1
|
Wu T, Chen Y, Wei W, Song W, Wu J, Wen J, Hu G, Li X, Gao C, Chen X, Liu L. Mechanism-Guided Computational Design Drives meso-Diaminopimelate Dehydrogenase to Efficient Synthesis of Aromatic d-amino Acids. ACS Synth Biol 2024; 13:1879-1892. [PMID: 38847341 DOI: 10.1021/acssynbio.4c00176] [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] [Indexed: 06/22/2024]
Abstract
Aromatic d-amino acids (d-AAs) play a pivotal role as important chiral building blocks and key intermediates in fine chemical and drug synthesis. Meso-diaminopimelate dehydrogenase (DAPDH) serves as an excellent biocatalyst in the synthesis of d-AAs and their derivatives. However, its strict substrate specificity and the lack of efficient engineering methods have hindered its widespread application. Therefore, this study aims to elucidate the catalytic mechanism underlying DAPDH from Proteus vulgaris (PvDAPDH) through the examination of its crystallographic structure, computational simulations of potential energies and molecular dynamics simulations, and site-directed mutagenesis. Mechanism-guided computational design showed that the optimal mutant PvDAPDH-M3 increased specific activity and catalytic efficiency (kcat/Km) for aromatic keto acids up to 124-fold and 92.4-fold, respectively, compared to that of the wild type. Additionally, it expanded the substrate scope to 10 aromatic keto acid substrates. Finally, six high-value-added aromatic d-AAs and their derivatives were synthesized using a one-pot three-enzyme cascade reaction, exhibiting a good conversion rate ranging from 32 to 84% and excellent stereoselectivity (enantiomeric excess >99%). These findings provide a potential synthetic pathway for the green industrial production of aromatic d-AAs.
Collapse
Affiliation(s)
- Tianfu Wu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Yihan Chen
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Wanqing Wei
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, 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
| | - Jian Wen
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Guipeng Hu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Xiaomin Li
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xiulai Chen
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| |
Collapse
|
2
|
Wu Y, Cui Y, Song W, Wei W, He Z, Tao J, Yin D, Chen X, Gao C, Liu J, Liu L, Wu J. Reprogramming the Transition States to Enhance C-N Cleavage Efficiency of Rhodococcus opacusl-Amino Acid Oxidase. JACS AU 2024; 4:557-569. [PMID: 38425913 PMCID: PMC10900486 DOI: 10.1021/jacsau.3c00672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/21/2023] [Accepted: 12/26/2023] [Indexed: 03/02/2024]
Abstract
l-Amino acid oxidase (LAAO) is an important biocatalyst used for synthesizing α-keto acids. LAAO from Rhodococcus opacus (RoLAAO) has a broad substrate spectrum; however, its low total turnover number limits its industrial use. To overcome this, we aimed to employ crystal structure-guided density functional theory calculations and molecular dynamic simulations to investigate the catalytic mechanism. Two key steps were identified: S → [TS1] in step 1 and Int1 → [TS2] in step 2. We reprogrammed the transition states [TS1] and [TS2] to reduce the identified energy barrier and obtain a RoLAAO variant capable of catalyzing 19 kinds of l-amino acids to the corresponding high-value α-keto acids with a high total turnover number, yield (≥95.1 g/L), conversion rate (≥95%), and space-time yields ≥142.7 g/L/d in 12-24 h, in a 5 L reactor. Our results indicated the promising potential of the developed RoLAAO variant for use in the industrial production of α-keto acids while providing a potential catalytic-mechanism-guided protein design strategy to achieve the desired physical and catalytic properties of enzymes.
