D, Xu Y, Nie Y, Mu X. Reshaping Substrate-Binding Pocket of Leucine Dehydrogenase for Bidirectionally Accessing Structurally Diverse Substrates. ACS Catal 2022. [DOI: 10.1021/acscatal.2c04735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Tao Wu
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi214122, China
- Suqian Jiangnan University Institute of Industrial Technology, Suqian223800, China
| | - Yinmiao Wang
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi214122, China
| | - Ningxin Zhang
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi214122, China
| | - Dejing Yin
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi214122, China
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi214122, China
| | - Yao Nie
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi214122, China
| | - Xiaoqing Mu
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi214122, China
- Suqian Jiangnan University Institute of Industrial Technology, Suqian223800, China
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Huang H, Chen J, Ao T, Chen Y, Xie J, Hu X, Yu Q. Exploration of the role of bound polyphenols on tea residues dietary fiber improving diabetic hepatorenal injury and metabolic disorders. Food Res Int 2022; 162:112062. [DOI: 10.1016/j.foodres.2022.112062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 09/12/2022] [Accepted: 10/16/2022] [Indexed: 11/04/2022]
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Gao D, Song W, Wu J, Guo L, Gao C, Liu J, Chen X, Liu L. Efficient Production of L‐Homophenylalanine by Enzymatic‐Chemical Cascade Catalysis. Angew Chem Int Ed Engl 2022; 61:e202207077. [DOI: 10.1002/anie.202207077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Dengke Gao
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi 214122 China
| | - Wei Song
- School of Life Sciences and Health Engineering Jiangnan University Wuxi 214122 China
| | - Jing Wu
- School of Life Sciences and Health Engineering Jiangnan University Wuxi 214122 China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi 214122 China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi 214122 China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi 214122 China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi 214122 China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi 214122 China
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6
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Efficient Production of L‐homophenylalanine by Enzymatic–Chemical Cascade Catalysis. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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7
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Wu T, Mu X, Xue Y, Xu Y, Nie Y. Structure-guided steric hindrance engineering of Bacillus badius phenylalanine dehydrogenase for efficient L-homophenylalanine synthesis. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:207. [PMID: 34689801 PMCID: PMC8543943 DOI: 10.1186/s13068-021-02055-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Direct reductive amination of prochiral 2-oxo-4-phenylbutyric acid (2-OPBA) catalyzed by phenylalanine dehydrogenase (PheDH) is highly attractive in the synthesis of the pharmaceutical chiral building block L-homophenylalanine (L-HPA) given that its sole expense is ammonia and that water is the only byproduct. Current issues in this field include a poor catalytic efficiency and a low substrate loading. RESULTS In this study, we report a structure-guided steric hindrance engineering of PheDH from Bacillus badius to create an enhanced biocatalyst for efficient L-HPA synthesis. Mutagenesis libraries based on molecular docking, double-proximity filtering, and a degenerate codon significantly increased catalytic efficiency. Seven superior mutants were acquired, and the optimal triple-site mutant, V309G/L306V/V144G, showed a 12.7-fold higher kcat value, and accordingly a 12.9-fold higher kcat/Km value, than that of the wild type. A paired reaction system comprising V309G/L306V/V144G and glucose dehydrogenase converted 1.08 M 2-OPBA to L-HPA in 210 min, and the specific space-time conversion was 30.9 mmol g-1 L-1 h-1. The substrate loading and specific space-time conversion are the highest values to date. Docking simulation revealed increases in substrate-binding volume and additional degrees of freedom of the substrate 2-OPBA in the pocket. Tunnel analysis suggested the formation of new enzyme tunnels and the expansion of existing ones. CONCLUSIONS Overall, the results show that the mutant V309G/L306V/V144G has the potential for the industrial synthesis of L-HPA. The modified steric hindrance engineering approach can be a valuable addition to the current enzyme engineering toolbox.
