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Núñez-Navarro N, Salazar Muñoz J, Castillo F, Ramírez-Sarmiento CA, Poblete-Castro I, Zacconi FC, Parra LP. Discovery of New Phenylacetone Monooxygenase Variants for the Development of Substituted Indigoids through Biocatalysis. Int J Mol Sci 2022; 23:ijms232012544. [PMID: 36293414 PMCID: PMC9604523 DOI: 10.3390/ijms232012544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/15/2022] [Accepted: 10/16/2022] [Indexed: 11/16/2022] Open
Abstract
Indigoids are natural pigments obtained from plants by ancient cultures. Romans used them mainly as dyes, whereas Asian cultures applied these compounds as treatment agents for several diseases. In the modern era, the chemical industry has made it possible to identify and develop synthetic routes to obtain them from petroleum derivatives. However, these processes require high temperatures and pressures and large amounts of solvents, acids, and alkali agents. Thus, enzyme engineering and the development of bacteria as whole-cell biocatalysts emerges as a promising green alternative to avoid the use of these hazardous materials and consequently prevent toxic waste generation. In this research, we obtained two novel variants of phenylacetone monooxygenase (PAMO) by iterative saturation mutagenesis. Heterologous expression of these two enzymes, called PAMOHPCD and PAMOHPED, in E. coli was serendipitously found to produce indigoids. These interesting results encourage us to characterize the thermal stability and enzyme kinetics of these new variants and to evaluate indigo and indirubin production in a whole-cell system by HPLC. The highest yields were obtained with PAMOHPCD supplemented with L-tryptophan, producing ~3000 mg/L indigo and ~130.0 mg/L indirubin. Additionally, both enzymes could oxidize and produce several indigo derivatives from substituted indoles, with PAMOHPCD being able to produce the well-known Tyrian purple. Our results indicate that the PAMO variants described herein have potential application in the textile, pharmaceutics, and semiconductors industries, prompting the use of environmentally friendly strategies to obtain a diverse variety of indigoids.
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Affiliation(s)
- Nicolás Núñez-Navarro
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Javier Salazar Muñoz
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Center for Nanomedicine, Diagnostic & Drug Development (ND3), Universidad de Talca, Talca 3460000, Chile
| | - Francisco Castillo
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - César A. Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Ignacio Poblete-Castro
- Biosystems Engineering Laboratory, Department of Chemical and Bioprocess Engineering, Universidad de Santiago de Chile (USACH), Santiago 8350709, Chile
| | - Flavia C. Zacconi
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Center for Nanomedicine, Diagnostic & Drug Development (ND3), Universidad de Talca, Talca 3460000, Chile
- Correspondence: (F.C.Z.); (L.P.P.)
| | - Loreto P. Parra
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Correspondence: (F.C.Z.); (L.P.P.)
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2
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Harwood LA, Wong LL, Robertson J. Enzymatic Kinetic Resolution by Addition of Oxygen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Lucy A. Harwood
- Department of Chemistry University of Oxford Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Luet L. Wong
- Department of Chemistry University of Oxford Inorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
- Oxford Suzhou Centre for Advanced Research Ruo Shui Road, Suzhou Industrial Park Jiangsu 215123 P. R. China
| | - Jeremy Robertson
- Department of Chemistry University of Oxford Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
- Oxford Suzhou Centre for Advanced Research Ruo Shui Road, Suzhou Industrial Park Jiangsu 215123 P. R. China
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3
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Harwood LA, Wong LL, Robertson J. Enzymatic Kinetic Resolution by Addition of Oxygen. Angew Chem Int Ed Engl 2021; 60:4434-4447. [PMID: 33037837 PMCID: PMC7986699 DOI: 10.1002/anie.202011468] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Indexed: 12/25/2022]
Abstract
Kinetic resolution using biocatalysis has proven to be an excellent complementary technique to traditional asymmetric catalysis for the production of enantioenriched compounds. Resolution using oxidative enzymes produces valuable oxygenated structures for use in synthetic route development. This Minireview focuses on enzymes which catalyse the insertion of an oxygen atom into the substrate and, in so doing, can achieve oxidative kinetic resolution. The Baeyer-Villiger rearrangement, epoxidation, and hydroxylation are included, and biological advancements in enzyme development, and applications of these key enantioenriched intermediates in natural product synthesis are discussed.
