1
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Mukhopadhyay A, Karu K, Dalby PA. Two-substrate enzyme engineering using small libraries that combine the substrate preferences from two different variant lineages. Sci Rep 2024; 14:1287. [PMID: 38218974 PMCID: PMC10787763 DOI: 10.1038/s41598-024-51831-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024] Open
Abstract
Improving the range of substrates accepted by enzymes with high catalytic activity remains an important goal for the industrialisation of biocatalysis. Many enzymes catalyse two-substrate reactions which increases the complexity in engineering them for the synthesis of alternative products. Often mutations are found independently that can improve the acceptance of alternatives to each of the two substrates. Ideally, we would be able to combine mutations identified for each of the two alternative substrates, and so reprogramme new enzyme variants that synthesise specific products from their respective two-substrate combinations. However, as we have previously observed for E. coli transketolase, the mutations that improved activity towards aromatic acceptor aldehydes, did not successfully recombine with mutations that switched the donor substrate to pyruvate. This likely results from several active site residues having multiple roles that can affect both of the substrates, as well as structural interactions between the mutations themselves. Here, we have designed small libraries, including both natural and non-natural amino acids, based on the previous mutational sites that impact on acceptance of the two substrates, to achieve up to 630× increases in kcat for the reaction with 3-formylbenzoic acid (3-FBA) and pyruvate. Computational docking was able to determine how the mutations shaped the active site to improve the proximity of the 3-FBA substrate relative to the enamine-TPP intermediate, formed after the initial reaction with pyruvate. This work opens the way for small libraries to rapidly reprogramme enzyme active sites in a plug and play approach to catalyse new combinations of two-substrate reactions.
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Affiliation(s)
- Arka Mukhopadhyay
- Department of Biochemical Engineering, UCL, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK
| | - Kersti Karu
- Department of Chemistry, UCL, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Paul A Dalby
- Department of Biochemical Engineering, UCL, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK.
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2
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Casajus H, Lagarde A, Nauton L, Ocal N, Leremboure M, Fessner WD, Duguet N, Charmantray F, Hecquet L. Cleavage of Aliphatic α-Hydroxy Ketones by Evolved Transketolase from Geobacillus stearothermophilus. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hubert Casajus
- Université Clermont Auvergne, CNRS, Clermont INP, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
| | - Aurélie Lagarde
- Université Clermont Auvergne, CNRS, Clermont INP, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
| | - Lionel Nauton
- Université Clermont Auvergne, CNRS, Clermont INP, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
| | - Nazim Ocal
- Université Clermont Auvergne, CNRS, Clermont INP, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
| | - Martin Leremboure
- Université Clermont Auvergne, CNRS, Clermont INP, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
| | - Wolf-Dieter Fessner
- Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, 64287 Darmstadt, Germany
| | - Nicolas Duguet
- Univ Lyon, Université Claude-Bernard Lyon 1, CNRS, INSA-Lyon, CPE-Lyon, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS), F-69100 Villeurbanne, France
| | - Franck Charmantray
- Université Clermont Auvergne, CNRS, Clermont INP, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
| | - Laurence Hecquet
- Université Clermont Auvergne, CNRS, Clermont INP, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
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3
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Morris P, García-Arrazola R, Rios-Solis L, Dalby PA. Biophysical characterization of the inactivation of E. coli transketolase by aqueous co-solvents. Sci Rep 2021; 11:23584. [PMID: 34880340 PMCID: PMC8654844 DOI: 10.1038/s41598-021-03001-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/24/2021] [Indexed: 11/09/2022] Open
Abstract
