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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Solhtalab M, Moller SR, Gu AZ, Jaisi D, Aristilde L. Selectivity in Enzymatic Phosphorus Recycling from Biopolymers: Isotope Effect, Reactivity Kinetics, and Molecular Docking with Fungal and Plant Phosphatases. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:16441-16452. [PMID: 36283689 PMCID: PMC9670850 DOI: 10.1021/acs.est.2c04948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/05/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Among ubiquitous phosphorus (P) reserves in environmental matrices are ribonucleic acid (RNA) and polyphosphate (polyP), which are, respectively, organic and inorganic P-containing biopolymers. Relevant to P recycling from these biopolymers, much remains unknown about the kinetics and mechanisms of different acid phosphatases (APs) secreted by plants and soil microorganisms. Here we investigated RNA and polyP dephosphorylation by two common APs, a plant purple AP (PAP) from sweet potato and a fungal phytase from Aspergillus niger. Trends of δ18O values in released orthophosphate during each enzyme-catalyzed reaction in 18O-water implied a different extent of reactivity. Subsequent enzyme kinetics experiments revealed that A. niger phytase had 10-fold higher maximum rate for polyP dephosphorylation than the sweet potato PAP, whereas the sweet potato PAP dephosphorylated RNA at a 6-fold faster rate than A. niger phytase. Both enzymes had up to 3 orders of magnitude lower reactivity for RNA than for polyP. We determined a combined phosphodiesterase-monoesterase mechanism for RNA and terminal phosphatase mechanism for polyP using high-resolution mass spectrometry and 31P nuclear magnetic resonance, respectively. Molecular modeling with eight plant and fungal AP structures predicted substrate binding interactions consistent with the relative reactivity kinetics. Our findings implied a hierarchy in enzymatic P recycling from P-polymers by phosphatases from different biological origins, thereby influencing the relatively longer residence time of RNA versus polyP in environmental matrices. This research further sheds light on engineering strategies to enhance enzymatic recycling of biopolymer-derived P, in addition to advancing environmental predictions of this P recycling by plants and microorganisms.
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Affiliation(s)
- Mina Solhtalab
- Department
of Biological and Environmental Engineering, College of Agriculture
and Life Sciences, Cornell University, Ithaca, New York 14853, United States
- Department
of Civil and Environmental Engineering, McCormick School of Engineering
and Applied Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Spencer R. Moller
- Department
of Plant and Soil Sciences, University of
Delaware, Newark, Delaware 19716, United States
| | - April Z. Gu
- School
of Civil and Environmental Engineering, College of Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Deb Jaisi
- Department
of Plant and Soil Sciences, University of
Delaware, Newark, Delaware 19716, United States
| | - Ludmilla Aristilde
- Department
of Biological and Environmental Engineering, College of Agriculture
and Life Sciences, Cornell University, Ithaca, New York 14853, United States
- Department
of Civil and Environmental Engineering, McCormick School of Engineering
and Applied Science, Northwestern University, Evanston, Illinois 60208, United States
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3
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Hot spots-making directed evolution easier. Biotechnol Adv 2022; 56:107926. [DOI: 10.1016/j.biotechadv.2022.107926] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/04/2022] [Accepted: 02/07/2022] [Indexed: 01/20/2023]
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4
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Cárdenas-Fernández M, Subrizi F, Dobrijevic D, Hailes HC, Ward JM. Characterisation of a hyperthermophilic transketolase from Thermotoga maritima DSM3109 as a biocatalyst for 7-keto-octuronic acid synthesis. Org Biomol Chem 2021; 19:6493-6500. [PMID: 34250527 PMCID: PMC8317047 DOI: 10.1039/d1ob01237a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 07/05/2021] [Indexed: 11/21/2022]
Abstract
Transketolase (TK) is a fundamentally important enzyme in industrial biocatalysis which carries out a stereospecific carbon-carbon bond formation, and is widely used in the synthesis of prochiral ketones. This study describes the biochemical and molecular characterisation of a novel and unusual hyperthermophilic TK from Thermotoga maritima DSM3109 (TKtmar). TKtmar has a low protein sequence homology compared to the already described TKs, with key amino acid residues in the active site highly conserved. TKtmar has a very high optimum temperature (>90 °C) and shows pronounced stability at high temperature (e.g. t1/2 99 and 9.3 h at 50 and 80 °C, respectively) and in presence of organic solvents commonly used in industry (DMSO, acetonitrile and methanol). Substrate screening showed activity towards several monosaccharides and aliphatic aldehydes. In addition, for the first time, TK specificity towards uronic acids was achieved with TKtmar catalysing the efficient conversion of d-galacturonic acid and lithium hydroxypyruvate into 7-keto-octuronic acid, a very rare C8 uronic acid, in high yields (98%, 49 mM).
