1
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Yang G, Pećanac O, Wijma HJ, Rozeboom HJ, de Gonzalo G, Fraaije MW, Mascotti ML. Evolution of the catalytic mechanism at the dawn of the Baeyer-Villiger monooxygenases. Cell Rep 2024; 43:114130. [PMID: 38640062 DOI: 10.1016/j.celrep.2024.114130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/15/2024] [Accepted: 04/04/2024] [Indexed: 04/21/2024] Open
Abstract
Enzymes are crucial for the emergence and sustenance of life on earth. How they became catalytically active during their evolution is still an open question. Two opposite explanations are plausible: acquiring a mechanism in a series of discrete steps or all at once in a single evolutionary event. Here, we use molecular phylogeny, ancestral sequence reconstruction, and biochemical characterization to follow the evolution of a specialized group of flavoprotein monooxygenases, the bacterial Baeyer-Villiger monooxygenases (BVMOs). These enzymes catalyze an intricate chemical reaction relying on three different elements: a reduced nicotinamide cofactor, dioxygen, and a substrate. Characterization of ancestral BVMOs shows that the catalytic mechanism evolved in a series of steps starting from a FAD-binding protein and further acquiring reactivity and specificity toward each of the elements participating in the reaction. Together, the results of our work portray how an intrinsically complex catalytic mechanism emerged during evolution.
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Affiliation(s)
- Guang Yang
- Molecular Enzymology Group, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Ognjen Pećanac
- Molecular Enzymology Group, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Hein J Wijma
- Molecular Enzymology Group, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Henriëtte J Rozeboom
- Molecular Enzymology Group, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Gonzalo de Gonzalo
- Departamento de Química Orgánica, Universidad de Sevilla, and Centro de Innovación en Química Avanzada (ORFEO-CINQA), 41012 Sevilla, Spain
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Maria Laura Mascotti
- Molecular Enzymology Group, University of Groningen, 9747 AG Groningen, the Netherlands; IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina.
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2
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Valotta A, Stelzer D, Reiter T, Kroutil W, Gruber-Woelfler H. A multistep (semi)-continuous biocatalytic setup for the production of polycaprolactone. REACT CHEM ENG 2024; 9:713-727. [PMID: 38433980 PMCID: PMC10903532 DOI: 10.1039/d3re00536d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/12/2023] [Indexed: 03/05/2024]
Abstract
Biocatalysis has gained increasing importance as an eco-friendly alternative for the production of bulk and fine chemicals. Within this paradigm, Baeyer Villiger monoxygenases (BVMOs) serve as enzymatic catalysts that provide a safe and sustainable route to the conventional synthesis of lactones, such as caprolactone, which is employed for the production of polycaprolactone (PCL), a biocompatible polymer for medicinal applications. In this work, we present a three-step, semi-continuous production of PCL using an entirely biocatalytic process, highlighting the merits of continuous manufacturing for enhancing biocatalysis. First, caprolactone is produced in batch from cyclohexanol using a coenzymatic cascade involving an alcohol dehydrogenase (ADH) and BVMO. Different process parameters and aeration modes were explored to optimize the cascade's productivity. Secondly, the continuous extraction of caprolactone into an organic solvent, needed for the polymerization step, was optimized. 3D-printed mixers were applied to enhance the mass transfer between the organic and the aqueous phases. Lastly, we investigated the ring-opening polymerization of caprolactone to PCL catalyzed by Candida antarctica lipase B (CAL-B), with a focus on eco-friendly solvents like cyclopentyl-methyl-ether (CPME). Space-time-yields up to 58.5 g L-1 h-1 were achieved with our overall setup. By optimizing the individual process steps, we present an efficient and sustainable pathway for PCL production.
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Affiliation(s)
- Alessia Valotta
- Institute of Process and Particle Engineering, Graz University of Technology Inffeldgasse 13 8010 Graz Austria
| | - Daniela Stelzer
- Institute of Process and Particle Engineering, Graz University of Technology Inffeldgasse 13 8010 Graz Austria
| | - Tamara Reiter
- Department of Chemistry, NAWI Graz, BioTechMed Graz, Field of Excellence BioHealth, University of Graz Heinrichstrasse 28 8010 Graz Austria
| | - Wolfgang Kroutil
- Department of Chemistry, NAWI Graz, BioTechMed Graz, Field of Excellence BioHealth, University of Graz Heinrichstrasse 28 8010 Graz Austria
| | - Heidrun Gruber-Woelfler
- Institute of Process and Particle Engineering, Graz University of Technology Inffeldgasse 13 8010 Graz Austria
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3
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Ding Y, Perez-Ortiz G, Peate J, Barry SM. Redesigning Enzymes for Biocatalysis: Exploiting Structural Understanding for Improved Selectivity. Front Mol Biosci 2022; 9:908285. [PMID: 35936784 PMCID: PMC9355150 DOI: 10.3389/fmolb.2022.908285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
The discovery of new enzymes, alongside the push to make chemical processes more sustainable, has resulted in increased industrial interest in the use of biocatalytic processes to produce high-value and chiral precursor chemicals. Huge strides in protein engineering methodology and in silico tools have facilitated significant progress in the discovery and production of enzymes for biocatalytic processes. However, there are significant gaps in our knowledge of the relationship between enzyme structure and function. This has demonstrated the need for improved computational methods to model mechanisms and understand structure dynamics. Here, we explore efforts to rationally modify enzymes toward changing aspects of their catalyzed chemistry. We highlight examples of enzymes where links between enzyme function and structure have been made, thus enabling rational changes to the enzyme structure to give predictable chemical outcomes. We look at future directions the field could take and the technologies that will enable it.
