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Bretschneider L, Heuschkel I, Ahmed A, Bühler K, Karande R, Bühler B. Characterization of different biocatalyst formats for BVMO-catalyzed cyclohexanone oxidation. Biotechnol Bioeng 2021; 118:2719-2733. [PMID: 33844297 DOI: 10.1002/bit.27791] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/03/2021] [Accepted: 04/04/2021] [Indexed: 01/05/2023]
Abstract
Cyclohexanone monooxygenase (CHMO), a member of the Baeyer-Villiger monooxygenase family, is a versatile biocatalyst that efficiently catalyzes the conversion of cyclic ketones to lactones. In this study, an Acidovorax-derived CHMO gene was expressed in Pseudomonas taiwanensis VLB120. Upon purification, the enzyme was characterized in vitro and shown to feature a broad substrate spectrum and up to 100% conversion in 6 h. Furthermore, we determined and compared the cyclohexanone conversion kinetics for different CHMO-biocatalyst formats, that is, isolated enzyme, suspended whole cells, and biofilms, the latter two based on recombinant CHMO-containing P. taiwanensis VLB120. Biofilms showed less favorable values for KS (9.3-fold higher) and kcat (4.8-fold lower) compared with corresponding KM and kcat values of isolated CHMO, but a favorable KI for cyclohexanone (5.3-fold higher). The unfavorable KS and kcat values are related to mass transfer- and possibly heterogeneity issues and deserve further investigation and engineering, to exploit the high potential of biofilms regarding process stability. Suspended cells showed only 1.8-fold higher KS , but 1.3- and 4.2-fold higher kcat and KI values than isolated CHMO. This together with the efficient NADPH regeneration via glucose metabolism makes this format highly promising from a kinetics perspective.
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Affiliation(s)
- Lisa Bretschneider
- Department of Solar Materials, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Ingeborg Heuschkel
- Department of Solar Materials, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Afaq Ahmed
- Department of Solar Materials, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Katja Bühler
- Department of Solar Materials, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Rohan Karande
- Department of Solar Materials, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Bruno Bühler
- Department of Solar Materials, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
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2
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Insights into the unique carboxylation reactions in the metabolism of propylene and acetone. Biochem J 2020; 477:2027-2038. [PMID: 32497192 DOI: 10.1042/bcj20200174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 01/16/2023]
Abstract
Alkenes and ketones are two classes of ubiquitous, toxic organic compounds in natural environments produced in several biological and anthropogenic processes. In spite of their toxicity, these compounds are utilized as primary carbon and energy sources or are generated as intermediate metabolites in the metabolism of other compounds by many diverse bacteria. The aerobic metabolism of some of the smallest and most volatile of these compounds (propylene, acetone, isopropanol) involves novel carboxylation reactions resulting in a common product acetoacetate. Propylene is metabolized in a four-step pathway involving five enzymes where the penultimate step is a carboxylation reaction catalyzed by a unique disulfide oxidoreductase that couples reductive cleavage of a thioether linkage with carboxylation to produce acetoacetate. The carboxylation of isopropanol begins with conversion to acetone via an alcohol dehydrogenase. Acetone is converted to acetoacetate in a single step by an acetone carboxylase which couples the hydrolysis of MgATP to the activation of both acetone and bicarbonate, generating highly reactive intermediates that are condensed into acetoacetate at a Mn2+ containing the active site. Acetoacetate is then utilized in central metabolism where it is readily converted to acetyl-coenzyme A and subsequently converted into biomass or utilized in energy metabolism via the tricarboxylic acid cycle. This review summarizes recent structural and biochemical findings that have contributed significant insights into the mechanism of these two unique carboxylating enzymes.
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A novel exopolysaccharide-producing and long-chain n-alkane degrading bacterium Bacillus licheniformis strain DM-1 with potential application for in-situ enhanced oil recovery. Sci Rep 2020; 10:8519. [PMID: 32444666 PMCID: PMC7244480 DOI: 10.1038/s41598-020-65432-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/05/2020] [Indexed: 11/12/2022] Open
Abstract
A novel Bacillus licheniformis strain (DM-1) was isolated from a mature reservoir in Dagang oilfield of China. DM-1 showed unique properties to utilize petroleum hydrocarbons and agroindustrial by-product (molasses) for exopolysaccharide (EPS) production under oil recovery conditions. The DM-1 EPS was proven to be a proteoglycan with a molecular weight of 568 kDa. The EPS showed shear thinning properties and had high viscosities at dilute concentrations (<1%, w/v), high salinities, and elevated temperatures. Strain DM-1 could degrade long-chain n-alkanes up to C36. Viscosity reduction test have shown that the viscosity of the crude oil was reduced by 40% compared with that before DM-1 treatment. Sand pack flooding test results under simulated reservoir conditions have shown that the enhanced oil recovery efficiency was 19.2% after 7 days of in-situ bioaugmentation with B. licheniformis DM-1. The obtained results indicate that strain DM-1 is a promising candidate for in situ microbial enhanced oil recovery (MEOR).
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Ceccoli RD, Bianchi DA, Carabajal MA, Rial DV. Genome mining reveals new bacterial type I Baeyer-Villiger monooxygenases with (bio)synthetic potential. MOLECULAR CATALYSIS 2020. [DOI: 10.1016/j.mcat.2020.110875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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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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Khosravinia S, Mahdavi MA, Gheshlaghi R, Dehghani H, Rasekh B. Construction and Characterization of a New Recombinant Vector to Remove Sulfate Repression of dsz Promoter Transcription in Biodesulfurization of Dibenzothiophene. Front Microbiol 2018; 9:1578. [PMID: 30065711 PMCID: PMC6056628 DOI: 10.3389/fmicb.2018.01578] [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: 03/09/2018] [Accepted: 06/25/2018] [Indexed: 11/13/2022] Open
Abstract
Biodesulfurization (BDS) is an environmentally friendly desulfurizing process with the potential of replacing or adding to the current expensive technologies for sulfur removal from fossil fuels. The BDS, however, still suffers from low biocatalyst activity. One reason is repression of dsz promoter transcription in presence of inorganic sulfate that impedes translation of Dsz enzymes required for desulfurization pathway. One approach to solve this problem is replacing the native promoter with a new promoter that is no longer repressed. In this study, dsz genes from desulfurizing strain Rhodococcus sp. FUM94 was cloned in an alkane responsive promoter, pCom8, and expressed in Escherichia coli BL21 (DE3) as a host. The recombinant was not susceptible to inorganic sulfate in the culture medium. Desulfurizing activity of recombinant strain versus wild type indicated that in a sulfate containing medium, BDS yield of recombinant increased from 16.0% ± 0.9 to 34.0% ± 1.9% when dibenzothiophene (DBT) concentration (dissolved in ethanol) increased from 25 to 100 ppm. Also, 2-hydroxy biphenyl (2-HBP) production rate improved 8.5-fold (from 0.302 ± 0.020 to 2.57 ± 0.14 mmol 2-HBP (kg DCW)-1 h-1) at the same DBT concentration range. This is while no 2-HBP production was detected in FUM94 biphasic reaction. In a sulfate-free medium, wild type strain demonstrated desulfurization activity, but decreasing with the increase of DBT concentration dissolved in n-tetradecane. Whereas, the recombinant strain demonstrated increasing desulfurizing activity in a sulfate-containing high DBT concentration environment. Overall, the result of this molecular manipulation can be considered as a step forward toward commercialization of BDS technology.
