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Matsuzawa M, Ito J, Danjo K, Fukui K. Vanillin production by Corynebacterium glutamicum using heterologous aromatic carboxylic acid reductases. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:58. [PMID: 38693567 PMCID: PMC11064420 DOI: 10.1186/s13068-024-02507-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/20/2024] [Indexed: 05/03/2024]
Abstract
BACKGROUND Vanillin is a flavoring substance derived from vanilla. We are currently developing a biotransformation method for vanillin production using glucose. This report describes the last step in vanillin production: the conversion of vanillic acid to vanillin. First, we selected Corynebacterium glutamicum as the host owing to its high vanillin resistance. The aromatic aldehyde reductase gene (NCgl0324) and vanillic acid demethylase protein subunits A and B gene (vanAB, NCgl2300-NCgl2301) were deleted in C. glutamicum genome to avoid vanillin degradation. Next, we searched for an aromatic carboxylic acid reductase (ACAR), which converts vanillic acid to vanillin. Seventeen ACAR homologs from various organisms were introduced into C. glutamicum. RESULTS In vivo conversion experiments showed that eight ACARs were successfully expressed and produced vanillin. In terms of conversion activity and substrate specificity, the ACARs from Gordonia effusa, Coccomyxa subellipsoidea, and Novosphingobium malaysiense are promising candidates for commercial production. CONCLUSIONS Corynebacterium glutamicum harboring Gordonia effusa ACAR produced 22 g/L vanillin, which is, to the best of our knowledge, the highest accumulation reported in the literature. At the same time, we discovered ACAR from Novosphingobium malaysiense and Coccomyxa subellipsoidea C-169 with high substrate specificity. These findings are useful for reducing the byproducts.
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Affiliation(s)
- Miku Matsuzawa
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc, Kawasaki, Kanagawa, 210-8681, Japan
| | - Junko Ito
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc, Kawasaki, Kanagawa, 210-8681, Japan
| | - Keiko Danjo
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc, Kawasaki, Kanagawa, 210-8681, Japan
| | - Keita Fukui
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc, Kawasaki, Kanagawa, 210-8681, Japan.
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Agosto-Maldonado A, Guo J, Niu W. Engineering carboxylic acid reductases and unspecific peroxygenases for flavor and fragrance biosynthesis. J Biotechnol 2024; 385:1-12. [PMID: 38428504 PMCID: PMC11062483 DOI: 10.1016/j.jbiotec.2024.02.013] [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: 01/08/2024] [Revised: 02/23/2024] [Accepted: 02/25/2024] [Indexed: 03/03/2024]
Abstract
Emerging consumer demand for safer, more sustainable flavors and fragrances has created new challenges for the industry. Enzymatic syntheses represent a promising green production route, but the broad application requires engineering advancements for expanded diversity, improved selectivity, and enhanced stability to be cost-competitive with current methods. This review discusses recent advances and future outlooks for enzyme engineering in this field. We focus on carboxylic acid reductases (CARs) and unspecific peroxygenases (UPOs) that enable selective productions of complex flavor and fragrance molecules. Both enzyme types consist of natural variants with attractive characteristics for biocatalytic applications. Applying protein engineering methods, including rational design and directed evolution in concert with computational modeling, present excellent examples for property improvements to unleash the full potential of enzymes in the biosynthesis of value-added chemicals.
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Affiliation(s)
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States; The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States; The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States.
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3
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Li JM, Shi K, Li AT, Zhang ZJ, Yu HL, Xu JH. Development of a Thermodynamically Favorable Multi-enzyme Cascade Reaction for Efficient Sustainable Production of ω-Amino Fatty Acids and α,ω-Diamines. CHEMSUSCHEM 2024; 17:e202301477. [PMID: 38117609 DOI: 10.1002/cssc.202301477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/25/2023] [Accepted: 12/19/2023] [Indexed: 12/22/2023]
Abstract
Aliphatic ω-amino fatty acids (ω-AFAs) and α,ω-diamines (α,ω-DMs) are essential monomers for the production of nylons. Development of a sustainable biosynthesis route for ω-AFAs and α,ω-DMs is crucial in addressing the challenges posed by climate change. Herein, we constructed an unprecedented thermodynamically favorable multi-enzyme cascade (TherFavMEC) for the efficient sustainable biosynthesis of ω-AFAs and α,ω-DMs from cheap α,ω-dicarboxylic acids (α,ω-DAs). This TherFavMEC was developed by incorporating bioretrosynthesis analysis tools, reaction Gibbs free energy calculations, thermodynamic equilibrium shift strategies and cofactor (NADPH&ATP) regeneration systems. The molar yield of 6-aminohexanoic acid (6-ACA) from adipic acid (AA) was 92.3 %, while the molar yield from 6-ACA to 1,6-hexanediamine (1,6-HMD) was 96.1 %, which were significantly higher than those of previously reported routes. Furthermore, the biosynthesis of ω-AFAs and α,ω-DMs from 20.0 mM α,ω-DAs (C6-C9) was also performed, giving 11.2 mM 1,6-HMD (56.0 % yield), 14.8 mM 1,7-heptanediamine (74.0 % yield), 17.4 mM 1,8-octanediamine (87.0 % yield), and 19.7 mM 1,9-nonanediamine (98.5 % yield), respectively. The titers of 1,9-nonanediamine, 1,8-octanediamine, 1,7-heptanediamine and 1,6-HMD were improved by 328-fold, 1740-fold, 87-fold and 3.8-fold compared to previous work. Therefore, this work holds great potential for the bioproduction of ω-AFAs and α,ω-DMs.
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Affiliation(s)
- Ju-Mou Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Kun Shi
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Ai-Tao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology School of Life Sciences, Hubei University, #368 Youyi Road, Wuhan, 430062, P.R. China
| | - Zhi-Jun Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
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4
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Qin N, Zhu F, Liu Y, Liu D, Chen Z. Metabolic Engineering of Escherichia coli for De Novo Production of 1,2-Butanediol. ACS Synth Biol 2024; 13:351-357. [PMID: 38110368 DOI: 10.1021/acssynbio.3c00606] [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: 12/20/2023]
Abstract
1,2-Butanediol (1,2-BDO) is an important platform chemical widely utilized in the synthesis of polyester polyols, plasticizers, cosmetics, and pharmaceuticals. However, no natural metabolic pathway for its biosynthesis has been identified, and biological production of 1,2-BDO from renewable bioresources has not been reported so far. In this study, we designed and experimentally verified a feasible non-natural synthesis pathway for the de novo production of 1,2-BDO from renewable carbohydrates for the first time. This pathway extends the l-threonine synthesis pathway by introducing two artificial metabolic modules to sequentially convert l-threonine into 2-hydroxybutyric acid and 1,2-BDO. Following key enzyme screening and enhancement of l-threonine synthesis module in the chassis microorganism, the best engineered Escherichia coli strain was able to produce 0.15 g/L 1,2-BDO using glucose as the sole carbon source. This work lays the foundation for the bioproduction of 1,2-BDO from renewable resources.
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Affiliation(s)
- Nan Qin
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Fanghuan Zhu
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Yanyan Liu
- School of Physiology, Pharmacology & Neuroscience, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Dehua Liu
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Zhen Chen
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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5
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Lu H, Ouyang J, Liu WQ, Wu C, Li J. Enzyme-Polymer-Conjugate-Based Pickering Emulsions for Cell-Free Expression and Cascade Biotransformation. Angew Chem Int Ed Engl 2023; 62:e202312906. [PMID: 37966024 DOI: 10.1002/anie.202312906] [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: 09/01/2023] [Revised: 10/28/2023] [Accepted: 11/15/2023] [Indexed: 11/16/2023]
Abstract
In this study, we addressed the limitations of conventional enzyme-polymer-conjugate-based Pickering emulsions for interfacial biocatalysis, which traditionally suffer from nonspecific and uncontrollable conjugation positions that can impede catalytic performance. By introducing a non-canonical amino acid (ncAA) at a specific site on target enzymes, we enabled precise polymer-enzyme conjugation. These engineered conjugates then acted as biocatalytically active emulsifiers to stabilize Pickering emulsions, while encapsulating a cell-free protein synthesis (CFPS) system in the aqueous phase for targeted enzyme expression. The resulting cascade reaction system leveraged enzymes expressed in the aqueous phase and on the emulsion interface for optimized chemical biosynthesis. The use of the cell-free system eliminated the need for intact whole cells or purified enzymes, representing a significant advancement in biocatalysis. Remarkably, the integration of Pickering emulsion, precise enzyme-polymer conjugation, and CFPS resulted in a fivefold enhancement in catalytic performance as compared to traditional single-phase reactions. Therefore, our approach harnesses the combined strengths of advanced biochemical engineering techniques, offering an efficient and practical solution for the synthesis of value-added chemicals in various biocatalysis and biotransformation applications.
