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Wang L, Xu Z, Zhang Y, Wang R, Wang J, Yang S, Su J, Li Y. Recent insights into function, structure and modification of cytochrome P450 153 a family. Mol Biol Rep 2023; 50:6955-6961. [PMID: 37355495 DOI: 10.1007/s11033-023-08553-8] [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: 03/25/2023] [Accepted: 05/26/2023] [Indexed: 06/26/2023]
Abstract
Cytochrome P450 153 A (CYP153A) is a versatile enzyme that can catalyze a wide range of oxidation reactions on various substrates. This review provides a comprehensive overview of the current state of knowledge on CYP153A, including its classification, structure, function, and potential applications in biotechnology and pharmaceuticals. The CYP153A family encompasses many enzymes with different functions on a variety of substrates. We also discuss the structural features that are responsible for the different substrate specificities. Additionally, the enzyme has been engineered to increase its catalytic activity and modifications have been made to enhance its properties further. Despite its potential, challenges and limitations associated with studying and exploiting CYP153A remain, such as low expression levels and substrate inhibition. Nonetheless, ongoing research is exploring new ways to harness the enzyme's capabilities, particularly in synthetic biology, biocatalysis, and drug discovery, making it an exciting target for future research.
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Affiliation(s)
- Leilei Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, 250353, China
| | - Ziqi Xu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, 250353, China
| | - Yisang Zhang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, 250353, China
| | - Ruiming Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, 250353, China
| | - Junqing Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, 250353, China
| | - Suzhen Yang
- Shandong Freda Biotech Co., Ltd, Jinan, 250101, Shandong, China
| | - Jing Su
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, 250353, China.
| | - Yan Li
- Shandong Freda Biotech Co., Ltd, Jinan, 250101, Shandong, China.
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2
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Yu J, Ge J, Yu H, Ye L. Improved Bioproduction of the Nylon 12 Monomer by Combining the Directed Evolution of P450 and Enhancing Heme Synthesis. Molecules 2023; 28:molecules28041758. [PMID: 36838746 PMCID: PMC9963201 DOI: 10.3390/molecules28041758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/04/2023] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
The nylon 12 (PA12) monomer ω-aminododecanoic acid (ω-AmDDA) could be synthesized from lauric acid (DDA) through multi-enzyme cascade transformation using engineered E. coli, with the P450 catalyzing terminal hydroxylation of DDA as a rate-limiting enzyme. Its activity is jointly determined by the heme domain and the reductase domain. To obtain a P450 mutant with higher activity, directed evolution was conducted using a colorimetric high-throughput screening (HTS) system with DDA as the real substrate. After two rounds of directed evolution, a positive double-site mutant (R14R/D629G) with 90.3% higher activity was obtained. Molecular docking analysis, kinetic parameter determination and protein electrophoresis suggested the improved soluble expression of P450 resulting from the synonymous mutation near the N-terminus and the shortened distance of the electron transfer between FMN and FAD caused by D629G mutation as the major reasons for activity improvement. The significantly increased kcat and unchanged Km provided further evidence for the increase in electron transfer efficiency. Considering the important role of heme in P450, its supply was strengthened by the metabolic engineering of the heme synthesis pathway. By combining P450-directed evolution and enhancing heme synthesis, 2.02 ± 0.03 g/L of ω-AmDDA was produced from 10 mM DDA, with a yield of 93.6%.
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Affiliation(s)
- Jiaming Yu
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
| | - Jiawei Ge
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
| | - Hongwei Yu
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
- Correspondence: (H.Y.); (L.Y.)
| | - Lidan Ye
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
- Correspondence: (H.Y.); (L.Y.)