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Affiliation(s)
- Somayeh Khosravinia
- Department of Chemical Engineering, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mahmood A Mahdavi
- Department of Chemical Engineering, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Reza Gheshlaghi
- Department of Chemical Engineering, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Hesam Dehghani
- Stem Cells and Regenerative Medicine Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran.,Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Behnam Rasekh
- Microbiology and Biotechnology Research Group, Research Institute of Petroleum Industry, Tehran, Iran
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Abstract
Chirality is a key factor in the safety and efficacy of many drug products and thus the production of single enantiomers of drug intermediates and drugs has become important and state of the art in the pharmaceutical industry. There has been an increasing awareness of the enormous potential of microorganisms and enzymes (biocatalysts) for the transformation of synthetic chemicals with high chemo-, regio- and enatioselectivities providing products in high yields and purity. In this article, biocatalytic processes are described for the synthesis of key chiral intermediates for development pharmaceuticals.
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Affiliation(s)
- Ramesh N Patel
- SLRP Associates, LLC, Consultation in Biocatalysis and Biotechnology, 572 Cabot Hill Road, Bridgewater, NJ 08807, USA.
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Synthesis of tetrahydrofuran-based natural products and their carba analogs via stereoselective enzyme mediated Baeyer–Villiger oxidation. Tetrahedron 2016. [DOI: 10.1016/j.tet.2015.11.048] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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9
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Baeyer-Villiger oxidations: biotechnological approach. Appl Microbiol Biotechnol 2016; 100:6585-6599. [DOI: 10.1007/s00253-016-7670-x] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 06/02/2016] [Accepted: 06/07/2016] [Indexed: 10/21/2022]
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10
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Purification of an amide hydrolase DamH from Delftia sp. T3-6 and its gene cloning, expression, and biochemical characterization. Appl Microbiol Biotechnol 2014; 98:7491-9. [DOI: 10.1007/s00253-014-5710-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Accepted: 03/17/2014] [Indexed: 11/26/2022]
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11
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Dudek HM, Fink MJ, Shivange AV, Dennig A, Mihovilovic MD, Schwaneberg U, Fraaije MW. Extending the substrate scope of a Baeyer–Villiger monooxygenase by multiple-site mutagenesis. Appl Microbiol Biotechnol 2013; 98:4009-20. [DOI: 10.1007/s00253-013-5364-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 10/25/2013] [Accepted: 10/28/2013] [Indexed: 10/26/2022]
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12
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Li Y, Chen Q, Wang CH, Cai S, He J, Huang X, Li SP. Degradation of acetochlor by consortium of two bacterial strains and cloning of a novel amidase gene involved in acetochlor-degrading pathway. BIORESOURCE TECHNOLOGY 2013; 148:628-631. [PMID: 24075675 DOI: 10.1016/j.biortech.2013.09.038] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Revised: 09/04/2013] [Accepted: 09/07/2013] [Indexed: 06/02/2023]
Abstract
Two bacterial strains Sphingobium quisquiliarum DC-2 and Sphingobium baderi DE-13 were isolated from activated sludge. Acetochlor was transformed by S. quisquiliarum DC-2 to a transitory intermediate 2-chloro-N-(2-methyl-6-ethylphenyl)acetamide (CMEPA), which was further transformed to 2-methyl-6-ethylaniline (MEA), and MEA could not be degraded by strain DC-2. S. baderi DE-13, incapable of degrading acetochlor, showed capability of degrading MEA to an intermediate 2-methyl-6-ethylaminophenol (MEAOH). MEAOH was further transformed to 2-methyl-6-ethylbenzoquinoneimine (MEBQI), which was mineralized by strain DE-13. A gene, cmeH, encoding an amidase that catalyzed the amide bond cleavage of CMEPA was cloned from strain DC-2. CmeH was expressed in Escherichia coli BL21 and homogenously purified using Ni-nitrilotriacetic acid affinity. CmeH efficiently hydrolyzed CMEPA and other important herbicide, such as propanil, fenoxaprop-p-ethyl and clodinafop-propargyl.
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Affiliation(s)
- Yi Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
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13
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Bianchi DA, Moran-Ramallal R, Iqbal N, Rudroff F, Mihovilovic MD. Enantiocomplementary access to carba-analogs of C-nucleoside derivatives by recombinant Baeyer–Villiger monooxygenases. Bioorg Med Chem Lett 2013; 23:2718-20. [DOI: 10.1016/j.bmcl.2013.02.085] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Revised: 02/13/2013] [Accepted: 02/14/2013] [Indexed: 10/27/2022]
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14
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Balke K, Kadow M, Mallin H, Sass S, Bornscheuer UT. Discovery, application and protein engineering of Baeyer-Villiger monooxygenases for organic synthesis. Org Biomol Chem 2012; 10:6249-65. [PMID: 22733152 DOI: 10.1039/c2ob25704a] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Baeyer-Villiger monooxygenases (BVMOs) are useful enzymes for organic synthesis as they enable the direct and highly regio- and stereoselective oxidation of ketones to esters or lactones simply with molecular oxygen. This contribution covers novel concepts such as searching in protein sequence databases using distinct motifs to discover new Baeyer-Villiger monooxygenases as well as high-throughput assays to facilitate protein engineering in order to improve BVMOs with respect to substrate range, enantioselectivity, thermostability and other properties. Recent examples for the application of BVMOs in synthetic organic synthesis illustrate the broad potential of these biocatalysts. Furthermore, methods to facilitate the more efficient use of BVMOs in organic synthesis by applying e.g. improved cofactor regeneration, substrate feed and in situ product removal or immobilization are covered in this perspective.
