1
|
Chen Q, Wang J, Zhang S, Chen X, Hao J, Wu Q, Zhu D. Discovery and directed evolution of C-C bond formation enzymes for the biosynthesis of β-hydroxy-α-amino acids and derivatives. Crit Rev Biotechnol 2024:1-20. [PMID: 38566472 DOI: 10.1080/07388551.2024.2332295] [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: 11/24/2023] [Accepted: 02/16/2024] [Indexed: 04/04/2024]
Abstract
β-Hydroxy-α-amino acids (β-HAAs) have extensive applications in the pharmaceutical, chemical synthesis, and food industries. The development of synthetic methodologies aimed at producing optically pure β-HAAs has been driven by practical applications. Among the various synthetic methods, biocatalytic asymmetric synthesis is considered a sustainable approach due to its capacity to generate two stereogenic centers from simple prochiral precursors in a single step. Therefore, extensive efforts have been made in recent years to search for effective enzymes which enable such biotransformation. This review provides an overview on the discovery and engineering of C-C bond formation enzymes for the biocatalytic synthesis of β-HAAs. We highlight examples where the use of threonine aldolases, threonine transaldolases, serine hydroxymethyltransferases, α-methylserine aldolases, α-methylserine hydroxymethyltransferases, and engineered alanine racemases facilitated the synthesis of β-HAAs. Additionally, we discuss the potential future advancements and persistent obstacles in the enzymatic synthesis of β-HAAs.
Collapse
Affiliation(s)
- Qijia Chen
- College of Food Science and Biology, University of Science and Technology, Shijiazhuang, China
| | - Jingmin Wang
- College of Food Science and Biology, University of Science and Technology, Shijiazhuang, China
| | - Sisi Zhang
- College of Food Science and Biology, University of Science and Technology, Shijiazhuang, China
| | - Xi Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jianxiong Hao
- College of Food Science and Biology, University of Science and Technology, Shijiazhuang, China
| | - Qiaqing Wu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Dunming Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| |
Collapse
|
2
|
Xu L, Shen JJ, Wu M, Su BM, Xu XQ, Lin J. An artificial biocatalytic cascade for efficient synthesis of norepinephrine by combination of engineered L-threonine transaldolase with multi-enzyme expression fine-tuning. Int J Biol Macromol 2024; 265:130819. [PMID: 38508550 DOI: 10.1016/j.ijbiomac.2024.130819] [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: 01/09/2024] [Revised: 02/19/2024] [Accepted: 03/10/2024] [Indexed: 03/22/2024]
Abstract
Norepinephrine, a kind of β-adrenergic receptor agonist, is commonly used for treating shocks and hypotension caused by a variety of symptoms. The development of a straightforward, efficient and environmentally friendly biocatalytic route for manufacturing norepinephrine remains a challenge. Here, we designed and realized an artificial biocatalytic cascade to access norepinephrine starting from 3, 4-dihydroxybenzaldehyde and L-threonine mediated by a tailored-made L-threonine transaldolase PsLTTA-Mu1 and a newly screened tyrosine decarboxylase ErTDC. To overcome the imbalance of multi-enzymes in a single cell, engineering of PsLTTA for improved activity and fine-tuning expression mode of multi-enzymes in single E.coli cells were combined, leading to a robust whole cell biocatalyst ES07 that could produce 100 mM norepinephrine with 99% conversion, delivering a highest time-space yield (3.38 g/L/h) ever reported. To summarized, the current study proposed an effective biocatalytic approach for the synthesis of norepinephrine from low-cost substrates, paving the way for industrial applications of enzymatic norepinephrine production.
Collapse
Affiliation(s)
- Lian Xu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350116, China
| | - Jun-Jiang Shen
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350116, China
| | - Ming Wu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350116, China
| | - Bing-Mei Su
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350116, China
| | - Xin-Qi Xu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350116, China
| | - Juan Lin
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350116, China.
| |
Collapse
|
3
|
Xu M, Tan Z, Qi S, Na Q, Zhang X, Zhuang W, Zhu C, Ying H, Shen T. Synthesis of 3-Phenylserine by a Two-enzyme Cascade System with PLP Cofactor. Chemistry 2024; 30:e202302959. [PMID: 38012090 DOI: 10.1002/chem.202302959] [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: 09/12/2023] [Revised: 11/12/2023] [Accepted: 11/27/2023] [Indexed: 11/29/2023]
Abstract
A two-enzyme cascade system containing ω-transaminase (ω-TA) and L-threonine aldolase (L-ThA) was reported for the synthesis of 3-Phenylserine starting from benzylamine, and PLP was utilized as the only cofactor in these both two enzymes reaction system. Based on the transamination results, benzylamine was optimized as an advantageous amino donor as confirmed by MD simulation results. This cascade reaction system could not only facilitate the in situ removal of the co-product benzaldehyde, enhancing the economic viability of the reaction, but also establish a novel pathway for synthesizing high-value phenyl-serine derivatives. In our study, nearly 95 % of benzylamine was converted, yielding over 54 % of 3-Phenylserine under the optimized conditions cascade reaction.
