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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.
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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
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2
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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.
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Guo L, Sun L, Huo YX. Toward bioproduction of oxo chemicals from C1 feedstocks using isobutyraldehyde as an example. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:80. [PMID: 35945564 PMCID: PMC9361566 DOI: 10.1186/s13068-022-02178-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 07/30/2022] [Indexed: 11/10/2022]
Abstract
AbstractOxo chemicals are valuable chemicals for synthesizing a wide array of industrial and consumer products. However, producing of oxo chemicals is predominately through the chemical process called hydroformylation, which requires petroleum-sourced materials and generates abundant greenhouse gas. Current concerns on global climate change have renewed the interest in reducing greenhouse gas emissions and recycling the plentiful greenhouse gas. A carbon–neutral manner in this regard is producing oxo chemicals biotechnologically using greenhouse gas as C1 feedstocks. Exemplifying isobutyraldehyde, this review demonstrates the significance of using greenhouse gas for oxo chemicals production. We highlight the current state and the potential of isobutyraldehyde synthesis with a special focus on the in vivo and in vitro scheme of C1-based biomanufacturing. Specifically, perspectives and scenarios toward carbon– and nitrogen–neutral isobutyraldehyde production are proposed. In addition, key challenges and promising approaches for enhancing isobutyraldehyde bioproduction are thoroughly discussed. This study will serve as a reference case in exploring the biotechnological potential and advancing oxo chemicals production derived from C1 feedstocks.
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Liu J, Wang K, Wang M, Deng H, Chen X, Shang Y, Liu X, Yu X. Efficient whole cell biotransformation of tyrosol from L-tyrosine by engineered Escherichia coli. Enzyme Microb Technol 2022; 160:110100. [PMID: 35872508 DOI: 10.1016/j.enzmictec.2022.110100] [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: 02/26/2022] [Revised: 07/14/2022] [Accepted: 07/17/2022] [Indexed: 11/03/2022]
Abstract
An engineered Escherichia coli was constructed by co-expressing L-amino acid deaminase, α-keto acid decarboxylase, alcohol dehydrogenase, and glucose dehydrogenase through two plasmids for tyrosol production. The activity of the rate-limiting enzyme L-amino acid deaminase from Cosenzaea myxofaciens (CmAAD) toward tyrosine was improved by structure-guided modification. The enzyme activity of triple mutant CmAAD V438G/K147V/R151E toward tyrosine was ~5.12-fold higher than that of the wild-type CmAAD. Secondly, the plasmid copy numbers and the gene orders were optimized to improve the titer of tyrosol. Finally, the recombinant strain CS-6 transformed 10 mM tyrosine into 9.56 ± 0.64 mM tyrosol at 45 ℃, and the space-time yield reached 0.478 mM·L-1·h-1. This study proposes a novel idea for the efficient and natural production of tyrosol, which has great potential for industrial application.
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Affiliation(s)
- Jinbin Liu
- School of Marine and Bioengineering, YanCheng Institute of Technology, Yancheng, Jiangsu 224051, China
| | - Kaipeng Wang
- School of Marine and Bioengineering, YanCheng Institute of Technology, Yancheng, Jiangsu 224051, China
| | - Mian Wang
- School of Marine and Bioengineering, YanCheng Institute of Technology, Yancheng, Jiangsu 224051, China
| | - Huaxiang Deng
- Center for Synthetic Biochemistry, Institute of Synthetic Biology, Institutes of Advanced Technologies, Shenzhen, China
| | - Xiaodong Chen
- School of Marine and Bioengineering, YanCheng Institute of Technology, Yancheng, Jiangsu 224051, China
| | - Yueling Shang
- School of Marine and Bioengineering, YanCheng Institute of Technology, Yancheng, Jiangsu 224051, China
| | - Xiaochen Liu
- School of Marine and Bioengineering, YanCheng Institute of Technology, Yancheng, Jiangsu 224051, China
| | - Xiaohong Yu
- School of Marine and Bioengineering, YanCheng Institute of Technology, Yancheng, Jiangsu 224051, China.