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Affiliation(s)
- Kathleen Balke
- Institute of Biochemistry, Dept of Biotechnology & Enzyme Catalysis, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
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15
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Linares-Pastén JA, Chávez-Lizárraga G, Villagomez R, Mamo G, Hatti-Kaul R. A method for rapid screening of ketone biotransformations: Detection of whole cell Baeyer–Villiger monooxygenase activity. Enzyme Microb Technol 2012; 50:101-6. [DOI: 10.1016/j.enzmictec.2011.10.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 10/19/2011] [Accepted: 10/26/2011] [Indexed: 10/15/2022]
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16
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Leipold F, Wardenga R, Bornscheuer UT. Cloning, expression and characterization of a eukaryotic cycloalkanone monooxygenase from Cylindrocarpon radicicola ATCC 11011. Appl Microbiol Biotechnol 2011; 94:705-17. [DOI: 10.1007/s00253-011-3670-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 10/09/2011] [Accepted: 10/23/2011] [Indexed: 01/24/2023]
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17
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Wang XB, Chi CQ, Nie Y, Tang YQ, Tan Y, Wu G, Wu XL. Degradation of petroleum hydrocarbons (C6-C40) and crude oil by a novel Dietzia strain. BIORESOURCE TECHNOLOGY 2011; 102:7755-7761. [PMID: 21715162 DOI: 10.1016/j.biortech.2011.06.009] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 06/03/2011] [Accepted: 06/04/2011] [Indexed: 05/31/2023]
Abstract
A novel bacterial strain, DQ12-45-1b, was isolated from the production water of a deep subterranean oil-reservoir. Morphological, physiological and phylogenetic analyses indicated that the strain belonged to the genus Dietzia with both alkB (coding for alkane monooxygenase) and CYP153 (coding for P450 alkane hydroxylase of the cytochrome CYP153 family) genes and their induction detected. It was capable of utilizing a wide range of n-alkanes (C6-C40), aromatic compounds and crude oil as the sole carbon sources for growth. In addition, it preferentially degraded short-chain hydrocarbons (≤C25) in the early cultivation phase and accumulated hydrocarbons with chain-lengths from C23 to C27 during later cultivation stage with crude oil as the sole carbon source. This is the first study to report the different behaviors of a bacterial species toward crude oil degradation as well as a species of Dietzia degrading a wide range of hydrocarbons.
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Affiliation(s)
- Xing-Biao Wang
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, PR China
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18
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Leisch H, Morley K, Lau PCK. Baeyer−Villiger Monooxygenases: More Than Just Green Chemistry. Chem Rev 2011; 111:4165-222. [DOI: 10.1021/cr1003437] [Citation(s) in RCA: 317] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Hannes Leisch
- Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada
| | - Krista Morley
- Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada
| | - Peter C. K. Lau
- Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada
- Department of Microbiology and Immunology, McGill University, 3775 University Street, Montreal, Quebec H3A 2B4, Canada
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de Gonzalo G, Mihovilovic MD, Fraaije MW. Recent developments in the application of Baeyer-Villiger monooxygenases as biocatalysts. Chembiochem 2011; 11:2208-31. [PMID: 20936617 DOI: 10.1002/cbic.201000395] [Citation(s) in RCA: 162] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Baeyer-Villiger monooxygenases (BVMOs) represent a specific class of monooxygenases that are capable of catalyzing a variety of oxidation reactions, including Baeyer-Villiger oxidations. The recently elucidated BVMO crystal structures have provided a more detailed insight into the complex mechanism of these flavin-containing enzymes. Biocatalytic studies on a number of newly discovered BVMOs have shown that they are very potent oxidative biocatalysts. In addition to catalyzing the regio- and enantioselective Baeyer-Villiger oxidations of a wide range of carbonylic compounds, epoxidations, and enantioselective sulfoxidations have also been shown to be part of their catalytic repertoire. This review provides an overview on the recent developments in BVMO-mediated biocatalytic processes, identification of the catalytic role of these enzymes in metabolic routes and prodrug activation, as well as the efforts in developing effective biocatalytic methodologies to apply BVMOs for the synthesis of high added value compounds.
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Affiliation(s)
- Gonzalo de Gonzalo
- Laboratory of Biochemistry, University of Groningen, Groningen, The Netherlands.
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20
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Rehdorf J, Mihovilovic M, Fraaije M, Bornscheuer U. Enzymatic Synthesis of Enantiomerically Pure β-Amino Ketones, β-Amino Esters, and β-Amino Alcohols with Baeyer-Villiger Monooxygenases. Chemistry 2010; 16:9525-35. [DOI: 10.1002/chem.201001480] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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21
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Torres Pazmiño DE, Riebel A, de Lange J, Rudroff F, Mihovilovic MD, Fraaije MW. Efficient biooxidations catalyzed by a new generation of self-sufficient Baeyer-Villiger monooxygenases. Chembiochem 2010; 10:2595-8. [PMID: 19795432 DOI: 10.1002/cbic.200900480] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Daniel E Torres Pazmiño
- Laboratory of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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22
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Lau PCK, Leisch H, Yachnin BJ, Mirza IA, Berghuis AM, Iwaki H, Hasegawa Y. Sustained Development in Baeyer-Villiger Biooxidation Technology. ACS SYMPOSIUM SERIES 2010. [DOI: 10.1021/bk-2010-1043.ch024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- Peter C. K. Lau
- Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
- Departments of Biochemistry and Microbiology & Immunology, McGill University, 3655 Prom Sir William Osler, Montreal, QC, H3G 1Y6, Canada
- Department of Life Science & Biotechnology and ORDIST, Kansai University, Suita, Osaka, 564-8680, Japan
| | - Hannes Leisch
- Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
- Departments of Biochemistry and Microbiology & Immunology, McGill University, 3655 Prom Sir William Osler, Montreal, QC, H3G 1Y6, Canada
- Department of Life Science & Biotechnology and ORDIST, Kansai University, Suita, Osaka, 564-8680, Japan
| | - Brahm J. Yachnin
- Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
- Departments of Biochemistry and Microbiology & Immunology, McGill University, 3655 Prom Sir William Osler, Montreal, QC, H3G 1Y6, Canada
- Department of Life Science & Biotechnology and ORDIST, Kansai University, Suita, Osaka, 564-8680, Japan
| | - I. Ahmad Mirza
- Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
- Departments of Biochemistry and Microbiology & Immunology, McGill University, 3655 Prom Sir William Osler, Montreal, QC, H3G 1Y6, Canada
- Department of Life Science & Biotechnology and ORDIST, Kansai University, Suita, Osaka, 564-8680, Japan
| | - Albert M. Berghuis
- Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
- Departments of Biochemistry and Microbiology & Immunology, McGill University, 3655 Prom Sir William Osler, Montreal, QC, H3G 1Y6, Canada
- Department of Life Science & Biotechnology and ORDIST, Kansai University, Suita, Osaka, 564-8680, Japan
| | - Hiroaki Iwaki
- Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
- Departments of Biochemistry and Microbiology & Immunology, McGill University, 3655 Prom Sir William Osler, Montreal, QC, H3G 1Y6, Canada
- Department of Life Science & Biotechnology and ORDIST, Kansai University, Suita, Osaka, 564-8680, Japan
| | - Yoshie Hasegawa
- Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
- Departments of Biochemistry and Microbiology & Immunology, McGill University, 3655 Prom Sir William Osler, Montreal, QC, H3G 1Y6, Canada
- Department of Life Science & Biotechnology and ORDIST, Kansai University, Suita, Osaka, 564-8680, Japan
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Park YC, Shaffer CEH, Bennett GN. Microbial formation of esters. Appl Microbiol Biotechnol 2009; 85:13-25. [PMID: 19714327 DOI: 10.1007/s00253-009-2170-x] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2009] [Revised: 07/27/2009] [Accepted: 07/28/2009] [Indexed: 12/22/2022]
Abstract
Small aliphatic esters are important natural flavor and fragrance compounds and have numerous uses as solvents and as chemical intermediates. Besides the chemical or lipase-catalyzed formation of esters from alcohols and organic acids, small volatile esters are made by several biochemical routes in microbes. This short review will cover the biosynthesis of esters from acyl-CoA and alcohol condensation, from oxidation of hemiacetals formed from aldehydes and alcohols, and from the insertion of oxygen adjacent to the carbonyl group in a straight chain or cyclic ketone by Baeyer-Villiger monooxygenases. The physiological role of the ester-forming reactions can allow degradation of ketones for use as a carbon source and may play a role in detoxification of aldehydes or recycling cofactors. The enzymes catalyzing each of these processes have been isolated and characterized, and a number of genes encoding the proteins from various microbes have been cloned and functionally expressed. The use of these ester-forming organisms or recombinant organisms expressing the appropriate genes as biocatalysts in biotechnology to make specific esters and chiral lactones has been studied in recent years.