Collapse
Affiliation(s)
- Mengjiao Xu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Zhuotao Tan
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Siyu Qi
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Qi Na
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Xiaowang Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Wei Zhuang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Chenjie Zhu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Hanjie Ying
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Tao Shen
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| |
Collapse
|
4
|
Jones MA, Butler ND, Anderson SR, Wirt SA, Govil I, Lyu X, Fang Y, Kunjapur AM. Discovery of L-threonine transaldolases for enhanced biosynthesis of beta-hydroxylated amino acids. Commun Biol 2023; 6:929. [PMID: 37696954 PMCID: PMC10495429 DOI: 10.1038/s42003-023-05293-0] [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: 03/24/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023] Open
Abstract
Beta-hydroxy non-standard amino acids (β-OH-nsAAs) have utility as small molecule drugs, precursors for beta-lactone antibiotics, and building blocks for polypeptides. While the L-threonine transaldolase (TTA), ObiH, is a promising enzyme for β-OH-nsAA biosynthesis, little is known about other natural TTA sequences. We ascertained the specificity of the TTA enzyme class more comprehensively by characterizing 12 candidate TTA gene products across a wide range (20-80%) of sequence identities. We found that addition of a solubility tag substantially enhanced the soluble protein expression level within this difficult-to-express enzyme family. Using an optimized coupled enzyme assay, we identified six TTAs, including one with less than 30% sequence identity to ObiH that exhibits broader substrate scope, two-fold higher L-Threonine (L-Thr) affinity, and five-fold faster initial reaction rates under conditions tested. We harnessed these TTAs for first-time bioproduction of β-OH-nsAAs with handles for bio-orthogonal conjugation from supplemented precursors during aerobic fermentation of engineered Escherichia coli, where we observed that higher affinity of the TTA for L-Thr increased titer. Overall, our work reveals an unexpectedly high level of sequence diversity and broad substrate specificity in an enzyme family whose members play key roles in the biosynthesis of therapeutic natural products that could benefit from chemical diversification.
Collapse
Affiliation(s)
- Michaela A Jones
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Neil D Butler
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Shelby R Anderson
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Sean A Wirt
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Ishika Govil
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Xinyi Lyu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Yinzhi Fang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Aditya M Kunjapur
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA.
| |
Collapse
|
5
|
Li L, Zhang R, Xu Y, Zhang W. Comprehensive screening strategy coupled with structure-guided engineering of l-threonine aldolase from Pseudomonas putida for enhanced catalytic efficiency towards l- threo-4-methylsulfonylphenylserine. Front Bioeng Biotechnol 2023; 11:1117890. [PMID: 36793440 PMCID: PMC9922994 DOI: 10.3389/fbioe.2023.1117890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/19/2023] [Indexed: 01/31/2023] Open
Abstract
l-Threonine aldolases (TAs) can catalyze aldol condensation reactions to form β-hydroxy-α-amino acids, but afford unsatisfactory conversion and poor stereoselectivity at the Cβ position. In this study, a directed evolution coupling high-throughput screening method was developed to screen more efficient l-TA mutants based on their aldol condensation activity. A mutant library with over 4000 l-TA mutants from Pseudomonas putida were obtained by random mutagenesis. About 10% of mutants retained activity toward 4-methylsulfonylbenzaldehyde, with five site mutations (A9L, Y13K, H133N, E147D, and Y312E) showing higher activity. Iterative combinatorial mutant A9V/Y13K/Y312R catalyzed l-threo-4-methylsulfonylphenylserine with a 72% conversion and 86% diastereoselectivity, representing 2.3-fold and 5.1-fold improvements relative to the wild-type. Molecular dynamics simulations illustrated that additional hydrogen bonds, water bridge force, hydrophobic interactions, and π-cation interactions were present in the A9V/Y13K/Y312R mutant compared with the wild-type to reshape the substrate-binding pocket, resulting in a higher conversion and Cβ stereoselectivity. This study provides a useful strategy for engineering TAs to resolve the low Cβ stereoselectivity problem and contributes to the industrial application of TAs.
Collapse
Affiliation(s)
- Lihong Li
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
| | - Rongzhen Zhang
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China,*Correspondence: Rongzhen Zhang,
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
| | - Wenchi Zhang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| |
Collapse
|
6
|
Improving the Cβ stereoselectivity of L-threonine aldolase for the preparation of L-threo-3,4-dihydroxyphenylserine, a powerful anti-Parkinson's disease drug. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108766] [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]
|
7
|
Reetz MT, Garcia-Borràs M. The Unexplored Importance of Fleeting Chiral Intermediates in Enzyme-Catalyzed Reactions. J Am Chem Soc 2021; 143:14939-14950. [PMID: 34491742 PMCID: PMC8461649 DOI: 10.1021/jacs.1c04551] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Indexed: 02/07/2023]
Abstract
Decades of extensive research efforts by biochemists, organic chemists, and protein engineers have led to an understanding of the basic mechanisms of essentially all known types of enzymes, but in a formidable number of cases an essential aspect has been overlooked. The occurrence of short-lived chiral intermediates formed by symmetry-breaking of prochiral precursors in enzyme catalyzed reactions has been systematically neglected. We designate these elusive species as fleeting chiral intermediates and analyze such crucial questions as "Do such intermediates occur in homochiral form?" If so, what is the absolute configuration, and why did Nature choose that particular stereoisomeric form, even when the isolable final product may be achiral? Does the absolute configuration of a chiral product depend in any way on the absolute configuration of the fleeting chiral precursor? How does this affect the catalytic proficiency of the enzyme? If these issues continue to be unexplored, then an understanding of the mechanisms of many enzyme types remains incomplete. We have systematized the occurrence of these chiral intermediates according to their structures and enzyme types. This is followed by critical analyses of selected case studies and by final conclusions and perspectives. We hope that the fascinating concept of fleeting chiral intermediates will attract the attention of scientists, thereby opening an exciting new research field.