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Affiliation(s)
- Haofan Lu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Jingping Ouyang
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Wan-Qiu Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Changzhu Wu
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
- Danish Institute for Advanced Study (DIAS), University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
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Zhang R, Liu WQ, Ling S, Li J. Combining Cell-Free Expression and Multifactor Optimization for Enhanced Biosynthesis of Cinnamyl Alcohol. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37216486 DOI: 10.1021/acs.jafc.3c02340] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cell-free expression systems have emerged as a potent and promising platform for the biosynthesis of chemicals by reconstituting in vitro expressed enzymes. Here, we report cell-free biosynthesis of cinnamyl alcohol (cinOH) with enhanced productivity by using the Plackett-Burman experimental design for multifactor optimization. Initially, four enzymes were individually expressed in vitro and directly mixed to reconstitute a biosynthetic route for the synthesis of cinOH. Then, the Plackett-Burman experimental design was used to screen multiple reaction factors and found three crucial parameters (i.e., reaction temperature, reaction volume, and carboxylic acid reductase) for the cinOH production. With the optimum reaction conditions, approximately 300 μM of cinOH was synthesized after 10 h of cell-free biosynthesis. Extending the production time to 24 h also increased the production to a maximum yield of 807 μM, which is nearly 10 times higher than the initial yield without optimization. This study demonstrates that cell-free biosynthesis can be combined with other powerful optimization methodologies such as the Plackett-Burman experimental design for enhanced production of valuable chemicals.
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Affiliation(s)
- Ren Zhang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wan-Qiu Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Shengjie Ling
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
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7
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Basri RS, Rahman RNZRA, Kamarudin NHA, Ali MSM. Carboxylic acid reductases: Structure, catalytic requirements, and applications in biotechnology. Int J Biol Macromol 2023; 240:124526. [PMID: 37080403 DOI: 10.1016/j.ijbiomac.2023.124526] [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: 02/03/2023] [Revised: 04/07/2023] [Accepted: 04/16/2023] [Indexed: 04/22/2023]
Abstract
Biocatalysts have been gaining extra attention in recent decades due to their industrial-relevance properties, which may hasten the transition to a cleaner environment. Carboxylic acid reductases (CARs) are large, multi-domain proteins that can catalyze the reduction of carboxylic acids to corresponding aldehydes, with the presence of adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide phosphate (NADPH). This biocatalytic reaction is of great interest due to the abundance of carboxylic acids in nature and the ability of CAR to convert carboxylic acids to a wide range of aldehydes essentially needed as end products such as vanillin or reaction intermediates for several compounds production such as alcohols, alkanes, and amines. This modular enzyme, found in bacteria and fungi, demands an activation via post-translational modification by the phosphopantetheinyl transferase (PPTase). Recent advances in the characterization and structural studies of CARs revealed valuable information about the enzymes' dynamics, mechanisms, and unique features. In this comprehensive review, we summarize the previous findings on the phylogeny, structural and mechanistic insight of the domains, post-translational modification requirement, strategies for the cofactors regeneration, the extensively broad aldehyde-related industrial application properties of CARs, as well as their recent immobilization approaches.
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Affiliation(s)
- Rose Syuhada Basri
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Nor Hafizah Ahmad Kamarudin
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Centre of Foundation Studies for Agricultural Science, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
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8
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Systematic metabolic engineering of Escherichia coli for the enhanced production of cinnamaldehyde. Metab Eng 2023; 76:63-74. [PMID: 36639020 DOI: 10.1016/j.ymben.2023.01.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/16/2022] [Accepted: 01/09/2023] [Indexed: 01/12/2023]
Abstract
Cinnamaldehyde (CAD) derived from cinnamon bark has received much attention for its potential as a nematicide and food additive. Previously, we have succeeded in developing an Escherichia coli strain (YHP05) capable of synthesizing cinnamaldehyde; however, the production titer (75 mg/L) was not sufficient for commercialization. Herein, to develop an economical and sustainable production bioprocess, we further engineered the YHP05 strain for non-auxotrophic, antibiotic-free, inducer-free hyperproduction of CAD using systematic metabolic engineering. First, the conversion of trans-cinnamic acid (t-CA) to CAD was improved by the co-expression of carboxylic acid reductase and phosphopantetheinyl transferase (PPTase) genes. Second, to prevent the spontaneous conversion of CAD to cinnamyl alcohol, 10 endogenous reductase and dehydrogenase genes were deleted. Third, all expression cassettes were integrated into the chromosomal DNA using an auto-inducible system for antibiotic- and inducer-free production. Subsequently, to facilitate CAD production, available pools of cofactors (NADPH, CoA, and ATP) were increased, and acetate pathways were deleted. With the final antibiotic-, plasmid-, and inducer-free strain (H-11MPmR), fed-batch cultivations combined with in situ product recovery (ISPR) were performed, and the production titer of CAD as high as 3.8 g/L could be achieved with 49.1 mg/L/h productivity, which is the highest CAD titer ever reported.
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Liu Y, Liu WQ, Huang S, Xu H, Lu H, Wu C, Li J. Cell-free metabolic engineering enables selective biotransformation of fatty acids to value-added chemicals. Metab Eng Commun 2022; 16:e00217. [PMID: 36578475 PMCID: PMC9791597 DOI: 10.1016/j.mec.2022.e00217] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022] Open
Abstract
Fatty acid-derived products such as alkanes, fatty aldehydes, and fatty alcohols have many applications in the chemical industry. These products are predominately produced from fossil resources, but their production processes are often not environmentally friendly. While microbes like Escherichia coli have been engineered to convert fatty acids to corresponding products, the design and optimization of metabolic pathways in cells for high productivity is challenging due to low mass transfer, heavy metabolic burden, and intermediate/product toxicity. Here, we describe an E. coli-based cell-free protein synthesis (CFPS) platform for in vitro conversion of long-chain fatty acids to value-added chemicals with product selectivity, which can also avoid the above issues when using microbial production systems. We achieve the selective biotransformation by cell-free expression of different enzymes and the use of different conditions (e.g., light and heating) to drive the biocatalysis toward different final products. Specifically, in response to blue light, cell-free expressed fatty acid photodecarboxylase (CvFAP, a photoenzyme) was able to convert fatty acids to alkanes with approximately 90% conversion. When the expressed enzyme was switched to carboxylic acid reductase (CAR), fatty acids were reduced to corresponding fatty aldehydes, which, however, could be further reduced to fatty alcohols by endogenous reductases in the cell-free system. By using a thermostable CAR and a heating treatment, the endogenous reductases were deactivated and fatty aldehydes could be selectively accumulated (>97% in the product mixture) without over-reduction to alcohols. Overall, our cell-free platform provides a new strategy to convert fatty acids to valuable chemicals with notable properties of operation flexibility, reaction controllability, and product selectivity.
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Affiliation(s)
- Yushi Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Wan-Qiu Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Shuhui Huang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Huiling Xu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Haofan Lu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Changzhu Wu
- Danish Institute for Advanced Study (DIAS) and Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, 5230, Denmark
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China,Corresponding author.
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Basri RS, Rahman RNZRA, Kamarudin NHA, Latip W, Ali MSM. Characterization of Carboxylic Acid Reductase from Mycobacterium phlei Immobilized onto Seplite LX120. Polymers (Basel) 2022; 14:polym14204375. [PMID: 36297953 PMCID: PMC9609965 DOI: 10.3390/polym14204375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/02/2022] [Accepted: 10/03/2022] [Indexed: 11/16/2022] Open
Abstract
A multi-domain oxidoreductase, carboxylic acid reductase (CAR), can catalyze the one-step reduction of carboxylic acid to aldehyde. This study aimed to immobilize bacterial CAR from a moderate thermophile Mycobacterium phlei (MpCAR). It was the first work reported on immobilizing bacterial CAR onto a polymeric support, Seplite LX120, via simple adsorption. Immobilization time and protein load were optimized for MpCAR immobilization. The immobilized MpCAR showed optimal activity at 60 °C and pH 9. It was stable over a wide range of temperatures (10 to 100 °C) and pHs (4–11), retaining more than 50% of its activity. The immobilized MpCAR also showed stability in polar solvents. The adsorption of MpCAR onto the support was confirmed by Scanning Electron Microscopy (SEM), Fourier-Transform Infrared (FTIR) spectroscopy, and Brunauer–Emmett–Teller (BET) analysis. The immobilized MpCAR could be stored for up to 6 weeks at 4 °C and 3 weeks at 25 °C. Immobilized MpCAR showed great operational stability, as 59.68% of its activity was preserved after 10 assay cycles. The immobilized MpCAR could also convert approximately 2.6 mM of benzoic acid to benzaldehyde at 60 °C. The successfully immobilized MpCAR on Seplite LX120 exhibited improved properties that benefit green industrial processes.