Transketolase (TK) has been previously engineered, using semi-rational directed evolution and substrate walking, to accept increasingly aliphatic, cyclic, and then aromatic substrates. This has ultimately led to the poor water solubility of new substrates, as a potential bottleneck to further exploitation of this enzyme in biocatalysis. Here we used a range of biophysical studies to characterise the response of both E. coli apo- and holo-TK activity and structure to a range of polar organic co-solvents: acetonitrile (AcCN), n-butanol (nBuOH), ethyl acetate (EtOAc), isopropanol (iPrOH), and tetrahydrofuran (THF). The mechanism of enzyme deactivation was found to be predominantly via solvent-induced local unfolding. Holo-TK is thermodynamically more stable than apo-TK and yet for four of the five co-solvents it retained less activity than apo-TK after exposure to organic solvents, indicating that solvent tolerance was not simply correlated to global conformational stability. The co-solvent concentrations required for complete enzyme inactivation was inversely proportional to co-solvent log(P), while the unfolding rate was directly proportional, indicating that the solvents interact with and partially unfold the enzyme through hydrophobic contacts. Small amounts of aggregate formed in some cases, but this was not sufficient to explain the enzyme inactivation. TK was found to be tolerant to 15% (v/v) iPrOH, 10% (v/v) AcCN, or 6% (v/v) nBuOH over 3 h. This work indicates that future attempts to engineer the enzyme to better tolerate co-solvents should focus on increasing the stability of the protein to local unfolding, particularly in and around the cofactor-binding loops.
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Affiliation(s)
- Phattaraporn Morris
- Department of Biochemical Engineering, University College London, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK
- Chemical Metrology and Biometry Department, National Institute of Metrology, 3/4-5 Moo 3, Klong 5, Klong Luang, 12120, Pathumthani, Thailand
| | - Ribia García-Arrazola
- Department of Biochemical Engineering, University College London, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh, EH9 3JL, UK
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, King's Buildings, Edinburgh, EH9 3JL, UK
| | - Paul A Dalby
- Department of Biochemical Engineering, University College London, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK.
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4
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Fúster Fernández I, Hecquet L, Fessner W. Transketolase Catalyzed Synthesis of
N
‐Aryl Hydroxamic Acids. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202101100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Inés Fúster Fernández
- Institut für Organische Chemie und Biochemie Technische Universität Darmstadt Alarich-Weiss-Str. 4 64287 Darmstadt Germany
| | - Laurence Hecquet
- Institut de Chimie de Clermont-Ferrand CNRS Auvergne Clermont INP Université Clermont Auverne 63000 Clermont-Ferrand France
| | - Wolf‐Dieter Fessner
- Institut für Organische Chemie und Biochemie Technische Universität Darmstadt Alarich-Weiss-Str. 4 64287 Darmstadt Germany
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5
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Ocal N, Lagarde A, L'enfant M, Charmantray F, Hecquet L. High-Throughput Solid-Phase Assay for Substrate Profiling and Directed Evolution of Transketolase. Chembiochem 2021; 22:2814-2820. [PMID: 34289225 DOI: 10.1002/cbic.202100356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Indexed: 11/10/2022]
Abstract
Thiamine diphosphate-dependent enzymes, and specifically transketolases, form one of the most important families of biocatalytic tools for enantioselective carbon-carbon bond formation yielding various hydroxyketones of biological interest. To enable substrate profiling of transketolases for acceptance of different donors and acceptors, a simple, direct colorimetric assay based on pH reaction variation was developed to establish a high-throughput solid-phase assay. This assay reduces the screening effort in the directed evolution of transketolases, as only active variants are selected for further analysis. Transketolase activity is detected as bicarbonate anions released from the α-ketoacid donor substrate, which causes the pH to rise. A pH indicator, bromothymol blue, which changes color from yellow to blue in alkaline conditions, was used to directly detect, with the naked eye, clones expressing active transketolase variants, obviating enzyme extraction.