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3
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Call A, Cianfanelli M, Besalú-Sala P, Olivo G, Palone A, Vicens L, Ribas X, Luis JM, Bietti M, Costas M. Carboxylic Acid Directed γ-Lactonization of Unactivated Primary C-H Bonds Catalyzed by Mn Complexes: Application to Stereoselective Natural Product Diversification. J Am Chem Soc 2022; 144:19542-19558. [PMID: 36228322 DOI: 10.1021/jacs.2c08620] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reactions that enable selective functionalization of strong aliphatic C-H bonds open new synthetic paths to rapidly increase molecular complexity and expand chemical space. Particularly valuable are reactions where site-selectivity can be directed toward a specific C-H bond by catalyst control. Herein we describe the catalytic site- and stereoselective γ-lactonization of unactivated primary C-H bonds in carboxylic acid substrates. The system relies on a chiral Mn catalyst that activates aqueous hydrogen peroxide to promote intramolecular lactonization under mild conditions, via carboxylate binding to the metal center. The system exhibits high site-selectivity and enables the oxidation of unactivated primary γ-C-H bonds even in the presence of intrinsically weaker and a priori more reactive secondary and tertiary ones at α- and β-carbons. With substrates bearing nonequivalent γ-C-H bonds, the factors governing site-selectivity have been uncovered. Most remarkably, by manipulating the absolute chirality of the catalyst, γ-lactonization at methyl groups in gem-dimethyl structural units of rigid cyclic and bicyclic carboxylic acids can be achieved with unprecedented levels of diastereoselectivity. Such control has been successfully exploited in the late-stage lactonization of natural products such as camphoric, camphanic, ketopinic, and isoketopinic acids. DFT analysis points toward a rebound type mechanism initiated by intramolecular 1,7-HAT from a primary γ-C-H bond of the bound substrate to a highly reactive MnIV-oxyl intermediate, to deliver a carbon radical that rapidly lactonizes through carboxylate transfer. Intramolecular kinetic deuterium isotope effect and 18O labeling experiments provide strong support to this mechanistic picture.
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Affiliation(s)
- Arnau Call
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi, Girona E-17003, Catalonia, Spain
| | - Marco Cianfanelli
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi, Girona E-17003, Catalonia, Spain
| | - Pau Besalú-Sala
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi, Girona E-17003, Catalonia, Spain
| | - Giorgio Olivo
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi, Girona E-17003, Catalonia, Spain
| | - Andrea Palone
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi, Girona E-17003, Catalonia, Spain.,Dipartimento di Scienze e Tecnologie Chimiche, Università "Tor Vergata", Via della Ricerca Scientifica 1, I-00133 Rome, Italy
| | - Laia Vicens
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi, Girona E-17003, Catalonia, Spain
| | - Xavi Ribas
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi, Girona E-17003, Catalonia, Spain
| | - Josep M Luis
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi, Girona E-17003, Catalonia, Spain
| | - Massimo Bietti
- Dipartimento di Scienze e Tecnologie Chimiche, Università "Tor Vergata", Via della Ricerca Scientifica 1, I-00133 Rome, Italy
| | - Miquel Costas
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi, Girona E-17003, Catalonia, Spain
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4
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Wang L, Wang L, Wang R, Wang Z, Wang J, Yuan H, Su J, Li Y, Yang S, Han T. Efficient Biosynthesis of 10-Hydroxy-2-decenoic Acid Using a NAD(P)H Regeneration P450 System and Whole-Cell Catalytic Biosynthesis. ACS OMEGA 2022; 7:17774-17783. [PMID: 35664602 PMCID: PMC9161381 DOI: 10.1021/acsomega.2c00972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/21/2022] [Indexed: 06/15/2023]
Abstract
10-Hydroxy-2-decenoic acid (10-HDA) is an α,β-unsaturated medium-chain carboxylic acid containing a terminal hydroxyl group. It has various unique properties and great economic value. We improved the two-step biosynthesis method of 10-HDA. The conversion rate of the intermediate product trans-2-decenoic acid in the first step of 10-HDA synthesis could reach 93.1 ± 1.3% by combining transporter overexpression and permeation technology strategies. Moreover, the extracellular trans-2-decenoic acid content was five times greater than the intracellular content when 2.0% (v/v) triton X-100 and 1.2% (v/v) tween-80 were each used. In the second step of 10-HDA synthesis, we regenerated NAD(P)H by overexpressing a glucose dehydrogenase with the P450 enzyme (CYP153A33/M228L-CPRBM3) in Escherichia coli, improving the catalytic performance of the trans-2-decenoic acid terminal hydroxylation. Finally, the yield of 10-HDA was 486.5 mg/L using decanoic acid as the substrate with two-step continuous biosynthesis. Our research provides a simplified production strategy to promote the two-step continuous whole-cell catalytic biosynthesis of 10-HDA and other α,β-unsaturated carboxylic acid derivatives.