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Affiliation(s)
- Lucy A. Harwood
- Department of ChemistryUniversity of OxfordChemistry Research LaboratoryMansfield RoadOxfordOX1 3TAUK
| | - Luet L. Wong
- Department of ChemistryUniversity of OxfordInorganic Chemistry LaboratorySouth Parks RoadOxfordOX1 3QRUK
- Oxford Suzhou Centre for Advanced ResearchRuo Shui Road, Suzhou Industrial ParkJiangsu215123P. R. China
| | - Jeremy Robertson
- Department of ChemistryUniversity of OxfordChemistry Research LaboratoryMansfield RoadOxfordOX1 3TAUK
- Oxford Suzhou Centre for Advanced ResearchRuo Shui Road, Suzhou Industrial ParkJiangsu215123P. R. China
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4
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Ren SM, Liu F, Wu YQ, Chen Q, Zhang ZJ, Yu HL, Xu JH. Identification two key residues at the intersection of domains of a thioether monooxygenase for improving its sulfoxidation performance. Biotechnol Bioeng 2020; 118:737-744. [PMID: 33073356 DOI: 10.1002/bit.27604] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/20/2020] [Accepted: 10/11/2020] [Indexed: 02/01/2023]
Abstract
AcCHMO, a cyclohexanone monooxygenase from Acinetobacter calcoaceticus, is a typical Type I Baeyer-Villiger monooxygenase (BVMO). We previously obtained the AcCHMOM6 mutant, which oxidizes omeprazole sulfide (OPS) to the chiral sulfoxide drug esomeprazole. To further improve the catalytic efficiency of the AcCHMOM6 mutant, a focused mutagenesis strategy was adopted at the intersections of the FAD-binding domain, NADPH-binding domain, and α-helical domain based on structural characteristics of AcCHMO. By using focused mutagenesis and subsequent global evolution two key residues (L55 and P497) at the intersections of the domains were identified. Mutant of L55Y improved catalytic efficiency significantly, whereas the P497S mutant alleviated substrate inhibition remarkably. AcCHMOM7 (L55Y/P497S) was obtained by combining the two mutations, which increased the specific activity from 18.5 (M6) to 108 U/g, and an increase in the Ki of the substrate OPS from 34 to 265 μM. The results indicate that catalytic performance can be elevated by modification of the sensitive sites at the intersection of the domains of AcCHMO. The results also provided some insights for the engineering of other Type I BVMOs or other multidomain proteins.
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Affiliation(s)
- Shi-Miao Ren
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Feng Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yin-Qi Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Qi Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Zhi-Jun Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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5
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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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Silva ALP, da Silva Caridade TN, Magalhães RR, de Sousa KT, de Sousa CC, Vale JA. Biocatalytic production of Ɛ-caprolactone using Geotrichum candidum cells immobilized on functionalized silica. Appl Microbiol Biotechnol 2020; 104:8887-8895. [PMID: 32902680 DOI: 10.1007/s00253-020-10875-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/18/2020] [Accepted: 08/31/2020] [Indexed: 11/30/2022]
Abstract
Immobilization of the Geotrichum candidum (CCT 1205) cell with functionalized silica creates promising biocatalysts for production of ɛ-caprolactone. The results obtained by immobilization of the whole cell on SiO2-NH2 and SiO2-SH supports indicate that the presence of reactive functional groups on the support may promote effective chemical bonds with the cell walls resulting the decreased dehydrogenases enzyme activity (5% yield in less than 2h) and consequently, increased Baeyer-Villiger monooxygenases enzyme activity with redacting of 25% of time reaction when is used SiO2-NH2 as support and 50% through use of SiO2-SH as support relative to free cells when cyclohexanone is used as a substrate. The catalysts SiO2-NH2-Geotrichum candidum and SiO2-SH-Geotrichum candidum were recycling and reused in the ɛ-caprolactone synthesis from cyclohexanone, and the biocatalysts promoted a quantitative conversion up to the eighth reaction cycle. KEY POINTS: • Immobilized microorganism is more efficient than free cell in the caprolactone synthesis. • The reaction times for amino and thiol groups in support were 3 h and 2 h, respectively. • These catalysts showed higher ɛ-caprolactone conversion at higher concentrations.