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Affiliation(s)
- Rose Syuhada Basri
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd. Rahman
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Nor Hafizah Ahmad Kamarudin
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Centre of Foundation Studies for Agricultural Science, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Wahhida Latip
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Correspondence:
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11
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Wang Q, Ma L, Wang Z, Chen Q, Wang Q, Qi Q. Construction and yield optimization of a cinnamylamine biosynthesis route in Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:100. [PMID: 36175923 PMCID: PMC9524069 DOI: 10.1186/s13068-022-02199-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/22/2022] [Indexed: 11/10/2022]
Abstract
Background With the development of metabolic engineering and synthetic biology, the biosynthesis of aromatic compounds has attracted much attention. Cinnamylamine is an aromatic compound derived from l-phenylalanine, which is used in the synthesis of biologically active molecules, including drugs, and energetic materials. Cinnamylamine has been mainly synthesized by chemical methods to date, and few reports have focused on the biosynthesis of cinnamylamine. Therefore, it is desirable to establish an efficient biosynthesis method for cinnamylamine. Results The ω-aminotransferase Cv-ωTA from Chromobacterium violaceum has been demonstrated to have high enzyme activity in the conversion of cinnamaldehyde to cinnamylamine. To prevent the preferable conversion of cinnamaldehyde to cinnamyl alcohol in wild-type Escherichia coli, the E. coli MG1655 strain with reduced aromatic aldehyde reduction (RARE) in which six aldehyde ketone reductase and alcohol dehydrogenase genes have been knocked out was employed. Then, the carboxylic acid reductase from Neurospora crassa (NcCAR) and phosphopantetheinyl transferase (PPTase) from E. coli were screened for a high conversion rate of cinnamic acid to cinnamaldehyde. To shift the equilibrium of the reaction toward cinnamylamine, saturation mutagenesis of Cv-ωTA at key amino acid residues was performed, and Cv-ωTA Y168G had the highest conversion rate with 88.56 mg/L cinnamylamine obtained after 4 h of fermentation. Finally, by optimizing the substrates and the supply of the cofactors, PLP and NADPH, in the fermentation, the yield of cinnamylamine in engineered E. coli reached 523.15 mg/L. Conclusion We achieved the first biosynthesis of cinnamylamine using cinnamic acid as the precursor in E. coli using a combinatorial metabolic engineering strategy. This study provides a reference for the biosynthesis of other amine compounds and lays a foundation for the de novo synthesis of cinnamylamine. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02199-7.
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12
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Winkler M, Ling JG. Biocatalytic carboxylate reduction – recent advances and new enzymes. ChemCatChem 2022. [DOI: 10.1002/cctc.202200441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Margit Winkler
- Technische Universitat Graz Austrian Centre of Industrial Biotechnology Petersgasse 14 8010 Graz AUSTRIA
| | - Jonathan Guyang Ling
- Universiti Kebangsaan Malaysia Fakulti Sains dan Teknologi Department of Biological Sciences and Biotechnology 43600 Bangi MALAYSIA
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13
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Carboxylic acid reductases enable intramolecular lactamization reactions. GREEN SYNTHESIS AND CATALYSIS 2022. [DOI: 10.1016/j.gresc.2022.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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14
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Maphatsoe MM, Hashem C, Ling JG, Horvat M, Rumbold K, Bakar FDA, Winkler M. Characterization and Immobilization of Pycnoporus cinnabarinus Carboxylic Acid Reductase, PcCAR2. J Biotechnol 2021; 345:47-54. [PMID: 34954290 DOI: 10.1016/j.jbiotec.2021.12.010] [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: 10/21/2021] [Revised: 12/14/2021] [Accepted: 12/20/2021] [Indexed: 10/19/2022]
Abstract
Carboxylic acid reductases (CARs) are well-known for their eminent selective one-step synthesis of carboxylic acids to aldehydes. To date, however, few CARs have been identified and characterized, especially from fungal sources. In this study, the CAR from the white rot fungus Pycnoporus cinnabarinus (PcCAR2) was expressed in Escherichia coli. PcCAR2's biochemical properties were explored in vitro after purification, revealing a melting temperature of 53°C, while the reaction temperature optimum was at 35°C. In the tested buffers, the enzyme showed a pH optimum of 6.0 and notably, a similar activity up to pH 7.5. PcCAR2 was immobilized to explore its potential as a recyclable biocatalyst. PcCAR2 showed no critical loss of activity after six cycles, with an average conversion to benzaldehyde of more than 85 percent per cycle. Immobilization yield and efficiency were 82% and 76%, respectively, on Ni-sepharose. Overall, our findings contribute to the characterization of a thermotolerant fungal CAR, and established a more sustainable use of the valuable biocatalyst.
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Affiliation(s)
- Masethabela Maria Maphatsoe
- Industrial Microbiology & Biotechnology Laboratory, School of Molecular and Cell Biology, University of the Witwatersrand, 2000 Johannesburg, South Africa
| | - Chiam Hashem
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
| | - Jonathan Guyang Ling
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Melissa Horvat
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
| | - Karl Rumbold
- Industrial Microbiology & Biotechnology Laboratory, School of Molecular and Cell Biology, University of the Witwatersrand, 2000 Johannesburg, South Africa
| | - Farah Diba Abu Bakar
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Margit Winkler
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria; Austrian Centre of Industrial Biotechnology (acib GmbH), Petersgasse 14, 8010 Graz, Austria.
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15
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Wang L, Sun Y, Diao S, Jiang S, Wang H, Wei D. Rational hinge engineering of carboxylic acid reductase from Mycobacterium smegmatis enhances its catalytic efficiency in biocatalysis. Biotechnol J 2021; 17:e2100441. [PMID: 34862729 DOI: 10.1002/biot.202100441] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/13/2021] [Accepted: 11/15/2021] [Indexed: 11/11/2022]
Abstract
BACKGROUND Carboxylic acid reductases (CARs) represent useful tools for the production of aldehydes from ubiquitous organic carboxylic acids. However, the low catalytic efficiency of these enzymes hampers their application. METHODS Herein, a CAR originating from Mycobacterium smegmatis was redesigned through rational hinge engineering to enhance the catalytic efficiency. RESULTS Based on the unique domain architecture of CARs and their superfamily, a mutagenesis library of the hinge region was designed. The best mutant R505I/N506K showed a 6.57-fold improved catalytic efficiency. Molecular dynamics simulations showed the increased catalytic efficiency was due to the strong binding of the acyl-AMP complex with it. Meanwhile, the ε-nitrogen atom of Lys610 frequently interacted with the ribose-ring oxygen atom of the complex, the distance (d1) between them represents a great indicator for that. The d1 value was used as a nimble indicator to evaluate unexplored mutants of that region for enhanced activity by in silico mutational experiments. Overall, eight mutants were identified to show higher enhanced activity compared with wild-type enzyme and R505F/N506G showed the highest catalytic efficiency. CONCLUSION Altogether, the two-step strategy used here provided useful references for the engineering of CARs and other similar multiple-domain enzymes.
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Affiliation(s)
- Liuzhu Wang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Yangyang Sun
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Shiqing Diao
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Shuiqin Jiang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Hualei Wang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
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16
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Dickey RM, Forti AM, Kunjapur AM. Advances in engineering microbial biosynthesis of aromatic compounds and related compounds. BIORESOUR BIOPROCESS 2021; 8:91. [PMID: 38650203 PMCID: PMC10992092 DOI: 10.1186/s40643-021-00434-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/18/2021] [Indexed: 01/14/2023] Open
Abstract
Aromatic compounds have broad applications and have been the target of biosynthetic processes for several decades. New biomolecular engineering strategies have been applied to improve production of aromatic compounds in recent years, some of which are expected to set the stage for the next wave of innovations. Here, we will briefly complement existing reviews on microbial production of aromatic compounds by focusing on a few recent trends where considerable work has been performed in the last 5 years. The trends we highlight are pathway modularization and compartmentalization, microbial co-culturing, non-traditional host engineering, aromatic polymer feedstock utilization, engineered ring cleavage, aldehyde stabilization, and biosynthesis of non-standard amino acids. Throughout this review article, we will also touch on unmet opportunities that future research could address.