Collapse
Affiliation(s)
- Manfred T. Reetz
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport
Economic Area, Tianjin 300308, China
| | - Marc Garcia-Borràs
- Institute
of Computational Chemistry and Catalysis (IQCC) and Departament de
Química, Universitat de Girona, Carrer Maria Aurèlia Capmany
69, 17003 Girona, Spain
| |
Collapse
|
8
|
Lee SH, Yeom SJ, Kim SE, Oh DK. Development of aldolase-based catalysts for the synthesis of organic chemicals. Trends Biotechnol 2021; 40:306-319. [PMID: 34462144 DOI: 10.1016/j.tibtech.2021.08.001] [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: 04/29/2021] [Revised: 08/01/2021] [Accepted: 08/02/2021] [Indexed: 11/28/2022]
Abstract
Aldol chemicals are synthesized by condensation reactions between the carbon units of ketones and aldehydes using aldolases. The efficient synthesis of diverse organic chemicals requires intrinsic modification of aldolases via engineering and design, as well as extrinsic modification through immobilization or combination with other catalysts. This review describes the development of aldolases, including their engineering and design, and the selection of desired aldolases using high-throughput screening, to enhance their catalytic properties and perform novel reactions. Aldolase-containing catalysts, which catalyze the aldol reaction combined with other enzymatic and/or chemical reactions, can efficiently synthesize diverse complex organic chemicals using inexpensive and simple materials as substrates. We also discuss the current challenges and emerging solutions for aldolase-based catalysts.
Collapse
Affiliation(s)
- Seon-Hwa Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Soo-Jin Yeom
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Seong-Eun Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Deok-Kun Oh
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea.
| |
Collapse
|
9
|
Wang L, Xu L, Su B, Lin W, Xu X, Lin J. Improving the C β Stereoselectivity of l-Threonine Aldolase for the Synthesis of l-threo-4-Methylsulfonylphenylserine by Modulating the Substrate-Binding Pocket To Control the Orientation of the Substrate Entrance. Chemistry 2021; 27:9654-9660. [PMID: 33843095 DOI: 10.1002/chem.202100752] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Indexed: 12/20/2022]
Abstract
l-Threonine aldolase from Actinocorallia herbida (AhLTA) is an ideal catalyst for producing l-threo-4-methylsulfonylphenylserine [(2S,3R)-1 b], a key chiral precursor for florfenicol and thiamphenicol. The moderate Cβ stereoselectivity is the main obstacle to the industrial application of AhLTA. To address this issue, a combinatorial active-site saturation test (CAST) together with sequence conservatism analysis was applied to engineer the AhLTA toward improved Cβ stereoselectivity. The optical mutant Y314R could asymmetrically synthesize l-threo-4-methylsulfonylphenylserine with 81 % diastereomeric excess (de), which is 23 % higher than wild-type AhLTA. Molecular dynamic (MD) simulations revealed that the mechanism for the improvement in Cβ stereoselectivity of Y314R is due to the acylamino group of residues Arg314 controlling the orientation of substrate 4-methylsulfonyl benzaldehyde (1 a) in the active pocket by directed interaction with the methylsulfonyl group; this leads to asymmetric synthesis of l-threo-4-methylsulfonylphenylserine. The success in this study demonstrates that direct control of substrates in an active pocket is an attract strategy to address the Cβ stereoselectivity problem of LTA and contribute to the industrial application of LTA.
Collapse
Affiliation(s)
- Lichao Wang
- College of Chemical Engineering, Fuzhou University, 350116, Fuzhou, P. R. China
| | - Lian Xu
- College of Chemical Engineering, Fuzhou University, 350116, Fuzhou, P. R. China
| | - Bingmei Su
- College of Chemistry, Fuzhou University, 350116, Fuzhou, P. R. China
| | - Wei Lin
- College of Chemistry, Fuzhou University, 350116, Fuzhou, P. R. China
| | - Xinqi Xu
- College of Biological Science and Engineering, Fuzhou University, 350116, Fuzhou, P. R. China
| | - Juan Lin
- College of Chemical Engineering, Fuzhou University, 350116, Fuzhou, P. R. China.,College of Biological Science and Engineering, Fuzhou University, 350116, Fuzhou, P. R. China
| |
Collapse
|