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Affiliation(s)
- Li Wang
- State
Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong 250353, China
- Key
Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong 250353, China
| | - Leilei Wang
- State
Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong 250353, China
- Key
Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong 250353, China
| | - Ruiming Wang
- State
Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong 250353, China
- Key
Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong 250353, China
| | - Zhaoyun Wang
- State
Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong 250353, China
- Key
Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong 250353, China
| | - Junqing Wang
- State
Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong 250353, China
- Key
Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong 250353, China
| | - Haibo Yuan
- State
Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong 250353, China
- Key
Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong 250353, China
| | - Jing Su
- State
Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong 250353, China
- Key
Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong 250353, China
| | - Yan Li
- Shandong
Freda Biotech Co., Ltd, Jinan, Shandong 250101, China
| | - Suzhen Yang
- Shandong
Freda Biotech Co., Ltd, Jinan, Shandong 250101, China
| | - Tingting Han
- Shandong
Freda Biotech Co., Ltd, Jinan, Shandong 250101, China
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5
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Li Y, Wang J, Wang F, Wang L, Wang L, Xu Z, Yuan H, Yang X, Li P, Su J, Wang R. Production of 10-Hydroxy-2-decenoic Acid from Decanoic Acid via Whole-Cell Catalysis in Engineered Escherichia coli. CHEMSUSCHEM 2022; 15:e202102152. [PMID: 34796684 DOI: 10.1002/cssc.202102152] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/18/2021] [Indexed: 06/13/2023]
Abstract
10-Hydroxy-2-decenoic acid (10-HDA) is a terminal hydroxylated medium-chain α,β-unsaturated carboxylic acid that performs various unique physiological activities and has a wide market value. Therefore, development of an environmentally friendly, safe, and high-efficiency route to synthesize 10-HDA is required. Here, the β-oxidation pathway of Escherichia coli was modified and a P450 terminal hydroxylase (CYP153A33-CPRBM3 ) was rationally designed to synthesize 10-HDA using decanoic acid as a substrate via two-step whole-cell catalysis. Different homologues of FadDs, FadEs, and YdiIs were analyzed in the first step of the conversion of decanoic acid to trans- -2- decenoic acid. In the second step, CYP153A33 (M228L)-CPRBM3 efficiently catalyzed the conversion of trans- -2- decenoic acid to 10-HDA. Finally, 217 mg L-1 10-HDA was obtained with 500 mg L-1 decanoic acid. This study provides a strategy for biosynthesis of 10-HDA and other α, β-unsaturated carboxylic acid derivatives from specific fatty acids.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Junqing Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Fen Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Li Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Leilei Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Ziqi Xu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Haibo Yuan
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Xiaohui Yang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Piwu Li
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Jing Su
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Ruiming Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
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6
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Yan Y, Wu J, Hu G, Gao C, Guo L, Chen X, Liu L, Song W. Current state and future perspectives of cytochrome P450 enzymes for C–H and C=C oxygenation. Synth Syst Biotechnol 2022; 7:887-899. [PMID: 35601824 PMCID: PMC9112060 DOI: 10.1016/j.synbio.2022.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 01/11/2023] Open
Abstract
Cytochrome P450 enzymes (CYPs) catalyze a series of C–H and C=C oxygenation reactions, including hydroxylation, epoxidation, and ketonization. They are attractive biocatalysts because of their ability to selectively introduce oxygen into inert molecules under mild conditions. This review provides a comprehensive overview of the C–H and C=C oxygenation reactions catalyzed by CYPs and the various strategies for achieving higher selectivity and enzymatic activity. Furthermore, we discuss the application of C–H and C=C oxygenation catalyzed by CYPs to obtain the desired chemicals or pharmaceutical intermediates in practical production. The rapid development of protein engineering for CYPs provides excellent biocatalysts for selective C–H and C=C oxygenation reactions, thereby promoting the development of environmentally friendly and sustainable production processes.
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Affiliation(s)
- Yu Yan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- 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
| | - Guipeng Hu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- 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
| | - 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
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
- Corresponding author.