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Affiliation(s)
- Max Cárdenas-Fernández
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, UK. and School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Fabiana Subrizi
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - Dragana Dobrijevic
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, UK.
| | - Helen C Hailes
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - John M Ward
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, UK.
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5
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James P, Isupov MN, De Rose SA, Sayer C, Cole IS, Littlechild JA. A 'Split-Gene' Transketolase From the Hyper-Thermophilic Bacterium Carboxydothermus hydrogenoformans: Structure and Biochemical Characterization. Front Microbiol 2020; 11:592353. [PMID: 33193259 PMCID: PMC7661550 DOI: 10.3389/fmicb.2020.592353] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/12/2020] [Indexed: 11/26/2022] Open
Abstract
A novel transketolase has been reconstituted from two separate polypeptide chains encoded by a ‘split-gene’ identified in the genome of the hyperthermophilic bacterium, Carboxydothermus hydrogenoformans. The reconstituted active α2β2 tetrameric enzyme has been biochemically characterized and its activity has been determined using a range of aldehydes including glycolaldehyde, phenylacetaldehyde and cyclohexanecarboxaldehyde as the ketol acceptor and hydroxypyruvate as the donor. This reaction proceeds to near 100% completion due to the release of the product carbon dioxide and can be used for the synthesis of a range of sugars of interest to the pharmaceutical industry. This novel reconstituted transketolase is thermally stable with no loss of activity after incubation for 1 h at 70°C and is stable after 1 h incubation with 50% of the organic solvents methanol, ethanol, isopropanol, DMSO, acetonitrile and acetone. The X-ray structure of the holo reconstituted α2β2 tetrameric transketolase has been determined to 1.4 Å resolution. In addition, the structure of an inactive tetrameric β4 protein has been determined to 1.9 Å resolution. The structure of the active reconstituted α2β2 enzyme has been compared to the structures of related enzymes; the E1 component of the pyruvate dehydrogenase complex and D-xylulose-5-phosphate synthase, in an attempt to rationalize differences in structure and substrate specificity between these enzymes. This is the first example of a reconstituted ‘split-gene’ transketolase to be biochemically and structurally characterized allowing its potential for industrial biocatalysis to be evaluated.
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Affiliation(s)
- Paul James
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Simone Antonio De Rose
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Christopher Sayer
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Isobel S Cole
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Jennifer A Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
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6
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Wilkinson HC, Dalby PA. Fine-tuning the activity and stability of an evolved enzyme active-site through noncanonical amino-acids. FEBS J 2020; 288:1935-1955. [PMID: 32897608 DOI: 10.1111/febs.15560] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/14/2020] [Accepted: 09/02/2020] [Indexed: 01/17/2023]
Abstract
Site-specific saturation mutagenesis within enzyme active sites can radically alter reaction specificity, though often with a trade-off in stability. Extending saturation mutagenesis with a range of noncanonical amino acids (ncAA) potentially increases the ability to improve activity and stability simultaneously. Previously, an Escherichia coli transketolase variant (S385Y/D469T/R520Q) was evolved to accept aromatic aldehydes not converted by wild-type. The aromatic residue Y385 was critical to the new acceptor substrate binding, and so was explored here beyond the natural aromatic residues, to probe side chain structure and electronics effects on enzyme function and stability. A series of five variants introduced decreasing aromatic ring electron density at position 385 in the order para-aminophenylalanine (pAMF), tyrosine (Y), phenylalanine (F), para-cyanophenylalanine (pCNF) and para-nitrophenylalanine (pNTF), and simultaneously modified the hydrogen-bonding potential of the aromatic substituent from accepting to donating. The fine-tuning of residue 385 yielded variants with a 43-fold increase in specific activity for 50 mm 3-HBA and 100% increased kcat (pCNF), 290% improvement in Km (pNTF), 240% improvement in kcat /Km (pAMF) and decreased substrate inhibition relative to Y. Structural modelling suggested switching of the ring-substituted functional group, from donating to accepting, stabilised a helix-turn (D259-H261) through an intersubunit H-bond with G262, to give a 7.8 °C increase in the thermal transition mid-point, Tm , and improved packing of pAMF. This is one of the first examples in which both catalytic activity and stability are simultaneously improved via site-specific ncAA incorporation into an enzyme active site, and further demonstrates the benefits of expanding designer libraries to include ncAAs.