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Affiliation(s)
- Roman M Dickey
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, USA
| | - Amanda M Forti
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, USA
| | - Aditya M Kunjapur
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, USA.
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17
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Intasian P, Prakinee K, Phintha A, Trisrivirat D, Weeranoppanant N, Wongnate T, Chaiyen P. Enzymes, In Vivo Biocatalysis, and Metabolic Engineering for Enabling a Circular Economy and Sustainability. Chem Rev 2021; 121:10367-10451. [PMID: 34228428 DOI: 10.1021/acs.chemrev.1c00121] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Since the industrial revolution, the rapid growth and development of global industries have depended largely upon the utilization of coal-derived chemicals, and more recently, the utilization of petroleum-based chemicals. These developments have followed a linear economy model (produce, consume, and dispose). As the world is facing a serious threat from the climate change crisis, a more sustainable solution for manufacturing, i.e., circular economy in which waste from the same or different industries can be used as feedstocks or resources for production offers an attractive industrial/business model. In nature, biological systems, i.e., microorganisms routinely use their enzymes and metabolic pathways to convert organic and inorganic wastes to synthesize biochemicals and energy required for their growth. Therefore, an understanding of how selected enzymes convert biobased feedstocks into special (bio)chemicals serves as an important basis from which to build on for applications in biocatalysis, metabolic engineering, and synthetic biology to enable biobased processes that are greener and cleaner for the environment. This review article highlights the current state of knowledge regarding the enzymatic reactions used in converting biobased wastes (lignocellulosic biomass, sugar, phenolic acid, triglyceride, fatty acid, and glycerol) and greenhouse gases (CO2 and CH4) into value-added products and discusses the current progress made in their metabolic engineering. The commercial aspects and life cycle assessment of products from enzymatic and metabolic engineering are also discussed. Continued development in the field of metabolic engineering would offer diversified solutions which are sustainable and renewable for manufacturing valuable chemicals.
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Affiliation(s)
- Pattarawan Intasian
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Kridsadakorn Prakinee
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Aisaraphon Phintha
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand.,Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Duangthip Trisrivirat
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Nopphon Weeranoppanant
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand.,Department of Chemical Engineering, Faculty of Engineering, Burapha University, 169, Long-hard Bangsaen, Saensook, Muang, Chonburi 20131, Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
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18
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LuxAB-Based Microbial Cell Factories for the Sensing, Manufacturing and Transformation of Industrial Aldehydes. Catalysts 2021. [DOI: 10.3390/catal11080953] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The application of genetically encoded biosensors enables the detection of small molecules in living cells and has facilitated the characterization of enzymes, their directed evolution and the engineering of (natural) metabolic pathways. In this work, the LuxAB biosensor system from Photorhabdus luminescens was implemented in Escherichia coli to monitor the enzymatic production of aldehydes from primary alcohols and carboxylic acid substrates. A simple high-throughput assay utilized the bacterial luciferase—previously reported to only accept aliphatic long-chain aldehydes—to detect structurally diverse aldehydes, including aromatic and monoterpene aldehydes. LuxAB was used to screen the substrate scopes of three prokaryotic oxidoreductases: an alcohol dehydrogenase (Pseudomonas putida), a choline oxidase variant (Arthrobacter chlorophenolicus) and a carboxylic acid reductase (Mycobacterium marinum). Consequently, high-value aldehydes such as cinnamaldehyde, citral and citronellal could be produced in vivo in up to 80% yield. Furthermore, the dual role of LuxAB as sensor and monooxygenase, emitting bioluminescence through the oxidation of aldehydes to the corresponding carboxylates, promises implementation in artificial enzyme cascades for the synthesis of carboxylic acids. These findings advance the bio-based detection, preparation and transformation of industrially important aldehydes in living cells.
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19
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Abstract
In this study, we present the synthesis of chiral fragrance aldehydes, which was tackled by a combination of chemo-catalysis and a multi-enzymatic in vivo cascade reaction and the development of a highly versatile high-throughput assay for the enzymatic reduction of carboxylic acids. We investigated a biocompatible metal-catalyzed synthesis for the preparation of α or β substituted cinnamic acid derivatives which were fed directly into the biocatalytic system. Subsequently, the target molecules were synthesized by an enzymatic cascade consisting of a carboxylate reduction, followed by the selective C-C double bond reduction catalyzed by appropriate enoate reductases. We investigated a biocompatible oxidative Heck protocol and combined it with cells expressing a carboxylic acid reductase from Neurospora crassa (NcCAR) and an ene reductase from Saccharomyces pastorianus for the production fragrance aldehydes.
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20
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Cha TY, Yong Y, Park H, Yun HJ, Jeon W, Ahn JO, Choi KY. Biosynthesis of C12 Fatty Alcohols by Whole Cell Biotransformation of C12 Derivatives Using Escherichia coli Two-cell Systems Expressing CAR and ADH. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-020-0239-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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21
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Production of Aldehydes by Biocatalysis. Int J Mol Sci 2021; 22:ijms22094949. [PMID: 34066641 PMCID: PMC8124467 DOI: 10.3390/ijms22094949] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 02/07/2023] Open
Abstract
The production of aldehydes, highly reactive and toxic chemicals, brings specific challenges to biocatalytic processes. Absence of natural accumulation of aldehydes in microorganisms has led to a combination of in vitro and in vivo strategies for both, bulk and fine production. Advances in genetic and metabolic engineering and implementation of computational techniques led to the production of various enzymes with special requirements. Cofactor synthesis, post-translational modifications and structure engineering are applied to prepare active enzymes for one-step or cascade reactions. This review presents the highlights in biocatalytical production of aldehydes with the potential to shape future industrial applications.
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22
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Park J, Lee HS, Oh J, Joo JC, Yeon YJ. A highly active carboxylic acid reductase from Mycobacterium abscessus for biocatalytic reduction of vanillic acid to vanillin. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107683] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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23
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Horvat M, Winkler M. In Vivo
Reduction of Medium‐ to Long‐Chain Fatty Acids by Carboxylic Acid Reductase (CAR) Enzymes: Limitations and Solutions. ChemCatChem 2020. [DOI: 10.1002/cctc.202000895] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Melissa Horvat
- acib –Austrian Center of Industrial Biotechnology Krenngasse 37 8010 Graz Austria
| | - Margit Winkler
- acib –Austrian Center of Industrial Biotechnology Krenngasse 37 8010 Graz Austria
- Institute of Molecular Biotechnology Graz University of Technology Petersgasse 14 8010 Graz Austria
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24
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Kramer L, Le X, Rodriguez M, Wilson MA, Guo J, Niu W. Engineering Carboxylic Acid Reductase (CAR) through a Whole-Cell Growth-Coupled NADPH Recycling Strategy. ACS Synth Biol 2020; 9:1632-1637. [PMID: 32589835 DOI: 10.1021/acssynbio.0c00290] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Rapid evolution of enzyme activities is often hindered by the lack of efficient and affordable methods to identify beneficial mutants. We report the development of a new growth-coupled selection method for evolving NADPH-consuming enzymes based on the recycling of this redox cofactor. The method relies on a genetically modified Escherichia coli strain, which overaccumulates NADPH. This method was applied to the engineering of a carboxylic acid reductase (CAR) for improved catalytic activities on 2-methoxybenzoate and adipate. Mutant enzymes with up to 17-fold improvement in catalytic efficiency were identified from single-site saturated mutagenesis libraries. Obtained mutants were successfully applied to whole-cell conversions of adipate into 1,6-hexanediol, a C6 monomer commonly used in polymer industry.