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7
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Dong YL, Chong GG, Li CX, Chen Q, Pan J, Li AT, Xu JH. Carving the Active Site of CYP153A7 Monooxygenase for Improving Terminal Hydroxylation of Medium-Chain Fatty Acids. Chembiochem 2022; 23:e202200063. [PMID: 35257464 DOI: 10.1002/cbic.202200063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/07/2022] [Indexed: 11/10/2022]
Abstract
The P450-mediated terminal hydroxylation of non-activated C-H bonds is a chemically challenging reaction. CYP153A7 monooxygenase discovered in Sphingomonas sp. HXN200 belongs to the CYP153A subfamily and shows a pronounced terminal selectivity. Herein, we report the significantly improved terminal hydroxylation activity of CYP153A7 by redesign of the substrate binding pocket based on molecular docking of CYP153A7-C 8:0 and sequence alignments. Some of the resultant single mutants were advantageous over the wild-type enzyme with higher reaction rates, achieving a complete conversion of n- octanoic acid (C 8:0. 1 mM) in a shorter period. Especially, a single-mutation variant, D258E, showed 3.8-fold higher catalytic efficiency than the wild type toward the terminal hydroxylation of medium-chain fatty acid C 8:0 into the high value-added product 8-hydroxyoctanoic acid.
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Affiliation(s)
- Ya-Li Dong
- East China University of Science and Technology, State Key Laboratory of Bioreactor Engineering, CHINA
| | - Gang-Gang Chong
- East China University of Science and Technology, State Key Laboratory of Bioreactor Engineering, 130 Meilong Road, Shanghai 200237, China, 200237, Shanghai, CHINA
| | - Chun-Xiu Li
- East China University of Science and Technology, State Key Laboratory of Bioreactor Engineering, CHINA
| | - Qi Chen
- East China University of Science and Technology, State Key Laboratory of Bioreactor Engineering, CHINA
| | - Jiang Pan
- East China University of Science and Technology, State Key Laboratory of Bioreactor Engineering, CHINA
| | - Ai-Tao Li
- Hubei University, College of Life Science, CHINA
| | - Jian-He Xu
- East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, CHINA
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8
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Seo E, Kim M, Park S, Park S, Oh D, Bornscheuer U, Park J. Enzyme Access Tunnel Engineering in Baeyer‐Villiger Monooxygenases to Improve Oxidative Stability and Biocatalyst Performance. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202101044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Eun‐Ji Seo
- Department of Food Science and Engineering Ewha Womans University Seoul 03760 Republic of Korea
| | - Myeong‐Ju Kim
- Department of Food Science and Engineering Ewha Womans University Seoul 03760 Republic of Korea
| | - So‐Yeon Park
- Department of Food Science and Engineering Ewha Womans University Seoul 03760 Republic of Korea
| | - Seongsoon Park
- Department of Chemistry, Center for NanoBio Applied Technology Sungshin Women's University Seoul 01133 Republic of Korea
| | - Deok‐Kun Oh
- Department of Bioscience and Biotechnology Konkuk University Seoul 05029 Republic of Korea
| | - Uwe Bornscheuer
- Institute of Biochemistry, Department of Biotechnology & Enzyme Catalysis Greifswald University Greifswald 17487 Germany
| | - Jin‐Byung Park
- Department of Food Science and Engineering Ewha Womans University Seoul 03760 Republic of Korea
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9
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Nieto-Domínguez M, Nikel PI. Intersecting Xenobiology and Neometabolism To Bring Novel Chemistries to Life. Chembiochem 2020; 21:2551-2571. [PMID: 32274875 DOI: 10.1002/cbic.202000091] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/09/2020] [Indexed: 12/19/2022]
Abstract
The diversity of life relies on a handful of chemical elements (carbon, oxygen, hydrogen, nitrogen, sulfur and phosphorus) as part of essential building blocks; some other atoms are needed to a lesser extent, but most of the remaining elements are excluded from biology. This circumstance limits the scope of biochemical reactions in extant metabolism - yet it offers a phenomenal playground for synthetic biology. Xenobiology aims to bring novel bricks to life that could be exploited for (xeno)metabolite synthesis. In particular, the assembly of novel pathways engineered to handle nonbiological elements (neometabolism) will broaden chemical space beyond the reach of natural evolution. In this review, xeno-elements that could be blended into nature's biosynthetic portfolio are discussed together with their physicochemical properties and tools and strategies to incorporate them into biochemistry. We argue that current bioproduction methods can be revolutionized by bridging xenobiology and neometabolism for the synthesis of new-to-nature molecules, such as organohalides.