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Affiliation(s)
- Henry C Wilkinson
- Department of Biochemical Engineering, University College London, London, UK
| | - Paul A Dalby
- Department of Biochemical Engineering, University College London, London, UK
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7
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Oxalyl‐CoA Decarboxylase katalysiert die nukleophile ein‐Kohlenstoff‐Verlängerung von Aldehyden zu chiralen α‐Hydroxysäuren. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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8
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Burgener S, Cortina NS, Erb TJ. Oxalyl-CoA Decarboxylase Enables Nucleophilic One-Carbon Extension of Aldehydes to Chiral α-Hydroxy Acids. Angew Chem Int Ed Engl 2020; 59:5526-5530. [PMID: 31894608 PMCID: PMC7154664 DOI: 10.1002/anie.201915155] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Indexed: 11/11/2022]
Abstract
The synthesis of complex molecules from simple, renewable carbon units is the goal of a sustainable economy. Here we explored the biocatalytic potential of the thiamine-diphosphate-dependent (ThDP) oxalyl-CoA decarboxylase (OXC)/2-hydroxyacyl-CoA lyase (HACL) superfamily that naturally catalyzes the shortening of acyl-CoA thioester substrates through the release of the C1 -unit formyl-CoA. We show that the OXC/HACL superfamily contains promiscuous members that can be reversed to perform nucleophilic C1 -extensions of various aldehydes to yield the corresponding 2-hydroxyacyl-CoA thioesters. We improved the catalytic properties of Methylorubrum extorquens OXC by rational enzyme engineering and combined it with two newly described enzymes-a specific oxalyl-CoA synthetase and a 2-hydroxyacyl-CoA thioesterase. This enzymatic cascade enabled continuous conversion of oxalate and aromatic aldehydes into valuable (S)-α-hydroxy acids with enantiomeric excess up to 99 %.
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Affiliation(s)
- Simon Burgener
- Department of Biochemistry & Synthetic MetabolismMax-Planck-Institute for terrestrial MicrobiologyKarl-von-Frisch-Str. 1035043MarburgGermany
| | - Niña Socorro Cortina
- Department of Biochemistry & Synthetic MetabolismMax-Planck-Institute for terrestrial MicrobiologyKarl-von-Frisch-Str. 1035043MarburgGermany
| | - Tobias J. Erb
- Department of Biochemistry & Synthetic MetabolismMax-Planck-Institute for terrestrial MicrobiologyKarl-von-Frisch-Str. 1035043MarburgGermany
- LOEWE-Center for Synthetic MicrobiologyPhilipps-University MarburgKarl-von-Frisch-Str. 835043MarburgGermany
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9
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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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10
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Henríquez M, Braun‐Galleani S, Nesbeth DN. Whole cell biosynthetic activity ofKomagataella phaffii(Pichia pastoris) GS115 strains engineered with transgenes encodingChromobacterium violaceumω‐transaminase alone or combined with native transketolase. Biotechnol Prog 2019; 36:e2893. [DOI: 10.1002/btpr.2893] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/18/2019] [Accepted: 08/01/2019] [Indexed: 01/25/2023]
Affiliation(s)
| | | | - Darren N. Nesbeth
- Department of Biochemical EngineeringUniversity College London London UK
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11
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Exploiting correlated molecular-dynamics networks to counteract enzyme activity-stability trade-off. Proc Natl Acad Sci U S A 2018; 115:E12192-E12200. [PMID: 30530661 PMCID: PMC6310800 DOI: 10.1073/pnas.1812204115] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rigidifying flexible sites is a powerful method to improve enzyme stability. However, if the highly flexible regions form the active site, modifying them risks losing activity due to the activity–stability trade-off. We hypothesized here that regions outside the active site whose dynamics were highly correlated to flexible active sites, would provide good targets for stabilizing mutations. To test this hypothesis, six variants were constructed in the 3M variant of Escherichia coli transketolase. The best variant had a 10.8-fold improved half-life at 55 °C, and increased the Tm and Tagg by 3 °C and 4.3 °C, respectively. The variants even increased the activity, by up to threefold. This study highlights how protein engineering strategies could be potentially improved by considering long-range dynamics. The directed evolution of enzymes for improved activity or substrate specificity commonly leads to a trade-off in stability. We have identified an activity–stability trade-off and a loss in unfolding cooperativity for a variant (3M) of Escherichia coli transketolase (TK) engineered to accept aromatic substrates. Molecular dynamics simulations of 3M revealed increased flexibility in several interconnected active-site regions that also form part of the dimer interface. Mutating the newly flexible active-site residues to regain stability risked losing the new activity. We hypothesized that stabilizing mutations could be targeted to residues outside of the active site, whose dynamics were correlated with the newly flexible active-site residues. We previously stabilized WT TK by targeting mutations to highly flexible regions. These regions were much less flexible in 3M and would not have been selected a priori as targets using the same strategy based on flexibility alone. However, their dynamics were highly correlated with the newly flexible active-site regions of 3M. Introducing the previous mutations into 3M reestablished the WT level of stability and unfolding cooperativity, giving a 10.8-fold improved half-life at 55 °C, and increased midpoint and aggregation onset temperatures by 3 °C and 4.3 °C, respectively. Even the activity toward aromatic aldehydes increased up to threefold. Molecular dynamics simulations confirmed that the mutations rigidified the active-site via the correlated network. This work provides insights into the impact of rigidifying mutations within highly correlated dynamic networks that could also be useful for developing improved computational protein engineering strategies.