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Affiliation(s)
- Nazim Ocal
- Université Clermont Auvergne, CNRS, Auvergne Clermont INP, ICCF, 63000, Clermont-Ferrand, France
| | - Aurélie Lagarde
- Université Clermont Auvergne, CNRS, Auvergne Clermont INP, ICCF, 63000, Clermont-Ferrand, France
| | - Mélanie L'enfant
- Université Clermont Auvergne, CNRS, Auvergne Clermont INP, ICCF, 63000, Clermont-Ferrand, France
| | - Franck Charmantray
- Université Clermont Auvergne, CNRS, Auvergne Clermont INP, ICCF, 63000, Clermont-Ferrand, France
| | - Laurence Hecquet
- Université Clermont Auvergne, CNRS, Auvergne Clermont INP, ICCF, 63000, Clermont-Ferrand, France
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6
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Nauton L, Hecquet L, Théry V. QM/MM Study of Human Transketolase: Thiamine Diphosphate Activation Mechanism and Complete Catalytic Cycle. J Chem Inf Model 2021; 61:3502-3515. [PMID: 34161071 DOI: 10.1021/acs.jcim.1c00190] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A computational model for human transketolase was proposed, showing that thiamine diphosphate activation was based on His110 in place of His481 reported in yeast transketolase. In addition, a complete catalytic reaction pathway was investigated using d-xylulose-5-phosphate and d-ribose-5-phosphate as substrates, showing at every step a perfect superimposition of our model with high-resolution crystallographic structures 3MOS, 4KXV, and 4KXX. This study shows that H2N4' of the active thiamine diphosphate "V form" no longer has a self-activating role but allows self-stabilization of the cofactor and of the Breslow intermediate. These advances in our knowledge of the human transketolase mechanism offer interesting prospects for the design of new drugs, this enzyme being involved in several diseases, and for a better understanding of the reactions catalyzed by transketolases from other sources.
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Affiliation(s)
- Lionel Nauton
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, ICCF, F-63000 Clermont-Ferrand, France
| | - Laurence Hecquet
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, ICCF, F-63000 Clermont-Ferrand, France
| | - Vincent Théry
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, ICCF, F-63000 Clermont-Ferrand, France
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7
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Casajus H, Lagarde A, Leremboure M, De Dios Miguel T, Nauton L, Thery V, Fessner W, Duguet N, Charmantray F, Hecquet L. Enzymatic Synthesis of Aliphatic Acyloins Catalyzed by Thermostable Transketolase. ChemCatChem 2020. [DOI: 10.1002/cctc.202001160] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hubert Casajus
- Université Clermont Auvergne, CNRS, SIGMA Clermont Institut de Chimie de Clermont-Ferrand (ICCF) F-63000 Clermont-Ferrand France
| | - Aurélie Lagarde
- Université Clermont Auvergne, CNRS, SIGMA Clermont Institut de Chimie de Clermont-Ferrand (ICCF) F-63000 Clermont-Ferrand France
| | - Martin Leremboure
- Université Clermont Auvergne, CNRS, SIGMA Clermont Institut de Chimie de Clermont-Ferrand (ICCF) F-63000 Clermont-Ferrand France
| | - Thomas De Dios Miguel
- Univ Lyon, Université Claude Bernard Lyon 1 CNRS, INSA-Lyon, CPE-Lyon, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS) F-69100 Villeurbanne France
| | - Lionel Nauton
- Université Clermont Auvergne, CNRS, SIGMA Clermont Institut de Chimie de Clermont-Ferrand (ICCF) F-63000 Clermont-Ferrand France
| | - Vincent Thery
- Université Clermont Auvergne, CNRS, SIGMA Clermont Institut de Chimie de Clermont-Ferrand (ICCF) F-63000 Clermont-Ferrand France
| | - Wolf‐Dieter Fessner
- Institut für Organische Chemie und Biochemie Technische Universität Darmstadt 64287 Darmstadt Germany
| | - Nicolas Duguet
- Univ Lyon, Université Claude Bernard Lyon 1 CNRS, INSA-Lyon, CPE-Lyon, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS) F-69100 Villeurbanne France
| | - Franck Charmantray
- Université Clermont Auvergne, CNRS, SIGMA Clermont Institut de Chimie de Clermont-Ferrand (ICCF) F-63000 Clermont-Ferrand France
| | - Laurence Hecquet
- Université Clermont Auvergne, CNRS, SIGMA Clermont Institut de Chimie de Clermont-Ferrand (ICCF) F-63000 Clermont-Ferrand France
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8