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Affiliation(s)
- Manuel Nieto-Domínguez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
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10
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Whole-cell biocatalysis using cytochrome P450 monooxygenases for biotransformation of sustainable bioresources (fatty acids, fatty alkanes, and aromatic amino acids). Biotechnol Adv 2020; 40:107504. [PMID: 31926255 DOI: 10.1016/j.biotechadv.2020.107504] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/09/2019] [Accepted: 01/06/2020] [Indexed: 12/25/2022]
Abstract
Cytochrome P450s (CYPs) are heme-thiolated enzymes that catalyze the oxidation of CH bonds in a regio and stereoselective manner. Activation of the non-activated carbon atom can be further enhanced by multistep chemo-enzymatic reactions; moreover, several useful chemicals can be synthesized to provide alternative organic synthesis routes. Given their versatile functionality, CYPs show promise in a number of biotechnological fields. Recently, various CYPs, along with their sequences and functionalities, have been identified owing to rapid developments in sequencing technology and molecular biotechnology. In addition to these discoveries, attempts have been made to utilize CYPs to industrially produce biochemicals from available and sustainable bioresources such as oil, amino acids, carbohydrates, and lignin. Here, these accomplishments, particularly those involving the use of CYP enzymes as whole-cell biocatalysts for bioresource biotransformation, will be reviewed. Further, recently developed biotransformation pathways that result in gram-scale yields of fatty acids and fatty alkanes as well as aromatic amino acids, which depend on the hosts used for CYP expression, and the nature of the multistep reactions will be discussed. These pathways are similar regardless of whether the hosts are CYP-producing or non-CYP-producing; the limitations of these methods and the ways to overcome them are reviewed here.
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11
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Fiorentini F, Hatzl AM, Schmidt S, Savino S, Glieder A, Mattevi A. The Extreme Structural Plasticity in the CYP153 Subfamily of P450s Directs Development of Designer Hydroxylases. Biochemistry 2018; 57:6701-6714. [DOI: 10.1021/acs.biochem.8b01052] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Filippo Fiorentini
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, Pavia 27100, Italy
| | - Anna-Maria Hatzl
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
| | - Sandy Schmidt
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
| | - Simone Savino
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, Pavia 27100, Italy
| | - Anton Glieder
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, Pavia 27100, Italy
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12
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Xu LH, Du YL. Rational and semi-rational engineering of cytochrome P450s for biotechnological applications. Synth Syst Biotechnol 2018; 3:283-290. [PMID: 30533540 PMCID: PMC6263019 DOI: 10.1016/j.synbio.2018.10.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/02/2018] [Accepted: 10/04/2018] [Indexed: 01/08/2023] Open
Abstract
The cytochrome P450 enzymes are ubiquitous heme-thiolate proteins performing regioselective and stereoselective oxygenation reactions in cellular metabolism. Due to their broad substrate scope and catalytic versatility, P450 enzymes are also attractive candidates for many industrial and biopharmaceutical applications. For particular uses, enzyme properties of P450s can be further optimized through directed evolution, rational, and semi-rational engineering approaches, all of which introduce mutations within the P450 structures. In this review, we describe the recent applications of these P450 engineering approaches and highlight the key regions and residues that have been identified using such approaches. These “hotspots” lie within critical functional areas of the P450 structure, including the active site, the substrate access channel, and the redox partner interaction interface.
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Affiliation(s)
- Lian-Hua Xu
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
- Corresponding author.
| | - Yi-Ling Du
- Institute of Pharmaceutical Biotechnology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Corresponding author.