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Production of phenylpyruvic acid by engineered l-amino acid deaminase from Proteus mirabilis. Biotechnol Lett 2022; 44:635-642. [DOI: 10.1007/s10529-022-03245-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/07/2022] [Indexed: 12/20/2022]
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Ishida C, Miyata R, Hasebe F, Miyata A, Kumazawa S, Ito S, Nakano S. Reconstruction of Hyper‐Thermostable Ancestral L‐Amino Acid Oxidase to Perform Deracemization to D‐Amino Acids. ChemCatChem 2021. [DOI: 10.1002/cctc.202101296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Chiharu Ishida
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences University of Shizuoka Shizuoka 422-8526 Japan
| | - Ryo Miyata
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences University of Shizuoka Shizuoka 422-8526 Japan
| | - Fumihito Hasebe
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences University of Shizuoka Shizuoka 422-8526 Japan
| | - Azusa Miyata
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences University of Shizuoka Shizuoka 422-8526 Japan
| | - Shigenori Kumazawa
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences University of Shizuoka Shizuoka 422-8526 Japan
| | - Sohei Ito
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences University of Shizuoka Shizuoka 422-8526 Japan
| | - Shogo Nakano
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences University of Shizuoka Shizuoka 422-8526 Japan
- PREST, Japan Science and Technology Agency Saitama 332-0012 Japan
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Wu Y, Zhang S, Song W, Liu J, Chen X, Hu G, Zhou Y, Liu L, Wu J. Enhanced Catalytic Efficiency of L‐amino Acid Deaminase Achieved by a Shorter Hydride Transfer Distance. ChemCatChem 2021. [DOI: 10.1002/cctc.202101067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Yaoyun Wu
- School of Pharmaceutical Science Jiangnan University Wuxi 214122 P. R. China
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi 214122 P. R. China
| | - Sheng Zhang
- Tianrui Chemical Co. Ltd Department of Chemistry Quzhou 324400 P. R. China
| | - Wei Song
- School of Pharmaceutical Science Jiangnan University Wuxi 214122 P. R. China
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi 214122 P. R. China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi 214122 P. R. China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi 214122 P. R. China
| | - Guipeng Hu
- School of Pharmaceutical Science Jiangnan University Wuxi 214122 P. R. China
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi 214122 P. R. China
| | - Yiwen Zhou
- School of Pharmaceutical Science Jiangnan University Wuxi 214122 P. R. China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi 214122 P. R. China
| | - Jing Wu
- School of Pharmaceutical Science Jiangnan University Wuxi 214122 P. R. China
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Liu K, Chen X, Zhong Y, Gao C, Hu G, Liu J, Guo L, Song W, Liu L. Rational design of a highly efficient catalytic system for the production of PAPS from ATP and its application in the synthesis of chondroitin sulfate. Biotechnol Bioeng 2021; 118:4503-4515. [PMID: 34406648 DOI: 10.1002/bit.27919] [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: 07/08/2021] [Revised: 08/09/2021] [Accepted: 08/14/2021] [Indexed: 12/19/2022]
Abstract
The compound 3'-phosphoadenosine-5'-phosphosulfate (PAPS) serves as a sulfate group donor in the production of valuable sulfated compounds. However, elevated costs and low conversion efficiency limit the industrial applicability of PAPS. Here, we designed and constructed an efficient and controllable catalytic system for the conversion of adenosine triphosphate (ATP) (disodium salt) into PAPS without inhibition from by-products. In vitro and in vivo testing in Escherichia coli identified adenosine-5'-phosphosulfate kinase from Penicillium chrysogenum (PcAPSK) as the rate-limiting enzyme. Based on analysis of the catalytic steps and molecular dynamics simulations, a mechanism-guided "ADP expulsion" strategy was developed to generate an improved PcAPSK variant (L7), with a specific activity of 48.94 U·mg-1 and 73.27-fold higher catalytic efficiency (kcat/Km) that of the wild-type enzyme. The improvement was attained chiefly by reducing the ADP-binding affinity of PcAPSK, as well as by changing the enzyme's flexibility and lid structure to a more open conformation. By introducing PcAPSK L7 in an in vivo catalytic system, 73.59 mM (37.32 g·L-1 ) PAPS was produced from 150 mM ATP in 18.5 h using a 3-L bioreactor, and achieved titer is the highest reported to date and corresponds to a 98.13% conversion rate. Then, the PAPS catalytic system was combined with the chondroitin 4-sulfotransferase using a one-pot method. Finally, chondroitin sulfate was transformed from chondroitin at a conversion rate of 98.75%. This strategy has great potential for scale biosynthesis of PAPS and chondroitin sulfate.