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Winning the numbers game in enzyme evolution - fast screening methods for improved biotechnology proteins. Curr Opin Struct Biol 2020; 63:123-133. [PMID: 32615371 DOI: 10.1016/j.sbi.2020.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 04/28/2020] [Accepted: 05/08/2020] [Indexed: 01/02/2023]
Abstract
The booming demand for environmentally benign industrial processes relies on the ability to quickly find or engineer a biocatalyst suitable to ideal process conditions. Both metagenomic approaches and directed evolution involve the screening of huge libraries of protein variants, which can only be managed reasonably by flexible platforms for (ultra)high-throughput profiling against the desired criteria. Here, we review the most recent additions toward a growing toolbox of versatile assays using fluorescence, absorbance and mass spectrometry readouts. While conventional solution based high-throughput screening in microtiter plate formats is still important, the implementation of novel screening protocols for microfluidic cell or droplet sorting systems supports technological advances for ultra-high-frequency screening that now can dramatically reduce the timescale of engineering projects. We discuss practical issues of scope, scalability, sensitivity and stereoselectivity for the improvement of biotechnologically relevant enzymes from different classes.
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9
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Ocal N, L’enfant M, Charmantray F, Pollegioni L, Martin J, Auffray P, Collin J, Hecquet L. d-Serine as a Key Building Block: Enzymatic Process Development and Smart Applications within the Cascade Enzymatic Concept. Org Process Res Dev 2020. [DOI: 10.1021/acs.oprd.0c00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nazim Ocal
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
| | - Mélanie L’enfant
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
| | - Franck Charmantray
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, Università degli Studi dell’Insubria, 21100 Varese, Italy
| | - Juliette Martin
- Protéus by Seqens, 70 Allée Graham Belln, F-30035 Nîmes, France
| | - Pascal Auffray
- Protéus by Seqens, 70 Allée Graham Belln, F-30035 Nîmes, France
| | - Jérôme Collin
- Protéus by Seqens, 70 Allée Graham Belln, F-30035 Nîmes, France
| | - Laurence Hecquet
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
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10
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Lorillière M, Guérard‐Hélaine C, Gefflaut T, Fessner W, Clapés P, Charmantray F, Hecquet L. Convergent
in situ
Generation of Both Transketolase Substrates
via
Transaminase and Aldolase Reactions for Sequential One‐Pot, Three‐Step Cascade Synthesis of Ketoses. ChemCatChem 2019. [DOI: 10.1002/cctc.201901756] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Marion Lorillière
- Université Clermont Auvergne, CNRS, SIGMA ClermontInstitut de Chimie de Clermont-Ferrand (ICCF) Clermont-Ferrand F63000 France
| | - Christine Guérard‐Hélaine
- Université Clermont Auvergne, CNRS, SIGMA ClermontInstitut de Chimie de Clermont-Ferrand (ICCF) Clermont-Ferrand F63000 France
| | - Thierry Gefflaut
- Université Clermont Auvergne, CNRS, SIGMA ClermontInstitut de Chimie de Clermont-Ferrand (ICCF) Clermont-Ferrand F63000 France
| | - Wolf‐Dieter Fessner
- Institut für Organische Chemie und BiochemieTechnische Universität Darmstadt Darmstadt 64287 Germany
| | - Pere Clapés
- Biotransformation and Bioactive Molecules GroupInstituto de Química Avanzada de Cataluña IQAC-CSIC Jordi Barcelona 08034 Spain
| | - Franck Charmantray
- Université Clermont Auvergne, CNRS, SIGMA ClermontInstitut de Chimie de Clermont-Ferrand (ICCF) Clermont-Ferrand F63000 France
| | - Laurence Hecquet
- Université Clermont Auvergne, CNRS, SIGMA ClermontInstitut de Chimie de Clermont-Ferrand (ICCF) Clermont-Ferrand F63000 France
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11
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Marsden SR, Mestrom L, McMillan DGG, Hanefeld U. Thermodynamically and Kinetically Controlled Reactions in Biocatalysis – from Concepts to Perspectives. ChemCatChem 2019. [DOI: 10.1002/cctc.201901589] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Stefan R. Marsden
- Biokatalyse, Afdeling BiotechnologieTechnische Universiteit Delft Van der Maasweg 9 Delft 2629HZ The Netherlands