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4
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Programmable chemical actuator control of soluble and membrane-bound enzymatic catalysis. Methods Enzymol 2022; 676:159-194. [DOI: 10.1016/bs.mie.2022.07.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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5
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Sun Z, Zhao Q, Haag R, Wu C. Chemoenzymatic Cascades Enabled by Combining Catalytically Active Emulsions and Biocatalysts. ChemCatChem 2021. [DOI: 10.1002/cctc.202101556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Zhiyong Sun
- University of Southern Denmark: Syddansk Universitet Department of Physic, Chemistry and Pharmacy DENMARK
| | - Qingcai Zhao
- Freie Universität Berlin: Freie Universitat Berlin Institute fur Chemie und Biochemie GERMANY
| | - Rainer Haag
- Freie Universität Berlin: Freie Universitat Berlin Institut fur Chemie und Biochemie Takustraße 3 14195 Berlin GERMANY
| | - Changzhu Wu
- University of Southern Denmark Department of Physics, Chemistry and Pharmacy Campusvej 555230Denmark 5230 Odense M DENMARK
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6
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Stamm A, Öhlin J, Mosbech C, Olsén P, Guo B, Söderberg E, Biundo A, Fogelström L, Bhattacharyya S, Bornscheuer UT, Malmström E, Syrén PO. Pinene-Based Oxidative Synthetic Toolbox for Scalable Polyester Synthesis. JACS AU 2021; 1:1949-1960. [PMID: 34849510 PMCID: PMC8620555 DOI: 10.1021/jacsau.1c00312] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Indexed: 05/27/2023]
Abstract
Generation of renewable polymers is a long-standing goal toward reaching a more sustainable society, but building blocks in biomass can be incompatible with desired polymerization type, hampering the full implementation potential of biomaterials. Herein, we show how conceptually simple oxidative transformations can be used to unlock the inherent reactivity of terpene synthons in generating polyesters by two different mechanisms starting from the same α-pinene substrate. In the first pathway, α-pinene was oxidized into the bicyclic verbanone-based lactone and subsequently polymerized into star-shaped polymers via ring-opening polymerization, resulting in a biobased semicrystalline polyester with tunable glass transition and melting temperatures. In a second pathway, polyesters were synthesized via polycondensation, utilizing the diol 1-(1'-hydroxyethyl)-3-(2'-hydroxy-ethyl)-2,2-dimethylcyclobutane (HHDC) synthesized by oxidative cleavage of the double bond of α-pinene, together with unsaturated biobased diesters such as dimethyl maleate (DMM) and dimethyl itaconate (DMI). The resulting families of terpene-based polyesters were thereafter successfully cross-linked by either transetherification, utilizing the terminal hydroxyl groups of the synthesized verbanone-based materials, or by UV irradiation, utilizing the unsaturation provided by the DMM or DMI moieties within the HHDC-based copolymers. This work highlights the potential to apply an oxidative toolbox to valorize inert terpene metabolites enabling generation of biosourced polyesters and coatings thereof by complementary mechanisms.
