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Cárdenas-Moreno Y, González-Bacerio J, García Arellano H, Del Monte-Martínez A. Oxidoreductase enzymes: Characteristics, applications, and challenges as a biocatalyst. Biotechnol Appl Biochem 2023; 70:2108-2135. [PMID: 37753743 DOI: 10.1002/bab.2513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 09/03/2023] [Indexed: 09/28/2023]
Abstract
Oxidoreductases are enzymes with distinctive characteristics that favor their use in different areas, such as agriculture, environmental management, medicine, and analytical chemistry. Among these enzymes, oxidases, dehydrogenases, peroxidases, and oxygenases are very interesting. Because their substrate diversity, they can be used in different biocatalytic processes by homogeneous and heterogeneous catalysis. Immobilization of these enzymes has favored their use in the solution of different biotechnological problems, with a notable increase in the study and optimization of this technology in the last years. In this review, the main structural and catalytical features of oxidoreductases, their substrate specificity, immobilization, and usage in biocatalytic processes, such as bioconversion, bioremediation, and biosensors obtainment, are presented.
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Affiliation(s)
- Yosberto Cárdenas-Moreno
- Laboratory for Enzyme Technology, Centre for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba
| | - Jorge González-Bacerio
- Laboratory for Enzyme Technology, Centre for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba
- Department of Biochemistry, Faculty of Biology, University of Havana, Havana, Cuba
| | - Humberto García Arellano
- Department of Environmental Sciences, Division of Health and Biological Sciences, Metropolitan Autonomous University, Lerma, Mexico, Mexico
| | - Alberto Del Monte-Martínez
- Laboratory for Enzyme Technology, Centre for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba
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2
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Grimm C, Pompei S, Egger K, Fuchs M, Kroutil W. Anaerobic demethylation of guaiacyl-derived monolignols enabled by a designed artificial cobalamin methyltransferase fusion enzyme. RSC Adv 2023; 13:5770-5777. [PMID: 36816070 PMCID: PMC9930637 DOI: 10.1039/d2ra08005b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
Lignin-derived aryl methyl ethers (e.g. coniferyl alcohol, ferulic acid) are expected to be a future carbon source for chemistry. The well-known P450 dependent biocatalytic O-demethylation of these aryl methyl ethers is prone to side product formation especially for the oxidation sensitive catechol products which get easily oxidized in the presence of O2. Alternatively, biocatalytic demethylation using cobalamin dependent enzymes may be used under anaerobic conditions, whereby two proteins, namely a methyltransferase and a carrier protein are required. To make this approach applicable for preparative transformations, fusion proteins were designed connecting the cobalamin-dependent methyltransferase (MT) with the corrinoid-binding protein (CP) from Desulfitobacterium hafniense by variable glycine linkers. From the proteins created, the fusion enzyme MT-L5-CP with the shortest linker performed best of all fusion enzymes investigated showing comparable and, in some aspects, even better performance than the separated proteins. The fusion enzymes provided several advantages like that the cobalamin cofactor loading step required originally for the CP could be skipped enabling a significantly simpler protocol. Consequently, the biocatalytic demethylation was performed using Schlenk conditions allowing the O-demethylation e.g. of the monolignol coniferyl alcohol on a 25 mL scale leading to 75% conversion. The fusion enzyme represents a promising starting point to be evolved for alternative demethylation reactions to diversify natural products and to valorize lignin.
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Affiliation(s)
- Christopher Grimm
- Institute of Chemistry, University of Graz, NAWI Graz Heinrichstraße 28 8010 Graz Austria
| | - Simona Pompei
- Institute of Chemistry, University of Graz, NAWI Graz Heinrichstraße 28 8010 Graz Austria
| | - Kristina Egger
- Institute of Chemistry, University of Graz, NAWI Graz Heinrichstraße 28 8010 Graz Austria
| | - Michael Fuchs
- Institute of Chemistry, University of Graz, NAWI Graz Heinrichstraße 28 8010 Graz Austria
| | - Wolfgang Kroutil
- Institute of Chemistry, University of Graz, NAWI Graz Heinrichstraße 28 8010 Graz Austria .,BioTechMed Graz 8010 Graz Austria.,Field of Excellence BioHealth, University of Graz 8010 Graz Austria
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3
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Ma Y, Zhang N, Vernet G, Kara S. Design of fusion enzymes for biocatalytic applications in aqueous and non-aqueous media. Front Bioeng Biotechnol 2022; 10:944226. [PMID: 35935496 PMCID: PMC9354712 DOI: 10.3389/fbioe.2022.944226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 06/30/2022] [Indexed: 12/26/2022] Open
Abstract
Biocatalytic cascades play a fundamental role in sustainable chemical synthesis. Fusion enzymes are one of the powerful toolboxes to enable the tailored combination of multiple enzymes for efficient cooperative cascades. Especially, this approach offers a substantial potential for the practical application of cofactor-dependent oxidoreductases by forming cofactor self-sufficient cascades. Adequate cofactor recycling while keeping the oxidized/reduced cofactor in a confined microenvironment benefits from the fusion fashion and makes the use of oxidoreductases in harsh non-aqueous media practical. In this mini-review, we have summarized the application of various fusion enzymes in aqueous and non-aqueous media with a focus on the discussion of linker design within oxidoreductases. The design and properties of the reported linkers have been reviewed in detail. Besides, the substrate loadings in these studies have been listed to showcase one of the key limitations (low solubility of hydrophobic substrates) of aqueous biocatalysis when it comes to efficiency and economic feasibility. Therefore, a straightforward strategy of applying non-aqueous media has been briefly discussed while the potential of using the fusion oxidoreductase of interest in organic media was highlighted.
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Affiliation(s)
- Yu Ma
- Biocatalysis and Bioprocessing Group, Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | - Ningning Zhang
- Institute of Technical Chemistry, Leibniz University Hannover, Hannover, Germany
| | - Guillem Vernet
- Institute of Technical Chemistry, Leibniz University Hannover, Hannover, Germany
| | - Selin Kara
- Biocatalysis and Bioprocessing Group, Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
- Institute of Technical Chemistry, Leibniz University Hannover, Hannover, Germany
- *Correspondence: Selin Kara,
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4
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Genetic fusion of P450 BM3 and formate dehydrogenase towards self-sufficient biocatalysts with enhanced activity. Sci Rep 2021; 11:21706. [PMID: 34737365 PMCID: PMC8568981 DOI: 10.1038/s41598-021-00957-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/08/2021] [Indexed: 11/09/2022] Open
Abstract
Fusion of multiple enzymes to multifunctional constructs has been recognized as a viable strategy to improve enzymatic properties at various levels such as stability, activity and handling. In this study, the genes coding for cytochrome P450 BM3 from B. megaterium and formate dehydrogenase from Pseudomonas sp. were fused to enable both substrate oxidation catalyzed by P450 BM3 and continuous cofactor regeneration by formate dehydrogenase within one construct. The order of the genes in the fusion as well as the linkers that bridge the enzymes were varied. The resulting constructs were compared to individual enzymes regarding substrate conversion, stability and kinetic parameters to examine whether fusion led to any substantial improvements of enzymatic properties. Most noticeably, an activity increase of up to threefold was observed for the fusion constructs with various substrates which were partly attributed to the increased diflavin reductase activity of the P450 BM3. We suggest that P450 BM3 undergoes conformational changes upon fusion which resulted in altered properties, however, no NADPH channeling was detected for the fusion constructs.