| | - Luuk Mestrom
- Biokatalyse, Afdeling BiotechnologieTechnische Universiteit Delft Van der Maasweg 9 Delft 2629HZ The Netherlands
| | - Duncan G. G. McMillan
- Biokatalyse, Afdeling BiotechnologieTechnische Universiteit Delft Van der Maasweg 9 Delft 2629HZ The Netherlands
| | - Ulf Hanefeld
- Biokatalyse, Afdeling BiotechnologieTechnische Universiteit Delft Van der Maasweg 9 Delft 2629HZ The Netherlands
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12
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Yu H, Hernández López RI, Steadman D, Méndez‐Sánchez D, Higson S, Cázares‐Körner A, Sheppard TD, Ward JM, Hailes HC, Dalby PA. Engineering transketolase to accept both unnatural donor and acceptor substrates and produce α‐hydroxyketones. FEBS J 2019; 287:1758-1776. [DOI: 10.1111/febs.15108] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/26/2019] [Accepted: 10/23/2019] [Indexed: 11/27/2022]
Affiliation(s)
- Haoran Yu
- Department of Biochemical Engineering University College London UK
| | | | | | | | - Sally Higson
- Department of Chemistry University College London UK
| | | | | | - John M. Ward
- Department of Biochemical Engineering University College London UK
| | | | - Paul A. Dalby
- Department of Biochemical Engineering University College London UK
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13
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Lorillière M, Dumoulin R, L’enfant M, Rambourdin A, Thery V, Nauton L, Fessner WD, Charmantray F, Hecquet L. Evolved Thermostable Transketolase for Stereoselective Two-Carbon Elongation of Non-Phosphorylated Aldoses to Naturally Rare Ketoses. ACS Catal 2019. [DOI: 10.1021/acscatal.9b01339] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Marion Lorillière
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
| | - Romain Dumoulin
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
| | - Mélanie L’enfant
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
| | - Agnès Rambourdin
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
| | - Vincent Thery
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
| | - Lionel Nauton
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
| | - Wolf-Dieter Fessner
- Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, 64287 Darmstadt, Germany
| | - Franck Charmantray
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
| | - Laurence Hecquet
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
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14
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L'enfant M, Bruna F, Lorillière M, Ocal N, Fessner W, Pollegioni L, Charmantray F, Hecquet L. One‐Pot Cascade Synthesis of (3 S)‐Hydroxyketones Catalyzed by Transketolase viaHydroxypyruvate Generated in Situfrom d‐Serine by d‐Amino Acid Oxidase. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Mélanie L'enfant
- Université Clermont AuvergneCNRSSIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF) F-63000 Clermont-Ferrand France
| | - Felipe Bruna
- Université Clermont AuvergneCNRSSIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF) F-63000 Clermont-Ferrand France
| | - Marion Lorillière
- Université Clermont AuvergneCNRSSIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF) F-63000 Clermont-Ferrand France
| | - Nazim Ocal
- Université Clermont AuvergneCNRSSIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF) F-63000 Clermont-Ferrand France
| | - Wolf‐Dieter Fessner
- Institut für Organische Chemie und BiochemieTechnische Universität Darmstadt 64287 Darmstadt Germany
| | - Loredano Pollegioni
- Department of Biotechnology and Life SciencesUniversità degli Studi dell'Insubria Varese Italy
| | - Franck Charmantray
- Université Clermont AuvergneCNRSSIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF) F-63000 Clermont-Ferrand France
| | - Laurence Hecquet
- Université Clermont AuvergneCNRSSIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF) F-63000 Clermont-Ferrand France
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15
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Saravanan T, Junker S, Kickstein M, Hein S, Link MK, Ranglack J, Witt S, Lorillière M, Hecquet L, Fessner WD. Donor-Promiskuität einer thermostabilen Transketolase durch gelenkte Evolution - effektive Komplementierung der 1-Desoxy-d