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Affiliation(s)
- Yong Cheol Park
- Department of General Education, Kookmin University, Seoul, South Korea
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Novel genes retrieved from environmental DNA by polymerase chain reaction: current genome-walking techniques for future metagenome applications. J Biotechnol 2009; 144:75-82. [PMID: 19712711 DOI: 10.1016/j.jbiotec.2009.08.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 08/11/2009] [Accepted: 08/17/2009] [Indexed: 11/24/2022]
Abstract
Environmental DNA is an extremely rich source of genes encoding enzymes with novel biocatalytic activities. To tap this source, function-based and sequence-based strategies have been established to isolate, clone, and express these novel metagenome-derived genes. Sequence-based strategies, which rely on PCR with consensus primers and genome walking, represent an efficient and inexpensive alternative to activity-based screening of recombinant strains harbouring fragments of environmental DNA. This review covers the diverse array of genome-walking techniques, which were originally developed for genomic DNA and currently are also used for PCR-based recovery of entire genes from the metagenome. These sequence-based gene mining methods appear to offer a powerful tool for retrieving from the metagenome novel genes encoding biocatalysts with potential applications in biotechnology.
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Kinetic resolution of aliphatic acyclic β-hydroxyketones by recombinant whole-cell Baeyer–Villiger monooxygenases—Formation of enantiocomplementary regioisomeric esters. Bioorg Med Chem Lett 2009; 19:3739-43. [DOI: 10.1016/j.bmcl.2009.05.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 05/04/2009] [Accepted: 05/06/2009] [Indexed: 11/21/2022]
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Beam MP, Bosserman MA, Noinaj N, Wehenkel M, Rohr J. Crystal structure of Baeyer-Villiger monooxygenase MtmOIV, the key enzyme of the mithramycin biosynthetic pathway . Biochemistry 2009; 48:4476-87. [PMID: 19364090 PMCID: PMC2713373 DOI: 10.1021/bi8023509] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Baeyer-Villiger monooxygenases (BVMOs), mostly flavoproteins, were shown to be powerful biocatalysts for synthetic organic chemistry applications and were also suggested to play key roles for the biosyntheses of various natural products. Here we present the three-dimensional structure of MtmOIV, a 56 kDa homodimeric FAD- and NADPH-dependent monooxygenase, which catalyzes the key frame-modifying step of the mithramycin biosynthetic pathway and currently the only BVMO proven to react with its natural substrate via a Baeyer-Villiger reaction. MtmOIV's structure was determined by X-ray crystallography using molecular replacement to a resolution of 2.9 A. MtmOIV cleaves a C-C bond, essential for the conversion of the biologically inactive precursor, premithramycin B, into the active drug mithramycin. The MtmOIV structure combined with substrate docking calculations and site-directed mutagenesis experiments identifies several residues that participate in cofactor and substrate binding. Future experimentation aimed at broadening the substrate specificity of the enzyme could facilitate the generation of chemically diverse mithramycin analogues through combinatorial biosynthesis.
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Affiliation(s)
- Miranda P. Beam
- Department of Pharmaceutical Sciences, College of Pharmacy, and the Kentucky Center for Structural Biology, University of Kentucky, Lexington, KY 40536
| | - Mary A. Bosserman
- Department of Pharmaceutical Sciences, College of Pharmacy, and the Kentucky Center for Structural Biology, University of Kentucky, Lexington, KY 40536
| | - Nicholas Noinaj
- Department of Molecular and Cellular Biochemistry and Kentucky Center of Structural Biology, University of Kentucky, Lexington, KY 40536
| | - Marie Wehenkel
- Department of Pharmaceutical Sciences, College of Pharmacy, and the Kentucky Center for Structural Biology, University of Kentucky, Lexington, KY 40536
| | - Jürgen Rohr
- Department of Pharmaceutical Sciences, College of Pharmacy, and the Kentucky Center for Structural Biology, University of Kentucky, Lexington, KY 40536
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Kayser MM. ‘Designer reagents’ recombinant microorganisms: new and powerful tools for organic synthesis. Tetrahedron 2009. [DOI: 10.1016/j.tet.2008.10.039] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Directed evolution of a Baeyer–Villiger monooxygenase to enhance enantioselectivity. Appl Microbiol Biotechnol 2008; 81:465-72. [DOI: 10.1007/s00253-008-1646-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Revised: 07/30/2008] [Accepted: 08/02/2008] [Indexed: 11/26/2022]
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Martínez I, Zhu J, Lin H, Bennett GN, San KY. Replacing Escherichia coli NAD-dependent glyceraldehyde 3-phosphate dehydrogenase (GAPDH) with a NADP-dependent enzyme from Clostridium acetobutylicum facilitates NADPH dependent pathways. Metab Eng 2008; 10:352-9. [PMID: 18852061 DOI: 10.1016/j.ymben.2008.09.001] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2007] [Revised: 09/05/2008] [Accepted: 09/10/2008] [Indexed: 11/18/2022]
Abstract
Reactions requiring reducing equivalents, NAD(P)H, are of enormous importance for the synthesis of industrially valuable compounds such as carotenoids, polymers, antibiotics and chiral alcohols among others. The use of whole-cell biocatalysis can reduce process cost by acting as catalyst and cofactor regenerator at the same time; however, product yields might be limited by cofactor availability within the cell. Thus, our study focussed on the genetic manipulation of a whole-cell system by modifying metabolic pathways and enzymes to improve the overall production process. In the present work, we genetically engineered an Escherichia coli strain to increase NADPH availability to improve the productivity of products that require NADPH in its biosynthesis. The approach involved an alteration of the glycolysis step where glyceraldehyde-3-phosphate (GAP) is oxidized to 1,3 bisphophoglycerate (1,3-BPG). This reaction is catalyzed by NAD-dependent endogenous glyceraldehyde-3-phosphate dehydrogenase (GAPDH) encoded by the gapA gene. We constructed a recombinant E. coli strain by replacing the native NAD-dependent gapA gene with a NADP-dependent GAPDH from Clostridium acetobutylicum, encoded by the gene gapC. The beauty of this approach is that the recombinant E. coli strain produces 2 mol of NADPH, instead of NADH, per mole of glucose consumed. Metabolic flux analysis showed that the flux through the pentose phosphate (PP) pathway, one of the main pathways that produce NADPH, was reduced significantly in the recombinant strain when compared to that of the parent strain. The effectiveness of the NADPH enhancing system was tested using the production of lycopene and epsilon-caprolactone as model systems using two different background strains. The recombinant strains, with increased NADPH availability, consistently showed significant higher productivity than the parent strains.