Collapse
Affiliation(s)
- Yaoyun Wu
- School
of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
- State
Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
- School
of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yaozhong Cui
- Jiangsu
Xishan Senior High School, Wuxi 214174, China
| | - Wei Song
- School
of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Wanqing Wei
- State
Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
| | - Zhizhen He
- School
of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Jinyang Tao
- School
of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Dejing Yin
- School
of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xiulai Chen
- State
Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State
Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
| | - Jia Liu
- State
Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State
Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
| | - Jing Wu
- School
of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| |
Collapse
|
3
|
Fang K, Xu Z, Yang L, Cui Q, Du B, Liu H, Wang R, Li P, Su J, Wang J. Biosynthesis of 10-Hydroxy-2-decenoic Acid through a One-Step Whole-Cell Catalysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:1190-1202. [PMID: 38175798 DOI: 10.1021/acs.jafc.3c08142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
10-Hydroxy-2-decenoic acid (10-HDA) is an important component of royal jelly, known for its antimicrobial, anti-inflammatory, blood pressure-lowering, and antiradiation effects. Currently, 10-HDA biosynthesis is limited by the substrate selectivity of acyl-coenzyme A dehydrogenase, which restricts the technique to a two-step process. This study aimed to develop an efficient and simplified method for synthesizing 10-HDA. In this study, ACOX from Candida tropicalis 1798, which catalyzes 10-hydroxydecanoyl coenzyme A desaturation for 10-HDA synthesis, was isolated and heterologously coexpressed with FadE, Macs, YdiI, and CYP in Escherichia coli/SK after knocking out FadB, FadJ, and FadR genes. The engineered E. coli/AKS strain achieved a 49.8% conversion of decanoic acid to 10-HDA. CYP expression was improved through ultraviolet mutagenesis and high-throughput screening, increased substrate conversion to 75.6%, and the synthesis of 10-HDA was increased to 0.628 g/L in 10 h. This is the highest conversion rate and product concentration achieved in the shortest time to date. This study provides a simple and efficient method for 10-HDA biosynthesis and offers an effective method for developing strains with high product yields.
Collapse
Affiliation(s)
- Ke Fang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP) (Qilu University of Technology), Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - Ziting Xu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP) (Qilu University of Technology), Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - Lu Yang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP) (Qilu University of Technology), Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - Quan Cui
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP) (Qilu University of Technology), Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - Bowen Du
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP) (Qilu University of Technology), Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - Huijing Liu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP) (Qilu University of Technology), Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - Ruiming Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP) (Qilu University of Technology), Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - Piwu Li
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP) (Qilu University of Technology), Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - Jing Su
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP) (Qilu University of Technology), Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - Junqing Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP) (Qilu University of Technology), Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| |
Collapse
|
4
|
Yang J, Wei W, Gao C, Song W, Gao C, Chen X, Liu J, Guo L, Liu L, Wu J. Efficient production of salvianic acid A from L-dihydroxyphenylalanine through a tri-enzyme cascade. BIORESOUR BIOPROCESS 2023; 10:31. [PMID: 38647923 PMCID: PMC10992476 DOI: 10.1186/s40643-023-00649-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/31/2023] [Indexed: 04/25/2024] Open
Abstract
Salvianic acid A (SAA), used for treating cardiovascular and cerebrovascular diseases, possesses several pharmacological properties. However, the current methods for the enzymatic synthesis of SAA show low efficiency. Here, we constructed a three-enzyme cascade pathway in Escherichia coli BL21 (DE3) to produce SAA from L-dihydroxyphenylalanine (L-DOPA). The phenylpyruvate reductase (LaPPR) from Lactobacillus sp. CGMCC 9967 is a rate-limiting enzyme in this process. Therefore, we employed a mechanism-guided protein engineering strategy to shorten the transfer distances of protons and hydrides, generating an optimal LaPPR mutant, LaPPRMu2 (H89M/H143D/P256C), with a 2.8-fold increase in specific activity and 9.3-time increase in kcat/Km value compared to that of the wild type. Introduction of the mutant LaPPRMu2 into the cascade pathway and the optimization of enzyme levels and transformation conditions allowed the obtainment of the highest SAA titer (82.6 g L-1) ever reported in vivo, good conversion rate (91.3%), excellent ee value (99%) and the highest productivity (6.9 g L-1 h-1) from 90 g L-1 L-DOPA in 12 h. This successful strategy provides a potential new method for the industrial production of SAA.
Collapse
Affiliation(s)
- Jiahui Yang
- School of Life Science and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Wanqing Wei
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Changzheng Gao
- Department of Cardiology, Affiliated Hospital of Jiangnan University, Wuxi, 214122, China
| | - Wei Song
- School of Life Science and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- 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
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Liang Guo
- 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
| | - Jing Wu
- School of Life Science and Health Engineering, Jiangnan University, Wuxi, 214122, China.