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12
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Coupled molecular dynamics mediate long- and short-range epistasis between mutations that affect stability and aggregation kinetics. Proc Natl Acad Sci U S A 2018; 115:E11043-E11052. [PMID: 30404916 PMCID: PMC6255212 DOI: 10.1073/pnas.1810324115] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Multiple mutations are typically required to significantly improve protein stability or aggregation kinetics. However, when several substitutions are made in a single protein, the mutations can potentially interact in a nonadditive manner, resulting in epistatic effects, which can hamper protein-engineering strategies to improve thermostability or aggregation kinetics. Here, we have examined the role of protein dynamics in mediating epistasis between pairs of mutations. With Escherichia coli transketolase (TK) as a model, we explored the epistatic interactions between two single variants H192P and A282P, and also between the double-mutant H192P/A282P and two single variants, I365L or G506A. Epistasis was determined for several measures of protein stability, including the following: the free-energy barrier to kinetic inactivation, ∆∆G ‡; thermal transition midpoint temperatures, T m; and aggregation onset temperatures, T agg Nonadditive epistasis was observed between neighboring mutations as expected, but also for distant mutations located in the surface and core regions of different domains. Surprisingly, the epistatic behaviors for each measure of stability were often different for any given pairwise recombination, highlighting that kinetic and thermodynamic stabilities do not always depend on the same structural features. Molecular-dynamics simulations and a pairwise cross-correlation analysis revealed that mutations influence the dynamics of their local environment, but also in some cases the dynamics of regions distant in the structure. This effect was found to mediate epistatic interactions between distant mutations and could therefore be exploited in future protein-engineering strategies.
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13
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Baierl A, Theorell A, Mackfeld U, Marquardt P, Hoffmann F, Moers S, Nöh K, Buchholz PCF, Pleiss J, Pohl M. Towards a Mechanistic Understanding of Factors Controlling the Stereoselectivity of Transketolase. ChemCatChem 2018. [DOI: 10.1002/cctc.201800299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anna Baierl
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH; 52425 Jülich Germany
| | - Axel Theorell
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH; 52425 Jülich Germany
| | - Ursula Mackfeld
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH; 52425 Jülich Germany
| | - Philipp Marquardt
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH; 52425 Jülich Germany
| | | | - Stephanie Moers
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH; 52425 Jülich Germany
| | - Katharina Nöh
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH; 52425 Jülich Germany
| | - Patrick C. F. Buchholz
- Institute of Biochemistry and Technical Biochemistry; University of Stuttgart; 70569 Stuttgart Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry; University of Stuttgart; 70569 Stuttgart Germany
| | - Martina Pohl
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH; 52425 Jülich Germany
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14
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Wei YC, Braun-Galleani S, Henríquez MJ, Bandara S, Nesbeth D. Biotransformation of β-hydroxypyruvate and glycolaldehyde to l-erythrulose by Pichia pastoris strain GS115 overexpressing native transketolase. Biotechnol Prog 2017; 34:99-106. [PMID: 29086489 PMCID: PMC5836872 DOI: 10.1002/btpr.2577] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 10/27/2017] [Indexed: 01/22/2023]
Abstract
Transketolase is a proven biocatalytic tool for asymmetric carbon-carbon bond formation, both as a purified enzyme and within bacterial whole-cell biocatalysts. The performance of Pichia pastoris as a host for transketolase whole-cell biocatalysis was investigated using a transketolase-overexpressing strain to catalyze formation of l-erythrulose from β-hydroxypyruvic acid and glycolaldehyde substrates. Pichia pastoris transketolase coding sequence from the locus PAS_chr1-4_0150 was subcloned downstream of the methanol-inducible AOX1 promoter in a plasmid for transformation of strain GS115, generating strain TK150. Whole and disrupted TK150 cells from shake flasks achieved 62% and 65% conversion, respectively, under optimal pH and methanol induction conditions. In a 300 μL reaction, TK150 samples from a 1L fed-batch fermentation achieved a maximum l-erythrulose space time yield (STY) of 46.58 g L-1 h-1 , specific activity of 155 U gCDW-1, product yield on substrate (Yp/s ) of 0.52 mol mol-1 and product yield on catalyst (Yp/x ) of 2.23g gCDW-1. We have successfully exploited the rapid growth and high biomass characteristics of Pichia pastoris in whole cell biocatalysis. At high cell density, the engineered TK150 Pichia pastoris strain tolerated high concentrations of substrate and product to achieve high STY of the chiral sugar l-erythrulose. © 2017 The Authors Biotechnology Progress published by Wiley Periodicals, Inc. on behalf of American Institute of Chemical Engineers Biotechnol. Prog., 34:99-106, 2018.