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Affiliation(s)
- Irene Martínez
- Department of Bioengineering, Rice University, Houston, TX, USA
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The genome of Polaromonas sp. strain JS666: insights into the evolution of a hydrocarbon- and xenobiotic-degrading bacterium, and features of relevance to biotechnology. Appl Environ Microbiol 2008; 74:6405-16. [PMID: 18723656 DOI: 10.1128/aem.00197-08] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Polaromonas sp. strain JS666 can grow on cis-1,2-dichloroethene (cDCE) as a sole carbon and energy source and may be useful for bioremediation of chlorinated solvent-contaminated sites. Analysis of the genome sequence of JS666 (5.9 Mb) shows a bacterium well adapted to pollution that carries many genes likely to be involved in hydrocarbon and xenobiotic catabolism and metal resistance. Clusters of genes coding for haloalkane, haloalkanoate, n-alkane, alicyclic acid, cyclic alcohol, and aromatic catabolism were analyzed in detail, and growth on acetate, catechol, chloroacetate, cyclohexane carboxylate, cyclohexanol, ferulate, heptane, 3-hydroxybenzoate, hydroxyquinol, gentisate, octane, protocatechuate, and salicylate was confirmed experimentally. Strain JS666 also harbors diverse putative mobile genetic elements, including retrons, inteins, a miniature inverted-repeat transposable element, insertion sequence transposases from 14 families, eight genomic islands, a Mu family bacteriophage, and two large (338- and 360-kb) plasmids. Both plasmids are likely to be self-transferable and carry genes for alkane, alcohol, aromatic, and haloacid metabolism. Overall, the JS666 genome sequence provides insights into the evolution of pollutant-degrading bacteria and provides a toolbox of catabolic genes with utility for biotechnology.
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31
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Cloning and characterization of a cyclohexanone monooxygenase gene from Arthrobacter sp. L661. BIOTECHNOL BIOPROC E 2008. [DOI: 10.1007/s12257-007-0162-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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32
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Rial DV, Bianchi DA, Kapitanova P, Lengar A, van Beilen JB, Mihovilovic MD. Stereoselective Desymmetrizations by Recombinant Whole Cells Expressing the Baeyer–Villiger Monooxygenase fromXanthobacter sp. ZL5: A New Biocatalyst Accepting Structurally Demanding Substrates. European J Org Chem 2008. [DOI: 10.1002/ejoc.200700872] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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33
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Biocatalyst assessment of recombinant whole-cells expressing the Baeyer-Villiger monooxygenase from Xanthobacter sp. ZL5. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.molcatb.2007.09.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Clouthier CM, Kayser MM, Reetz MT. Designing new Baeyer-Villiger monooxygenases using restricted CASTing. J Org Chem 2007; 71:8431-7. [PMID: 17064016 DOI: 10.1021/jo0613636] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper outlines the design and execution of the first mini-evolution of cyclopentanone monooxygenase (CPMO). The methodology described is a relatively inexpensive and rapid way to obtain mutant enzymes with the desired characteristics. Several successful mutants with enhanced enantioselectivities were identified. For example, mutant-catalyzed oxidation of 4-methoxycyclohexanone gave the corresponding lactone with 92% entantiometric excess (ee) compared to the 46% ee achieved with wild-type cyclohexanone monoxygenase (WT-CHMO). The original design of the mini-evolution and the following evaluation of mutants can provide valuable insights into the active site's construction and dynamics and can suggest other catalytically profitable mutations within the putative active site.
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Affiliation(s)
- Christopher M Clouthier
- Department of Physical Sciences, University of New Brunswick, Saint John, New Brunswick, E2L 4L5 Canada
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Rudroff F, Rydz J, Ogink F, Fink M, Mihovilovic M. Comparing the Stereoselective Biooxidation of Cyclobutanones by Recombinant Strains Expressing Bacterial Baeyer–Villiger Monooxygenases. Adv Synth Catal 2007. [DOI: 10.1002/adsc.200700072] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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36
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Onaca C, Kieninger M, Engesser KH, Altenbuchner J. Degradation of alkyl methyl ketones by Pseudomonas veronii MEK700. J Bacteriol 2007; 189:3759-67. [PMID: 17351032 PMCID: PMC1913341 DOI: 10.1128/jb.01279-06] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas veronii MEK700 was isolated from a biotrickling filter cleaning 2-butanone-loaded waste air. The strain is able to grow on 2-butanone and 2-hexanol. The genes for degradation of short chain alkyl methyl ketones were identified by transposon mutagenesis using a newly designed transposon, mini-Tn5495, and cloned in Escherichia coli. DNA sequence analysis of a 15-kb fragment revealed three genes involved in methyl ketone degradation. The deduced amino acid sequence of the first gene, mekA, had high similarity to Baeyer-Villiger monooxygenases; the protein of the second gene, mekB, had similarity to homoserine acetyltransferases; the third gene, mekR, encoded a putative transcriptional activator of the AraC/XylS family. The three genes were located between two gene groups: one comprising a putative phosphoenolpyruvate synthase and glycogen synthase, and the other eight genes for the subunits of an ATPase. Inactivation of mekA and mekB by insertion of the mini-transposon abolished growth of P. veronii MEK700 on 2-butanone and 2-hexanol. The involvement of mekR in methyl ketone degradation was observed by heterologous expression of mekA and mekB in Pseudomonas putida. A fragment containing mekA and mekB on a plasmid was not sufficient to allow P. putida KT2440 to grow on 2-butanone. Not until all three genes were assembled in the recombinant P. putida was it able to use 2-butanone as carbon source. The Baeyer-Villiger monooxygenase activity of MekA was clearly demonstrated by incubating a mekB transposon insertion mutant of P. veronii with 2-butanone. Hereby, ethyl acetate was accumulated. To our knowledge, this is the first time that ethyl acetate by gas chromatographic analysis has been definitely demonstrated to be an intermediate of MEK degradation. The mekB-encoded protein was heterologously expressed in E. coli and purified by immobilized metal affinity chromatography. The protein exhibited high esterase activity towards short chain esters like ethyl acetate and 4-nitrophenyl acetate.