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Colombo D, Brenna E, Casali B, Ghezzi MC, Parmeggiani F, Tentori F, Tessaro D, Boratyński F. Oxidation of
threo
‐9,10‐Dihydroxystearic Acid Mediated by
Micrococcus luteus
as a Key Step in the Conversion of Oleic Acid into Pelargonic and Azelaic Acids. ChemCatChem 2021. [DOI: 10.1002/cctc.202100514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Danilo Colombo
- Dipartimento di Chimica Materiali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano Piazza Leonardo da Vinci, 32 20133 Milano Italy
| | - Elisabetta Brenna
- Dipartimento di Chimica Materiali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano Piazza Leonardo da Vinci, 32 20133 Milano Italy
| | - Beatrice Casali
- Dipartimento di Chimica Materiali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano Piazza Leonardo da Vinci, 32 20133 Milano Italy
| | - Maria Chiara Ghezzi
- Dipartimento di Chimica Materiali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano Piazza Leonardo da Vinci, 32 20133 Milano Italy
| | - Fabio Parmeggiani
- Dipartimento di Chimica Materiali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano Piazza Leonardo da Vinci, 32 20133 Milano Italy
| | - Francesca Tentori
- Dipartimento di Chimica Materiali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano Piazza Leonardo da Vinci, 32 20133 Milano Italy
| | - Davide Tessaro
- Dipartimento di Chimica Materiali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano Piazza Leonardo da Vinci, 32 20133 Milano Italy
| | - Filip Boratyński
- Department of Chemistry Wroclaw University of Environmental and Life Sciences Norwida 25 50-375 Wrocław Poland
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Abstract
Baeyer–Villiger monooxygenases (BVMOs) are flavin-dependent oxidative enzymes capable of catalyzing the insertion of an oxygen atom between a carbonylic Csp2 and the Csp3 at the alpha position, therefore transforming linear and cyclic ketones into esters and lactones. These enzymes are dependent on nicotinamides (NAD(P)H) for the flavin reduction and subsequent reaction with molecular oxygen. BVMOs can be included in cascade reactions, coupled to other redox enzymes, such as alcohol dehydrogenases (ADHs) or ene-reductases (EREDs), so that the direct conversion of alcohols or α,β-unsaturated carbonylic compounds to the corresponding esters can be achieved. In the present review, the different synthetic methodologies that have been performed by employing multienzymatic strategies with BVMOs combining whole cells or isolated enzymes, through sequential or parallel methods, are described, with the aim of highlighting the advantages of performing multienzymatic systems, and show the recent advances for overcoming the drawbacks of using BVMOs in these techniques.
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Optimizing the linker length for fusing an alcohol dehydrogenase with a cyclohexanone monooxygenase. Methods Enzymol 2020; 647:107-143. [PMID: 33482986 DOI: 10.1016/bs.mie.2020.09.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The use of enzymes in organic synthesis is highly appealing due their remarkably high chemo-, regio- and enantioselectivity. Nevertheless, for biosynthetic routes to be industrially useful, the enzymes must fulfill several requirements. Particularly, in case of cofactor-dependent enzymes self-sufficient systems are highly valuable. This can be achieved by fusing enzymes with complementary cofactor dependency. Such bifunctional enzymes are also relatively easy to handle, may enhance stability, and promote product intermediate channeling. However, usually the characteristics of the linker, fusing the target enzymes, are not thoroughly evaluated. A poor linker design can lead to detrimental effects on expression levels, enzyme stability and/or enzyme performance. In this chapter, the effect of the length of a glycine-rich linker was explored for the case study of ɛ-caprolactone synthesis through an alcohol dehydrogenase-cyclohexanone monooxygenase fusion system. The procedure includes cloning of linker variants, expression analysis, determination of thermostability and effect on activity and conversion levels of 15 variants of different linker sizes. The protocols can also be used for the creation of other protein-protein fusions.
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Kim TH, Kang SH, Han JE, Seo EJ, Jeon EY, Choi GE, Park JB, Oh DK. Multilayer Engineering of Enzyme Cascade Catalysis for One-Pot Preparation of Nylon Monomers from Renewable Fatty Acids. ACS Catal 2020. [DOI: 10.1021/acscatal.9b05426] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Tae-Hun Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Su-Hwan Kang
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Jeong-Eun Han
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Eun-Ji Seo
- Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Eun-Yeong Jeon
- Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Go-Eun Choi
- Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jin-Byung Park
- Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Deok-Kun Oh
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
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9
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Knockout of secondary alcohol dehydrogenase in Nocardia cholesterolicum NRRL 5767 by CRISPR/Cas9 genome editing technology. PLoS One 2020; 15:e0230915. [PMID: 32218601 PMCID: PMC7101164 DOI: 10.1371/journal.pone.0230915] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 03/11/2020] [Indexed: 11/19/2022] Open
Abstract
Nocardia cholesterolicum NRRL 5767 is well-known for its ability to convert oleic acid to 10-hydroxystearic acid (~88%, w/w) and 10-ketostearic acid (~11%, w/w). Conversion of oleic acid to 10-hydroxystearic acid and then to 10-ketostearic acid has been proposed to be catalyzed by oleate hydratase and secondary alcohol dehydrogenase, respectively. Hydroxy fatty acids are value-added with many industrial applications. The objective of this study was to improve the Nocardia cholesterolicum NRRL5767 strain by CRISPR/Cas9 genome editing technology to knockout the secondary alcohol dehydrogenase gene, thus blocking the conversion of 10-hydroxystearic acid to 10-ketostearic acid. The improved strain would produce 10-hydroxystearic acid solely from oleic acid. Such improvement would enhance the production of 10-hydroxystearic acid by eliminating downstream separation of 10-hydroxystearic acid from 10-ketostearic acid. Here, we report: (1) Molecular cloning and characterization of two functional recombinant oleate hydratase isozymes and a functional recombinant secondary alcohol dehydrogenase from Nocardia cholesterolicum NRRL5767. Existence of two oleate hydratase isozymes may explain the high conversion yield of 10-hydroxystearic acid from oleic acid. (2) Construction of a CRISPR/Cas9/sgRNA chimeric plasmid that specifically targeted the secondary alcohol dehydrogenase gene by Golden Gate Assembly. (3) Transformation of the chimeric plasmid into Nocardia cholesterolicum NRRL 5767 by electroporation and screening of secondary alcohol dehydrogenase knockout mutants. Two mutants were validated by their lack of secondary alcohol dehydrogenase activity at the protein level and mutation at the targeted 5’ coding region and the 5’ upstream at the DNA level. The knockout mutants offer improvements by converting added oleic acid to solely 10-hydroxystearic acid, thus eliminating downstream separation of 10-hydroxystearic acid from 10-ketostearic acid. To the best of our knowledge, we report the first successful knockout of a target gene in the Nocardia species using CRISPR/Cas9/sgRNA-mediated genome editing technology.