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Kim J, Yoo HW, Kim M, Kim EJ, Sung C, Lee PG, Park BG, Kim BG. Rewiring FadR regulon for the selective production of ω-hydroxy palmitic acid from glucose in Escherichia coli. Metab Eng 2018; 47:414-422. [PMID: 29719215 DOI: 10.1016/j.ymben.2018.04.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/19/2018] [Accepted: 04/28/2018] [Indexed: 12/28/2022]
Abstract
ω-Hydroxy palmitic acid (ω-HPA) is a valuable compound for an ingredient of artificially synthesized ceramides and an additive for lubricants and adhesives. Production of such a fatty acid derivative is limited by chemical catalysis, but plausible by biocatalysis. However, its low productivity issue, including formations of unsaturated fatty acid (UFA) byproducts in host cells, remains as a hurdle toward industrial biological processes. In this study, to achieve selective and high-level production of ω-HPA from glucose in Escherichia coli, FadR, a native transcriptional regulator of fatty acid metabolism, and its regulon were engineered. First, FadR was co-expressed with a thioesterase with a specificity toward palmitic acid production to enhance palmitic acid production yield, but a considerable quantity of UFAs was also produced. In order to avoid the UFA production caused by fadR overexpression, FadR regulon was rewired by i) mutating FadR consensus binding sites of fabA or fabB, ii) integrating fabZ into fabI operon, and iii) enhancing the strength of fabI promoter. This approach led to dramatic increases in both proportion (48.3-83.0%) and titer (377.8 mg/L to 675.8 mg/L) of palmitic acid, mainly due to the decrease in UFA synthesis. Introducing a fatty acid ω-hydroxylase, CYP153A35, into the engineered strain resulted in a highly selective production of ω-HPA (83.5 mg/L) accounting for 87.5% of total ω-hydroxy fatty acids. Furthermore, strategies, such as i) enhancement in CYP153A35 activity, ii) expression of a fatty acid transporter, iii) supplementation of triton X-100, and iv) separation of the ω-HPA synthetic pathway into two strains for a co-culture system, were applied and resulted in 401.0 mg/L of ω-HPA production. For such selective productions of palmitic acid and ω-HPA, the rewiring of FadR regulation in E. coli is a promising strategy to develop an industrial process with economical downstream processing.
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Affiliation(s)
- Joonwon Kim
- School of Chemical and Biological Engineering, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Hee-Wang Yoo
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea; Interdisciplinary Program of Bioengineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Minsuk Kim
- Institute of Engineering Research, Seoul National University, Seoul 08826, Republic of Korea
| | - Eun-Jung Kim
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea; Bio-MAX Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Changmin Sung
- Doping Control Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Pyung-Gang Lee
- School of Chemical and Biological Engineering, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Beom Gi Park
- School of Chemical and Biological Engineering, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Byung-Gee Kim
- School of Chemical and Biological Engineering, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea; Interdisciplinary Program of Bioengineering, Seoul National University, Seoul 08826, Republic of Korea; Institute of Engineering Research, Seoul National University, Seoul 08826, Republic of Korea.
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14
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Affiliation(s)
- Yujie Liang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
| | - Jialiang Wei
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
| | - Xu Qiu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
| | - Ning Jiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
- State Key Laboratory of Organometallic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
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15
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16
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Microbial synthesis of medium-chain chemicals from renewables. Nat Biotechnol 2017; 35:1158-1166. [PMID: 29220020 DOI: 10.1038/nbt.4022] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 10/31/2017] [Indexed: 12/28/2022]
Abstract
Linear, medium-chain (C8-C12) hydrocarbons are important components of fuels as well as commodity and specialty chemicals. As industrial microbes do not contain pathways to produce medium-chain chemicals, approaches such as overexpression of endogenous enzymes or deletion of competing pathways are not available to the metabolic engineer; instead, fatty acid synthesis and reversed β-oxidation are manipulated to synthesize medium-chain chemical precursors. Even so, chain lengths remain difficult to control, which means that purification must be used to obtain the desired products, titers of which are typically low and rarely exceed milligrams per liter. By engineering the substrate specificity and activity of the pathway enzymes that generate the fatty acyl intermediates and chain-tailoring enzymes, researchers can boost the type and yield of medium-chain chemicals. Development of technologies to both manipulate chain-tailoring enzymes and to assay for products promises to enable the generation of g/L yields of medium-chain chemicals.
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17
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Jung E, Park BG, Yoo HW, Kim J, Choi KY, Kim BG. Semi-rational engineering of CYP153A35 to enhance ω-hydroxylation activity toward palmitic acid. Appl Microbiol Biotechnol 2017; 102:269-277. [DOI: 10.1007/s00253-017-8584-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 09/01/2017] [Accepted: 10/09/2017] [Indexed: 01/14/2023]
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18
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Li G, Yao P, Gong R, Li J, Liu P, Lonsdale R, Wu Q, Lin J, Zhu D, Reetz MT. Simultaneous engineering of an enzyme's entrance tunnel and active site: the case of monoamine oxidase MAO-N. Chem Sci 2017; 8:4093-4099. [PMID: 30155214 PMCID: PMC6099926 DOI: 10.1039/c6sc05381e] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/30/2017] [Indexed: 12/19/2022] Open
Abstract
A new directed evolution approach is presented to enhance the activity of an enzyme and to manipulate stereoselectivity by focusing iterative saturation mutagenesis (ISM) simultaneously on residues lining the entrance tunnel and the binding pocket. This combined mutagenesis strategy was applied successfully to the monoamine oxidase from Aspergillus niger (MAO-N) in the reaction of sterically demanding substrates which are of interest in the synthesis of chiral pharmaceuticals based on the benzo-piperidine scaffold. Reversal of enantioselectivity of Turner-type deracemization was achieved in the synthesis of (S)-1,2,3,4-tetrahydro-1-methyl-isoquinoline, (S)-1,2,3,4-tetrahydro-1-ethylisoquinoline and (S)-1,2,3,4-tetrahydro-1-isopropylisoquinoline. Extensive molecular dynamics simulations indicate that the altered catalytic profile is due to increased hydrophobicity of the entrance tunnel acting in concert with the altered shape of the binding pocket.