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Affiliation(s)
- Christina Onaca
- Institut für Industrielle Genetik, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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38
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Kotani T, Yurimoto H, Kato N, Sakai Y. Novel acetone metabolism in a propane-utilizing bacterium, Gordonia sp. strain TY-5. J Bacteriol 2007; 189:886-93. [PMID: 17071761 PMCID: PMC1797311 DOI: 10.1128/jb.01054-06] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Accepted: 10/16/2006] [Indexed: 11/20/2022] Open
Abstract
In the propane-utilizing bacterium Gordonia sp. strain TY-5, propane was shown to be oxidized to 2-propanol and then further oxidized to acetone. In this study, the subsequent metabolism of acetone was studied. Acetone-induced proteins were found in extracts of cells induced by acetone, and a gene cluster designated acmAB was cloned on the basis of the N-terminal amino acid sequences of acetone-induced proteins. The acmA and acmB genes encode a Baeyer-Villiger monooxygenase (BVMO) and esterase, respectively. The BVMO encoded by acmA was purified from acetone-induced cells of Gordonia sp. strain TY-5 and characterized. The BVMO exhibited NADPH-dependent oxidation activity for linear ketones (C3 to C10) and cyclic ketones (C4 to C8). Escherichia coli expressing the acmA gene oxidized acetone to methyl acetate, and E. coli expressing the acmB gene hydrolyzed methyl acetate. Northern blot analyses revealed that polycistronic transcription of the acmAB gene cluster was induced by propane, 2-propanol, and acetone. These results indicate that the acmAB gene products play an important role in the metabolism of acetone derived from propane oxidation and clarify the propane metabolism pathway of strain TY-5 (propane --> 2-propanol --> acetone --> methyl acetate --> acetic acid + methanol). This paper provides the first evidence for BVMO-dependent acetone metabolism.
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Affiliation(s)
- Tetsuya Kotani
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Kyoto 606-8502, Japan
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Kirschner A, Altenbuchner J, Bornscheuer UT. Cloning, expression, and characterization of a Baeyer–Villiger monooxygenase from Pseudomonas fluorescens DSM 50106 in E. coli. Appl Microbiol Biotechnol 2007; 73:1065-72. [PMID: 16944127 DOI: 10.1007/s00253-006-0556-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2006] [Revised: 06/23/2006] [Accepted: 06/26/2006] [Indexed: 11/25/2022]
Abstract
A gene encoding a Baeyer-Villiger monooxygenase (BVMO) identified in Pseudomonas fluorescens DSM 50106 was cloned and functionally expressed in Escherichia coli JM109. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot analysis showed an estimated 56 kDa-size protein band corresponding to the recombinant enzyme. Expression in BL21 (DE3) resulted mainly in the formation of inclusion bodies. This could be overcome by coexpression of molecular chaperones, especially the DnaK/DnaJ/GrpE complex, leading to increased production of soluble BVMO enzyme in recombinant E. coli. Examination of the substrate spectra using whole-cell biocatalysis revealed a high specificity of the BVMO for aliphatic open-chain ketones. Thus, octyl acetate, heptyl propionate, and hexyl butyrate were quantitatively formed from the corresponding ketone substrates. Several other esters were obtained in conversion >68%. Selected esters were also produced on preparative scale.
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Affiliation(s)
- Anett Kirschner
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Friedrich-Ludwig-Jahn-Str. 18c, 17487, Greifswald, Germany
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Powell SM, Ferguson SH, Bowman JP, Snape I. Using real-time PCR to assess changes in the hydrocarbon-degrading microbial community in Antarctic soil during bioremediation. MICROBIAL ECOLOGY 2006; 52:523-32. [PMID: 16944337 DOI: 10.1007/s00248-006-9131-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2006] [Accepted: 06/13/2006] [Indexed: 05/11/2023]
Abstract
A real-time polymerase chain reaction (PCR) method to quantify the proportion of microorganisms containing alkane monooxygenase was developed and used to follow changes in the microbial community in hydrocarbon-contaminated Antarctic soil during a bioremediation field trial. Assays for the alkB and rpoB genes were validated and found to be both sensitive and reproducible (less than 2% intrarun variation and 25-38% interrun variation). Results from the real-time PCR analysis were compared to analysis of the microbial population by a culture-based technique [most probable number (MPN) counts]. Both types of analysis indicated that fertilizer addition to hydrocarbon-contaminated soil stimulated the indigenous bacterial population within 1 year. The proportion of alkB containing microorganisms was positively correlated to the concentration of n-alkanes in the soil. After the concentration of n-alkanes in the soil decreased, the proportion of alkane-degrading microorganisms decreased, but the proportion of total hydrocarbon-degrading microorganisms increased, indicating another shift in the microbial community structure and ongoing biodegradation.
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Affiliation(s)
- Shane M Powell
- Tasmanian Institute of Agricultural Research, University of Tasmania, Hobart 7001, Australia.