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10
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Sheldon RA, Brady D, Bode ML. The Hitchhiker's guide to biocatalysis: recent advances in the use of enzymes in organic synthesis. Chem Sci 2020; 11:2587-2605. [PMID: 32206264 PMCID: PMC7069372 DOI: 10.1039/c9sc05746c] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/12/2020] [Indexed: 12/12/2022] Open
Abstract
Enzymes are excellent catalysts that are increasingly being used in industry and academia. This perspective is primarily aimed at synthetic organic chemists with limited experience using enzymes and provides a general and practical guide to enzymes and their synthetic potential, with particular focus on recent applications.
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Affiliation(s)
- Roger A Sheldon
- Molecular Sciences Institute , School of Chemistry , University of the Witwatersrand , Johannesburg , South Africa .
- Department of Biotechnology , Delft University of Technology , Delft , The Netherlands
| | - Dean Brady
- Molecular Sciences Institute , School of Chemistry , University of the Witwatersrand , Johannesburg , South Africa .
| | - Moira L Bode
- Molecular Sciences Institute , School of Chemistry , University of the Witwatersrand , Johannesburg , South Africa .
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11
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Fürst MJLJ, Gran-Scheuch A, Aalbers FS, Fraaije MW. Baeyer–Villiger Monooxygenases: Tunable Oxidative Biocatalysts. ACS Catal 2019. [DOI: 10.1021/acscatal.9b03396] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Maximilian J. L. J. Fürst
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, Groningen 9747AG, The Netherlands
| | - Alejandro Gran-Scheuch
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, Groningen 9747AG, The Netherlands
- Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Santiago 7820436, Chile
| | - Friso S. Aalbers
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, Groningen 9747AG, The Netherlands
| | - Marco W. Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, Groningen 9747AG, The Netherlands
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12
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Ribeiro LF, Amarelle V, Alves LDF, Viana de Siqueira GM, Lovate GL, Borelli TC, Guazzaroni ME. Genetically Engineered Proteins to Improve Biomass Conversion: New Advances and Challenges for Tailoring Biocatalysts. Molecules 2019; 24:molecules24162879. [PMID: 31398877 PMCID: PMC6719137 DOI: 10.3390/molecules24162879] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 07/30/2019] [Accepted: 08/06/2019] [Indexed: 01/02/2023] Open
Abstract
Protein engineering emerged as a powerful approach to generate more robust and efficient biocatalysts for bio-based economy applications, an alternative to ecologically toxic chemistries that rely on petroleum. On the quest for environmentally friendly technologies, sustainable and low-cost resources such as lignocellulosic plant-derived biomass are being used for the production of biofuels and fine chemicals. Since most of the enzymes used in the biorefinery industry act in suboptimal conditions, modification of their catalytic properties through protein rational design and in vitro evolution techniques allows the improvement of enzymatic parameters such as specificity, activity, efficiency, secretability, and stability, leading to better yields in the production lines. This review focuses on the current application of protein engineering techniques for improving the catalytic performance of enzymes used to break down lignocellulosic polymers. We discuss the use of both classical and modern methods reported in the literature in the last five years that allowed the boosting of biocatalysts for biomass degradation.
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Affiliation(s)
- Lucas Ferreira Ribeiro
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-901, Brazil.
| | - Vanesa Amarelle
- Department of Microbial Biochemistry and Genomics, Biological Research Institute Clemente Estable, Montevideo, PC 11600, Uruguay
| | - Luana de Fátima Alves
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Ribeirão Preto 14049-900, Brazil
| | | | - Gabriel Lencioni Lovate
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Ribeirão Preto 14049-900, Brazil
| | - Tiago Cabral Borelli
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-901, Brazil
| | - María-Eugenia Guazzaroni
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-901, Brazil.
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13
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Sheldon RA, Brady D. Broadening the Scope of Biocatalysis in Sustainable Organic Synthesis. CHEMSUSCHEM 2019; 12:2859-2881. [PMID: 30938093 DOI: 10.1002/cssc.201900351] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 02/05/2019] [Accepted: 03/04/2019] [Indexed: 05/21/2023]
Abstract
This Review is aimed at synthetic organic chemists who may be familiar with organometallic catalysis but have no experience with biocatalysis, and seeks to provide an answer to the perennial question: if it is so attractive, why wasn't it extensively used in the past? The development of biocatalysis in industrial organic synthesis is traced from the middle of the last century. Advances in molecular biology in the last two decades, in particular genome sequencing, gene synthesis and directed evolution of proteins, have enabled remarkable improvements in scope and substantially reduced biocatalyst development times and cost contributions. Additionally, improvements in biocatalyst recovery and reuse have been facilitated by developments in enzyme immobilization technologies. Biocatalysis has become eminently competitive with chemocatalysis and the biocatalytic production of important pharmaceutical intermediates, such as enantiopure alcohols and amines, has become mainstream organic synthesis. The synthetic space of biocatalysis has significantly expanded and is currently being extended even further to include new-to-nature biocatalytic reactions.
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Affiliation(s)
- Roger A Sheldon
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, 2050, South Africa
- Department of Biotechnology, Delft University of Technology, Section BOC, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Dean Brady
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, 2050, South Africa
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14
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Huang L, Aalbers FS, Tang W, Röllig R, Fraaije MW, Kara S. Convergent Cascade Catalyzed by Monooxygenase-Alcohol Dehydrogenase Fusion Applied in Organic Media. Chembiochem 2019; 20:1653-1658. [PMID: 30811825 DOI: 10.1002/cbic.201800814] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/26/2019] [Indexed: 01/13/2023]
Abstract
With the aim of applying redox-neutral cascade reactions in organic media, fusions of a type II flavin-containing monooxygenase (FMO-E) and horse liver alcohol dehydrogenase (HLADH) were designed. The enzyme orientation and expression vector were found to influence the overall fusion enzyme activity. The resulting bifunctional enzyme retained the catalytic properties of both individual enzymes. The lyophilized cell-free extract containing the bifunctional enzyme was applied for the convergent cascade reaction consisting of cyclobutanone and butane-1,4-diol in different microaqueous media with only 5 % (v/v) aqueous buffer without any addition of external cofactor. Methyl tert-butyl ether and cyclopentyl methyl ether were found to be the best organic media for the synthesis of γ-butyrolactone, resulting in about 27 % analytical yield.