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Affiliation(s)
- Arne Stamm
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Department
of Fibre and Polymer Technology, Division of Coating Technology, KTH Royal Institute of Technology, Teknikringen 56-58, SE-100 44 Stockholm, Sweden
| | - Johannes Öhlin
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Department
of Fibre and Polymer Technology, Division of Coating Technology, KTH Royal Institute of Technology, Teknikringen 56-58, SE-100 44 Stockholm, Sweden
| | - Caroline Mosbech
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Department
of Fibre and Polymer Technology, Division of Coating Technology, KTH Royal Institute of Technology, Teknikringen 56-58, SE-100 44 Stockholm, Sweden
| | - Peter Olsén
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Department
of Fibre and Polymer Technology, Division of Coating Technology, KTH Royal Institute of Technology, Teknikringen 56-58, SE-100 44 Stockholm, Sweden
| | - Boyang Guo
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Science
for Life Laboratory, KTH Royal Institute
of Technology, Tomtebodavägen
23, Box 1031, SE-171 21 Solna, Sweden
| | - Elisabeth Söderberg
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Science
for Life Laboratory, KTH Royal Institute
of Technology, Tomtebodavägen
23, Box 1031, SE-171 21 Solna, Sweden
| | - Antonino Biundo
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Science
for Life Laboratory, KTH Royal Institute
of Technology, Tomtebodavägen
23, Box 1031, SE-171 21 Solna, Sweden
| | - Linda Fogelström
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Department
of Fibre and Polymer Technology, Division of Coating Technology, KTH Royal Institute of Technology, Teknikringen 56-58, SE-100 44 Stockholm, Sweden
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Department
of Fibre and Polymer Technology, Wallenberg Wood Science Center, KTH Royal Institute of Technology, Teknikringen 56-58, Stockholm SE-100 44 Sweden
| | | | - Uwe T. Bornscheuer
- Department
of Biotechnology and Enzyme Catalysis, University
of Greifswald, Institute of Biochemistry, Felix-Hausdorff-Strasse 4, 17487 Greifswald, Germany
| | - Eva Malmström
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Department
of Fibre and Polymer Technology, Division of Coating Technology, KTH Royal Institute of Technology, Teknikringen 56-58, SE-100 44 Stockholm, Sweden
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Department
of Fibre and Polymer Technology, Wallenberg Wood Science Center, KTH Royal Institute of Technology, Teknikringen 56-58, Stockholm SE-100 44 Sweden
| | - Per-Olof Syrén
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Department
of Fibre and Polymer Technology, Division of Coating Technology, KTH Royal Institute of Technology, Teknikringen 56-58, SE-100 44 Stockholm, Sweden
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Science
for Life Laboratory, KTH Royal Institute
of Technology, Tomtebodavägen
23, Box 1031, SE-171 21 Solna, Sweden
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Department
of Fibre and Polymer Technology, Wallenberg Wood Science Center, KTH Royal Institute of Technology, Teknikringen 56-58, Stockholm SE-100 44 Sweden
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7
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Leferink NGH, Scrutton NS. Predictive Engineering of Class I Terpene Synthases Using Experimental and Computational Approaches. Chembiochem 2021; 23:e202100484. [PMID: 34669250 PMCID: PMC9298401 DOI: 10.1002/cbic.202100484] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/15/2021] [Indexed: 12/18/2022]
Abstract
Terpenoids are a highly diverse group of natural products with considerable industrial interest. Increasingly, engineered microbes are used for the production of terpenoids to replace natural extracts and chemical synthesis. Terpene synthases (TSs) show a high level of functional plasticity and are responsible for the vast structural diversity observed in natural terpenoids. Their relatively inert active sites guide intrinsically reactive linear carbocation intermediates along one of many cyclisation paths via exertion of subtle steric and electrostatic control. Due to the absence of a strong protein interaction with these intermediates, there is a remarkable lack of sequence‐function relationship within the TS family, making product‐outcome predictions from sequences alone challenging. This, in combination with the fact that many TSs produce multiple products from a single substrate hampers the design and use of TSs in the biomanufacturing of terpenoids. This review highlights recent advances in genome mining, computational modelling, high‐throughput screening, and machine‐learning that will allow more predictive engineering of these fascinating enzymes in the near future.
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Affiliation(s)
- Nicole G H Leferink
- Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Nigel S Scrutton
- Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
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8
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Abstract
Baeyer–Villiger monooxygenases (BVMOs) are flavin-dependent oxidative enzymes capable of catalyzing the insertion of an oxygen atom between a carbonylic Csp2 and the Csp3 at the alpha position, therefore transforming linear and cyclic ketones into esters and lactones. These enzymes are dependent on nicotinamides (NAD(P)H) for the flavin reduction and subsequent reaction with molecular oxygen. BVMOs can be included in cascade reactions, coupled to other redox enzymes, such as alcohol dehydrogenases (ADHs) or ene-reductases (EREDs), so that the direct conversion of alcohols or α,β-unsaturated carbonylic compounds to the corresponding esters can be achieved. In the present review, the different synthetic methodologies that have been performed by employing multienzymatic strategies with BVMOs combining whole cells or isolated enzymes, through sequential or parallel methods, are described, with the aim of highlighting the advantages of performing multienzymatic systems, and show the recent advances for overcoming the drawbacks of using BVMOs in these techniques.