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Affiliation(s)
- Tao Wu
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Suqian Jiangnan University Institute of Industrial Technology, Suqian, 223800, China
| | - Xiaoqing Mu
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
- Suqian Jiangnan University Institute of Industrial Technology, Suqian, 223800, China.
| | - Yuyan Xue
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Yao Nie
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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8
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Metal-phenolic network-coated hollow fiber catalytic membranes via solvent transfer induced phase separation (STRIPS) for Suzuki coupling reaction. J Memb Sci 2021. [DOI: 10.1016/j.memsci.2021.119386] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Yong K, Luo ZZ, Luo Q, Yang QW, Huang YX, Zhao XX, Zhang Y, Cao SZ. Plasma metabolome alteration in dairy cows with left displaced abomasum before and after surgical correction. J Dairy Sci 2021; 104:8177-8187. [PMID: 33865591 DOI: 10.3168/jds.2020-19761] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 03/12/2021] [Indexed: 12/12/2022]
Abstract
Left displaced abomasum (LDA) leads to substantial changes in the metabolism of dairy cows. Surgical correction of LDA can rapidly improve the health of cows; however, changes in metabolism following surgery are rarely described. To investigate the changes of plasma metabolome in cows with LDA before and after surgical correction, blood samples were collected from 10 healthy postpartum cows and 10 cows with LDA on the day of diagnosis, then again from the LDA cows 14 d after surgery. Serum nonesterified fatty acid, β-hydroxybutyric acid, cortisol and histamine concentration, and antioxidant enzyme (superoxide dismutase and glutathione peroxidase) activities were evaluated, and the metabolic profile in plasma was analyzed using ultra-high-performance liquid chromatography time-of-flight mass spectrometry. The results demonstrated that cows with LDA experienced severe negative energy balance and oxidative stress, which can be improved by surgical correction. The metabolic profile was analyzed using multidimensional and univariate statistical analyses, and different metabolites were identified. In total, 102 metabolites differed between cows with LDA and healthy cows. After surgical correction, 65 metabolites changed in cows with LDA, compared with these cows during the LDA event. Following surgical correction, AA levels tended to increase, and lipid levels tended to decrease in cows with LDA. Pathway analysis indicated marked changes in linoleic acid metabolism, Arg biosynthesis, and Gly, Ser, and Thr metabolism in cows at the onset of LDA and following surgical correction. Surgical treatment reversed the changes in AA and lipid metabolism in cows with LDA.
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Affiliation(s)
- K Yong
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China; Department of Animal Husbandry and Veterinary Medicine, College of Animal Science and Technology, Chongqing Three Gorges Vocational College, Chongqing 404100, China
| | - Z Z Luo
- Department of Animal Husbandry and Veterinary Medicine, College of Animal Science and Technology, Chongqing Three Gorges Vocational College, Chongqing 404100, China; Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Q Luo
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Q W Yang
- Department of Animal Husbandry and Veterinary Medicine, College of Animal Science and Technology, Chongqing Three Gorges Vocational College, Chongqing 404100, China
| | - Y X Huang
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, United Kingdom
| | - X X Zhao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Y Zhang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China.
| | - S Z Cao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China.
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10
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Liu Z, Lei D, Qiao B, Li S, Qiao J, Zhao GR. Integrative Biosynthetic Gene Cluster Mining to Optimize a Metabolic Pathway to Efficiently Produce l-Homophenylalanine in Escherichia coli. ACS Synth Biol 2020; 9:2943-2954. [PMID: 33078922 DOI: 10.1021/acssynbio.0c00363] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mining biosynthetic genes for the exploration of hybrid metabolic pathways is a promising approach in heterologous production of natural and unnatural products. Here, we developed an integrative biosynthetic gene cluster (BGC) mining strategy to engineer the biosynthesis of l-homophenylalanine (l-Hph), an important intermediate for the synthesis of angiotensin-converting enzyme inhibitors. We assembled the putative l-Hph BGCs and integrated phylogenetic analysis with target metabolite abundance mapping to prioritize candidate BGCs. To obtain an effective l-Hph pathway, various combinations of candidate genes from different species were screened in an iterative design-build-test stepwise manner. After the pathway was strength balanced and the metabolic flux was enhanced, engineered Escherichia coli produced 1.41 g/L of l-Hph from glucose in feeding shake-flask fermentation. Our cluster mining strategy enabled optimization of the target metabolic pathway, and it would be promising for production of other valuable products in the postgenomic era.