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Affiliation(s)
| | | | | | | | | | - Juliana Alves Vale
- Department of Chemistry, Federal University of Paraíba, João Pessoa, PB, 58051-970, Brazil.
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Natural Variation in the ‘Control Loop’ of BVMOAFL210 and Its Influence on Regioselectivity and Sulfoxidation. Catalysts 2020. [DOI: 10.3390/catal10030339] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Baeyer-Villiger monooxygenases (BVMOs) are flavin-dependent enzymes that primarily convert ketones to esters, but can also catalyze heteroatom oxidation. Several structural studies have highlighted the importance of the ‘control loop’ in BVMOs, which adopts different conformations during catalysis. Central to the ‘control loop’ is a conserved tryptophan that has been implicated in NADP(H) binding. BVMOAFL210 from Aspergillus flavus, however, contains a threonine in the equivalent position. Here, we report the structure of BVMOAFL210 in complex with NADP+ in both the ‘open’ and ‘closed’ conformations. In neither conformation does Thr513 contact the NADP+. Although mutagenesis of Thr513 did not significantly alter the substrate scope, changes in peroxyflavin stability and reaction rates were observed. Mutation of this position also brought about changes in the regio- and enantioselectivity of the enzyme. Moreover, lower rates of overoxidation during sulfoxidation of thioanisole were also observed.
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8
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Unbiased libraries in protein directed evolution. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140321. [DOI: 10.1016/j.bbapap.2019.140321] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/03/2019] [Accepted: 10/31/2019] [Indexed: 12/17/2022]
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9
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Schmidt S, Bornscheuer UT. Baeyer-Villiger monooxygenases: From protein engineering to biocatalytic applications. FLAVIN-DEPENDENT ENZYMES: MECHANISMS, STRUCTURES AND APPLICATIONS 2020; 47:231-281. [DOI: 10.1016/bs.enz.2020.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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10
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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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11
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Fürst MJLJ, Boonstra M, Bandstra S, Fraaije MW. Stabilization of cyclohexanone monooxygenase by computational and experimental library design. Biotechnol Bioeng 2019; 116:2167-2177. [PMID: 31124128 PMCID: PMC6836875 DOI: 10.1002/bit.27022] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/14/2019] [Accepted: 05/18/2019] [Indexed: 12/23/2022]
Abstract
Enzymes often by far exceed the activity, selectivity, and sustainability achieved with chemical catalysts. One of the main reasons for the lack of biocatalysis in the chemical industry is the poor stability exhibited by many enzymes when exposed to process conditions. This dilemma is exemplified in the usually very temperature‐sensitive enzymes catalyzing the Baeyer–Villiger reaction, which display excellent stereo‐ and regioselectivity and offer a green alternative to the commonly used, explosive peracids. Here we describe a protein engineering approach applied to cyclohexanone monooxygenase from Rhodococcus sp. HI‐31, a substrate‐promiscuous enzyme that efficiently catalyzes the production of the nylon‐6 precursor ε‐caprolactone. We used a framework for rapid enzyme stabilization by computational libraries (FRESCO), which predicts protein‐stabilizing mutations. From 128 screened point mutants, approximately half had a stabilizing effect, albeit mostly to a small degree. To overcome incompatibility effects observed upon combining the best hits, an easy shuffled library design strategy was devised. The most stable and highly active mutant displayed an increase in unfolding temperature of 13°C and an approximately 33x increase in half‐life at 30°C. In contrast to the wild‐type enzyme, this thermostable 8x mutant is an attractive biocatalyst for biotechnological applications.