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9
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Paul CE, Eggerichs D, Westphal AH, Tischler D, van Berkel WJH. Flavoprotein monooxygenases: Versatile biocatalysts. Biotechnol Adv 2021; 51:107712. [PMID: 33588053 DOI: 10.1016/j.biotechadv.2021.107712] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/27/2021] [Accepted: 02/06/2021] [Indexed: 12/13/2022]
Abstract
Flavoprotein monooxygenases (FPMOs) are single- or two-component enzymes that catalyze a diverse set of chemo-, regio- and enantioselective oxyfunctionalization reactions. In this review, we describe how FPMOs have evolved from model enzymes in mechanistic flavoprotein research to biotechnologically relevant catalysts that can be applied for the sustainable production of valuable chemicals. After a historical account of the development of the FPMO field, we explain the FPMO classification system, which is primarily based on protein structural properties and electron donor specificities. We then summarize the most appealing reactions catalyzed by each group with a focus on the different types of oxygenation chemistries. Wherever relevant, we report engineering strategies that have been used to improve the robustness and applicability of FPMOs.
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Affiliation(s)
- Caroline E Paul
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Daniel Eggerichs
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dirk Tischler
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands.
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10
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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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11
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Figueiredo PR, Almeida BC, Dourado DFAR, Sousa AF, Silvestre AJD, Carvalho ATP. Enzymatic Synthesis of Poly(caprolactone): A QM/MM Study. ChemCatChem 2020. [DOI: 10.1002/cctc.202000780] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Pedro R. Figueiredo
- CNC – Center for Neuroscience and Cell Biology Institute for Interdisciplinary Research (IIIUC) University of Coimbra 3004-504 Coimbra Portugal
| | - Beatriz C. Almeida
- CNC – Center for Neuroscience and Cell Biology Institute for Interdisciplinary Research (IIIUC) University of Coimbra 3004-504 Coimbra Portugal
| | - Daniel F. A. R. Dourado
- Almac Sciences Department of Biocatalysis and Isotope Chemistry Almac House 20 Seagoe Industrial Estate Craigavon BT63 5QD Northern Ireland UK
| | | | | | - Alexandra T. P. Carvalho
- CNC – Center for Neuroscience and Cell Biology Institute for Interdisciplinary Research (IIIUC) University of Coimbra 3004-504 Coimbra Portugal
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12
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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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13
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Farhat W, Biundo A, Stamm A, Malmström E, Syrén P. Lactone monomers obtained by enzyme catalysis and their use in reversible thermoresponsive networks. J Appl Polym Sci 2020. [DOI: 10.1002/app.48949] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Wissam Farhat
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer TechnologyKTH Royal Institute of Technology Teknikringen 56‐58, 100 44 Stockholm Sweden
- Science for Life Laboratory, Division of Protein TechnologyKTH Royal Institute of Technology Tomtebodavägen 23, Box 1031, 171 21 Solna Stockholm Sweden
| | - Antonino Biundo
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer TechnologyKTH Royal Institute of Technology Teknikringen 56‐58, 100 44 Stockholm Sweden
- Science for Life Laboratory, Division of Protein TechnologyKTH Royal Institute of Technology Tomtebodavägen 23, Box 1031, 171 21 Solna Stockholm Sweden
| | - Arne Stamm
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer TechnologyKTH Royal Institute of Technology Teknikringen 56‐58, 100 44 Stockholm Sweden
- Science for Life Laboratory, Division of Protein TechnologyKTH Royal Institute of Technology Tomtebodavägen 23, Box 1031, 171 21 Solna Stockholm Sweden
| | - Eva Malmström
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer TechnologyKTH Royal Institute of Technology Teknikringen 56‐58, 100 44 Stockholm Sweden
- Wallenberg Wood Science CenterKTH Royal Institute of Technology Teknikringen 56‐58, 100 44 Stockholm Sweden
| | - Per‐Olof Syrén
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer TechnologyKTH Royal Institute of Technology Teknikringen 56‐58, 100 44 Stockholm Sweden
- Science for Life Laboratory, Division of Protein TechnologyKTH Royal Institute of Technology Tomtebodavägen 23, Box 1031, 171 21 Solna Stockholm Sweden
- Wallenberg Wood Science CenterKTH Royal Institute of Technology Teknikringen 56‐58, 100 44 Stockholm Sweden
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14
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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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15
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Howe GW, van der Donk WA. Temperature-Independent Kinetic Isotope Effects as Evidence for a Marcus-like Model of Hydride Tunneling in Phosphite Dehydrogenase. Biochemistry 2019; 58:4260-4268. [PMID: 31535852 PMCID: PMC6852621 DOI: 10.1021/acs.biochem.9b00732] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Phosphite dehydrogenase catalyzes the transfer of a hydride from phosphite to NAD+, producing phosphate and NADH. We have evaluated the role of hydride tunneling in a thermostable variant of this enzyme (17X-PTDH) by measuring the temperature dependence of the primary 2H kinetic isotope effects (KIEs) between 5 and 45 °C. Pre-steady-state kinetic measurements were used to demonstrate that the hydride transfer is rate-determining across this temperature range and that the observed KIEs are equal to the intrinsic isotope effect on the chemical step. The KIEs on the pre-exponential factor (AH/AD) and the activation energy (ΔEa) were 1.6 ± 0.1 and 0.21 ± 0.05 kcal/mol, respectively, suggesting that 17X-PTDH facilitates extensive tunneling of both isotopes via a Marcus-like model. Site-directed mutagenesis was used to evaluate the role of an active site threonine (Thr104) found on the back face of the nicotinamide in promoting the close packing of the substrates. In mutants with reduced steric bulk at this position, values of AH/AD and ΔEa fall within the range describing semiclassical "over the barrier" reactivity, suggesting that Thr104 acts as a steric backstop to promote tunneling in 17X-PTDH. Whereas hydrogen tunneling is now a widely appreciated feature of C-H activating enzymes, these observations with a P-H activating system are consistent with the proposal that tunneling is likely to be a common feature on all enzymes that catalyze hydrogen transfers.