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Affiliation(s)
- Zhenning Liu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Dengwei Lei
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Bin Qiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Shilin Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Jianjun Qiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Guang-Rong Zhao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
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11
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Cheng F, Li JM, Zhou SP, Liu Q, Jin LQ, Xue YP, Zheng YG. A Single-Transaminase-Catalyzed Biocatalytic Cascade for Efficient Asymmetric Synthesis of l-Phosphinothricin. Chembiochem 2020; 22:345-348. [PMID: 32815302 DOI: 10.1002/cbic.202000488] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/13/2020] [Indexed: 12/11/2022]
Abstract
A single-transaminase-catalyzed biocatalytic cascade was developed by employing the desired biocatalyst, ATA-117-Rd11, that showed high activity toward 2-oxo-4-[(hydroxy)(methyl)phosphinoyl] butyric acid (PPO) and α-ketoglutarate, and low activity against pyruvate. The cascade successfully promotes a highly asymmetric amination reaction for the synthesis of l-phosphinothricin (l-PPT) with high conversion (>95 %) and>99 % ee. In a scale-up experiment, using 10 kg pre-frozen E. coli cells harboring ATA-117-Rd11 as catalyst, 80 kg PPO was converted to ≈70 kg l-PPT after 24 hours with a high ee value (>99 %).
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Affiliation(s)
- Feng Cheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
| | - Ju-Mou Li
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
| | - Shi-Peng Zhou
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
| | - Qi Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
| | - Li-Qun Jin
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
| | - Ya-Ping Xue
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
| | - Yu-Guo Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
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12
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Martínez-Rodríguez S, Torres JM, Sánchez P, Ortega E. Overview on Multienzymatic Cascades for the Production of Non-canonical α-Amino Acids. Front Bioeng Biotechnol 2020; 8:887. [PMID: 32850740 PMCID: PMC7431475 DOI: 10.3389/fbioe.2020.00887] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/09/2020] [Indexed: 12/11/2022] Open
Abstract
The 22 genetically encoded amino acids (AAs) present in proteins (the 20 standard AAs together with selenocysteine and pyrrolysine), are commonly referred as proteinogenic AAs in the literature due to their appearance in ribosome-synthetized polypeptides. Beyond the borders of this key set of compounds, the rest of AAs are generally named imprecisely as non-proteinogenic AAs, even when they can also appear in polypeptide chains as a result of post-transductional machinery. Besides their importance as metabolites in life, many of D-α- and L-α-"non-canonical" amino acids (NcAAs) are of interest in the biotechnological and biomedical fields. They have found numerous applications in the discovery of new medicines and antibiotics, drug synthesis, cosmetic, and nutritional compounds, or in the improvement of protein and peptide pharmaceuticals. In addition to the numerous studies dealing with the asymmetric synthesis of NcAAs, many different enzymatic pathways have been reported in the literature allowing for the biosynthesis of NcAAs. Due to the huge heterogeneity of this group of molecules, this review is devoted to provide an overview on different established multienzymatic cascades for the production of non-canonical D-α- and L-α-AAs, supplying neophyte and experienced professionals in this field with different illustrative examples in the literature. Whereas the discovery of new or newly designed enzymes is of great interest, dusting off previous enzymatic methodologies by a "back and to the future" strategy might accelerate the implementation of new or improved multienzymatic cascades.