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Affiliation(s)
| | - Marjon Boonstra
- Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands
| | - Selle Bandstra
- Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands
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12
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Expanding the substrate scope of phenylacetone monooxygenase from Thermobifida fusca towards cyclohexanone by protein engineering. CATAL COMMUN 2019. [DOI: 10.1016/j.catcom.2018.10.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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13
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Fürst MJLJ, Romero E, Gómez Castellanos JR, Fraaije MW, Mattevi A. Side-Chain Pruning Has Limited Impact on Substrate Preference in a Promiscuous Enzyme. ACS Catal 2018; 8:11648-11656. [PMID: 30687578 PMCID: PMC6345240 DOI: 10.1021/acscatal.8b03793] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/26/2018] [Indexed: 01/02/2023]
Abstract
![]()
Detoxifying
enzymes such as flavin-containing monooxygenases deal
with a huge array of highly diverse xenobiotics and toxic compounds.
In addition to being of high physiological relevance, these drug-metabolizing
enzymes are useful catalysts for synthetic chemistry. Despite the
wealth of studies, the molecular basis of their relaxed substrate
selectivity remains an open question. Here, we addressed this issue
by applying a cumulative alanine mutagenesis approach to cyclohexanone
monooxygenase from Thermocrispum municipale, a flavin-dependent
Baeyer–Villiger monooxygenase which we chose as a model system
because of its pronounced thermostability and substrate promiscuity.
Simultaneous removal of up to eight noncatalytic active-site side
chains including four phenylalanines had no effect on protein folding,
thermostability, and cofactor loading. We observed a linear decrease
in activity, rather than a selectivity switch, and attributed this
to a less efficient catalytic environment in the enlarged active-site
space. Time-resolved kinetic studies confirmed this interpretation.
We also determined the crystal structure of the enzyme in complex
with a mimic of the reaction intermediate that shows an unaltered
overall protein conformation. These findings led us to propose that
this cyclohexanone monooxygenase may lack a distinct substrate selection
mechanism altogether. We speculate that the main or exclusive function
of the protein shell in promiscuous enzymes might be the stabilization
and accessibility of their very reactive catalytic intermediates.
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Affiliation(s)
- Maximilian J. L. J. Fürst
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Elvira Romero
- 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
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 1, 27100, Pavia, Italy
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Hollmann F, Kara S, Opperman DJ, Wang Y. Biocatalytic synthesis of lactones and lactams. Chem Asian J 2018; 13:3601-3610. [PMID: 30256534 PMCID: PMC6348383 DOI: 10.1002/asia.201801180] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/26/2018] [Indexed: 01/15/2023]
Abstract
Cyclic esters and amides (lactones and lactams) are important active ingredients and polymer building blocks. In recent years, numerous biocatalytic methods for their preparation have been developed including enzymatic and chemoenzymatic Baeyer-Villiger oxidations, oxidative lactonisation of diols, and reductive lactonisation and lactamisation of ketoesters. The current state of the art of these methods is reviewed.