- xylulose-5-phosphat-Synthase-Aktivität. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701169] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Thangavelu Saravanan
- Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Straße 4 64287 Darmstadt Deutschland
| | - Sebastian Junker
- Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Straße 4 64287 Darmstadt Deutschland
| | - Michael Kickstein
- Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Straße 4 64287 Darmstadt Deutschland
| | - Sascha Hein
- Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Straße 4 64287 Darmstadt Deutschland
| | - Marie-Kristin Link
- Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Straße 4 64287 Darmstadt Deutschland
| | - Jan Ranglack
- Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Straße 4 64287 Darmstadt Deutschland
| | - Samantha Witt
- Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Straße 4 64287 Darmstadt Deutschland
| | - Marion Lorillière
- Clermont Université, Université Blaise Pascal; Institut de Chimie de Clermont-Ferrand, CNRS UMR 6296, ICCF; BP10448 63177 Aubière Frankreich
| | - Laurence Hecquet
- Clermont Université, Université Blaise Pascal; Institut de Chimie de Clermont-Ferrand, CNRS UMR 6296, ICCF; BP10448 63177 Aubière Frankreich
| | - Wolf-Dieter Fessner
- Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Straße 4 64287 Darmstadt Deutschland
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16
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Saravanan T, Junker S, Kickstein M, Hein S, Link MK, Ranglack J, Witt S, Lorillière M, Hecquet L, Fessner WD. Donor Promiscuity of a Thermostable Transketolase by Directed Evolution: Efficient Complementation of 1-Deoxy-d
-xylulose-5-phosphate Synthase Activity. Angew Chem Int Ed Engl 2017; 56:5358-5362. [DOI: 10.1002/anie.201701169] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Thangavelu Saravanan
- Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
| | - Sebastian Junker
- Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
| | - Michael Kickstein
- Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
| | - Sascha Hein
- Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
| | - Marie-Kristin Link
- Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
| | - Jan Ranglack
- Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
| | - Samantha Witt
- Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
| | - Marion Lorillière
- Université Clermont Auvergne; CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-; 63000 Clermont-Ferrand France
| | - Laurence Hecquet
- Université Clermont Auvergne; CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-; 63000 Clermont-Ferrand France
| | - Wolf-Dieter Fessner
- Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
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17
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Yu H, Yan Y, Zhang C, Dalby PA. Two strategies to engineer flexible loops for improved enzyme thermostability. Sci Rep 2017; 7:41212. [PMID: 28145457 PMCID: PMC5286519 DOI: 10.1038/srep41212] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 12/16/2016] [Indexed: 11/19/2022] Open
Abstract
Flexible sites are potential targets for engineering the stability of enzymes. Nevertheless, the success rate of the rigidifying flexible sites (RFS) strategy is still low due to a limited understanding of how to determine the best mutation candidates. In this study, two parallel strategies were applied to identify mutation candidates within the flexible loops of Escherichia coli transketolase (TK). The first was a “back to consensus mutations” approach, and the second was computational design based on ΔΔG calculations in Rosetta. Forty-nine single variants were generated and characterised experimentally. From these, three single-variants I189H, A282P, D143K were found to be more thermostable than wild-type TK. The combination of A282P with H192P, a variant constructed previously, resulted in the best all-round variant with a 3-fold improved half-life at 60 °C, 5-fold increased specific activity at 65 °C, 1.3-fold improved kcat and a Tm increased by 5 °C above that of wild type. Based on a statistical analysis of the stability changes for all variants, the qualitative prediction accuracy of the Rosetta program reached 65.3%. Both of the two strategies investigated were useful in guiding mutation candidates to flexible loops, and had the potential to be used for other enzymes.