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13
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Zhang Y, Li JK, Zhang FG, Ma JA. Catalytic Asymmetric Access to Noncanonical Chiral α-Amino Acids from Cyclic Iminoglyoxylates and Enamides. J Org Chem 2020; 85:5580-5589. [PMID: 32223256 DOI: 10.1021/acs.joc.0c00436] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Here we describe an enantioselective Mannich reaction of cyclic iminoglyoxylates with enamides by virtue of chiral phosphoric acid catalysis in a one-pot manner. The wide substrate scope, mild reaction conditions, and constantly excellent enantioselectivities (>95% ee in most cases) render this protocol highly practical for the rapid construction of valuable noncanonical chiral α-amino-acid building blocks.
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Affiliation(s)
- Yue Zhang
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, and Tianjin Collaborative Innovation Center of Chemical Science & Engineering, Tianjin University, Tianjin 300072, P. R. of China
| | - Jun-Kuan Li
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, and Tianjin Collaborative Innovation Center of Chemical Science & Engineering, Tianjin University, Tianjin 300072, P. R. of China
| | - Fa-Guang Zhang
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, and Tianjin Collaborative Innovation Center of Chemical Science & Engineering, Tianjin University, Tianjin 300072, P. R. of China.,Joint School of NUS & TJU, International Campus of Tianjin University, Fuzhou 350207, P. R. of China
| | - Jun-An Ma
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, and Tianjin Collaborative Innovation Center of Chemical Science & Engineering, Tianjin University, Tianjin 300072, P. R. of China.,Joint School of NUS & TJU, International Campus of Tianjin University, Fuzhou 350207, P. R. of China
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Abstract
Natural nonproteinogenic amino acids vastly outnumber the well-known 22 proteinogenic amino acids. Such amino acids are generated in specialized metabolic pathways. In these pathways, diverse biosynthetic transformations, ranging from isomerizations to the stereospecific functionalization of C-H bonds, are employed to generate structural diversity. The resulting nonproteinogenic amino acids can be integrated into more complex natural products. Here we review recently discovered biosynthetic routes to freestanding nonproteinogenic α-amino acids, with an emphasis on work reported between 2013 and mid-2019.
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Affiliation(s)
- Jason B Hedges
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Katherine S Ryan
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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15
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Asymmetric synthesis of l-phosphinothricin using thermostable alpha-transaminase mined from Citrobacter koseri. J Biotechnol 2019; 302:10-17. [PMID: 31201835 DOI: 10.1016/j.jbiotec.2019.06.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/30/2019] [Accepted: 06/11/2019] [Indexed: 11/22/2022]
Abstract
α-Transaminase (α-TA) responsible for catalyzing the reversible transfer of amino groups between amine donors and amine acceptors, is applicable to enzymatic route for asymmetric synthesis of herbicide l-phosphinothricin (l-PPT). In the search for α-TAs with better catalysis performance, three α-TAs were discovered by genome mining approach using a known sequence encoding Escherichia coli tyrosine TA (TyrB) as probe. Through detailed comparison of their expression amount, activities and characteristics, Citrobacter koseri TA (CkTA) exhibited better activity and thermostability, which retain 65.9% of initial activity after incubation at 57 °C for 4 h. The Km and kcat/Km values of CkTA were 36.75 mM and 34.29 mM-1 min-1, respectively. In addition, recombinant CkTA cells were immobilized onto Celite 545 using tris(hydroxymethyl)phosphine as crosslinker. During five repetitive asymmetric synthesis of l-PPT from 20 g/L prostereogenic ketone using l-Glu as amine donor, all the yields of l-PPT reached up to 91.2% (>99% ee). These characteristics made CkTA a valuable addition to the currently scarce α-TA library for stereospecific synthesis of l-PPT.