| |
Collapse
|
5
|
Song Y, Wang R, Zhang Z, Liu X, Qi L, Shentu X, Yu X. Semi-rational engineering membrane binding domain of L-amino acid deaminase from Proteus vulgaris for enhanced α-ketoisocaproate. Front Microbiol 2022; 13:1025845. [PMID: 36246292 PMCID: PMC9561763 DOI: 10.3389/fmicb.2022.1025845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/16/2022] [Indexed: 12/01/2022] Open
Abstract
α-Keto acids are important raw materials for pharmaceuticals and functional foods, which could be produced from cheap feed stock by whole cell biocatalysts containing L-amino acid deaminases (L-AADs). However, the production capacity is limited by the low activity of L-AADs. The L-AAD mediated redox reaction employs the electron transport chain to transfer electrons from the reduced FADH2 to O2, implying that the interaction between L-AAD and the cell membrane affects its catalytic activity. To improve the catalytic activity of L-AAD from Proteus vulgaris, we redesigned the membrane-bound hydrophobic insertion sequences (INS, residues 325–375) by saturation mutagenesis and high-throughput screening. Mutants D340N and L363N exhibited higher affinity and catalytic efficiency for L-leucine, with half-life 1.62-fold and 1.28-fold longer than that of wild-type L-AAD. D340N catalyzed L-leucine to produce 81.21 g⋅L–1 α-ketoisocaproate, with a bioconversion rate of 89.06%, which was 17.57% higher than that of the wild-type. It is predicted that the mutations enhanced the interaction between the protein and the cell membrane.
Collapse
|
6
|
Cheng Y, Song W, Chen X, Gao C, Liu J, Guo L, Zhu M, Liu L, Wu J. Efficient synthesis 1,4-cyclohexanedicarboxaldehyde by an engineered alcohol oxidase. BIORESOUR BIOPROCESS 2022; 9:80. [PMID: 38647772 PMCID: PMC10991250 DOI: 10.1186/s40643-022-00570-y] [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: 06/08/2022] [Accepted: 08/01/2022] [Indexed: 11/10/2022] Open
Abstract
In this study, we selected and engineered a flavin adenine dinucleotide (FAD)-dependent alcohol oxidase (AOX) to produce 1,4-cyclohexanedicarboxaldehyde (CHDA), an initial raw material for spiral compounds, from 1,4-cyclohexanedimethanol (CHDM). First, the structure of alcohol oxidase from Arthrobacter cholorphenolicus (AcCO) was analyzed, and the mechanism of AcCO-catalyzed primary alcohol oxidation was elucidated, demonstrating that the energy barrier of the hydride (H-) transfer (13.4 kcal·mol-1 and 20.4 kcal·mol-1) decreases the catalytic efficiency of the primary alcohol oxidation reaction. Therefore, we designed a protein engineering strategy to adjust the catalytically active conformation to shorten the distance of hydride (H-) transfer and further decreased the core energy barrier. Following this strategy, variant W4 (S101A/H351V/N378S/Q329N) was obtained with 112.5-fold increased catalytic efficiency to produce CHDA compared to that of the wild-type strain. The 3 L scale preparation of CHDA reached a titer up to 29.6 g·L-1 with a 42.2% yield by an Escherichia coli whole-cell catalyst, which demonstrates the potential of this system for industrial application.
Collapse
Affiliation(s)
- Yaqi Cheng
- School of Life Sciences and Health Engineering, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Meng Zhu
- Wuxi Acryl Technology Co., Ltd, Wuxi, 214122, China
| | - Liming Liu
- School of Life Sciences and Health Engineering, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
| |
Collapse
|
7
|
Semi-Rational Design of Proteus mirabilis l-Amino Acid Deaminase for Expanding Its Substrate Specificity in α-Keto Acid Synthesis from l-Amino Acids. Catalysts 2022. [DOI: 10.3390/catal12020175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
l-amino acid deaminases (LAADs) are flavoenzymes that catalyze the stereospecific oxidative deamination of l-amino acids into α-keto acids, which are widely used in the pharmaceutical, food, chemical, and cosmetic industries. However, the substrate specificity of available LAADs is limited, and most substrates are concentrated on several bulky or basic l-amino acids. In this study, we employed a LAAD from Proteus mirabilis (PmiLAAD) and broadened its substrate specificity using a semi-rational design strategy. Molecular docking and alanine scanning identified F96, Q278, and E417 as key residues around the substrate-binding pocket of PmiLAAD. Site-directed saturation mutagenesis identified E417 as the key site for substrate specificity expansion. Expansion of the substrate channel with mutations of E417 (E417L, E417A) improved activity toward the bulky substrate l-Trp, and mutation of E417 to basic amino acids (E417K, E417H, E417R) enhanced the universal activity toward various l-amino acid substrates. The variant PmiLAADE417K showed remarkable catalytic activity improvement on seven substrates (l-Ala, l-Asp, l-Ile, l-Leu, l-Phe, l-Trp, and l-Val). The catalytic efficiency improvement obtained by E417 mutation may be attributed to the expansion of the entrance channel and its electrostatic interactions. These PmiLAAD variants with a broadened substrate spectrum can extend the application potential of LAADs.
Collapse
|