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Affiliation(s)
- Lei Huang
- Department of Engineering, Biocatalysis and Bioprocessing Group, Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus, Denmark.,Institute of Technical Biocatalysis, Hamburg University of Technology, Denickestrasse 15, 21073, Hamburg, Germany
| | - Friso S Aalbers
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Wei Tang
- Institute of Technical Biocatalysis, Hamburg University of Technology, Denickestrasse 15, 21073, Hamburg, Germany
| | - Robert Röllig
- Institute of Technical Biocatalysis, Hamburg University of Technology, Denickestrasse 15, 21073, Hamburg, Germany.,Chair of Molecular Biotechnology, Technische Universität Dresden, Zellescher Weg 20b, 01062, Dresden, Germany
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Selin Kara
- Department of Engineering, Biocatalysis and Bioprocessing Group, Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus, Denmark.,Institute of Technical Biocatalysis, Hamburg University of Technology, Denickestrasse 15, 21073, Hamburg, Germany
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15
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Kuzmak A, Carmali S, von Lieres E, Russell AJ, Kondrat S. Can enzyme proximity accelerate cascade reactions? Sci Rep 2019; 9:455. [PMID: 30679600 PMCID: PMC6345930 DOI: 10.1038/s41598-018-37034-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/26/2018] [Indexed: 01/23/2023] Open
Abstract
The last decade has seen an exponential expansion of interest in conjugating multiple enzymes of cascades in close proximity to each other, with the overarching goal being to accelerate the overall reaction rate. However, some evidence has emerged that there is no effect of proximity channeling on the reaction velocity of the popular GOx-HRP cascade, particularly in the presence of a competing enzyme (catalase). Herein, we rationalize these experimental results quantitatively. We show that, in general, proximity channeling can enhance reaction velocity in the presence of competing enzymes, but in steady state a significant enhancement can only be achieved for diffusion-limited reactions or at high concentrations of competing enzymes. We provide simple equations to estimate the effect of channeling quantitatively and demonstrate that proximity can have a more pronounced effect under crowding conditions in vivo, particularly that crowding can enhance the overall rates of channeled cascade reactions.
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Affiliation(s)
- Andrij Kuzmak
- Department for Theoretical Physics, I. Franko National University of Lviv, Lviv, Ukraine
| | - Sheiliza Carmali
- Department of Chemistry, Aarhus University, 8000, Aarhus C, Denmark.,Center for Polymer-Based Protein Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA
| | - Eric von Lieres
- Forschungszentrum Jülich, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Alan J Russell
- Center for Polymer-Based Protein Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA.,Department of Chemical Engineering, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Svyatoslav Kondrat
- Forschungszentrum Jülich, IBG-1: Biotechnology, 52425, Jülich, Germany. .,Department of Complex Systems, Institute of Physical Chemistry, Warsaw, Poland.
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16
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Cha HJ, Park JB, Park S. Esterification of Secondary Alcohols and Multi-hydroxyl Compounds by Candida antarctica Lipase B and Subtilisin. BIOTECHNOL BIOPROC E 2019. [DOI: 10.1007/s12257-018-0379-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Abstract
One approach to bringing enzymes together for multienzyme biocatalysis is genetic fusion. This enables the production of multifunctional enzymes that can be used for whole-cell biotransformations or for in vitro (cascade) reactions. In some cases and in some aspects, such as expression and conversions, the fused enzymes outperform a combination of the individual enzymes. In contrast, some enzyme fusions are greatly compromised in activity and/or expression. In this Minireview, we give an overview of studies on fusions between two or more enzymes that were used for biocatalytic applications, with a focus on oxidative enzymes. Typically, the enzymes are paired to facilitate cofactor recycling or cosubstrate supply. In addition, different linker designs are briefly discussed. Although enzyme fusion is a promising tool for some biocatalytic applications, future studies could benefit from integrating the findings of previous studies in order to improve reliability and effectiveness.
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Affiliation(s)
- Friso S. Aalbers
- Molecular Enzymology GroupUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Marco W. Fraaije
- Molecular Enzymology GroupUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
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18
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Biosynthesis of ω-hydroxy fatty acids and related chemicals from natural fatty acids by recombinant Escherichia coli. Appl Microbiol Biotechnol 2018; 103:191-199. [DOI: 10.1007/s00253-018-9503-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/01/2018] [Accepted: 11/05/2018] [Indexed: 10/27/2022]
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19
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Aalbers FS, Fraaije MW. Design of Artificial Alcohol Oxidases: Alcohol Dehydrogenase-NADPH Oxidase Fusions for Continuous Oxidations. Chembiochem 2018; 20:51-56. [PMID: 30184296 PMCID: PMC6899577 DOI: 10.1002/cbic.201800421] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Indexed: 01/22/2023]
Abstract
To expand the arsenal of industrially applicable oxidative enzymes, fusions of alcohol dehydrogenases with an NADPH-oxidase were designed. Three different alcohol dehydrogenases (LbADH, TbADH, ADHA) were expressed with a thermostable NADPH-oxidase fusion partner (PAMO C65D) and purified. The resulting bifunctional biocatalysts retained the catalytic properties of the individual enzymes, and acted essentially like alcohol oxidases: transforming alcohols to ketones by using dioxygen as mild oxidant, while merely requiring a catalytic amount of NADP+ . In small-scale reactions, the purified fusion enzymes show good performances, with 69-99 % conversion, 99 % ee with a racemic substrate, and high cofactor and enzyme total turnover numbers. As the fusion enzymes essentially act as oxidases, we found that commonly used high-throughput oxidase-activity screening methods can be used. Therefore, if needed, the fusion enzymes could be easily engineered to tune their properties.
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Affiliation(s)
- Friso S Aalbers
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
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20
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Jäger VD, Lamm R, Kloß R, Kaganovitch E, Grünberger A, Pohl M, Büchs J, Jaeger KE, Krauss U. A Synthetic Reaction Cascade Implemented by Colocalization of Two Proteins within Catalytically Active Inclusion Bodies. ACS Synth Biol 2018; 7:2282-2295. [PMID: 30053372 DOI: 10.1021/acssynbio.8b00274] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In nature, enzymatic reaction cascades, i.e., realized in metabolic networks, operate with unprecedented efficacy, with the reactions often being spatially and temporally orchestrated. The principle of "learning from nature" has in recent years inspired the setup of synthetic reaction cascades combining biocatalytic reaction steps to artificial cascades. Hereby, the spatial organization of multiple enzymes, e.g., by coimmobilization, remains a challenging task, as currently no generic principles are available that work for every enzyme. We here present a tunable, genetically programmed coimmobilization strategy that relies on the fusion of a coiled-coil domain as aggregation inducing-tag, resulting in the formation of catalytically active inclusion body coimmobilizates (Co-CatIBs). Coexpression and coimmobilization was proven using two fluorescent proteins, and the strategy was subsequently extended to two enzymes, which enabled the realization of an integrated enzymatic two-step cascade for the production of (1 R,2 R)-1-phenylpropane-1,2-diol (PPD), a precursor of the calicum channel blocker diltiazem. In particular, the easy production and preparation of Co-CatIBs, readily yielding a biologically produced enzyme immobilizate renders the here presented strategy an interesting alternative to existing cascade immobilization techniques.
