1
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Liu Y, Zhong X, Luo Z, Meng X, Li R, Zhong W, Yang L, Wang H, Wei D. The identification of a robust leucine dehydrogenase from a directed soil metagenome for efficient synthesis of L-2-aminobutyric acid. Biotechnol J 2023; 18:e2200590. [PMID: 37149736 DOI: 10.1002/biot.202200590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 04/29/2023] [Accepted: 05/03/2023] [Indexed: 05/08/2023]
Abstract
L-2-aminobutyric acid (L-2-ABA) is a chiral precursor for the synthesis of anti-epileptic drug levetiracetam and anti-tuberculosis drug ethambutol. Asymmetric synthesis of L-2-ABA by leucine dehydrogenases has been widely developed. However, the limitations of natural enzymes, such as poor stability, low catalytic efficiency, and inhibition of high-concentration substrates, limit large-scale applications. Herein, by directed screening of a metagenomic library from unnatural amino acid-enriched environments, a robust leucine dehydrogenase, TvLeuDH, was identified, which exhibited high substrate tolerance and excellent enzymatic activity towards 2-oxobutyric acid. In addition, TvLeuDH has strong affinity for NADH. Subsequently, a three-enzyme co-expression system containing L-threonine deaminase, TvLeuDH, and glucose dehydrogenase was established. By optimizing reaction conditions, 1.5 M L-threonine could be converted to L-2-ABA with a 99% molar conversion rate and a space-time yield of 51.5 g·L-1 ·h-1 . In this process, no external coenzyme was added. The robustness of TvLeuDH allowed the reaction to be performed without the addition of extra salt as the buffer, demonstrating the simplest reaction system currently reported. These unique properties for the efficient and environmentally friendly production of chiral amino acids make TvLeuDH a particularly promising candidate for industrial applications, which reveals the great potential of directed metagenomics for industrial biotechnology.
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Affiliation(s)
- Yan Liu
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Xuezhao Zhong
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Zi Luo
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Xiangqi Meng
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Rui Li
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Wa Zhong
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Lin Yang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Hualei Wang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
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2
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Zhao L, Zhang W, Wang Q, Wang H, Gao X, Qin B, Jia X, You S. A novel NADH-dependent leucine dehydrogenase for multi-step cascade synthesis of L-phosphinothricin. Enzyme Microb Technol 2023; 166:110225. [PMID: 36921551 DOI: 10.1016/j.enzmictec.2023.110225] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/29/2023] [Accepted: 03/02/2023] [Indexed: 03/11/2023]
Abstract
L-Phosphinothricin (L-PPT) is the effective constituent in racemic PPT (a high-efficiency and broad-spectrum herbicide), and the exploitation of green and sustainable synthesis route for L-PPT has always been the focus in pesticide industry. In recent years, "one-pot, two-step" enzyme-mediated cascade strategy is a mainstream pathway to obtain L-PPT. Herein, RgDAAO and BsLeuDH were applied to expand "one-pot, two-step" process. Notably, a NADH-dependent leucine dehydrogenase from Bacillus subtilis (BsLeuDH) was firstly characterized and attempted to generate L-PPT, achieving an excellent enantioselectivity (99.9% ee). Meanwhile, a formate dehydrogenase from Pichia pastoris (PpFDH) was utilized to implement NADH cofactor regeneration and only CO2 was by-product. Sufficient amount of the corresponding keto acid precursor PPO was obtained by oxidation of D-PPT relying on a D-amino acid oxidase from Rhodotorula gracilis (RgDAAO) with content conversion (46.1%). L-PPT was ultimately prepared from racemized PPT via oxidative deamination catalyzed by RgDAAO and reductive amination catalyzed by BsLeuDH, achieving 80.3% overall yield and > 99.9% ee value.
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Affiliation(s)
- Lu Zhao
- School of Life Sciences and Biopharmaceutical Sciences, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe, Shenyang 110016, People's Republic of China
| | - Wenhe Zhang
- School of Life Sciences and Biopharmaceutical Sciences, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe, Shenyang 110016, People's Republic of China
| | - Qi Wang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe, Shenyang 110016, People's Republic of China
| | - Huibin Wang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Xiao Gao
- School of Life Sciences and Biopharmaceutical Sciences, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe, Shenyang 110016, People's Republic of China
| | - Bin Qin
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe, Shenyang 110016, People's Republic of China
| | - Xian Jia
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe, Shenyang 110016, People's Republic of China.
| | - Song You
- School of Life Sciences and Biopharmaceutical Sciences, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe, Shenyang 110016, People's Republic of China.