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Affiliation(s)
- Frank Hollmann
- Department of Biotechnology, Delft University of Technology, The Netherlands
| | - Selin Kara
- Department of Engineering, Biological and Chemical Engineering, Aarhus University, Denmark
| | | | - Yonghua Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
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15
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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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16
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Carvalho ATP, Dourado DFAR, Skvortsov T, de Abreu M, Ferguson LJ, Quinn DJ, Moody TS, Huang M. Spatial requirement for PAMO for transformation of non-native linear substrates. Phys Chem Chem Phys 2018; 20:2558-2570. [PMID: 29318252 DOI: 10.1039/c7cp07172h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Phenylacetone monooxygenase is the most stable and thermo-tolerant member of the Baeyer-Villiger monooxygenases family, and therefore it is an ideal candidate for the synthesis of industrially relevant ester or lactone compounds. However, its limited substrate scope has largely limited its industrial applications. Linear substrates are interesting from an industrial point of view, it is thus necessary to identify the essential spatial requirement for achieving high conversions for non-native linear substrates. Here using molecular dynamics simulations, we compared the conversion of a non-native linear substrate 2-octanone and the native substrate phenylacetone, catalyzed by the WT enzyme and a quadruple variant P253F/G254A/R258M/L443F that exhibits significantly improved activity towards 2-octanone. We uncovered that a remarkable movement of L289 is crucial for a reshaping of the active site of the quadruple variant so as to prevent the aliphatic substrate from moving away from the C4a-peroxyflavin, thus enabling it to keep a catalytically relevant pose during the oxygenation process. By performing steady-state kinetic analysis of two single-mutation variants at position 258, we further validated that the L289 reposition is attributed to the combined effect of quadruple mutations. In order to further explore the substrate scope of PAMO we also studied the binding of cyclopentanone and 2-phenylcyclohexanone, which are the typical substrates of CPMO in group I and CHMO in group III, respectively. Our study provides fundamental atomic-level insights in rational engineering of PAMO for wide applications in industrial biocatalysis, in particular, in the biotransformation of long-chain aliphatic oils into potential biodiesels.
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Affiliation(s)
- Alexandra T P Carvalho
- School of Chemistry and Chemical Engineering, Queen's University, David Keir Building, Stranmillis Road, Belfast BT9 5AG, Northern Ireland, UK.
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17
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Carvalho ATP, Dourado DFAR, Skvortsov T, de Abreu M, Ferguson LJ, Quinn DJ, Moody TS, Huang M. Catalytic mechanism of phenylacetone monooxygenases for non-native linear substrates. Phys Chem Chem Phys 2018; 19:26851-26861. [PMID: 28951930 DOI: 10.1039/c7cp03640j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Phenylacetone monooxygenase (PAMO) is the most stable and thermo-tolerant member of the Baeyer-Villiger monooxygenase family, and therefore it is an ideal candidate for the synthesis of industrially relevant compounds. However, its limited substrate scope has largely limited its industrial applications. In the present work, we provide, for the first time, the catalytic mechanism of PAMO for the native substrate phenylacetone as well as for a linear non-native substrate 2-octanone, using molecular dynamics simulations, quantum mechanics and quantum mechanics/molecular mechanics calculations. We provide a theoretical basis for the preference of the enzyme for the native aromatic substrate over non-native linear substrates. Our study provides fundamental atomic-level insights that can be employed in the rational engineering of PAMO for wide applications in industrial biocatalysis, in particular, in the biotransformation of long-chain aliphatic oils into potential biodiesels.
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Affiliation(s)
- Alexandra T P Carvalho
- School of Chemistry and Chemical Engineering, Queen's University, David Keir Building, Stranmillis Road, Belfast BT9 5AG, Northern Ireland, UK.