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Affiliation(s)
- Guangyue Li
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 , Mülheim an der Ruhr , Germany .
- Fachbereich Chemie , Philipps-Universität , Hans-Meerwein-Strasse , 35032 Marburg , Germany
| | - Peiyuan Yao
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China . ;
| | - Rui Gong
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China . ;
| | - Jinlong Li
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China . ;
| | - Pi Liu
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China . ;
| | - Richard Lonsdale
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 , Mülheim an der Ruhr , Germany .
- Fachbereich Chemie , Philipps-Universität , Hans-Meerwein-Strasse , 35032 Marburg , Germany
| | - Qiaqing Wu
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China . ;
| | - Jianping Lin
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China . ;
| | - Dunming Zhu
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China . ;
| | - Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 , Mülheim an der Ruhr , Germany .
- Fachbereich Chemie , Philipps-Universität , Hans-Meerwein-Strasse , 35032 Marburg , Germany
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Ebert MC, Pelletier JN. Computational tools for enzyme improvement: why everyone can - and should - use them. Curr Opin Chem Biol 2017; 37:89-96. [PMID: 28231515 DOI: 10.1016/j.cbpa.2017.01.021] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/25/2017] [Accepted: 01/30/2017] [Indexed: 12/12/2022]
Abstract
This review presents computational methods that experimentalists can readily use to create smart libraries for enzyme engineering and to obtain insights into protein-substrate complexes. Computational tools have the reputation of being hard to use and inaccurate compared to experimental methods in enzyme engineering, yet they are essential to probe datasets of ever-increasing size and complexity. In recent years, bioinformatics groups have made a huge leap forward in providing user-friendly interfaces and accurate algorithms for experimentalists. These methods guide efficient experimental planning and allow the enzyme engineer to rationalize time and resources. Computational tools nevertheless face challenges in the realm of transient modern technology.
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Affiliation(s)
- Maximilian Ccjc Ebert
- Département de biochimie and Center for Green Chemistry and Catalysis (CGCC), Université de Montréal, Montréal, QC H3T 1J4, Canada; PROTEO, The Québec Network for Research on Protein Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
| | - Joelle N Pelletier
- Département de biochimie and Center for Green Chemistry and Catalysis (CGCC), Université de Montréal, Montréal, QC H3T 1J4, Canada; PROTEO, The Québec Network for Research on Protein Function, Engineering and Applications, Québec, QC G1V 0A6, Canada; Département de chimie, Université de Montréal, Montréal, QC H3T 1J4, Canada.
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20
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Hoffmann SM, Danesh-Azari HR, Spandolf C, Weissenborn MJ, Grogan G, Hauer B. Structure-Guided Redesign of CYP153AM.aqfor the Improved Terminal Hydroxylation of Fatty Acids. ChemCatChem 2016. [DOI: 10.1002/cctc.201600680] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Sara M. Hoffmann
- Institute of Technical Biochemistry; Universität Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Hamid-Reza Danesh-Azari
- York Structural Biology Laboratory; Department of Chemistry; University of York; YO10 5DD York United Kingdom
| | - Claudia Spandolf
- York Structural Biology Laboratory; Department of Chemistry; University of York; YO10 5DD York United Kingdom
| | - Martin J. Weissenborn
- Institute of Technical Biochemistry; Universität Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Gideon Grogan
- York Structural Biology Laboratory; Department of Chemistry; University of York; YO10 5DD York United Kingdom
| | - Bernhard Hauer
- Institute of Technical Biochemistry; Universität Stuttgart; Allmandring 31 70569 Stuttgart Germany
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