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3
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Meng X, Liu Y, Yang L, Li R, Wang H, Shen Y, Wei D. Rational identification of a high catalytic efficiency leucine dehydrogenase and process development for efficient synthesis of l-phenylglycine. Biotechnol J 2023; 18:e2200465. [PMID: 36738237 DOI: 10.1002/biot.202200465] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 01/01/2023] [Accepted: 02/02/2023] [Indexed: 02/05/2023]
Abstract
Enzymatic asymmetric synthesis of chiral amino acids has great industrial potential. However, the low catalytic efficiency of high-concentration substrates limits their industrial application. Herein, using a combination of substrate catalytic efficiency prediction based on "open to closed" conformational change and substrate specificity prediction, a novel leucine dehydrogenase (TsLeuDH), with high substrate catalytic efficiency toward benzoylformic acid (BFA) for producing l-phenylglycine (l-Phg), was directly identified from 4695 putative leucine dehydrogenases in a public database. The specific activity of TsLeuDH was determined to be as high as 4253.8 U mg-1 . Through reaction process optimization, a high-concentration substrate (0.7 m) was efficiently and completely converted within 90 min in a single batch, without any external coenzyme addition. Moreover, a continuous flow-feeding approach was designed using gradient control of the feed rate to reduce substrate accumulation. Finally, the highest overall substrate concentration of up to 1.2 m BFA could be aminated to l-Phg with conversion of >99% in 3 h, demonstrating that this new combination of enzyme process development is promising for large-scale application of l-Phg.
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Affiliation(s)
- Xiangqi Meng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Yan Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Lin Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Rui Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Hualei Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Yaling Shen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
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4
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Huang B, Yang K, Amanze C, Yan Z, Zhou H, Liu X, Qiu G, Zeng W. Sequence and structure-guided discovery of a novel NADH-dependent 7β-hydroxysteroid dehydrogenase for efficient biosynthesis of ursodeoxycholic acid. Bioorg Chem 2023; 131:106340. [PMID: 36586301 DOI: 10.1016/j.bioorg.2022.106340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/11/2022] [Accepted: 12/23/2022] [Indexed: 12/25/2022]
Abstract
7β-Hydroxysteroid dehydrogenases (7β-HSDHs) have attracted increasing attention due to their crucial roles in the biosynthesis of ursodeoxycholic acid (UDCA). However, most published 7β-HSDHs are strictly NADPH-dependent oxidoreductases with poor activity and low productivity. Compared with NADPH, NADH is more stable and cheaper, making it the more popular cofactor for industrial applications of dehydrogenases. Herein, by using a sequence and structure-guided genome mining approach based on the structural information of conserved cofactor-binding motifs, we uncovered a novel NADH-dependent 7β-HSDH (Cle7β-HSDH). The Cle7β-HSDH was overexpressed, purified, and characterized. It exhibited high specific activity (9.6 U/mg), good pH stability and thermostability, significant methanol tolerance, and showed excellent catalytic efficiencies (kcat/Km) towards 7-oxo-lithocholic acid (7-oxo-LCA) and NADH (70.8 mM-1s-1 and 31.8 mM-1s-1, respectively). Molecular docking and mutational analyses revealed that Asp42 could play a considerable role in NADH binding and recognition. Coupling with a glucose dehydrogenase for NADH regeneration, up to 20 mM 7-oxo-LCA could be completely transformed to UDCA within 90 min by Cle7β-HSDH. This study provides an efficient approach for mining promising enzymes from genomic databases for cost-effective biotechnological applications.
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Affiliation(s)
- Bin Huang
- School of Minerals Processing and Bioengineering, Central South University, Hunan 410083, China
| | - Kai Yang
- School of Minerals Processing and Bioengineering, Central South University, Hunan 410083, China
| | - Charles Amanze
- School of Minerals Processing and Bioengineering, Central South University, Hunan 410083, China
| | - Zhen Yan
- School of Minerals Processing and Bioengineering, Central South University, Hunan 410083, China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Hunan 410083, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Hunan 410083, China
| | - Guanzhou Qiu
- School of Minerals Processing and Bioengineering, Central South University, Hunan 410083, China
| | - Weimin Zeng
- School of Minerals Processing and Bioengineering, Central South University, Hunan 410083, China.
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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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6
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Yin X, Gong W, Zhan Z, Wei W, Li M, Jiao J, Chen B, Liu L, Li W, Gao Z. Mining and engineering of valine dehydrogenases from a hot spring sediment metagenome for the synthesis of chiral non-natural L-amino acids. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Characterization of a New Marine Leucine Dehydrogenase from Pseudomonas balearica and Its Application for L-tert-Leucine Production. Catalysts 2022. [DOI: 10.3390/catal12090971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Leucine dehydrogenase (LeuDH) has emerged as the most promising biocatalyst for L-tert-leucine (L-Tle) production via asymmetric reduction in trimethylpyruvate (TMP). In this study, a new LeuDH named PbLeuDH from marine Pseudomonas balearica was heterologously over-expressed in Escherichia coli, followed by purification and characterization. PbLeuDH possessed a broad substrate scope, displaying activities toward numerous L-amino acids and α-keto acids. Notably, compared with those reported LeuDHs, PbLeuDH exhibited excellent catalytic efficiency for TMP with a Km value of 4.92 mM and a kcat/Km value of 24.49 s−1 mM−1. Subsequently, L-Tle efficient production was implemented from TMP by whole-cell biocatalysis using recombinant E. coli as a catalyst, which co-expressed PbLeuDH and glucose dehydrogenase (GDH). Ultimately, using a fed-batch feeding strategy, 273 mM (35.8 g L−1) L-Tle was achieved with a 96.1% yield and 2.39 g L−1 h−1 productivity. In summary, our research provides a competitive biocatalyst for L-Tle green biosynthesis and lays a solid foundation for the realization of large-scale L-Tle industrial production.