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18
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Balke K, Beier A, Bornscheuer UT. Hot spots for the protein engineering of Baeyer-Villiger monooxygenases. Biotechnol Adv 2018; 36:247-263. [DOI: 10.1016/j.biotechadv.2017.11.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 11/15/2017] [Accepted: 11/17/2017] [Indexed: 10/18/2022]
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Bisagni S, Abolhalaj M, de Brevern AG, Rebehmed J, Hatti-Kaul R, Mamo G. Enhancing the Activity of a Dietzia
sp. D5 Baeyer-Villiger Monooxygenase towards Cyclohexanone by Saturation Mutagenesis. ChemistrySelect 2017. [DOI: 10.1002/slct.201701212] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Serena Bisagni
- Biotechnology, Department of Chemistry; Centre for Chemistry and Chemical Engineering; Lund University; Box 124 SE-221 00 Lund Sweden
- Johnson Matthey; Cambridge Science Park 28 CB4 0FP Cambridge United Kingdom
| | - Milad Abolhalaj
- Department of Immunotechnology; Medicon Village; Scheelevägen 2 22100 Lund Sweden
| | - Alexandre G. de Brevern
- Inserm U1134; Paris France
- Université Paris Diderot; Sorbonne, Paris Cité, UMR_S 1134; Paris France
- Institut National de la Transfusion Sanguine; Paris France
- Laboratory of Excellence GR-Ex; Paris France
| | - Joseph Rebehmed
- Inserm U1134; Paris France
- Université Paris Diderot; Sorbonne, Paris Cité, UMR_S 1134; Paris France
- Institut National de la Transfusion Sanguine; Paris France
- Laboratory of Excellence GR-Ex; Paris France
- Department of Computer Science and Mathematics; Lebanese American University; Byblos 1 h401 2010 Lebanon
| | - Rajni Hatti-Kaul
- Biotechnology, Department of Chemistry; Centre for Chemistry and Chemical Engineering; Lund University; Box 124 SE-221 00 Lund Sweden
| | - Gashaw Mamo
- Biotechnology, Department of Chemistry; Centre for Chemistry and Chemical Engineering; Lund University; Box 124 SE-221 00 Lund Sweden
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20
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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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21
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Balke K, Bäumgen M, Bornscheuer UT. Controlling the Regioselectivity of Baeyer-Villiger Monooxygenases by Mutation of Active-Site Residues. Chembiochem 2017; 18:1627-1638. [PMID: 28504873 DOI: 10.1002/cbic.201700223] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Indexed: 11/12/2022]
Abstract
Baeyer-Villiger monooxygenase (BVMO)-mediated regiodivergent conversions of asymmetric ketones can lead to the formation of "normal" or "abnormal" lactones. In a previous study, we were able to change the regioselectivity of a BVMO by mutation of the active-site residues to smaller amino acids, which thus created more space. In this study, we demonstrate that this method can also be used for other BVMO/substrate combinations. We investigated the regioselectivity of 2-oxo-Δ3 -4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase from Pseudomonas putida (OTEMO) for cis-bicyclo[3.2.0]hept-2-en-6-one (1) and trans-dihydrocarvone (2), and we were able to switch the regioselectivity of this enzyme for one of the substrate enantiomers. The OTEMO wild-type enzyme converted (-)-1 into an equal (50:50) mixture of the normal and abnormal products. The F255A/F443V variant produced 90 % of the normal product, whereas the W501V variant formed up to 98 % of the abnormal product. OTEMO F255A exclusively produced the normal lactone from (+)-2, whereas the wild-type enzyme was selective for the production of the abnormal product. The positions of these amino acids were equivalent to those mutated in the cyclohexanone monooxygenases from Arthrobacter sp. and Acinetobacter sp. (CHMOArthro and CHMOAcineto ) to switch their regioselectivity towards (+)-2, which suggests that there are hot spots in the active site of BVMOs that can be targeted with the aim to change the regioselectivity.
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Affiliation(s)
- Kathleen Balke
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Marcus Bäumgen
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Uwe T Bornscheuer
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
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22
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Engineering a lipase B from Candida antactica with efficient perhydrolysis performance by eliminating its hydrolase activity. Sci Rep 2017; 7:44599. [PMID: 28317884 PMCID: PMC5357956 DOI: 10.1038/srep44599] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 02/09/2017] [Indexed: 12/02/2022] Open
Abstract
A Ser105Ala mutant of the lipase B from Candida antarctica enables ‘perhydrolase-only’ reactions. At the example of the chemoenzymatic Baeyer-Villiger oxidation of cyclohexanone, we demonstrate that with this mutant selective oxidation can be achieved in deep eutectic solvent while essentially eliminating the undesired hydrolysis reaction of the product.