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Affiliation(s)
- Graeme W Howe
- Department of Chemistry , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States.,Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , 1206 West Gregory Drive , Urbana , Illinois 61801 , United States
| | - Wilfred A van der Donk
- Department of Chemistry , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States.,Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , 1206 West Gregory Drive , Urbana , Illinois 61801 , United States.,Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , 1206 West Gregory Drive , Urbana , Illinois 61801 , United States
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16
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Toplishek M, Žagar E, Pahovnik D. Synthesis of dicyano-substituted ε-caprolactone and its (co)polymers. Eur Polym J 2019. [DOI: 10.1016/j.eurpolymj.2019.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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17
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Busch H, Hagedoorn PL, Hanefeld U. Rhodococcus as A Versatile Biocatalyst in Organic Synthesis. Int J Mol Sci 2019; 20:E4787. [PMID: 31561555 PMCID: PMC6801914 DOI: 10.3390/ijms20194787] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 12/11/2022] Open
Abstract
The application of purified enzymes as well as whole-cell biocatalysts in synthetic organic chemistry is becoming more and more popular, and both academia and industry are keen on finding and developing novel enzymes capable of performing otherwise impossible or challenging reactions. The diverse genus Rhodococcus offers a multitude of promising enzymes, which therefore makes it one of the key bacterial hosts in many areas of research. This review focused on the broad utilization potential of the genus Rhodococcus in organic chemistry, thereby particularly highlighting the specific enzyme classes exploited and the reactions they catalyze. Additionally, close attention was paid to the substrate scope that each enzyme class covers. Overall, a comprehensive overview of the applicability of the genus Rhodococcus is provided, which puts this versatile microorganism in the spotlight of further research.
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Affiliation(s)
- Hanna Busch
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Peter-Leon Hagedoorn
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Ulf Hanefeld
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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18
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Farhat W, Stamm A, Robert-Monpate M, Biundo A, Syrén PO. Biocatalysis for terpene-based polymers. ACTA ACUST UNITED AC 2019; 74:91-100. [PMID: 30789828 DOI: 10.1515/znc-2018-0199] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/24/2019] [Indexed: 12/11/2022]
Abstract
Accelerated generation of bio-based materials is vital to replace current synthetic polymers obtained from petroleum with more sustainable options. However, many building blocks available from renewable resources mainly contain unreactive carbon-carbon bonds, which obstructs their efficient polymerization. Herein, we highlight the potential of applying biocatalysis to afford tailored functionalization of the inert carbocyclic core of multicyclic terpenes toward advanced materials. As a showcase, we unlock the inherent monomer reactivity of norcamphor, a bicyclic ketone used as a monoterpene model system in this study, to afford polyesters with unprecedented backbones. The efficiencies of the chemical and enzymatic Baeyer-Villiger transformation in generating key lactone intermediates are compared. The concepts discussed herein are widely applicable for the valorization of terpenes and other cyclic building blocks using chemoenzymatic strategies.