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Affiliation(s)
- Yu-Chia Wei
- Dept. of Biochemical Engineering, University College London, Bernard Katz Building, London, WC1E 6BT, U.K
| | | | - Maria José Henríquez
- Dept. of Biochemical Engineering, University College London, Bernard Katz Building, London, WC1E 6BT, U.K
| | - Sahan Bandara
- Dept. of Biochemical Engineering, University College London, Bernard Katz Building, London, WC1E 6BT, U.K
| | - Darren Nesbeth
- Dept. of Biochemical Engineering, University College London, Bernard Katz Building, London, WC1E 6BT, U.K
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15
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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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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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Affaticati PE, Dai SB, Payongsri P, Hailes HC, Tittmann K, Dalby PA. Structural Analysis of an Evolved Transketolase Reveals Divergent Binding Modes. Sci Rep 2016; 6:35716. [PMID: 27767080 PMCID: PMC5073344 DOI: 10.1038/srep35716] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 09/22/2016] [Indexed: 11/09/2022] Open
Abstract
The S385Y/D469T/R520Q variant of E. coli transketolase was evolved previously with three successive smart libraries, each guided by different structural, bioinformatical or computational methods. Substrate-walking progressively shifted the target acceptor substrate from phosphorylated aldehydes, towards a non-phosphorylated polar aldehyde, a non-polar aliphatic aldehyde, and finally a non-polar aromatic aldehyde. Kinetic evaluations on three benzaldehyde derivatives, suggested that their active-site binding was differentially sensitive to the S385Y mutation. Docking into mutants generated in silico from the wild-type crystal structure was not wholly satisfactory, as errors accumulated with successive mutations, and hampered further smart-library designs. Here we report the crystal structure of the S385Y/D469T/R520Q variant, and molecular docking of three substrates. This now supports our original hypothesis that directed-evolution had generated an evolutionary intermediate with divergent binding modes for the three aromatic aldehydes tested. The new active site contained two binding pockets supporting π-π stacking interactions, sterically separated by the D469T mutation. While 3-formylbenzoic acid (3-FBA) preferred one pocket, and 4-FBA the other, the less well-accepted substrate 3-hydroxybenzaldehyde (3-HBA) was caught in limbo with equal preference for the two pockets. This work highlights the value of obtaining crystal structures of evolved enzyme variants, for continued and reliable use of smart library strategies.