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41
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Iwaki H, Wang S, Grosse S, Bergeron H, Nagahashi A, Lertvorachon J, Yang J, Konishi Y, Hasegawa Y, Lau PCK. Pseudomonad cyclopentadecanone monooxygenase displaying an uncommon spectrum of Baeyer-Villiger oxidations of cyclic ketones. Appl Environ Microbiol 2006; 72:2707-20. [PMID: 16597975 PMCID: PMC1449013 DOI: 10.1128/aem.72.4.2707-2720.2006] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Baeyer-Villiger monooxygenases (BVMOs) are biocatalysts that offer the prospect of high chemo-, regio-, and enantioselectivity in the organic synthesis of lactones or esters from a variety of ketones. In this study, we have cloned, sequenced, and overexpressed in Escherichia coli a new BVMO, cyclopentadecanone monooxygenase (CpdB or CPDMO), originally derived from Pseudomonas sp. strain HI-70. The 601-residue primary structure of CpdB revealed only 29% to 50% sequence identity to those of known BVMOs. A new sequence motif, characterized by a cluster of charged residues, was identified in a subset of BVMO sequences that contain an N-terminal extension of approximately 60 to 147 amino acids. The 64-kDa CPDMO enzyme was purified to apparent homogeneity, providing a specific activity of 3.94 micromol/min/mg protein and a 20% yield. CPDMO is monomeric and NADPH dependent and contains approximately 1 mol flavin adenine dinucleotide per mole of protein. A deletion mutant suggested the importance of the N-terminal 54 amino acids to CPDMO activity. In addition, a Ser261Ala substitution in a Rossmann fold motif resulted in an improved stability and increased affinity of the enzyme towards NADPH compared to the wild-type enzyme (K(m) = 8 microM versus K(m) = 24 microM). Substrate profiling indicated that CPDMO is unusual among known BVMOs in being able to accommodate and oxidize both large and small ring substrates that include C(11) to C(15) ketones, methyl-substituted C(5) and C(6) ketones, and bicyclic ketones, such as decalone and beta-tetralone. CPDMO has the highest affinity (K(m) = 5.8 microM) and the highest catalytic efficiency (k(cat)/K(m) ratio of 7.2 x 10(5) M(-1) s(-1)) toward cyclopentadecanone, hence the Cpd designation. A number of whole-cell biotransformations were carried out, and as a result, CPDMO was found to have an excellent enantioselectivity (E > 200) as well as 99% S-selectivity toward 2-methylcyclohexanone for the production of 7-methyl-2-oxepanone, a potentially valuable chiral building block. Although showing a modest selectivity (E = 5.8), macrolactone formation of 15-hexadecanolide from the kinetic resolution of 2-methylcyclopentadecanone using CPDMO was also demonstrated.
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Affiliation(s)
- Hiroaki Iwaki
- National Research Council Canada, Biotechnology Research Institute, 6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada
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Mihovilovic MD, Snajdrova R, Grötzl B. Microbial Baeyer–Villiger oxidation of 4,4-disubstituted cyclohexan- and cyclohexenones by recombinant whole-cells expressing monooxygenases of bacterial origin. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.molcatb.2006.01.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Mihovilovic MD, Müller B, Spina M, Durrani AI, Stanetty P, Dazinger G, Kirchner K. Microbial Baeyer-Villiger Oxidation of Ketones by Cyclohexanone and Cyclopentanone Monooxygenase – A Computational Rational for Biocatalyst Performance. MONATSHEFTE FUR CHEMIE 2006. [DOI: 10.1007/s00706-006-0468-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Weinitschke S, Denger K, Smits THM, Hollemeyer K, Cook AM. The sulfonated osmolyte N-methyltaurine is dissimilated by Alcaligenes faecalis and by Paracoccus versutus with release of methylamine. Microbiology (Reading) 2006; 152:1179-1186. [PMID: 16549680 DOI: 10.1099/mic.0.28622-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Selective enrichments yielded bacterial cultures able to utilize the osmolyte N-methyltaurine as sole source of carbon and energy or as sole source of fixed nitrogen for aerobic growth. Strain MT1, which degraded N-methyltaurine as a sole source of carbon concomitantly with growth, was identified as a strain of Alcaligenes faecalis. Stoichiometric amounts of methylamine, whose identity was confirmed by matrix-assisted, laser-desorption ionization time-of-flight mass spectrometry, and of sulfate were released during growth. Inducible N-methyltaurine dehydrogenase, sulfoacetaldehyde acetyltransferase (Xsc) and a sulfite dehydrogenase could be detected. Taurine dehydrogenase was also present and it was hypothesized that taurine dehydrogenase has a substrate range that includes N-methyltaurine. Partial sequences of a tauY-like gene (encoding the putative large component of taurine dehydrogenase) and an xsc gene were obtained by PCR with degenerate primers. Strain N-MT utilized N-methyltaurine as a sole source of fixed nitrogen for growth and could also utilize the compound as sole source of carbon. This bacterium was identified as a strain of Paracoccus versutus. This organism also expressed inducible (N-methyl)taurine dehydrogenase, Xsc and a sulfite dehydrogenase. The presence of a gene cluster with high identity to a larger cluster from Paracoccus pantotrophus NKNCYSA, which is now known to dissimilate N-methyltaurine via Xsc, allowed most of the overall pathway, including transport and excretion, to be defined. N-Methyltaurine is thus another compound whose catabolism is channelled directly through sulfoacetaldehyde.
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Affiliation(s)
- Sonja Weinitschke
- Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Karin Denger
- Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Theo H M Smits
- Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Klaus Hollemeyer
- Institute of Biochemical Engineering, Saarland University, Box 50 11 50, D-66041 Saarbrücken, Germany
| | - Alasdair M Cook
- Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
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Mihovilovic MD, Bianchi DA, Rudroff F. Accessing tetrahydrofuran-based natural products by microbial Baeyer–Villiger biooxidation. Chem Commun (Camb) 2006:3214-6. [PMID: 17028747 DOI: 10.1039/b606633j] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A heterobicyclic lactone obtained by stereoselective Baeyer-Villiger biooxidation with recombinant whole-cells expressing cyclopentanone monooxygenase from Comamonas sp. NCIMB 9872 was used for formal total syntheses of various natural products containing a tetrahydrofuran structural motif.
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Affiliation(s)
- Marko D Mihovilovic
- Vienna University of Technology, Institute of Applied Synthetic Chemistry, Getreidemarkt 9/163-OC, A-1060 Vienna, Austria.
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46
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Biooxidation of ketones with a cyclobutanone structural motif by recombinant whole-cells expressing 4-hydroxyacetophenone monooxygenase. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.molcatb.2004.11.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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47
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Fraaije MW, Wu J, Heuts DPHM, van Hellemond EW, Spelberg JHL, Janssen DB. Discovery of a thermostable Baeyer–Villiger monooxygenase by genome mining. Appl Microbiol Biotechnol 2004; 66:393-400. [PMID: 15599520 DOI: 10.1007/s00253-004-1749-5] [Citation(s) in RCA: 188] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2004] [Accepted: 08/31/2004] [Indexed: 11/26/2022]
Abstract
Baeyer-Villiger monooxygenases represent useful biocatalytic tools, as they can catalyze reactions which are difficult to achieve using chemical means. However, only a limited number of these atypical monooxygenases are available in recombinant form. Using a recently described protein sequence motif, a putative Baeyer-Villiger monooxygenase (BVMO) was identified in the genome of the thermophilic actinomycete Thermobifida fusca. Heterologous expression of the respective protein in Escherichia coli and subsequent enzyme characterization showed that it indeed represents a BVMO. The NADPH-dependent and FAD-containing monooxygenase is active with a wide range of aromatic ketones, while aliphatic substrates are also converted. The best substrate discovered so far is phenylacetone (k(cat) = 1.9 s(-1), K(M) = 59 microM). The enzyme exhibits moderate enantioselectivity with alpha-methylphenylacetone (enantiomeric ratio of 7). In addition to Baeyer-Villiger reactions, the enzyme is able to perform sulfur oxidations. Different from all known BVMOs, this newly identified biocatalyst is relatively thermostable, displaying an activity half-life of 1 day at 52 degrees C. This study demonstrates that, using effective annotation tools, genomes can efficiently be exploited as a source of novel BVMOs.