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Affiliation(s)
- Wissam Farhat
- Department of Fibre and Polymer Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Teknikringen 56-58, 100 44 Stockholm, Sweden.,Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Tomtebodavägen 23, Box 1031, 171 21 Solna, Stockholm, Sweden
| | - Arne Stamm
- Department of Fibre and Polymer Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Teknikringen 56-58, 100 44 Stockholm, Sweden.,Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Tomtebodavägen 23, Box 1031, 171 21 Solna, Stockholm, Sweden
| | - Maxime Robert-Monpate
- Department of Fibre and Polymer Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Teknikringen 56-58, 100 44 Stockholm, Sweden.,Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Tomtebodavägen 23, Box 1031, 171 21 Solna, Stockholm, Sweden
| | - Antonino Biundo
- Department of Fibre and Polymer Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Teknikringen 56-58, 100 44 Stockholm, Sweden.,Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Tomtebodavägen 23, Box 1031, 171 21 Solna, Stockholm, Sweden
| | - Per-Olof Syrén
- Department of Fibre and Polymer Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Teknikringen 56-58, 100 44 Stockholm, Sweden.,Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Tomtebodavägen 23, Box 1031, 171 21 Solna, Stockholm, Sweden.,Wallenberg Wood Science Center, Teknikringen 56-58, SE-100 44 Stockholm, Sweden
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19
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Roberts AD, Finnigan W, Wolde-Michael E, Kelly P, Blaker JJ, Hay S, Breitling R, Takano E, Scrutton NS. Synthetic biology for fibres, adhesives and active camouflage materials in protection and aerospace. MRS COMMUNICATIONS 2019; 9:486-504. [PMID: 31281737 PMCID: PMC6609449 DOI: 10.1557/mrc.2019.35] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/12/2019] [Indexed: 05/03/2023]
Abstract
Synthetic biology has huge potential to produce the next generation of advanced materials by accessing previously unreachable (bio)chemical space. In this prospective review, we take a snapshot of current activity in this rapidly developing area, focussing on prominent examples for high-performance applications such as those required for protective materials and the aerospace sector. The continued growth of this emerging field will be facilitated by the convergence of expertise from a range of diverse disciplines, including molecular biology, polymer chemistry, materials science and process engineering. This review highlights the most significant recent advances and address the cross-disciplinary challenges currently being faced.
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Affiliation(s)
- Aled D. Roberts
- Manchester Institute of Biotechnology, Manchester Synthetic Biology
Research Centre SYBIOCHEM, School of Chemistry, The University of Manchester,
Manchester, UK, M1 7DN
- Bio-Active Materials Group, School of Materials, The University of
Manchester, Manchester, UK, M13 9PL
| | - William Finnigan
- Manchester Institute of Biotechnology, Manchester Synthetic Biology
Research Centre SYBIOCHEM, School of Chemistry, The University of Manchester,
Manchester, UK, M1 7DN
| | - Emmanuel Wolde-Michael
- Manchester Institute of Biotechnology, Manchester Synthetic Biology
Research Centre SYBIOCHEM, School of Chemistry, The University of Manchester,
Manchester, UK, M1 7DN
| | - Paul Kelly
- Manchester Institute of Biotechnology, Manchester Synthetic Biology
Research Centre SYBIOCHEM, School of Chemistry, The University of Manchester,
Manchester, UK, M1 7DN
| | - Jonny J. Blaker
- Bio-Active Materials Group, School of Materials, The University of
Manchester, Manchester, UK, M13 9PL
| | - Sam Hay
- Manchester Institute of Biotechnology, Manchester Synthetic Biology
Research Centre SYBIOCHEM, School of Chemistry, The University of Manchester,
Manchester, UK, M1 7DN
| | - Rainer Breitling
- Manchester Institute of Biotechnology, Manchester Synthetic Biology
Research Centre SYBIOCHEM, School of Chemistry, The University of Manchester,
Manchester, UK, M1 7DN
| | - Eriko Takano
- Manchester Institute of Biotechnology, Manchester Synthetic Biology
Research Centre SYBIOCHEM, School of Chemistry, The University of Manchester,
Manchester, UK, M1 7DN
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology, Manchester Synthetic Biology
Research Centre SYBIOCHEM, School of Chemistry, The University of Manchester,
Manchester, UK, M1 7DN
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20
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Chemo-enzymatic routes towards the synthesis of bio-based monomers and polymers. MOLECULAR CATALYSIS 2019. [DOI: 10.1016/j.mcat.2019.01.036] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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21
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Recent preparative applications of redox enzymes. Curr Opin Chem Biol 2019; 49:105-112. [DOI: 10.1016/j.cbpa.2018.11.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/12/2018] [Accepted: 11/13/2018] [Indexed: 01/02/2023]
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22
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Ascue Avalos GA, Toogood HS, Tait S, Messiha HL, Scrutton NS. From Bugs to Bioplastics: Total (+)-Dihydrocarvide Biosynthesis by Engineered Escherichia coli. Chembiochem 2019; 20:785-792. [PMID: 30431225 PMCID: PMC6850611 DOI: 10.1002/cbic.201800606] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Indexed: 11/15/2022]
Abstract
The monoterpenoid lactone derivative (+)-dihydrocarvide ((+)-DHCD) can be polymerised to form shape-memory polymers. Synthetic biology routes from simple, inexpensive carbon sources are an attractive, alternative route over chemical synthesis from (R)-carvone. We have demonstrated a proof-of-principle in vivo approach for the complete biosynthesis of (+)-DHCD from glucose in Escherichia coli (6.6 mg L-1 ). The pathway is based on the Mentha spicata route to (R)-carvone, with the addition of an 'ene'-reductase and Baeyer-Villiger cyclohexanone monooxygenase. Co-expression with a limonene synthesis pathway enzyme enables complete biocatalytic production within one microbial chassis. (+)-DHCD was successfully produced by screening multiple homologues of the pathway genes, combined with expression optimisation by selective promoter and/or ribosomal binding-site screening. This study demonstrates the potential application of synthetic biology approaches in the development of truly sustainable and renewable bioplastic monomers.