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Affiliation(s)
- Levi Kramer
- Department of Chemical & Biomolecular Engineering, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | - Xuan Le
- Department of Chemical & Biomolecular Engineering, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | - Marisa Rodriguez
- Department of Chemical & Biomolecular Engineering, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | - Mark A. Wilson
- Department of Biochemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
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25
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Fedorchuk TP, Khusnutdinova AN, Evdokimova E, Flick R, Di Leo R, Stogios P, Savchenko A, Yakunin AF. One-Pot Biocatalytic Transformation of Adipic Acid to 6-Aminocaproic Acid and 1,6-Hexamethylenediamine Using Carboxylic Acid Reductases and Transaminases. J Am Chem Soc 2020; 142:1038-1048. [PMID: 31886667 DOI: 10.1021/jacs.9b11761] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Production of platform chemicals from renewable feedstocks is becoming increasingly important due to concerns on environmental contamination, climate change, and depletion of fossil fuels. Adipic acid (AA), 6-aminocaproic acid (6-ACA) and 1,6-hexamethylenediamine (HMD) are key precursors for nylon synthesis, which are currently produced primarily from petroleum-based feedstocks. In recent years, the biosynthesis of adipic acid from renewable feedstocks has been demonstrated using both bacterial and yeast cells. Here we report the biocatalytic conversion/transformation of AA to 6-ACA and HMD by carboxylic acid reductases (CARs) and transaminases (TAs), which involves two rounds (cascades) of reduction/amination reactions (AA → 6-ACA → HMD). Using purified wild type CARs and TAs supplemented with cofactor regenerating systems for ATP, NADPH, and amine donor, we established a one-pot enzyme cascade catalyzing up to 95% conversion of AA to 6-ACA. To increase the cascade activity for the transformation of 6-ACA to HMD, we determined the crystal structure of the CAR substrate-binding domain in complex with AMP and succinate and engineered three mutant CARs with enhanced activity against 6-ACA. In combination with TAs, the CAR L342E protein showed 50-75% conversion of 6-ACA to HMD. For the transformation of AA to HMD (via 6-ACA), the wild type CAR was combined with the L342E variant and two different TAs resulting in up to 30% conversion to HMD and 70% to 6-ACA. Our results highlight the suitability of CARs and TAs for several rounds of reduction/amination reactions in one-pot cascade systems and their potential for the biobased synthesis of terminal amines.
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Affiliation(s)
- Tatiana P Fedorchuk
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada.,Institute of Basic Biological Problems , Russian Academy of Sciences , Pushchino , Moscow Region 142290 , Russia
| | - Anna N Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada.,Institute of Basic Biological Problems , Russian Academy of Sciences , Pushchino , Moscow Region 142290 , Russia
| | - Elena Evdokimova
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - Rosa Di Leo
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - Peter Stogios
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada.,Department of Microbiology, Immunology and Infectious Diseases , University of Calgary , Calgary , Alberta T2N 4N1 , Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada.,Centre for Environmental Biotechnology, School of Natural Sciences , Bangor University , Gwynedd LL57 2UW , U.K
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26
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Carboxylic acid reductases in metabolic engineering. J Biotechnol 2020; 307:1-14. [DOI: 10.1016/j.jbiotec.2019.10.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/30/2019] [Accepted: 10/01/2019] [Indexed: 01/29/2023]
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27
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Derrington SR, Turner NJ, France SP. Carboxylic acid reductases (CARs): An industrial perspective. J Biotechnol 2019; 304:78-88. [DOI: 10.1016/j.jbiotec.2019.08.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/14/2019] [Accepted: 08/14/2019] [Indexed: 01/09/2023]
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28
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Horvat M, Fiume G, Fritsche S, Winkler M. Discovery of carboxylic acid reductase (CAR) from Thermothelomyces thermophila and its evaluation for vanillin synthesis. J Biotechnol 2019; 304:44-51. [DOI: 10.1016/j.jbiotec.2019.08.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/12/2019] [Accepted: 08/12/2019] [Indexed: 11/26/2022]
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29
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Kramer L, Le X, Hankore ED, Wilson MA, Guo J, Niu W. Engineering and characterization of hybrid carboxylic acid reductases. J Biotechnol 2019; 304:52-56. [DOI: 10.1016/j.jbiotec.2019.08.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/12/2019] [Accepted: 08/13/2019] [Indexed: 02/04/2023]
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30
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Kunjapur AM, Prather KLJ. Development of a Vanillate Biosensor for the Vanillin Biosynthesis Pathway in E. coli. ACS Synth Biol 2019; 8:1958-1967. [PMID: 31461264 DOI: 10.1021/acssynbio.9b00071] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The engineered de novo vanillin biosynthesis pathway constructed in Escherichia coli is industrially relevant but limited by the reaction catalyzed by catechol O-methyltransferase, which is intended to catalyze the conversion of protocatechuate to vanillate. To identify alternative O-methyltransferases, we constructed a vanillate sensor based on the Caulobacter crescentus VanR-VanO system. Using an E. coli promoter library, we achieved greater than 14-fold dynamic range in our best rationally constructed sensor. We found that this construct and an evolved variant demonstrate remarkable substrate selectivity, exhibiting no detectable response to the regioisomer byproduct isovanillate and minimal response to structurally similar pathway intermediates. We then harnessed the evolved biosensor to conduct rapid bioprospecting of natural catechol O-methyltransferases and identified three previously uncharacterized but active O-methyltransferases. Collectively, these efforts enrich our knowledge of how biosensing can aid metabolic engineering and constitute the foundation for future improvements in vanillin pathway productivity.
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Affiliation(s)
- Aditya M. Kunjapur
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Kristala L. J. Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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31
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Fedorchuk TP, Khusnutdinova AN, Flick R, Yakunin AF. Site-directed mutagenesis and stability of the carboxylic acid reductase MAB4714 from Mycobacterium abscessus. J Biotechnol 2019; 303:72-79. [DOI: 10.1016/j.jbiotec.2019.07.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 11/30/2022]
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32
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Horvat M, Fritsche S, Kourist R, Winkler M. Characterization of Type IV Carboxylate Reductases (CARs) for Whole Cell-Mediated Preparation of 3-Hydroxytyrosol. ChemCatChem 2019; 11:4171-4181. [PMID: 31681448 PMCID: PMC6813634 DOI: 10.1002/cctc.201900333] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/18/2019] [Indexed: 11/18/2022]
Abstract
Fragrance and flavor industries could not imagine business without aldehydes. Processes for their commercial production raise environmental and ecological concerns. The chemical reduction of organic acids to aldehydes is challenging. To fulfill the demand of a mild and selective reduction of carboxylic acids to aldehydes, carboxylic acid reductases (CARs) are gaining importance. We identified two new subtype IV fungal CARs from Dichomitus squalens CAR (DsCAR) and Trametes versicolor CAR (Tv2CAR) in addition to literature known Trametes versicolor CAR (TvCAR). Expression levels were improved by the co-expression of GroEL-GroES with either the trigger factor or the DnaJ-DnaK-GrpE system. Investigation of the substrate scope of the three enzymes revealed overlapping substrate-specificities. Tv2CAR and DsCAR showed a preferred pH range of 7.0 to 8.0 in bicine buffer. TvCAR showed highest activity at pH 6.5 to 7.5 in MES buffer and slightly reduced activity at pH 6.0 or 8.0. TvCAR appeared to tolerate a wider pH range without significant loss of activity. Type IV fungal CARs optimal temperature was in the range of 25-35 °C. TvCAR showed a melting temperature (Tm) of 55 °C indicating higher stability compared to type III and the other type IV fungal CARs (Tm 51-52 °C). Finally, TvCAR was used as the key enzyme for the bioreduction of 3,4-dihydroxyphenylacetic acid to the antioxidant 3-hydroxytyrosol (3-HT) and gave 58 mM of 3-HT after 24 h, which correlates to a productivity of 0.37 g L-1 h-1.