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Affiliation(s)
- Vera D. Jäger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Robin Lamm
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, D-52074 Aachen, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Ramona Kloß
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Eugen Kaganovitch
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Alexander Grünberger
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Multiscale Bioengineering group, Bielefeld University, D-33615 Bielefeld, Germany
| | - Martina Pohl
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Jochen Büchs
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, D-52074 Aachen, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Karl-Erich Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Ulrich Krauss
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
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21
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Jeon EY, Song JW, Cha HJ, Lee SM, Lee J, Park JB. Intracellular transformation rates of fatty acids are influenced by expression of the fatty acid transporter FadL in Escherichia coli cell membrane. J Biotechnol 2018; 281:161-167. [DOI: 10.1016/j.jbiotec.2018.07.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/10/2018] [Accepted: 07/14/2018] [Indexed: 10/28/2022]
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22
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Improving catalytic activity of the Baeyer-Villiger monooxygenase-based Escherichia coli biocatalysts for the overproduction of (Z)-11-(heptanoyloxy)undec-9-enoic acid from ricinoleic acid. Sci Rep 2018; 8:10280. [PMID: 29980730 PMCID: PMC6035261 DOI: 10.1038/s41598-018-28575-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 06/21/2018] [Indexed: 12/21/2022] Open
Abstract
Baeyer–Villiger monooxygenases (BVMOs) can be used for the biosynthesis of lactones and esters from ketones. However, the BVMO-based biocatalysts are not so stable under process conditions. Thereby, this study focused on enhancing stability of the BVMO-based biocatalysts. The biotransformation of ricinoleic acid into (Z)-11-(heptanoyloxy)undec-9-enoic acid by the recombinant Escherichia coli expressing the BVMO from Pseudomonas putida and an alcohol dehydrogenase from Micrococcus luteus was used as a model system. After thorough investigation of the key factors to influence stability of the BVMO, Cys302 was identified as an engineering target. The substitution of Cys302 to Leu enabled the engineered enzyme (i.e., E6BVMOC302L) to become more stable toward oxidative and thermal stresses. The catalytic activity of E6BVMOC302L-based E. coli biocatalysts was also greater than the E6BVMO-based biocatalysts. Another factor to influence biocatalytic performance of the BVMO-based whole-cell biocatalysts was availability of carbon and energy source during biotransformations. Glucose feeding into the reaction medium led to a marked increase of final product concentrations. Overall, the bioprocess engineering to improve metabolic stability of host cells in addition to the BVMO engineering allowed us to produce (Z)-11-(heptanoyloxy)undec-9-enoic acid to a concentration of 132 mM (41 g/L) from 150 mM ricinoleic acid within 8 h.
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Microbial synthesis of undec-9-enoic acid, heptyl ester from renewable fatty acids using recombinant Corynebacterium glutamicum-based whole-cell biocatalyst. Process Biochem 2018. [DOI: 10.1016/j.procbio.2017.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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24
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Liu J, Wu S, Li Z. Recent advances in enzymatic oxidation of alcohols. Curr Opin Chem Biol 2017; 43:77-86. [PMID: 29258054 DOI: 10.1016/j.cbpa.2017.12.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 11/03/2017] [Accepted: 12/04/2017] [Indexed: 01/07/2023]
Abstract
Enzymatic alcohol oxidation plays an important role in chemical synthesis. In the past two years, new alcohol oxidation enzymes were developed through genome-mining and protein engineering, such as new copper radical oxidases with broad substrate scope, alcohol dehydrogenases with altered cofactor preference and a flavin-dependent alcohol oxidase with enhanced oxygen coupling. New cofactor recycling methods were reported for alcohol dehydrogenase-catalyzed oxidation with photocatalyst and coupled glutaredoxin-glutathione reductase as promising examples. Different alcohol oxidation systems were used for the oxidation of primary and secondary alcohols, especially in the cascade conversion of alcohols to lactones, lactams, chiral amines, chiral alcohols and hydroxyketones. Among them, biocatalyst with low enantioselectivity demonstrated an interesting feature for complete conversion of racemic secondary alcohols through non-enantioselective oxidation.
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Affiliation(s)
- Ji Liu
- Department of Chemical and Biomolecular Engineering, 4 Engineering Drive 4, National University of Singapore, Singapore 117585, Singapore
| | - Shuke Wu
- Department of Chemical and Biomolecular Engineering, 4 Engineering Drive 4, National University of Singapore, Singapore 117585, Singapore
| | - Zhi Li
- Department of Chemical and Biomolecular Engineering, 4 Engineering Drive 4, National University of Singapore, Singapore 117585, Singapore.
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25
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Coupled reactions by coupled enzymes: alcohol to lactone cascade with alcohol dehydrogenase-cyclohexanone monooxygenase fusions. Appl Microbiol Biotechnol 2017; 101:7557-7565. [PMID: 28916997 PMCID: PMC5624969 DOI: 10.1007/s00253-017-8501-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/01/2017] [Accepted: 08/23/2017] [Indexed: 12/20/2022]
Abstract
The combination of redox enzymes for redox-neutral cascade reactions has received increasing appreciation. An example is the combination of an alcohol dehydrogenase (ADH) with a cyclohexanone monooxygenase (CHMO). The ADH can use NADP+ to oxidize cyclohexanol to form cyclohexanone and NADPH. Both products are then used by CHMO to produce ε-caprolactone. In this study, these two redox-complementary enzymes were fused, to create a self-sufficient bifunctional enzyme that can convert alcohols to esters or lactones. Three different ADH genes were fused to a gene coding for a thermostable CHMO, in both orientations (ADH-CHMO and CHMO-ADH). All six fusion enzymes could be produced and purified. For two of the three ADHs, we found a clear difference between the two orientations: one that showed the expected ADH activity, and one that showed low to no activity. The ADH activity of each fusion enzyme correlated with its oligomerization state. All fusions retained CHMO activity, and stability was hardly affected. The TbADH-TmCHMO fusion was selected to perform a cascade reaction, producing ε-caprolactone from cyclohexanol. By circumventing substrate and product inhibition, a > 99% conversion of 200 mM cyclohexanol could be achieved in 24 h, with > 13,000 turnovers per fusion enzyme molecule.
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26
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Peters C, Rudroff F, Mihovilovic MD, T Bornscheuer U. Fusion proteins of an enoate reductase and a Baeyer-Villiger monooxygenase facilitate the synthesis of chiral lactones. Biol Chem 2017; 398:31-37. [PMID: 27289001 DOI: 10.1515/hsz-2016-0150] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/08/2016] [Indexed: 11/15/2022]
Abstract
Nature uses the advantages of fusion proteins for multi-step reactions to facilitate the metabolism in cells as the conversion of substrates through intermediates to the final product can take place more rapidly and with less side-product formation. In a similar fashion, also for enzyme cascade reactions, the fusion of biocatalysts involved can be advantageous. In the present study, we investigated fusion of an alcohol dehydrogenase (ADH), an enoate reductase (ERED) and a Baeyer-Villiger monooxygenase (BVMO) to enable the synthesis of (chiral) lactones starting from unsaturated alcohols as substrates. The domain order and various linkers were studied to find optimal conditions with respect to expression levels and enzymatic activities. Best results were achieved for the ERED xenobiotic reductase B (XenB) from Pseudomonas putida and the cyclohexanone monooxygenase (CHMO) from Acinetobacter sp., whereas none of the ADHs studied could be fused successfully. This fusion protein together with separately supplied ADH resulted in similar reaction rates in in vivo biocatalysis reactions. After 1.5 h we could detect 40% more dihydrocarvone lactone in in vivo reactions with the fusion protein and ADH then with the single enzymes.