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Kim S, Koh S, Kang W, Yang JK. The Crystal Structure of L-Leucine Dehydrogenase from Pseudomonas aeruginosa. Mol Cells 2022; 45:495-501. [PMID: 35698914 PMCID: PMC9260137 DOI: 10.14348/molcells.2022.0012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/04/2022] [Accepted: 02/24/2022] [Indexed: 11/27/2022] Open
Abstract
Leucine dehydrogenase (LDH, EC 1.4.1.9) catalyzes the reversible deamination of branched-chain L-amino acids to their corresponding keto acids using NAD+ as a cofactor. LDH generally adopts an octameric structure with D4 symmetry, generating a molecular mass of approximately 400 kDa. Here, the crystal structure of the LDH from Pseudomonas aeruginosa (Pa-LDH) was determined at 2.5 Å resolution. Interestingly, the crystal structure shows that the enzyme exists as a dimer with C2 symmetry in a crystal lattice. The dimeric structure was also observed in solution using multiangle light scattering coupled with size-exclusion chromatography. The enzyme assay revealed that the specific activity was maximal at 60°C and pH 8.5. The kinetic parameters for three different amino acid and the cofactor (NAD+) were determined. The crystal structure represents that the subunit has more compact structure than homologs' structure. In addition, the crystal structure along with sequence alignments indicates a set of non-conserved arginine residues which are important in stability. Subsequent mutation analysis for those residues revealed that the enzyme activity reduced to one third of the wild type. These results provide structural and biochemical insights for its future studies on its application for industrial purposes.
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Affiliation(s)
- Seheon Kim
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Korea
| | - Seri Koh
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Korea
| | - Wonchull Kang
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Korea
- Department of Physics and Integrative Institute of Basic Science, Soongsil University, Seoul 06978, Korea
| | - Jin Kuk Yang
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Korea
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Li J, Mu X, Wu T, Xu Y. High coenzyme affinity chimeric amine dehydrogenase based on domain engineering. BIORESOUR BIOPROCESS 2022; 9:33. [PMID: 38647888 PMCID: PMC10992376 DOI: 10.1186/s40643-022-00528-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/17/2022] [Indexed: 11/10/2022] Open
Abstract
NADH-dependent phenylalanine amine dehydrogenase (F-AmDH) engineered from phenylalanine dehydrogenase (PheDH) catalyzes the synthesis of aromatic chiral amines from prochiral ketone substrates. However, its low coenzyme affinity and catalytic efficiency limit its industrial application. Here, we developed a chimeric amine dehydrogenase, cFLF-AmDH, based on the relative independence of the structure at the domain level, combined with a substrate-binding domain from F-AmDH and a high-affinity cofactor-binding domain from leucine amine dehydrogenase (L-AmDH). The kinetic parameters indicated that cFLF-AmDH showed a twofold improvement in affinity for NADH and a 4.4-fold increase in catalytic efficiency (kcat/Km) compared with the parent F-AmDH. Meanwhile, cFLF-AmDH also showed higher thermal stability, with the half-life increased by 60% at 55 °C and a broader substrate spectrum, than the parent F-AmDH. Molecular dynamics simulations suggested that the constructed cFLF-AmDH had a more stable structure than the parent F-AmDH, thereby improving the affinity of the coenzyme. The reaction rate increased by 150% in the reductive amination reaction catalyzed by cFLF-AmDH. When the NAD+ concentration was 0.05 mM, the conversion rate was increased by 150%. These results suggest that the chimeric protein by domain shuffling from different domain donors not only increased the cofactor affinity and catalytic efficiency, but also changed the specificity and thermal stability. Our study highlights that domain engineering is another effective method for creating biodiversity with different catalytic properties.
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Affiliation(s)
- Jialin Li
- 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.
| | - 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
| | - 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
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Abstract
Biocatalysis has an enormous impact on chemical synthesis. The waves in which biocatalysis has developed, and in doing so changed our perception of what organic chemistry is, were reviewed 20 and 10 years ago. Here we review the consequences of these waves of development. Nowadays, hydrolases are widely used on an industrial scale for the benign synthesis of commodity and bulk chemicals and are fully developed. In addition, further enzyme classes are gaining ever increasing interest. Particularly, enzymes catalysing selective C-C-bond formation reactions and enzymes catalysing selective oxidation and reduction reactions are solving long-standing synthetic challenges in organic chemistry. Combined efforts from molecular biology, systems biology, organic chemistry and chemical engineering will establish a whole new toolbox for chemistry. Recent developments are critically reviewed.
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Affiliation(s)
- Ulf Hanefeld
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, The Netherlands.
| | - Frank Hollmann
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, The Netherlands.
| | - Caroline E Paul
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, The Netherlands.
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