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16
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Dennig A, Blaschke F, Gandomkar S, Tassano E, Nidetzky B. Preparative Asymmetric Synthesis of Canonical and Non‐canonical α‐amino Acids Through Formal Enantioselective Biocatalytic Amination of Carboxylic Acids. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201801377] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Alexander Dennig
- Institute of Biotechnology and Biochemical Engineering, Graz University of TechnologyNAWI Graz Petersgasse 12 8010 Graz Austria
- Austrian Centre of Industrial Biotechnology (acib) Petersgasse 14 8010 Graz Austria
| | - Fabio Blaschke
- Institute of Biotechnology and Biochemical Engineering, Graz University of TechnologyNAWI Graz Petersgasse 12 8010 Graz Austria
| | - Somayyeh Gandomkar
- Institute of Biotechnology and Biochemical Engineering, Graz University of TechnologyNAWI Graz Petersgasse 12 8010 Graz Austria
| | - Erika Tassano
- Department of ChemistryUniversity of Graz Heinrichstrasse 28 8010 Graz Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of TechnologyNAWI Graz Petersgasse 12 8010 Graz Austria
- Austrian Centre of Industrial Biotechnology (acib) Petersgasse 14 8010 Graz Austria
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17
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Slabu I, Galman JL, Lloyd RC, Turner NJ. Discovery, Engineering, and Synthetic Application of Transaminase Biocatalysts. ACS Catal 2017. [DOI: 10.1021/acscatal.7b02686] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Iustina Slabu
- School
of Chemistry, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, M1 7DN Manchester, United Kingdom
| | - James L. Galman
- School
of Chemistry, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, M1 7DN Manchester, United Kingdom
| | - Richard C. Lloyd
- Dr.
Reddy’s Laboratories, Chirotech Technology Centre, CB4 0PE Cambridge, United Kingdom
| | - Nicholas J. Turner
- School
of Chemistry, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, M1 7DN Manchester, United Kingdom
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18
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Luo C, Lin Q, Lin S, Meng C, Wang H. Cosynthesis of l-homophenylalanine and 2-phenylethanol by recombinant Saccharomyces cerevisiae expressing aspartate aminotransferase from Escherichia coli BL21(DE3). J Biosci Bioeng 2017; 123:1-7. [DOI: 10.1016/j.jbiosc.2016.06.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 06/21/2016] [Accepted: 06/22/2016] [Indexed: 11/25/2022]
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19
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Huihui KM, Caputo JA, Melchor Z, Olivares AM, Spiewak A, Johnson KA, DiBenedetto TA, Kim S, Ackerman LKG, Weix DJ. Decarboxylative Cross-Electrophile Coupling of N-Hydroxyphthalimide Esters with Aryl Iodides. J Am Chem Soc 2016; 138:5016-9. [PMID: 27029833 PMCID: PMC4841236 DOI: 10.1021/jacs.6b01533] [Citation(s) in RCA: 306] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Indexed: 12/22/2022]
Abstract
A new method for the decarboxylative coupling of alkyl N-hydroxyphthalimide esters (NHP esters) with aryl iodides is presented. In contrast to previous studies that form alkyl radicals from carboxylic acid derivatives, no photocatalyst, light, or arylmetal reagent is needed, only nickel and a reducing agent (Zn). Methyl, primary, and secondary alkyl groups can all be coupled in good yield (77% ave yield). One coupling with an acid chloride is also presented. Stoichiometric reactions of (dtbbpy)Ni(2-tolyl)I with an NHP ester show for the first time that arylnickel(II) complexes can directly react with NHP esters to form alkylated arenes.