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Affiliation(s)
- Kaifang Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Yunlu Zhong
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Guipeng Hu
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China.,School of Pharmaceutical Science, Jiangnan University, Wuxi, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Wei Song
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China.,School of Pharmaceutical Science, Jiangnan University, Wuxi, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
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Wang J, Gao C, Chen X, Liu L. Expanding the lysine industry: biotechnological production of l-lysine and its derivatives. ADVANCES IN APPLIED MICROBIOLOGY 2021; 115:1-33. [PMID: 34140131 DOI: 10.1016/bs.aambs.2021.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
l-lysine is an essential amino acid that contains various functional groups including α-amino, ω-amino, and α-carboxyl groups, exhibiting high reaction potential. The derivatization of these functional groups produces a series of value-added chemicals, such as cadaverine, glutarate, and d-lysine, that are widely applied in the chemical synthesis, cosmetics, food, and pharmaceutical industries. Here, we review recent advances in the biotechnological production of l-lysine and its derivatives and expatiate key technological strategies. Furthermore, we also discuss the existing challenges and potential strategies for more efficient production of these chemicals.
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Affiliation(s)
- Jiaping Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China.
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Ancestral L-amino acid oxidases for deracemization and stereoinversion of amino acids. Commun Chem 2020; 3:181. [PMID: 36703379 PMCID: PMC9814856 DOI: 10.1038/s42004-020-00432-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/10/2020] [Indexed: 01/29/2023] Open
Abstract
L-amino acid oxidases (LAAOs) can be applied to convert racemic amino acids to D-isomers, which are potential precursors of pharmaceuticals. However, this application is hampered by the lack of available stable and structure-determined LAAOs. In this study, we attempt to address this limitation by utilizing two ancestral LAAOs: AncLAAO-N4 and AncLAAO-N5. AncLAAO-N4 has the highest thermal and temporal stabilities among the designed LAAOs that can be used for deracemization and stereoinversion. AncLAAO-N5 can provide X-ray crystal structures, which are helpful to reveal substrate recognition and reaction mechanisms of LAAOs at the molecular level. Next, we attempted to improve activity of AncLAAO-N4 toward L-Val through a semi-rational protein engineering method. Three variants with enhanced activity toward L-Val were obtained. Taken together, we believe that the activity and substrate selectivity of AncLAAOs give them the potential to be key enzymes in various chemoenzymatic reactions.
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Pei S, Ruan X, Liu J, Song W, Chen X, Luo Q, Liu L, Wu J. Enhancement of α-ketoisovalerate production by relieving the product inhibition of l-amino acid deaminase from Proteus mirabilis. Chin J Chem Eng 2020. [DOI: 10.1016/j.cjche.2020.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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12
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Song W, Chen X, Wu J, Xu J, Zhang W, Liu J, Chen J, Liu L. Biocatalytic derivatization of proteinogenic amino acids for fine chemicals. Biotechnol Adv 2020; 40:107496. [DOI: 10.1016/j.biotechadv.2019.107496] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 11/13/2019] [Accepted: 11/18/2019] [Indexed: 01/09/2023]
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