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Affiliation(s)
- Marco W Fraaije
- Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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Gürtler V, Mayall BC, Seviour R. Can whole genome analysis refine the taxonomy of the genus Rhodococcus? FEMS Microbiol Rev 2004; 28:377-403. [PMID: 15449609 DOI: 10.1016/j.femsre.2004.01.001] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The current systematics of the genus Rhodococcus is unclear, partly because many members were originally included before the application of a polyphasic taxonomic approach, central to which is the acquisition of 16S rRNA sequence data. This has resulted in the reclassification and description of many new species. Hence, the literature is replete with new species names that have not been brought together in an organized and easily interpreted form. This taxonomic confusion has been compounded by assigning many xenobiotic degrading isolates with phylogenetic positions but without formal taxonomic descriptions. In order to provide a framework for a taxonomic approach based on multiple genetic loci, a survey was undertaken of the known genome characteristics of members of the genus Rhodococcus including: (i) genetics of cell envelope biosynthesis; (ii) virulence genes; (iii) gene clusters involved in metabolic degradation and industrially relevant pathways; (iv) genetic analysis tools; (v) rapid identification of bacteria including rhodococci with specific gene RFLPs; (vi) genomic organization of rrn operons. Genes encoding virulence factors have been characterized for Rhodococcus equi and Rhodococcus fascians. Based on peptide signature comparisons deduced from gene sequences for cytochrome P-450, mono- and dioxygenases, alkane degradation, nitrile metabolism, proteasomes and desulfurization, phylogenetic relationships can be deduced for Rhodococcus erythropolis, Rhodococcus globerulus, Rhodococcus ruber and a number of undesignated Rhodococcus spp. that may distinguish the genus Rhodococcus into two further genera. The linear genome topologies that exist in some Rhodococcus species may alter a previously proposed model for the analysis of genomic fingerprinting techniques used in bacterial systematics.
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Affiliation(s)
- Volker Gürtler
- Department of Microbiology, Austin Health, Studley Road, Heidelberg, Vic. 3084, Australia.
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Kamerbeek NM, Fraaije MW, Janssen DB. Identifying determinants of NADPH specificity in Baeyer-Villiger monooxygenases. ACTA ACUST UNITED AC 2004; 271:2107-16. [PMID: 15153101 DOI: 10.1111/j.1432-1033.2004.04126.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Baeyer-Villiger monooxygenase (BVMO), 4-hydroxyacetophenone monooxygenase (HAPMO), uses NADPH and O(2) to oxidize a variety of aromatic ketones and sulfides. The FAD-containing enzyme has a 700-fold preference for NADPH over NADH. Sequence alignment with other BVMOs, which are all known to be selective for NADPH, revealed three conserved basic residues, which could account for the observed coenzyme specificity. The corresponding residues in HAPMO (Arg339, Lys439 and Arg440) were mutated and the properties of the purified mutant enzymes were studied. For Arg440 no involvement in coenzyme recognition could be shown as mutant R440A was totally inactive. Although this mutant could still be fully reduced by NADPH, no oxygenation occurred, indicating that this residue is crucial for completing the catalytic cycle of HAPMO. Characterization of several Arg339 and Lys439 mutants revealed that these residues are indeed both involved in coenzyme recognition. Mutant R339A showed a largely decreased affinity for NADPH, as judged from kinetic analysis and binding experiments. Replacing Arg339 also resulted in a decreased catalytic efficiency with NADH. Mutant K439A displayed a 100-fold decrease in catalytic efficiency with NADPH, mainly caused by an increased K(m). However, the efficiency with NADH increased fourfold. Saturation mutagenesis at position 439 showed that the presence of an asparagine or a phenylalanine improves the catalytic efficiency with NADH by a factor of 6 to 7. All Lys439 mutants displayed a lower affinity for AADP(+), confirming a role of the lysine in recognizing the 2'-phosphate of NADPH. The results obtained could be extrapolated to the sequence-related cyclohexanone monooxygenase. Replacing Lys326 in this BVMO, which is analogous to Lys439 in HAPMO, again changed the coenzyme specificity towards NADH. These results indicate that the strict NADPH dependency of this class of monooxygenases is based upon recognition of the coenzyme by several basic residues.
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Affiliation(s)
- Nanne M Kamerbeek
- Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
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Kyte BG, Rouvière P, Cheng Q, Stewart JD. Assessing the Substrate Selectivities and Enantioselectivities of Eight Novel Baeyer−Villiger Monooxygenases toward Alkyl-Substituted Cyclohexanones. J Org Chem 2003; 69:12-7. [PMID: 14703373 DOI: 10.1021/jo030253l] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Genes encoding eight Baeyer-Villiger monooxygenases have recently been cloned from bacteria inhabiting a wastewater treatment plant. We have carried out a systematic investigation in which each newly cloned enzyme, as well as the cyclohexanone monooxygenase from Acinetobacter sp. NCIB 9871, was used to oxidize 15 different alkyl-substituted cyclohexanones. The panel of substrates included equal numbers of 2-, 3-, and 4-alkyl-substituted compounds to probe each enzyme's stereoselectivity toward a homologous series of synthetically important compounds. For all 4-alkyl-substituted cyclohexanones tested, enzymes were discovered that afforded each of the corresponding (S)-lactones in >/=98% ee. This was also true for the 2-alkyl-substituted cyclohexanones examined. The situation was more complex for 3-akyl-substituted cyclohexanones. In a few cases, single Baeyer-Villiger monooxygenases possessed both high regio- and enantioselectivities toward these compounds. More commonly, however, they showed only one type of selectivity. Nonetheless, enzymes with such properties might be useful as parts of a two-step bioprocess where an initial kinetic resolution is followed by a regioselective oxidation on the isolated, optically pure ketone.
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Affiliation(s)
- Brian G Kyte
- 127 Chemistry Research Building, University of Florida, Gainesville, Florida 32611, USA
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