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Affiliation(s)
| | | | - Zulema Melchor
- Department
of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
| | - Astrid M. Olivares
- Department
of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
| | - Amanda
M. Spiewak
- Department
of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
| | - Keywan A. Johnson
- Department
of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
| | - Tarah A. DiBenedetto
- Department
of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
| | - Seoyoung Kim
- Department
of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
| | | | - Daniel J. Weix
- Department
of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
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20
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Grulich M, Brezovský J, ŠtĿpánek V, Palyzová A, Kyslíková E, Kyslík P. Resolution of α/β-amino acids by enantioselective penicillin G acylase from Achromobacter sp . ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2015.09.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Sohn WY, Ishiuchi SI, Çarçabal P, Oba H, Fujii M. UV–UV hole burning and IR dip spectroscopy of homophenylalanine by laser desorption supersonic jet technique. Chem Phys 2014. [DOI: 10.1016/j.chemphys.2014.10.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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22
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Ghaffari-Moghaddam M, Eslahi H, Omay D, Zakipour-Rahimabadi E. Industrial applications of enzymes. ACTA ACUST UNITED AC 2014. [DOI: 10.1134/s2079978014040037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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23
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Wang L, Murai Y, Yoshida T, Okamoto M, Tachrim ZP, Hashidoko Y, Hashimoto M. Utilization of acidic α-amino acids as acyl donors: an effective stereo-controllable synthesis of aryl-keto α-amino acids and their derivatives. Molecules 2014; 19:6349-67. [PMID: 24840903 PMCID: PMC6271428 DOI: 10.3390/molecules19056349] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 05/08/2014] [Accepted: 05/12/2014] [Indexed: 12/03/2022] Open
Abstract
Aryl-keto-containing α-amino acids are of great importance in organic chemistry and biochemistry. They are valuable intermediates for the construction of hydroxyl α-amino acids, nonproteinogenic α-amino acids, as well as other biofunctional components. Friedel-Crafts acylation is an effective method to prepare aryl-keto derivatives. In this review, we summarize the preparation of aryl-keto containing α-amino acids by Friedel-Crafts acylation using acidic α-amino acids as acyl-donors and Lewis acids or Brönsted acids as catalysts.
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Affiliation(s)
- Lei Wang
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan
| | - Yuta Murai
- Faculty of Advanced Life Science, Frontier Research Center for Post-Genome Science and Technology, Hokkaido University, Kita 21, Nishi 11, Kita-ku, Sapporo 001-0021, Japan
| | - Takuma Yoshida
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan
| | - Masashi Okamoto
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan
| | - Zetryana Puteri Tachrim
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan
| | - Yasuyuki Hashidoko
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan
| | - Makoto Hashimoto
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan.
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24
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Li H, Liao JC. Development of an NADPH-dependent homophenylalanine dehydrogenase by protein engineering. ACS Synth Biol 2014; 3:13-20. [PMID: 24053171 DOI: 10.1021/sb400093x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
l-Homophenylalanine is a nonproteinogenic amino acid and can be used as a versatile pharmaceutical intermediate. Production of l-homophenylalanine involves amination of the keto acid precursor 2-oxo-4-phenylbutyric acid (2-OPBA), which can be accomplished by bioenzymatic processes. Current biocatalysts for this reaction include transaminases and NADH-dependent phenylalanine dehydrogenases, which are not optimal for metabolic engineering of whole-cell biocatalysis. Here, we report the development of an NADPH-dependent homophenylalanine dehydrogenase by engineering the NADPH-dependent glutamate dehydrogenase (GDH) from Escherichia coli, which provides a new tool for in vitro catalysis and in vivo metabolic engineering. We took a stepwise substrate walking strategy: the first round directed evolution switched GDH's substrate specificity from its natural substrate 2-ketoglutarate to the intermediate target phenylpyruvate, which has similar structure as 2-OPBA; and the second round further improved the enzyme's catalytic efficiency toward the final target 2-OPBA. Compared to wild type GDH, the catalytic efficiency (kcat/Km) of the final mutant was ∼100 fold higher for 2-OPBA and ∼3000 fold lower for the original substrate 2-ketoglutarate. When overexpressed in E. coli, the engineered GDH aminated 2-OPBA to l-homophenylalanine more effectively than the transaminases and NADH-dependent phenylalanine dehydrogenase, possibly because it utilizes the strong anabolic driving force NADPH under aerobic condition.