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Affiliation(s)
- Gabriel A. Ascue Avalos
- School of ChemistryFaculty of Science and EngineeringUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Helen S. Toogood
- School of ChemistryFaculty of Science and EngineeringUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Shirley Tait
- School of ChemistryFaculty of Science and EngineeringUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Hanan L. Messiha
- School of ChemistryFaculty of Science and EngineeringUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Nigel S. Scrutton
- School of ChemistryFaculty of Science and EngineeringUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
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23
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What to sacrifice? Fusions of cofactor regenerating enzymes with Baeyer-Villiger monooxygenases and alcohol dehydrogenases for self-sufficient redox biocatalysis. Tetrahedron 2019. [DOI: 10.1016/j.tet.2019.02.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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24
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Issa IS, Toogood HS, Johannissen LO, Raftery J, Scrutton NS, Gardiner JM. C3 and C6 Modification-Specific OYE Biotransformations of Synthetic Carvones and Sequential BVMO Chemoenzymatic Synthesis of Chiral Caprolactones. Chemistry 2019; 25:2983-2988. [PMID: 30468546 PMCID: PMC6468273 DOI: 10.1002/chem.201805219] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/21/2018] [Indexed: 11/06/2022]
Abstract
The scope for biocatalytic modification of non-native carvone derivatives for speciality intermediates has hitherto been limited. Additionally, caprolactones are important feedstocks with diverse applications in the polymer industry and new non-native terpenone-derived biocatalytic caprolactone syntheses are thus of potential value for industrial biocatalytic materials applications. Biocatalytic reduction of synthetic analogues of R-(-)-carvone with additional substituents at C3 or C6, or both C3 and C6, using three types of OYEs (OYE2, PETNR and OYE3) shows significant impact of both regio-substitution and the substrate diastereomer. Bioreduction of (-)-carvone derivatives substituted with a Me and/or OH group at C6 is highly dependent on the diastereomer of the substrate. Derivatives bearing C6 substituents larger than methyl moieties are not substrates. Computer docking studies of PETNR with both (6S)-Me and (6R)-Me substituted (-)-carvone provides a model consistent with the outcomes of bioconversion. The products of bioreduction were efficiently biotransformed by the Baeyer-Villiger monooxygenase (BVase) CHMO_Phi1 to afford novel trisubstituted lactones with complete regioselectivity to provide a new biocatalytic entry to these chiral caprolactones. This provides both new non-native polymerization feedstock chemicals, but also with enhanced efficiency and selectivity over native (+)-dihydrocarvone Baeyer-Villigerase expansion. Optimum enzymatic reactions were scaled up to 60-100 mg, demonstrating the utility for preparative biocatalytic synthesis of both new synthetic scaffold-modified dihydrocarvones and efficient biocatalytic entry to new chiral caprolactones, which are potential single-isomer chiral polymer feedstocks.
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Affiliation(s)
- Issa S. Issa
- Manchester Institute of Biotechnology and the School of ChemistryThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Helen S. Toogood
- BBSRC/EPSRC Manchester Synthetic Biology Research Centre, for Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and the School of ChemistryThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Linus O. Johannissen
- BBSRC/EPSRC Manchester Synthetic Biology Research Centre, for Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and the School of ChemistryThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - James Raftery
- Manchester Institute of Biotechnology and the School of ChemistryThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Nigel S. Scrutton
- BBSRC/EPSRC Manchester Synthetic Biology Research Centre, for Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and the School of ChemistryThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - John M. Gardiner
- Manchester Institute of Biotechnology and the School of ChemistryThe University of Manchester131 Princess StreetManchesterM1 7DNUK
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25
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Mattioli EJ, Bottoni A, Calvaresi M. DNAzymes at Work: A DFT Computational Investigation on the Mechanism of 9DB1. J Chem Inf Model 2019; 59:1547-1553. [DOI: 10.1021/acs.jcim.8b00815] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Edoardo Jun Mattioli
- Dipartimento di Chimica “G. Ciamician”, Alma Mater Studiorum - Università di Bologna, V. F. Selmi 2, 40126 Bologna, Italy
| | - Andrea Bottoni
- Dipartimento di Chimica “G. Ciamician”, Alma Mater Studiorum - Università di Bologna, V. F. Selmi 2, 40126 Bologna, Italy
| | - Matteo Calvaresi
- Dipartimento di Chimica “G. Ciamician”, Alma Mater Studiorum - Università di Bologna, V. F. Selmi 2, 40126 Bologna, Italy
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26