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Affiliation(s)
- Haoran Yu
- Department of Biochemical Engineering, University College London, Gordon Street, London, WC1H 0AH, United Kingdom
| | - Yihan Yan
- Department of Biochemical Engineering, University College London, Gordon Street, London, WC1H 0AH, United Kingdom
| | - Cheng Zhang
- Department of Biochemical Engineering, University College London, Gordon Street, London, WC1H 0AH, United Kingdom
| | - Paul A Dalby
- Department of Biochemical Engineering, University College London, Gordon Street, London, WC1H 0AH, United Kingdom
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18
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Zhou C, Saravanan T, Lorillière M, Wei D, Charmantray F, Hecquet L, Fessner WD, Yi D. Second-Generation Engineering of a Thermostable Transketolase (TKGst) for Aliphatic Aldehyde Acceptors with Either Improved or Reversed Stereoselectivity. Chembiochem 2017; 18:455-459. [DOI: 10.1002/cbic.201600609] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Chaoqiang Zhou
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; Meilong Road 130 200237 Shanghai P.R. China
| | - Thangavelu Saravanan
- Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
| | - Marion Lorillière
- Université Blaise Pascal ou Université Clermont Auvergne; Institut de Chimie de Clermont-Ferrand; B. P. 10448 63000 Clermont-Ferrand France
- CNRS; UMR 6296; ICCF; 63177 Aubière France
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; Meilong Road 130 200237 Shanghai P.R. China
| | - Franck Charmantray
- Université Blaise Pascal ou Université Clermont Auvergne; Institut de Chimie de Clermont-Ferrand; B. P. 10448 63000 Clermont-Ferrand France
- CNRS; UMR 6296; ICCF; 63177 Aubière France
| | - Laurence Hecquet
- Université Blaise Pascal ou Université Clermont Auvergne; Institut de Chimie de Clermont-Ferrand; B. P. 10448 63000 Clermont-Ferrand France
- CNRS; UMR 6296; ICCF; 63177 Aubière France
| | - Wolf-Dieter Fessner
- Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
| | - Dong Yi
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; Meilong Road 130 200237 Shanghai P.R. China
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19
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Pinsolle A, Charmantray F, Hecquet L, Sarrazin F. Droplet millifluidics for kinetic study of transketolase. BIOMICROFLUIDICS 2016; 10:064103. [PMID: 27917251 PMCID: PMC5106428 DOI: 10.1063/1.4966619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 10/18/2016] [Indexed: 06/06/2023]
Abstract
We present a continuous-flow reactor at the millifluidic scale coupled with an online, non-intrusive spectroscopic monitoring method for determining the kinetic parameters of an enzyme, transketolase (TK) used in biocatalysis for the synthesis of polyols by carboligation. The millifluidic system used is based on droplet flow, a well-established method for kinetic chemical data acquisition. The TK assay is based on the direct quantitative measurement of bicarbonate ions released during the transketolase-catalysed reaction in the presence of hydroxypyruvic acid as the donor, thanks to an irreversible reaction: bicarbonate ions react with phosphoenolpyruvate (PEP) in the presence of PEP carboxylase as the first auxiliary enzyme. The oxaloacetate formed is reduced to malate by NADH in the reaction catalysed by malate dehydrogenase as the second auxiliary enzyme. The extent of oxidation of NADH was measured by spectrophotometry at 340 nm. This system gives a direct, quantitative, generic method to evaluate the TK activity versus different substrates. We demonstrate the accuracy of this strategy to determine the enzymatic kinetic parameters and to study the substrate specificity of a thermostable TK from thermophilic microorganism Geobacillus stearothermophilus, offering promising prospects in biocatalysis. Millifluidic systems are useful in this regard as they can be used to rapidly evaluate the TK activity towards various substrates, and also different sets of conditions, identifying the optimal operating environment while minimizing resource consumption and ensuring high control over the operating conditions.