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23
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Thirty-degree shift in optimum temperature of a thermophilic lipase by a single-point mutation: effect of serine to threonine mutation on structural flexibility. Mol Cell Biochem 2017; 430:21-30. [DOI: 10.1007/s11010-017-2950-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/17/2017] [Indexed: 10/20/2022]
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24
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Li G, Fürst MJLJ, Mansouri HR, Ressmann AK, Ilie A, Rudroff F, Mihovilovic MD, Fraaije MW, Reetz MT. Manipulating the stereoselectivity of the thermostable Baeyer–Villiger monooxygenase TmCHMO by directed evolution. Org Biomol Chem 2017; 15:9824-9829. [DOI: 10.1039/c7ob02692g] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The thermostable Baeyer–Villiger monooxygenase TmCHMO and evolved mutants are viable catalysts in stereoselective reactions of structurally different ketones.
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Affiliation(s)
- Guangyue Li
- Max-Planck-Institut für Kohlenforschung
- Mülheim an der Ruhr
- Germany
- Fachbereich Chemie
- Philipps-Universität
| | | | | | - Anna K. Ressmann
- Institute of Applied Synthetic Chemistry
- TU Wien
- 1060 Vienna
- Austria
| | - Adriana Ilie
- Max-Planck-Institut für Kohlenforschung
- Mülheim an der Ruhr
- Germany
- Fachbereich Chemie
- Philipps-Universität
| | - Florian Rudroff
- Institute of Applied Synthetic Chemistry
- TU Wien
- 1060 Vienna
- Austria
| | | | - Marco W. Fraaije
- Molecular Enzymology Group
- University of Groningen
- 9747 AG Groningen
- The Netherlands
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung
- Mülheim an der Ruhr
- Germany
- Fachbereich Chemie
- Philipps-Universität
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25
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Romero E, Castellanos JRG, Mattevi A, Fraaije MW. Characterization and Crystal Structure of a Robust Cyclohexanone Monooxygenase. Angew Chem Int Ed Engl 2016; 55:15852-15855. [PMID: 27873437 PMCID: PMC5213842 DOI: 10.1002/anie.201608951] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Indexed: 12/03/2022]
Abstract
Cyclohexanone monooxygenase (CHMO) is a promising biocatalyst for industrial reactions owing to its broad substrate spectrum and excellent regio‐, chemo‐, and enantioselectivity. However, the low stability of many Baeyer–Villiger monooxygenases is an obstacle for their exploitation in industry. Characterization and crystal structure determination of a robust CHMO from Thermocrispum municipale is reported. The enzyme efficiently converts a variety of aliphatic, aromatic, and cyclic ketones, as well as prochiral sulfides. A compact substrate‐binding cavity explains its preference for small rather than bulky substrates. Small‐scale conversions with either purified enzyme or whole cells demonstrated the remarkable properties of this newly discovered CHMO. The exceptional solvent tolerance and thermostability make the enzyme very attractive for biotechnology.
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Affiliation(s)
- Elvira Romero
- Department of Biotechnology, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - J Rubén Gómez Castellanos
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Andrea Mattevi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Marco W Fraaije
- Department of Biotechnology, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
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26
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Romero E, Castellanos JRG, Mattevi A, Fraaije MW. Characterization and Crystal Structure of a Robust Cyclohexanone Monooxygenase. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608951] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Elvira Romero
- Department of Biotechnology; University of Groningen; Nijenborgh 4 9747AG Groningen The Netherlands
| | - J. Rubén Gómez Castellanos
- Department of Biology and Biotechnology “Lazzaro Spallanzani”; University of Pavia; Via Ferrata 9 27100 Pavia Italy
| | - Andrea Mattevi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”; University of Pavia; Via Ferrata 9 27100 Pavia Italy
| | - Marco W. Fraaije
- Department of Biotechnology; University of Groningen; Nijenborgh 4 9747AG Groningen The Netherlands
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27
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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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28
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Schmidt S, Genz M, Balke K, Bornscheuer UT. The effect of disulfide bond introduction and related Cys/Ser mutations on the stability of a cyclohexanone monooxygenase. J Biotechnol 2015; 214:199-211. [DOI: 10.1016/j.jbiotec.2015.09.026] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 09/16/2015] [Accepted: 09/22/2015] [Indexed: 01/30/2023]
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