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Affiliation(s)
- Melissa Horvat
- acib – Austrian Center of Industrial BiotechnologyPetersgasse 148010GrazAustria
| | - Susanne Fritsche
- acib – Austrian Center of Industrial BiotechnologyPetersgasse 148010GrazAustria
| | - Robert Kourist
- Institute of Molecular BiotechnologyGraz University of TechnologyPetersgasse 148010GrazAustria
| | - Margit Winkler
- acib – Austrian Center of Industrial BiotechnologyPetersgasse 148010GrazAustria
- Institute of Molecular BiotechnologyGraz University of TechnologyPetersgasse 148010GrazAustria
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33
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Lubbers RJM, Dilokpimol A, Visser J, Mäkelä MR, Hildén KS, de Vries RP. A comparison between the homocyclic aromatic metabolic pathways from plant-derived compounds by bacteria and fungi. Biotechnol Adv 2019; 37:107396. [PMID: 31075306 DOI: 10.1016/j.biotechadv.2019.05.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 04/18/2019] [Accepted: 05/03/2019] [Indexed: 12/13/2022]
Abstract
Aromatic compounds derived from lignin are of great interest for renewable biotechnical applications. They can serve in many industries e.g. as biochemical building blocks for bioplastics or biofuels, or as antioxidants, flavor agents or food preservatives. In nature, lignin is degraded by microorganisms, which results in the release of homocyclic aromatic compounds. Homocyclic aromatic compounds can also be linked to polysaccharides, tannins and even found freely in plant biomass. As these compounds are often toxic to microbes already at low concentrations, they need to be degraded or converted to less toxic forms. Prior to ring cleavage, the plant- and lignin-derived aromatic compounds are converted to seven central ring-fission intermediates, i.e. catechol, protocatechuic acid, hydroxyquinol, hydroquinone, gentisic acid, gallic acid and pyrogallol through complex aromatic metabolic pathways and used as energy source in the tricarboxylic acid cycle. Over the decades, bacterial aromatic metabolism has been described in great detail. However, the studies on fungal aromatic pathways are scattered over different pathways and species, complicating a comprehensive view of fungal aromatic metabolism. In this review, we depicted the similarities and differences of the reported aromatic metabolic pathways in fungi and bacteria. Although both microorganisms share the main conversion routes, many alternative pathways are observed in fungi. Understanding the microbial aromatic metabolic pathways could lead to metabolic engineering for strain improvement and promote valorization of lignin and related aromatic compounds.
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Affiliation(s)
- Ronnie J M Lubbers
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Adiphol Dilokpimol
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Jaap Visser
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, Finland.
| | - Kristiina S Hildén
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, Finland.
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, Finland.
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34
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Schwendenwein D, Ressmann AK, Doerr M, Höhne M, Bornscheuer UT, Mihovilovic MD, Rudroff F, Winkler M. Random Mutagenesis‐Driven Improvement of Carboxylate Reductase Activity using an Amino Benzamidoxime‐Mediated High‐Throughput Assay. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900155] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | - Anna K. Ressmann
- Institute of Applied Synthetic ChemistryTU Wien Getreidemarkt 9/OC-163 1060 Vienna Austria
| | - Mark Doerr
- Institute of Biochemistry, Dept. of Biotechnology & Enzyme CatalysisGreifswald University Felix-Hausdorff-Str. 4 17487 Greifswald Germany
| | - Matthias Höhne
- Institute of Biochemistry, Dept. of Biotechnology & Enzyme CatalysisGreifswald University Felix-Hausdorff-Str. 4 17487 Greifswald Germany
| | - Uwe T. Bornscheuer
- Institute of Biochemistry, Dept. of Biotechnology & Enzyme CatalysisGreifswald University Felix-Hausdorff-Str. 4 17487 Greifswald Germany
| | - Marko D. Mihovilovic
- Institute of Applied Synthetic ChemistryTU Wien Getreidemarkt 9/OC-163 1060 Vienna Austria
| | - Florian Rudroff
- Institute of Applied Synthetic ChemistryTU Wien Getreidemarkt 9/OC-163 1060 Vienna Austria
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35
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Ressmann AK, Schwendenwein D, Leonhartsberger S, Mihovilovic MD, Bornscheuer UT, Winkler M, Rudroff F. Substrate‐Independent High‐Throughput Assay for the Quantification of Aldehydes. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900154] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anna K. Ressmann
- Institute of Applied Synthetic ChemistryTU Wien Getreidemarkt 9/OC-163 1060 Vienna Austria
| | | | - Simon Leonhartsberger
- Institute of Applied Synthetic ChemistryTU Wien Getreidemarkt 9/OC-163 1060 Vienna Austria
| | - Marko D. Mihovilovic
- Institute of Applied Synthetic ChemistryTU Wien Getreidemarkt 9/OC-163 1060 Vienna Austria
| | - Uwe T. Bornscheuer
- Institute of BiochemistryDept. of Biotechnology & Enzyme CatalysisGreifswald University Felix-Hausdorff-Str. 4 17487 Greifswald Germany
| | | | - Florian Rudroff
- Institute of Applied Synthetic ChemistryTU Wien Getreidemarkt 9/OC-163 1060 Vienna Austria
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36
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Strohmeier GA, Eiteljörg IC, Schwarz A, Winkler M. Enzymatic One-Step Reduction of Carboxylates to Aldehydes with Cell-Free Regeneration of ATP and NADPH. Chemistry 2019; 25:6119-6123. [PMID: 30866114 PMCID: PMC6563805 DOI: 10.1002/chem.201901147] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Indexed: 11/12/2022]
Abstract
The direct generation of aldehydes from carboxylic acids is often a challenging synthetic task but undoubtedly attractive in view of abundant supply of such feedstocks from nature. Though long known, biocatalytic carboxylate reductions are at an early stage of development, presumably because of their co-factor requirement. To establish an alternative to whole-cell-based carboxylate reductions which are limited by side reactions, we developed an in vitro multi-enzyme system that allows for quantitative reductions of various carboxylic acids with full recycling of all cofactors and prevention of undesired over-reductions. Regeneration of adenosine 5'-triphosphate is achieved through the simultaneous action of polyphosphate kinases from Meiothermus ruber and Sinorhizobium meliloti and β-nicotinamide adenine dinucleotide 2'-phosphate is reduced by a glucose dehydrogenase. Under these conditions and in the presence of the carboxylate reductases from Neurospora crassa or Nocardia iowensis, various aromatic, heterocyclic and aliphatic carboxylic acids were quantitatively reduced to the respective aldehydes.
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Affiliation(s)
- Gernot A Strohmeier
- acib-Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria
| | - Inge C Eiteljörg
- acib-Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria
| | - Anna Schwarz
- acib-Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria
| | - Margit Winkler
- acib-Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria.,Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
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37
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Thompson MP, Derrington SR, Heath RS, Porter JL, Mangas-Sanchez J, Devine PN, Truppo MD, Turner NJ. A generic platform for the immobilisation of engineered biocatalysts. Tetrahedron 2019. [DOI: 10.1016/j.tet.2018.12.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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38
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Kramer L, Hankore ED, Liu Y, Liu K, Jimenez E, Guo J, Niu W. Characterization of Carboxylic Acid Reductases for Biocatalytic Synthesis of Industrial Chemicals. Chembiochem 2018; 19:1452-1460. [DOI: 10.1002/cbic.201800157] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Levi Kramer
- Department of Chemical and Biomolecular Engineering University of Nebraska–Lincoln Lincoln NE 68588 USA
| | | | - Yilan Liu
- Department of Chemical and Biomolecular Engineering University of Nebraska–Lincoln Lincoln NE 68588 USA
| | - Kun Liu
- Department of Chemistry University of Nebraska–Lincoln Lincoln NE 68588 USA
| | - Esteban Jimenez
- Department of Chemical Engineering University of Arizona Tucson Arizona 85721 USA
| | - Jiantao Guo
- Department of Chemistry University of Nebraska–Lincoln Lincoln NE 68588 USA
| | - Wei Niu
- Department of Chemical and Biomolecular Engineering University of Nebraska–Lincoln Lincoln NE 68588 USA
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39
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Wang S, Bilal M, Hu H, Wang W, Zhang X. 4-Hydroxybenzoic acid-a versatile platform intermediate for value-added compounds. Appl Microbiol Biotechnol 2018. [PMID: 29516141 DOI: 10.1007/s00253-018-8815-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
4-Hydroxybenzoic acid (4-HBA) has recently emerged as a promising intermediate for several value-added bioproducts with potential biotechnological applications in food, cosmetics, pharmacy, fungicides, etc. Over the past years, a variety of biosynthetic techniques have been developed for producing the 4-HBA and 4-HBA-based products. At this juncture, synthetic biology and metabolic engineering approaches enabled the biosynthesis of 4-HBA to address the increasing demand for high-value bioproducts. This review summarizes the biosynthesis of a variety of industrially pertinent compounds such as resveratrol, muconic acid, gastrodin, xiamenmycin, and vanillyl alcohol using 4-HBA as the starting feedstock. Moreover, potential research activities with a close-up look at the future perspectives to produce new compounds using 4-HBA have also been discussed.