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Affiliation(s)
- Han Li
- Department of Chemical and Biomolecular
Engineering ‡The Molecular Biology Institute §Department of Chemistry
and Biochemistry, ∥Institute of Genomics and Proteomics, University of California, Los Angeles, Los
Angeles, California 90095, United States
| | - James C. Liao
- Department of Chemical and Biomolecular
Engineering ‡The Molecular Biology Institute §Department of Chemistry
and Biochemistry, ∥Institute of Genomics and Proteomics, University of California, Los Angeles, Los
Angeles, California 90095, United States
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25
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Zhang J, Zhu T, Wu X, Chen Y. Enhancement of biocatalytic efficiency by increasing substrate loading: enzymatic preparation of L-homophenylalanine. Appl Microbiol Biotechnol 2013; 97:8487-94. [PMID: 23893309 DOI: 10.1007/s00253-013-5117-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 05/27/2013] [Accepted: 07/10/2013] [Indexed: 10/26/2022]
Abstract
Enantiomerically pure L-homophenylalanine (L-HPA) is a key building block for the synthesis of angiotensin-converting enzyme inhibitors and other chiral pharmaceuticals. Among the processes developed for the L-HPA production, biocatalytic synthesis employing phenylalanine dehydrogenase has been proven as the most promising route. However, similar to other dehydrogenase-catalyzed reactions, the viability of this process is markedly affected by insufficient substrate loading and high costs of the indispensable cofactors. In the present work, a highly efficient and economic biocatalytic process for L-HPA was established by coupling genetically modified phenylalanine dehydrogenase and formate dehydrogenase. Combination of fed-batch substrate addition and a continuous product removal greatly increased substrate loading and cofactor utilization. After systemic optimization, 40 g (0.22 mol) of keto acid substrate was transformed to L-HPA within 24 h and a total of 0.2 mM NAD(+) was reused effectively in eight cycles of fed-batch operation, consequently giving an average substrate concentration of 510 mM and a productivity of 84.1 g l(-1) day(-1) for L-HPA. The present study provides an efficient and feasible enzymatic process for the production of L-HPA and a general solution for the increase of substrate loading.
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Affiliation(s)
- Jielin Zhang
- Laboratory of Chemical Biology and State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjia St., Nanjing, Jiangsu Province, 210009, China
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26
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Morcelle SR, Cánepa AS, Padró JM, Llerena-Suster CR, Clapés P. Syntheses of dipeptide alcohols and dipeptide aldehyde precursors catalyzed by plant cysteine peptidases. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2012.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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27
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Immobilization of phenylalanine dehydrogenase onto Eupergit CM for the synthesis of (S)-2-amino-4-phenylbutyric acid. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2012.11.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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28
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Identification of homophenylalanine biosynthetic genes from the cyanobacterium Nostoc punctiforme PCC73102 and application to its microbial production by Escherichia coli. Appl Environ Microbiol 2013; 79:2201-8. [PMID: 23354699 DOI: 10.1128/aem.03596-12] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
L-Homophenylalanine (L-Hph) is a useful chiral building block for synthesis of several drugs, including angiotensin-converting enzyme inhibitors and the novel proteasome inhibitor carfilzomib. While the chemoenzymatic route of synthesis is fully developed, we investigated microbial production of L-Hph to explore the possibility of a more efficient and sustainable approach to L-Hph production. We hypothesized that L-Hph is synthesized from L-Phe via a mechanism homologous to 3-methyl-2-oxobutanoic acid conversion to 4-methyl-2-oxopentanoic acid during leucine biosynthesis. Based on bioinformatics analysis, we found three putative homophenylalanine biosynthesis genes, hphA (Npun_F2464), hphB (Npun_F2457), and hphCD (Npun_F2458), in the cyanobacterium Nostoc punctiforme PCC73102, located around the gene cluster responsible for anabaenopeptin biosynthesis. We constructed Escherichia coli strains harboring hphABCD-expressing plasmids and achieved the fermentative production of L-Hph from L-Phe. To our knowledge, this is the first identification of the genes responsible for homophenylalanine synthesis in any organism. Furthermore, to improve the low conversion efficiency of the initial strain, we optimized the expression of hphA, hphB, and hphCD, which increased the yield to ∼630 mg/liter. The L-Hph biosynthesis and L-Leu biosynthesis genes from E. coli were also compared. This analysis revealed that HphB has comparatively relaxed substrate specificity and can perform the function of LeuB, but HphA and HphCD show tight substrate specificity and cannot complement the LeuA and LeuC/LeuD functions, and vice versa. Finally, the range of substrate tolerance of the L-Hph-producing strain was examined, which showed that m-fluorophenylalanine, o-fluorophenylalanine, and L-tyrosine were accepted as substrates and that the corresponding homoamino acids were generated.