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27
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Mthethwa KS, Kassier K, Engel J, Kara S, Smit MS, Opperman DJ. Fungal BVMOs as alternatives to cyclohexanone monooxygenase. Enzyme Microb Technol 2017; 106:11-17. [PMID: 28859804 DOI: 10.1016/j.enzmictec.2017.06.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/19/2017] [Accepted: 06/30/2017] [Indexed: 12/12/2022]
Abstract
FAD-dependent Baeyer-Villiger monooxygenases (BVMOs) have proven to be useful biocatalysts in the selective and specific oxygenation of various ketones. Despite the cloning, heterologous expression and characterization of close to 80 members of this enzyme family, some sub-groups of BVMOs still remain underrepresented and their evolutionary relationship uncertain. Until recently, very few fungal BVMOs have been described. Our previous investigations into BVMOs from the fungus Aspergillus flavus, yielded very little activity on simple cyclic ketones. Here we report on another four BVMOs from A. flavus that are more closely related to cyclohexanone monooxygenase (CHMO) from Acinetobacter sp. NCIMB 9871. Evolutionary analysis with other characterized BVMOs show their closest relationship to be with either cycloalkanone monooxygenase (CAMO) or 2-oxo-Δ3-4,5,5-trimethylcyclopentenylacetyl-coenzyme A monooxygenase (OTEMO). The OTEMO-related BVMOAFL706 and BVMOAFL334 were heterologously expressed in E. coli, purified and shown to be able to convert a range of cyclic and substituted cyclic ketones. Of the unsubstituted cyclic ketones, cyclohexanone showed the highest conversion with maximum turnover frequencies reaching 4.3s-1 for BVMOAFL706. Unlike CHMOacinet, and many of the closely related BVMOs, no substrate inhibition was observed with cyclohexanone to a concentration of up to 30mM, creating the possibility for applications requiring high substrate loading. Aliphatic ketones were also readily converted with excellent regioselectivity. Similar to CHMOacinet, acetophenones were not converted and the oxidation of rac-cis-bicyclo[3.2.0]hept-2-en-6-one occurs enantiodivergently, with the (1R,5S) isomer converted to the "normal" lactone and the (1S,5R) isomer to the "abnormal" lactone.
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Affiliation(s)
- Katlego Siphamandla Mthethwa
- Department of Biotechnology, University of the Free State, 205 Nelson Mandela Drive, Bloemfontein, 9300, South Africa
| | - Karin Kassier
- Department of Biotechnology, University of the Free State, 205 Nelson Mandela Drive, Bloemfontein, 9300, South Africa
| | - Jennifer Engel
- Institute of Technical Biocatalysis, Hamburg University of Technology, Denickestr. 15, Hamburg, 21073, Germany
| | - Selin Kara
- Institute of Technical Biocatalysis, Hamburg University of Technology, Denickestr. 15, Hamburg, 21073, Germany
| | - Martha Sophia Smit
- Department of Biotechnology, University of the Free State, 205 Nelson Mandela Drive, Bloemfontein, 9300, South Africa
| | - Diederik Johannes Opperman
- Department of Biotechnology, University of the Free State, 205 Nelson Mandela Drive, Bloemfontein, 9300, South Africa.
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28
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Cho YH, Kim SJ, Kim HW, Kim JY, Gwak JS, Chung D, Kim KH, Park K, Park YC. Continuous supply of glucose and glycerol enhances biotransformation of ricinoleic acid to ( E )-11-(heptanoyloxy) undec-9-enoic acid in recombinant Escherichia coli. J Biotechnol 2017; 253:34-39. [DOI: 10.1016/j.jbiotec.2017.05.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 04/29/2017] [Accepted: 05/19/2017] [Indexed: 11/25/2022]
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29
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Bioprocess engineering to produce 9-(nonanoyloxy) nonanoic acid by a recombinant Corynebacterium glutamicum-based biocatalyst. J Ind Microbiol Biotechnol 2017; 44:1301-1311. [PMID: 28567672 DOI: 10.1007/s10295-017-1945-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 04/16/2017] [Indexed: 10/19/2022]
Abstract
Here, Corynebacterium glutamicum ATCC13032 expressing Baeyer-Villiger monooxygenase from Pseudomonas putida KT2440 was designed to produce 9-(nonanoyloxy) nonanoic acid from 10-ketostearic acid. Diverse parameters including cultivation and reaction temperatures, type of detergent, and pH were found to improve biotransformation efficiency. The optimal temperature of cultivation for the production of 9-(nonanoyloxy) nonanoic acid from 10-ketostearic acid using whole cells of recombinant C. glutamicum was 15 °C, but the reaction temperature was optimal at 30 °C. Enhanced conversion efficiency was obtained by supplying 0.05 g/L of Tween 80 at pH 7.5. Under these optimal conditions, recombinant C. glutamicum produced 0.28 mM of 9-(nonanoyloxy) nonanoic acid with a 75.6% (mol/mol) conversion yield in 2 h. This is the first report on the biotransformation of 10-ketostearic acid to 9-(nonanoyloxy) nonanoic acid with a recombinant whole-cell C. glutamicum-based biocatalyst and the results demonstrate the feasibility of using C. glutamicum as a whole-cell biocatalyst.
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30
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Schrittwieser JH, Velikogne S, Hall M, Kroutil W. Artificial Biocatalytic Linear Cascades for Preparation of Organic Molecules. Chem Rev 2017; 118:270-348. [DOI: 10.1021/acs.chemrev.7b00033] [Citation(s) in RCA: 371] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Joerg H. Schrittwieser
- Institute
of Chemistry, Organic and Bioorganic Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, Heinrichstrasse 28, 8010 Graz, Austria
| | - Stefan Velikogne
- ACIB
GmbH, Department of Chemistry, University of Graz, Heinrichstrasse
28, 8010 Graz, Austria
| | - Mélanie Hall
- Institute
of Chemistry, Organic and Bioorganic Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, Heinrichstrasse 28, 8010 Graz, Austria
| | - Wolfgang Kroutil
- Institute
of Chemistry, Organic and Bioorganic Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, Heinrichstrasse 28, 8010 Graz, Austria
- ACIB
GmbH, Department of Chemistry, University of Graz, Heinrichstrasse
28, 8010 Graz, Austria
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31
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Poshyvailo L, von Lieres E, Kondrat S. Does metabolite channeling accelerate enzyme-catalyzed cascade reactions? PLoS One 2017; 12:e0172673. [PMID: 28234973 PMCID: PMC5325314 DOI: 10.1371/journal.pone.0172673] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 02/08/2017] [Indexed: 12/30/2022] Open
Abstract
Metabolite or substrate channeling is a direct transfer of metabolites from one enzyme to the next enzyme in a cascade. Among many potential advantages of substrate channeling, acceleration of the total reaction rate is considered as one of the most important and self-evident. However, using a simple model, supported by stochastic simulations, we show that it is not always the case; particularly at long times (i.e. in steady state) and high substrate concentrations, a channeled reaction cannot be faster, and can even be slower, than the original non-channeled cascade reaction. In addition we show that increasing the degree of channeling may lead to an increase of the metabolite pool size. We substantiate that the main advantage of channeling likely lies in protecting metabolites from degradation or competing side reactions.