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Affiliation(s)
- A Pinsolle
- Laboratory of the Future (LOF) , SOLVAY/CNRS UMR 5258, 178 avenue du Docteur Schweitzer, F-33608 Pessac Cedex, France
| | | | | | - F Sarrazin
- Laboratory of the Future (LOF) , SOLVAY/CNRS UMR 5258, 178 avenue du Docteur Schweitzer, F-33608 Pessac Cedex, France
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20
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Richter C, Berndt F, Kunde T, Mahrwald R. Decarboxylative Cascade Reactions of Dihydroxyfumaric Acid: A Preparative Approach to the Glyoxylate Scenario. Org Lett 2016; 18:2950-3. [DOI: 10.1021/acs.orglett.6b01287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Celin Richter
- Institute of Chemistry, Humboldt-University, Brook-Taylor Str. 2, 12489 Berlin, Germany
| | - Falko Berndt
- Institute of Chemistry, Humboldt-University, Brook-Taylor Str. 2, 12489 Berlin, Germany
| | - Tom Kunde
- Institute of Chemistry, Humboldt-University, Brook-Taylor Str. 2, 12489 Berlin, Germany
| | - Rainer Mahrwald
- Institute of Chemistry, Humboldt-University, Brook-Taylor Str. 2, 12489 Berlin, Germany
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21
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Ali G, Moreau T, Forano C, Mousty C, Prevot V, Charmantray F, Hecquet L. Chiral Polyol Synthesis Catalyzed by a Thermostable Transketolase Immobilized on Layered Double Hydroxides in Ionic liquids. ChemCatChem 2015. [DOI: 10.1002/cctc.201500524] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ghina Ali
- Institut de Chimie de Clermont-Ferrand; Clermont Université, Université Blaise Pascal, BP 10448; 63000 Clermont-Ferrand France
- CNRS, UMR 6296; ICCF; 63177 Aubière France
| | - Thomas Moreau
- Institut de Chimie de Clermont-Ferrand; Clermont Université, Université Blaise Pascal, BP 10448; 63000 Clermont-Ferrand France
- CNRS, UMR 6296; ICCF; 63177 Aubière France
| | - Claude Forano
- Institut de Chimie de Clermont-Ferrand; Clermont Université, Université Blaise Pascal, BP 10448; 63000 Clermont-Ferrand France
- CNRS, UMR 6296; ICCF; 63177 Aubière France
| | - Christine Mousty
- Institut de Chimie de Clermont-Ferrand; Clermont Université, Université Blaise Pascal, BP 10448; 63000 Clermont-Ferrand France
- CNRS, UMR 6296; ICCF; 63177 Aubière France
| | - Vanessa Prevot
- Institut de Chimie de Clermont-Ferrand; Clermont Université, Université Blaise Pascal, BP 10448; 63000 Clermont-Ferrand France
- CNRS, UMR 6296; ICCF; 63177 Aubière France
| | - Franck Charmantray
- Institut de Chimie de Clermont-Ferrand; Clermont Université, Université Blaise Pascal, BP 10448; 63000 Clermont-Ferrand France
- CNRS, UMR 6296; ICCF; 63177 Aubière France
| | - Laurence Hecquet
- Institut de Chimie de Clermont-Ferrand; Clermont Université, Université Blaise Pascal, BP 10448; 63000 Clermont-Ferrand France
- CNRS, UMR 6296; ICCF; 63177 Aubière France
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