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Affiliation(s)
- Songwei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Muhammad Bilal
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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40
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Stolterfoht H, Steinkellner G, Schwendenwein D, Pavkov-Keller T, Gruber K, Winkler M. Identification of Key Residues for Enzymatic Carboxylate Reduction. Front Microbiol 2018. [PMID: 29515539 PMCID: PMC5826065 DOI: 10.3389/fmicb.2018.00250] [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] [Indexed: 11/21/2022] Open
Abstract
Carboxylate reductases (CARs, E.C. 1.2.1.30) generate aldehydes from their corresponding carboxylic acid with high selectivity. Little is known about the structure of CARs and their catalytically important amino acid residues. The identification of key residues for carboxylate reduction provides a starting point to gain deeper understanding of enzymatic carboxylate reduction. A multiple sequence alignment of CARs with confirmed activity recently identified in our lab and from the literature revealed a fingerprint of conserved amino acids. We studied the function of conserved residues by multiple sequence alignments and mutational replacements of these residues. In this study, single-site alanine variants of Neurospora crassa CAR were investigated to determine the contribution of conserved residues to the function, expressability or stability of the enzyme. The effect of amino acid replacements was investigated by analyzing enzymatic activity of the variants in vivo and in vitro. Supported by molecular modeling, we interpreted that five of these residues are essential for catalytic activity, or substrate and co-substrate binding. We identified amino acid residues having significant impact on CAR activity. Replacement of His 237, Glu 433, Ser 595, Tyr 844, and Lys 848 by Ala abolish CAR activity, indicating their key role in acid reduction. These results may assist in the functional annotation of CAR coding genes in genomic databases. While some other conserved residues decreased activity or had no significant impact, four residues increased the specific activity of NcCAR variants when replaced by alanine. Finally, we showed that NcCAR wild-type and mutants efficiently reduce aliphatic acids.
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Affiliation(s)
- Holly Stolterfoht
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Graz, Austria.,Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Georg Steinkellner
- Austrian Centre of Industrial Biotechnology, Graz, Austria.,Structural Biology, Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | | | - Tea Pavkov-Keller
- Austrian Centre of Industrial Biotechnology, Graz, Austria.,Structural Biology, Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Karl Gruber
- Austrian Centre of Industrial Biotechnology, Graz, Austria.,Structural Biology, Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Margit Winkler
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Graz, Austria.,Austrian Centre of Industrial Biotechnology, Graz, Austria
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41
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Carboxylic acid reductase enzymes (CARs). Curr Opin Chem Biol 2017; 43:23-29. [PMID: 29127833 DOI: 10.1016/j.cbpa.2017.10.006] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 09/02/2017] [Accepted: 10/06/2017] [Indexed: 11/20/2022]
Abstract
Carboxylate reductases (CARs) are emerging as valuable catalysts for the selective one-step reduction of carboxylic acids to their corresponding aldehydes. The substrate scope of CARs is exceptionally broad and offers potential for their application in diverse synthetic processes. Two major fields of application are the preparation of aldehydes as end products for the flavor and fragrance sector and the integration of CARs in cascade reactions with aldehydes as the key intermediates. The latest applications of CARs are dominated by in vivo cascades and chemo-enzymatic reaction sequences. The challenge to fully exploit product selectivity is discussed. Recent developments in the characterization of CARs are summarized, with a focus on aspects related to the domain architecture and protein sequences of CAR enzymes.
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42
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Khusnutdinova AN, Flick R, Popovic A, Brown G, Tchigvintsev A, Nocek B, Correia K, Joo JC, Mahadevan R, Yakunin AF. Exploring Bacterial Carboxylate Reductases for the Reduction of Bifunctional Carboxylic Acids. Biotechnol J 2017; 12. [PMID: 28762640 DOI: 10.1002/biot.201600751] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 05/31/2017] [Indexed: 11/12/2022]
Abstract
Carboxylic acid reductases (CARs) selectively reduce carboxylic acids to aldehydes using ATP and NADPH as cofactors under mild conditions. Although CARs attracts significant interest, only a few enzymes have been characterized to date, whereas the vast majority of CARs have yet to be examined. Herein the authors report that 12 bacterial CARs reduces a broad range of bifunctional carboxylic acids containing oxo-, hydroxy-, amino-, or second carboxyl groups with several enzymes showing activity toward 4-hydroxybutanoic (4-HB) and adipic acids. These CARs exhibits significant reductase activity against substrates whose second functional group is separated from the carboxylate by at least three carbons with both carboxylate groups being reduced in dicarboxylic acids. Purified CARs supplemented with cofactor regenerating systems (for ATP and NADPH), an inorganic pyrophosphatase, and an aldo-keto reductase catalyzes a high conversion (50-76%) of 4-HB to 1,4-butanediol (1,4-BDO) and adipic acid to 1,6-hexanediol (1,6-HDO). Likewise, Escherichia coli strains expressing eight different CARs efficiently reduces 4-HB to 1,4-BDO with 50-95% conversion, whereas adipic acid is reduced to a mixture of 6-hydroxyhexanoic acid (6-HHA) and 1,6-HDO. Thus, our results illustrate the broad biochemical diversity of bacterial CARs and their compatibility with other enzymes for applications in biocatalysis.
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Affiliation(s)
- Anna N Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, ON, M5S 3E5, Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, ON, M5S 3E5, Canada
| | - Ana Popovic
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, ON, M5S 3E5, Canada
| | - Greg Brown
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, ON, M5S 3E5, Canada
| | - Anatoli Tchigvintsev
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, ON, M5S 3E5, Canada
| | - Boguslaw Nocek
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Kevin Correia
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, ON, M5S 3E5, Canada
| | - Jeong C Joo
- Center for Bio-Based Chemistry, Division of Convergence Chemistry, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, 34114, Republic of Korea
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, ON, M5S 3E5, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, ON, M5S 3E5, Canada
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43
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Stolterfoht H, Schwendenwein D, Sensen CW, Rudroff F, Winkler M. Four distinct types of E.C. 1.2.1.30 enzymes can catalyze the reduction of carboxylic acids to aldehydes. J Biotechnol 2017; 257:222-232. [DOI: 10.1016/j.jbiotec.2017.02.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/08/2017] [Accepted: 02/14/2017] [Indexed: 11/25/2022]
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44
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Tang X, Feng L, Chen L, Chen WN. Engineering Saccharomyces cerevisiae for Efficient Biosynthesis of Fatty Alcohols Based on Enhanced Supply of Free Fatty Acids. ACS OMEGA 2017; 2:3284-3290. [PMID: 30023691 PMCID: PMC6044801 DOI: 10.1021/acsomega.7b00065] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 04/20/2017] [Indexed: 05/05/2023]
Abstract
In recent years, production of fatty acid derivatives has attracted much attention because of their wide range of applications in renewable oleochemicals. Microorganisms such as Saccharomyces cerevisiae provided an ideal cell factory for such chemical synthesis. In this study, an efficient strategy for the synthesis of fatty alcohols based on enhanced supply of free fatty acids (FFAs) was constructed. The FAA1 and FAA4 genes encoding two acyl-CoA synthetases in S. cerevisiae were deleted, resulting in the accumulation of FFAs with carbon chain length from C8 to C18. The coexpression of the carboxylic acid reductase gene (car) from Mycobacterium marinum and the phosphopantetheinyl transferase gene (sfp) from Bacillus subtilis successfully converted the accumulated FFAs into fatty alcohols. The concentration of the total fatty alcohols reached 24.3 mg/L, which is in agreement with that of the accumulated FFAs. To further increase the supply of FFAs, the DGAI encoding the acyl-CoA:diacylglycerol acyltransferase involved in the rate-limiting step of triacylglycerols storage was codeleted with FAA1 and FAA4, and the acyl-CoA thioesterase gene (acot) was expressed together with car and sfp, resulting in an enhanced production of fatty alcohols, the content of which increased to 31.2 mg/L. The results herein demonstrated the efficiency of the engineered pathway for the production of fatty acid derivatives using FFAs as precursors.