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Affiliation(s)
- Pierre E Affaticati
- Department of Biochemical Engineering, Gordon Street, University College London, WC1H 0AH, UK
| | - Shao-Bo Dai
- Albrecht-von-Haller Institute, Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Panwajee Payongsri
- Department of Biochemical Engineering, Gordon Street, University College London, WC1H 0AH, UK
| | - Helen C Hailes
- Department of Chemistry, 20 Gordon Street, University College London, WC1H 0AJ, UK
| | - Kai Tittmann
- Albrecht-von-Haller Institute, Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Paul A Dalby
- Department of Biochemical Engineering, Gordon Street, University College London, WC1H 0AH, UK
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Morris P, Rios-Solis L, García-Arrazola R, Lye G, Dalby P. Impact of cofactor-binding loop mutations on thermotolerance and activity of E. coli transketolase. Enzyme Microb Technol 2016; 89:85-91. [DOI: 10.1016/j.enzmictec.2016.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 03/08/2016] [Accepted: 04/03/2016] [Indexed: 10/22/2022]
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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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20
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Payongsri P, Steadman D, Hailes HC, Dalby PA. Second generation engineering of transketolase for polar aromatic aldehyde substrates. Enzyme Microb Technol 2015; 71:45-52. [DOI: 10.1016/j.enzmictec.2015.01.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 01/20/2015] [Accepted: 01/22/2015] [Indexed: 10/24/2022]
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21
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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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The modular structure of ThDP-dependent enzymes. Proteins 2014; 82:2523-37. [DOI: 10.1002/prot.24615] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 05/06/2014] [Accepted: 05/20/2014] [Indexed: 01/12/2023]
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23
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Mutational Analysis of the C–C Bond Cleaving Enzyme Phloretin Hydrolase from Eubacterium ramulus. Top Catal 2013. [DOI: 10.1007/s11244-013-0196-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Lawrence J, O'Sullivan B, Lye GJ, Wohlgemuth R, Szita N. Microfluidic multi-input reactor for biocatalytic synthesis using transketolase. JOURNAL OF MOLECULAR CATALYSIS. B, ENZYMATIC 2013; 95:111-117. [PMID: 24187515 PMCID: PMC3724052 DOI: 10.1016/j.molcatb.2013.05.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 05/08/2013] [Accepted: 05/17/2013] [Indexed: 11/14/2022]
Abstract
Biocatalytic synthesis in continuous-flow microreactors is of increasing interest for the production of specialty chemicals. However, the yield of production achievable in these reactors can be limited by the adverse effects of high substrate concentration on the biocatalyst, including inhibition and denaturation. Fed-batch reactors have been developed in order to overcome this problem, but no continuous-flow solution exists. We present the design of a novel multi-input microfluidic reactor, capable of substrate feeding at multiple points, as a first step towards overcoming these problems in a continuous-flow setting. Using the transketolase-(TK) catalysed reaction of lithium hydroxypyruvate (HPA) and glycolaldehyde (GA) to l-erythrulose (ERY), we demonstrate the transposition of a fed-batch substrate feeding strategy to our microfluidic reactor. We obtained a 4.5-fold increase in output concentration and a 5-fold increase in throughput compared with a single input reactor.
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Affiliation(s)
- James Lawrence
- Department of Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
| | - Brian O'Sullivan
- Department of Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
| | - Gary J. Lye
- Department of Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
| | | | - Nicolas Szita
- Department of Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
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25
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Hailes HC, Rother D, Müller M, Westphal R, Ward JM, Pleiss J, Vogel C, Pohl M. Engineering stereoselectivity of ThDP-dependent enzymes. FEBS J 2013; 280:6374-94. [DOI: 10.1111/febs.12496] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 08/16/2013] [Accepted: 08/21/2013] [Indexed: 01/12/2023]
Affiliation(s)
- Helen C. Hailes
- Department of Chemistry; Christopher Ingold Laboratories; University College London; UK
| | - Dörte Rother
- IBG-1: Biotechnology; Forschungszentrum Jülich Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences; University of Freiburg; Germany
| | | | - John M. Ward
- Department of Biochemical Engineering; University College London; UK
| | - Jürgen Pleiss
- Institute of Technical Biochemistry; University of Stuttgart; Germany
| | - Constantin Vogel
- Institute of Technical Biochemistry; University of Stuttgart; Germany
| | - Martina Pohl
- IBG-1: Biotechnology; Forschungszentrum Jülich Germany
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Müller M, Sprenger GA, Pohl M. CC bond formation using ThDP-dependent lyases. Curr Opin Chem Biol 2013; 17:261-70. [PMID: 23523314 DOI: 10.1016/j.cbpa.2013.02.017] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 02/02/2013] [Accepted: 02/14/2013] [Indexed: 01/17/2023]
Abstract
The present review summarizes recent achievements in enzymatic thiamine catalysis during the past three years. With well-established enzymes such as BAL, PDC and TK new reactions have been identified and respective variants were prepared, which enable access to stereoisomeric products. Further we highlight recent progress with 'new' ThDP-dependent enzymes like MenD and PigD, which catalyze the Stetter-like 1,4 addition of aldehydes and YerE, which is the first known ThDP-dependent enzyme accepting ketones as acceptors.
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Affiliation(s)
- Michael Müller
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstr. 25, 79104 Freiburg, Germany.
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