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Jervis AJ, Carbonell P, Vinaixa M, Dunstan MS, Hollywood KA, Robinson CJ, Rattray NJW, Yan C, Swainston N, Currin A, Sung R, Toogood H, Taylor S, Faulon JL, Breitling R, Takano E, Scrutton NS. Machine Learning of Designed Translational Control Allows Predictive Pathway Optimization in Escherichia coli. ACS Synth Biol 2019; 8:127-136. [PMID: 30563328 DOI: 10.1021/acssynbio.8b00398] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The field of synthetic biology aims to make the design of biological systems predictable, shrinking the huge design space to practical numbers for testing. When designing microbial cell factories, most optimization efforts have focused on enzyme and strain selection/engineering, pathway regulation, and process development. In silico tools for the predictive design of bacterial ribosome binding sites (RBSs) and RBS libraries now allow translational tuning of biochemical pathways; however, methods for predicting optimal RBS combinations in multigene pathways are desirable. Here we present the implementation of machine learning algorithms to model the RBS sequence-phenotype relationship from representative subsets of large combinatorial RBS libraries allowing the accurate prediction of optimal high-producers. Applied to a recombinant monoterpenoid production pathway in Escherichia coli, our approach was able to boost production titers by over 60% when screening under 3% of a library. To facilitate library screening, a multiwell plate fermentation procedure was developed, allowing increased screening throughput with sufficient resolution to discriminate between high and low producers. High producers from one library did not translate during scale-up, but the reduced screening requirements allowed rapid rescreening at the larger scale. This methodology is potentially compatible with any biochemical pathway and provides a powerful tool toward predictive design of bacterial production chassis.
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Affiliation(s)
- Adrian J. Jervis
- Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Pablo Carbonell
- Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Maria Vinaixa
- Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Mark S. Dunstan
- Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Katherine A. Hollywood
- Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Christopher J. Robinson
- Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Nicholas J. W. Rattray
- Strathclyde Institute of Pharmacy and Biomedical Sciences, Strathclyde University, 161 Cathedral Street, Glasgow G4 0RE, United Kingdom
| | - Cunyu Yan
- Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Neil Swainston
- Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Andrew Currin
- Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Rehana Sung
- Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Helen Toogood
- Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Sandra Taylor
- Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Jean-Loup Faulon
- Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
- MICALIS, INRA-AgroParisTech, Domaine de Vilvert, 78352 Jouy en Josas Cedex, France
| | - Rainer Breitling
- Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Eriko Takano
- Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Nigel S. Scrutton
- Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
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27
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Howe GW, van der Donk WA. 18O Kinetic Isotope Effects Reveal an Associative Transition State for Phosphite Dehydrogenase Catalyzed Phosphoryl Transfer. J Am Chem Soc 2018; 140:17820-17824. [PMID: 30525552 DOI: 10.1021/jacs.8b06301] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Phosphite dehydrogenase (PTDH) catalyzes an unusual phosphoryl transfer reaction in which water displaces a hydride leaving group. Despite extensive effort, it remains unclear whether PTDH catalysis proceeds via an associative or dissociative mechanism. Here, primary 2H and secondary 18O kinetic isotope effects (KIEs) were determined and used together with computation to characterize the transition state (TS) catalyzed by a thermostable PTDH (17X-PTDH). The large, normal 18O KIEs suggest an associative mechanism. Various transition state structures were computed within a model of the enzyme active site and 2H and 18O KIEs were predicted to evaluate the accuracy of each TS. This analysis suggests that 17X-PTDH catalyzes an associative process with little leaving group displacement and extensive nucleophilic participation. This tight TS is likely a consequence of the extremely poor leaving group requiring significant P-O bond formation to expel the hydride. This finding contrasts with the dissociative TSs in most phosphoryl transfer reactions from phosphate mono- and diesters.
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Affiliation(s)
- Graeme W Howe
- Department of Chemistry , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States.,Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , 1206 West Gregory Drive , Urbana , Illinois 61801 , United States
| | - Wilfred A van der Donk
- Department of Chemistry , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States.,Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , 1206 West Gregory Drive , Urbana , Illinois 61801 , United States.,Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , 1206 West Gregory Drive , Urbana , Illinois 61801 , United States
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28
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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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29
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Bistoni G, Polyak I, Sparta M, Thiel W, Neese F. Toward Accurate QM/MM Reaction Barriers with Large QM Regions Using Domain Based Pair Natural Orbital Coupled Cluster Theory. J Chem Theory Comput 2018; 14:3524-3531. [DOI: 10.1021/acs.jctc.8b00348] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Giovanni Bistoni
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz, D-45470 Mülheim an der Ruhr, Germany
| | - Iakov Polyak
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz, D-45470 Mülheim an der Ruhr, Germany
| | - Manuel Sparta
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz, D-45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz, D-45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz, D-45470 Mülheim an der Ruhr, Germany
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