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Affiliation(s)
- Liubov Poshyvailo
- Forschungszentrum Jülich, IBG-1: Biotechnology, Jülich, Germany
- Forschungszentrum Jülich, IEK-7: Institute of Energy and Climate Research, Jülich, Germany
| | - Eric von Lieres
- Forschungszentrum Jülich, IBG-1: Biotechnology, Jülich, Germany
| | - Svyatoslav Kondrat
- Forschungszentrum Jülich, IBG-1: Biotechnology, Jülich, Germany
- * E-mail: ,
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32
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Quin MB, Wallin KK, Zhang G, Schmidt-Dannert C. Spatial organization of multi-enzyme biocatalytic cascades. Org Biomol Chem 2017; 15:4260-4271. [DOI: 10.1039/c7ob00391a] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Multi-enzyme cascades provide a wealth of valuable chemicals. Efficiency of reaction schemes can be improved by spatial organization of biocatalysts. This review will highlight various methods of spatial organization of biocatalysts: fusion, immobilization, scaffolding and encapsulation.
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Affiliation(s)
- M. B. Quin
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
| | - K. K. Wallin
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
| | - G. Zhang
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
| | - C. Schmidt-Dannert
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
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33
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Sivaperumal P, Kamala K, Rajaram R. Bioremediation of Industrial Waste Through Enzyme Producing Marine Microorganisms. MARINE ENZYMES BIOTECHNOLOGY: PRODUCTION AND INDUSTRIAL APPLICATIONS, PART III - APPLICATION OF MARINE ENZYMES 2017; 80:165-179. [DOI: 10.1016/bs.afnr.2016.10.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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34
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Jeon EY, Seo JH, Kang WR, Kim MJ, Lee JH, Oh DK, Park JB. Simultaneous Enzyme/Whole-Cell Biotransformation of Plant Oils into C9 Carboxylic Acids. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01884] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Eun-Yeong Jeon
- Department
of Food Science and Engineering, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Joo-Hyun Seo
- Department
of Food Science and Engineering, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Woo-Ri Kang
- Department
of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
| | - Min-Ji Kim
- Department
of Food Science and Engineering, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Jung-Hoo Lee
- Department
of Food Science and Engineering, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Deok-Kun Oh
- Department
of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
| | - Jin-Byung Park
- Department
of Food Science and Engineering, Ewha Womans University, Seoul 120-750, Republic of Korea
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35
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Woo JM, Kim JW, Song JW, Blank LM, Park JB. Activation of the Glutamic Acid-Dependent Acid Resistance System in Escherichia coli BL21(DE3) Leads to Increase of the Fatty Acid Biotransformation Activity. PLoS One 2016; 11:e0163265. [PMID: 27681369 PMCID: PMC5040553 DOI: 10.1371/journal.pone.0163265] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 09/05/2016] [Indexed: 01/29/2023] Open
Abstract
The biosynthesis of carboxylic acids including fatty acids from biomass is central in envisaged biorefinery concepts. The productivities are often, however, low due to product toxicity that hamper whole-cell biocatalyst performance. Here, we have investigated factors that influence the tolerance of Escherichia coli to medium chain carboxylic acid (i.e., n-heptanoic acid)-induced stress. The metabolic and genomic responses of E. coli BL21(DE3) and MG1655 grown in the presence of n-heptanoic acid indicated that the GadA/B-based glutamic acid-dependent acid resistance (GDAR) system might be critical for cellular tolerance. The GDAR system, which is responsible for scavenging intracellular protons by catalyzing decarboxylation of glutamic acid, was inactive in E. coli BL21(DE3). Activation of the GDAR system in this strain by overexpressing the rcsB and dsrA genes, of which the gene products are involved in the activation of GadE and RpoS, respectively, resulted in acid tolerance not only to HCl but also to n-heptanoic acid. Furthermore, activation of the GDAR system allowed the recombinant E. coli BL21(DE3) expressing the alcohol dehydrogenase of Micrococcus luteus and the Baeyer-Villiger monooxygenase of Pseudomonas putida to reach 60% greater product concentration in the biotransformation of ricinoleic acid (i.e., 12-hydroxyoctadec-9-enoic acid (1)) into n-heptanoic acid (5) and 11-hydroxyundec-9-enoic acid (4). This study may contribute to engineering E. coli-based biocatalysts for the production of carboxylic acids from renewable biomass.
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Affiliation(s)
- Ji-Min Woo
- Department of Food Science & Engineering, Ewha Womans University, Seoul, 120-750, Republic of Korea
| | - Ji-Won Kim
- Department of Food Science & Engineering, Ewha Womans University, Seoul, 120-750, Republic of Korea
| | - Ji-Won Song
- Department of Food Science & Engineering, Ewha Womans University, Seoul, 120-750, Republic of Korea
| | - Lars M. Blank
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Jin-Byung Park
- Department of Food Science & Engineering, Ewha Womans University, Seoul, 120-750, Republic of Korea
- * E-mail:
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3'-UTR engineering to improve soluble expression and fine-tuning of activity of cascade enzymes in Escherichia coli. Sci Rep 2016; 6:29406. [PMID: 27406241 PMCID: PMC4942690 DOI: 10.1038/srep29406] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/20/2016] [Indexed: 02/06/2023] Open
Abstract
3′-Untranslated region (3′UTR) engineering was investigated to improve solubility of heterologous proteins (e.g., Baeyer-Villiger monooxygenases (BVMOs)) in Escherichia coli. Insertion of gene fragments containing putative RNase E recognition sites into the 3′UTR of the BVMO genes led to the reduction of mRNA levels in E. coli. Importantly, the amounts of soluble BVMOs were remarkably enhanced resulting in a proportional increase of in vivo catalytic activities. Notably, this increase in biocatalytic activity correlated to the number of putative RNase E endonucleolytic cleavage sites in the 3′UTR. For instance, the biotransformation activity of the BVMO BmoF1 (from Pseudomonas fluorescens DSM50106) in E. coli was linear to the number of RNase E cleavage sites in the 3′UTR. In summary, 3′UTR engineering can be used to improve the soluble expression of heterologous enzymes, thereby fine-tuning the enzyme activity in microbial cells.