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Affiliation(s)
- Xiaoling Tang
- Key
Laboratory of Bioorganic Synthesis of Zhejiang Province, College of
Biotechnology and Bioengineering, Zhejiang
University of Technology, Hangzhou 310014, P. R. China
- School
of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459, Singapore
| | - Lilin Feng
- Key
Laboratory of Bioorganic Synthesis of Zhejiang Province, College of
Biotechnology and Bioengineering, Zhejiang
University of Technology, Hangzhou 310014, P. R. China
| | - Liwei Chen
- School
of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459, Singapore
| | - Wei Ning Chen
- School
of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459, Singapore
- E-mail: . Phone: +6563162870. Fax: +6562259865
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45
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Structures of carboxylic acid reductase reveal domain dynamics underlying catalysis. Nat Chem Biol 2017; 13:975-981. [PMID: 28719588 PMCID: PMC5563451 DOI: 10.1038/nchembio.2434] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 06/08/2017] [Indexed: 01/10/2023]
Abstract
Carboxylic acid reductase (CAR) catalyzes the ATP- and NADPH-dependent reduction of carboxylic acids to the corresponding aldehydes. The enzyme is related to the nonribosomal peptide synthetases, consisting of an adenylation domain fused via a peptidyl carrier protein (PCP) to a reductase termination domain. Crystal structures of the CAR adenylation-PCP didomain demonstrate that large-scale domain motions occur between the adenylation and thiolation states. Crystal structures of the PCP-reductase didomain reveal that phosphopantetheine binding alters the orientation of a key Asp, resulting in a productive orientation of the bound nicotinamide. This ensures that further reduction of the aldehyde product does not occur. Combining crystallography with small-angle X-ray scattering (SAXS), we propose that molecular interactions between initiation and termination domains are limited to competing PCP docking sites. This theory is supported by the fact that (R)-pantetheine can support CAR activity for mixtures of the isolated domains. Our model suggests directions for further development of CAR as a biocatalyst.
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46
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In Vivo Synthesis of Polyhydroxylated Compounds from a “Hidden Reservoir” of Toxic Aldehyde Species. ChemCatChem 2017. [DOI: 10.1002/cctc.201700469] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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47
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Younes SHH, Ni Y, Schmidt S, Kroutil W, Hollmann F. Alcohol Dehydrogenases Catalyze the Reduction of Thioesters. ChemCatChem 2017. [DOI: 10.1002/cctc.201700165] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sabry H. H. Younes
- Department of Biotechnology; Delft University of Technology; Van der Maasweg 9 2629 HZ Delft The Netherlands
- Department of Chemistry; Faculty of Sciences; Sohag University; Sohag 82524 Egypt
| | - Yan Ni
- Department of Biotechnology; Delft University of Technology; Van der Maasweg 9 2629 HZ Delft The Netherlands
| | - Sandy Schmidt
- Department of Biotechnology; Delft University of Technology; Van der Maasweg 9 2629 HZ Delft The Netherlands
| | - Wolfgang Kroutil
- Department of Chemistry; Organic and Bioorganic Chemistry; University of Graz; 8010 Graz Austria
| | - Frank Hollmann
- Department of Biotechnology; Delft University of Technology; Van der Maasweg 9 2629 HZ Delft The Netherlands
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48
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Hepworth LJ, France SP, Hussain S, Both P, Turner NJ, Flitsch SL. Enzyme Cascades in Whole Cells for the Synthesis of Chiral Cyclic Amines. ACS Catal 2017. [DOI: 10.1021/acscatal.7b00513] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lorna J. Hepworth
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess
Street, Manchester M1 7DN, United Kingdom
| | - Scott P. France
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess
Street, Manchester M1 7DN, United Kingdom
| | - Shahed Hussain
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess
Street, Manchester M1 7DN, United Kingdom
| | - Peter Both
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess
Street, Manchester M1 7DN, United Kingdom
| | - Nicholas J. Turner
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess
Street, Manchester M1 7DN, United Kingdom
| | - Sabine L. Flitsch
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess
Street, Manchester M1 7DN, United Kingdom
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49
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Finnigan W, Thomas A, Cromar H, Gough B, Snajdrova R, Adams JP, Littlechild JA, Harmer NJ. Characterization of Carboxylic Acid Reductases as Enzymes in the Toolbox for Synthetic Chemistry. ChemCatChem 2017; 9:1005-1017. [PMID: 28450969 PMCID: PMC5396282 DOI: 10.1002/cctc.201601249] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/14/2016] [Indexed: 11/26/2022]
Abstract
Carboxylic acid reductase enzymes (CARs) meet the demand in synthetic chemistry for a green and regiospecific route to aldehydes from their respective carboxylic acids. However, relatively few of these enzymes have been characterized. A sequence alignment with members of the ANL (Acyl‐CoA synthetase/ NRPS adenylation domain/Luciferase) superfamily of enzymes shed light on CAR functional dynamics. Four unstudied enzymes were selected by using a phylogenetic analysis of known and hypothetical CARs, and for the first time, a thorough biochemical characterization was performed. Kinetic analysis of these enzymes with various substrates shows that they have a broad but similar substrate specificity. Electron‐rich acids are favored, which suggests that the first step in the proposed reaction mechanism, attack by the carboxylate on the α‐phosphate of adenosine triphosphate (ATP), is the step that determines the substrate specificity and reaction kinetics. The effects of pH and temperature provide a clear operational window for the use of these CARs, whereas an investigation of product inhibition by NADP+, adenosine monophosphate, and pyrophosphate indicates that the binding of substrates at the adenylation domain is ordered with ATP binding first. This study consolidates CARs as important and exciting enzymes in the toolbox for sustainable chemistry and provides specifications for their use as a biocatalyst.
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Affiliation(s)
- William Finnigan
- Biosciences, College of Life and Environmental Sciences University of Exeter, Stocker Road Devon Exeter EX4 4QD UK
| | - Adam Thomas
- Biosciences, College of Life and Environmental Sciences University of Exeter, Stocker Road Devon Exeter EX4 4QD UK
| | - Holly Cromar
- Biosciences, College of Life and Environmental Sciences University of Exeter, Stocker Road Devon Exeter EX4 4QD UK
| | - Ben Gough
- Biosciences, College of Life and Environmental Sciences University of Exeter, Stocker Road Devon Exeter EX4 4QD UK
| | - Radka Snajdrova
- Synthetic Chemistry, AC-API Chem-UK, GlaxoSmithKline R&D Ltd Medicines Research Centre Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - Joseph P Adams
- Synthetic Chemistry, AC-API Chem-UK, GlaxoSmithKline R&D Ltd Medicines Research Centre Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - Jennifer A Littlechild
- Biosciences, College of Life and Environmental Sciences University of Exeter, Stocker Road Devon Exeter EX4 4QD UK
| | - Nicholas J Harmer
- Biosciences, College of Life and Environmental Sciences University of Exeter, Stocker Road Devon Exeter EX4 4QD UK
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Sas C, Müller F, Kappel C, Kent TV, Wright SI, Hilker M, Lenhard M. Repeated Inactivation of the First Committed Enzyme Underlies the Loss of Benzaldehyde Emission after the Selfing Transition in Capsella. Curr Biol 2016; 26:3313-3319. [PMID: 27916528 DOI: 10.1016/j.cub.2016.10.026] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/11/2016] [Accepted: 10/13/2016] [Indexed: 01/05/2023]
Abstract
The enormous species richness of flowering plants is at least partly due to floral diversification driven by interactions between plants and their animal pollinators [1, 2]. Specific pollinator attraction relies on visual and olfactory floral cues [3-5]; floral scent can not only attract pollinators but also attract or repel herbivorous insects [6-8]. However, despite its central role for plant-animal interactions, the genetic control of floral scent production and its evolutionary modification remain incompletely understood [9-13]. Benzenoids are an important class of floral scent compounds that are generated from phenylalanine via several enzymatic pathways [14-17]. Here we address the genetic basis of the loss of floral scent associated with the transition from outbreeding to selfing in the genus Capsella. While the outbreeding C. grandiflora emits benzaldehyde as a major constituent of its floral scent, this has been lost in the selfing C. rubella. We identify the Capsella CNL1 gene encoding cinnamate:CoA ligase as responsible for this variation. Population genetic analysis indicates that CNL1 has been inactivated twice independently in C. rubella via different novel mutations to its coding sequence. Together with a recent study in Petunia [18], this identifies cinnamate:CoA ligase as an evolutionary hotspot for mutations causing the loss of benzenoid scent compounds in association with a shift in the reproductive strategy of Capsella from pollination by insects to self-fertilization.
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Affiliation(s)
- Claudia Sas
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam-Golm, Germany
| | - Frank Müller
- Institute of Biology, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Haderslebener Straße 9, 12163 Berlin, Germany
| | - Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam-Golm, Germany
| | - Tyler V Kent
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Monika Hilker
- Institute of Biology, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Haderslebener Straße 9, 12163 Berlin, Germany
| | - Michael Lenhard
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam-Golm, Germany.
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