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29
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Identification of important residues in diketoreductase from Acinetobacter baylyi by molecular modeling and site-directed mutagenesis. Biochimie 2011; 94:471-8. [PMID: 21893158 DOI: 10.1016/j.biochi.2011.08.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 08/23/2011] [Indexed: 11/21/2022]
Abstract
Diketoreductase (DKR) from Acinetobacter baylyi exhibits a unique property of double reduction of a β, δ-diketo ester with excellent stereoselectivity, which can serve as an efficient biocatalyst for the preparation of an important chiral intermediate for cholesterol lowering statin drugs. Taken the advantage of high homology between DKR and human heart 3-hydroxyacyl-CoA dehydrogenase (HAD), a molecular model was created to compare the tertiary structures of DKR and HAD. In addition to the possible participation of His-143 in the enzyme catalysis by pH profile, three key amino acid residues, Ser-122, His-143 and Glu-155, were identified and mutated to explore the possibility of involving in the catalytic process. The catalytic activities for mutants S122A/C, H143A/K and E155Q were below detectable level, while their binding affinities to the diketo ester substrate and cofactor NADH did not change obviously. The experimental results were further supported by molecular docking, suggesting that Ser-122 and His-143 were essential for the proton transfer to the carbonyl functional groups of the substrate. Moreover, Glu-155 was crucial for maintaining the proper orientation and protonation of the imidazole ring of His-143 for efficient catalysis.
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30
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Schultheisz HL, Szymczyna BR, Scott LG, Williamson JR. Enzymatic de novo pyrimidine nucleotide synthesis. J Am Chem Soc 2011; 133:297-304. [PMID: 21166398 PMCID: PMC3134529 DOI: 10.1021/ja1059685] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The use of stable isotope labeling has revolutionized NMR studies of nucleic acids, and there is a need for methods of incorporation of specific isotope labels to facilitate specific NMR experiments and applications. Enzymatic synthesis offers an efficient and flexible means to synthesize nucleoside triphosphates from a variety of commercially available specifically labeled precursors, permitting isotope labeling of RNAs prepared by in vitro transcription. Here, we recapitulate de novo pyrimidine biosynthesis in vitro, using recombinantly expressed enzymes to perform efficient single-pot syntheses of UTP and CTP that bear a variety of stable isotope labeling patterns. Filtered NMR experiments on (13)C, (15)N, (2)H-labeled HIV-2 TAR RNA demonstrate the utility and value of this approach. This flexible enzymatic synthesis will make implementing detailed and informative RNA stable isotope labeling schemes substantially more cost-effective and efficient, providing advanced tools for the study of structure and dynamics of RNA molecules.
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Affiliation(s)
- Heather L Schultheisz
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, MB33, La Jolla, California 92037, USA
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31
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Crystallisation-induced asymmetric transformation (CIAT) for the synthesis of dipeptides containing homophenylalanine. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.tetasy.2010.11.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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Ahmad A, Oh P, Shukor SA. Synthesis of l-homophenylalanine via integrated membrane bioreactor: Influence of pH on yield. Biochem Eng J 2010. [DOI: 10.1016/j.bej.2010.08.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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33
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