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Seo JH, Kim HH, Jeon EY, Song YH, Shin CS, Park JB. Engineering of Baeyer-Villiger monooxygenase-based Escherichia coli biocatalyst for large scale biotransformation of ricinoleic acid into (Z)-11-(heptanoyloxy)undec-9-enoic acid. Sci Rep 2016; 6:28223. [PMID: 27311560 PMCID: PMC4911592 DOI: 10.1038/srep28223] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 06/01/2016] [Indexed: 01/25/2023] Open
Abstract
Baeyer-Villiger monooxygenases (BVMOs) are able to catalyze regiospecific Baeyer-Villiger oxygenation of a variety of cyclic and linear ketones to generate the corresponding lactones and esters, respectively. However, the enzymes are usually difficult to express in a functional form in microbial cells and are rather unstable under process conditions hindering their large-scale applications. Thereby, we investigated engineering of the BVMO from Pseudomonas putida KT2440 and the gene expression system to improve its activity and stability for large-scale biotransformation of ricinoleic acid (1) into the ester (i.e., (Z)-11-(heptanoyloxy)undec-9-enoic acid) (3), which can be hydrolyzed into 11-hydroxyundec-9-enoic acid (5) (i.e., a precursor of polyamide-11) and n-heptanoic acid (4). The polyionic tag-based fusion engineering of the BVMO and the use of a synthetic promoter for constitutive enzyme expression allowed the recombinant Escherichia coli expressing the BVMO and the secondary alcohol dehydrogenase of Micrococcus luteus to produce the ester (3) to 85 mM (26.6 g/L) within 5 h. The 5 L scale biotransformation process was then successfully scaled up to a 70 L bioreactor; 3 was produced to over 70 mM (21.9 g/L) in the culture medium 6 h after biotransformation. This study demonstrated that the BVMO-based whole-cell reactions can be applied for large-scale biotransformations.
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Affiliation(s)
- Joo-Hyun Seo
- Department of Food Science and Engineering, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Hwan-Hee Kim
- Department of Food Science and Engineering, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Eun-Yeong Jeon
- Department of Food Science and Engineering, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Young-Ha Song
- AP Technology, Suwon, Kyunggi 443-702, Republic of Korea
| | - Chul-Soo Shin
- AP Technology, Suwon, Kyunggi 443-702, Republic of Korea
| | - Jin-Byung Park
- Department of Food Science and Engineering, Ewha Womans University, Seoul 120-750, Republic of Korea
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Preparation of 11-hexyloxy-9-undecenoic acid from crude castor oil hydrolysates by recombinant Escherichia coli expressing alcohol dehydrogenase and Baeyer–Villiger monooxygenase. Process Biochem 2016. [DOI: 10.1016/j.procbio.2015.12.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Ferrer M, Martínez-Martínez M, Bargiela R, Streit WR, Golyshina OV, Golyshin PN. Estimating the success of enzyme bioprospecting through metagenomics: current status and future trends. Microb Biotechnol 2016; 9:22-34. [PMID: 26275154 PMCID: PMC4720405 DOI: 10.1111/1751-7915.12309] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 06/26/2015] [Accepted: 07/02/2015] [Indexed: 12/01/2022] Open
Abstract
Recent reports have suggested that the establishment of industrially relevant enzyme collections from environmental genomes has become a routine procedure. Across the studies assessed, a mean number of approximately 44 active clones were obtained in an average size of approximately 53,000 clones tested using naïve screening protocols. This number could be significantly increased in shorter times when novel metagenome enzyme sequences obtained by direct sequencing are selected and subjected to high-throughput expression for subsequent production and characterization. The pre-screening of clone libraries by naïve screens followed by the pyrosequencing of the inserts allowed for a 106-fold increase in the success rate of identifying genes encoding enzymes of interest. However, a much longer time, usually on the order of years, is needed from the time of enzyme identification to the establishment of an industrial process. If the hit frequency for the identification of enzymes performing at high turnover rates under real application conditions could be increased while still covering a high natural diversity, the very expensive and time-consuming enzyme optimization phase would likely be significantly shortened. At this point, it is important to review the current knowledge about the success of fine-tuned naïve- and sequence-based screening protocols for enzyme selection and to describe the environments worldwide that have already been subjected to enzyme screen programmes through metagenomic tools. Here, we provide such estimations and suggest the current challenges and future actions needed before environmental enzymes can be successfully introduced into the market.
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Affiliation(s)
- Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Marie Curie 2, 28049, Madrid, Spain
| | - Mónica Martínez-Martínez
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Marie Curie 2, 28049, Madrid, Spain
| | - Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Marie Curie 2, 28049, Madrid, Spain
| | - Wolfgang R Streit
- Biozentrum Klein Flottbek, Universität Hamburg, Ohnhorststraße 18, D-22609, Hamburg, Germany
| | - Olga V Golyshina
- School of Biological Sciences, Bangor University, LL57 2UW, Gwynedd, UK
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, LL57 2UW, Gwynedd, UK
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Jung SM, Seo JH, Lee JH, Park JB, Seo JH. Fatty acid hydration activity of a recombinant Escherichia coli-based biocatalyst is improved through targeting the oleate hydratase into the periplasm. Biotechnol J 2015; 10:1887-93. [PMID: 26429801 DOI: 10.1002/biot.201500141] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/11/2015] [Accepted: 09/29/2015] [Indexed: 11/12/2022]
Abstract
Whole-cell biotransformation of fatty acids can be influenced by the activities of catalytic enzymes and by the efficiency of substrate transport into host cells. Here, we improved fatty acid hydration activity of the recombinant Escherichia coli expressing an oleate hydratase of Stenotrophomonas maltophilia by targeting the catalytic enzyme into the periplasm instead of the cytoplasm. Recombinant E. coli producing OhyA in the periplasm under guidance of the PelB signal sequence (E. coli OhyA_PP) exhibited significantly greater hydration activity with oleic acid and linoleic acid compared to a recombinant E. coli producing OhyA in the cytoplasm (E. coli OhyA_CS). For example, the oleate double bond hydration rate of E. coli OhyA_PP was >400 μmol/g dry cells/min (400 U/g dry cells), which is >10-fold higher than that of E. coli OhyA_CS. As the specific activities of the enzymes targeted into the cytoplasm and periplasm were comparable, we assumed that targeting OhyA into the periplasm could accelerate fatty acid transport to the catalytic enzymes by skipping the major mass transport barrier of the cytoplasmic membrane. Our results will contribute to the development of whole-cell biocatalysts for fatty acid biotransformation.
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Affiliation(s)
- Sang-Min Jung
- Department of Agricultural Biotechnology and Center for Food and Bioconvergence, Seoul National University, Seoul, Republic of Korea
| | - Joo-Hyun Seo
- Department of Food Science & Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Jung-Hoo Lee
- Department of Food Science & Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Jin-Byung Park
- Department of Food Science & Engineering, Ewha Womans University, Seoul, Republic of Korea.
| | - Jin-Ho Seo
- Department of Agricultural Biotechnology and Center for Food and Bioconvergence, Seoul National University, Seoul, Republic of Korea.
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