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Frazão CJR, Wagner N, Rabe K, Walther T. Construction of a synthetic metabolic pathway for biosynthesis of 2,4-dihydroxybutyric acid from ethylene glycol. Nat Commun 2023; 14:1931. [PMID: 37024485 PMCID: PMC10079672 DOI: 10.1038/s41467-023-37558-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 03/22/2023] [Indexed: 04/08/2023] Open
Abstract
Ethylene glycol is an attractive two-carbon alcohol substrate for biochemical product synthesis as it can be derived from CO2 or syngas at no sacrifice to human food stocks. Here, we disclose a five-step synthetic metabolic pathway enabling the carbon-conserving biosynthesis of the versatile platform molecule 2,4-dihydroxybutyric acid (DHB) from this compound. The linear pathway chains ethylene glycol dehydrogenase, D-threose aldolase, D-threose dehydrogenase, D-threono-1,4-lactonase, D-threonate dehydratase and 2-oxo-4-hydroxybutyrate reductase enzyme activities in succession. We screen candidate enzymes with D-threose dehydrogenase and D-threonate dehydratase activities on cognate substrates with conserved carbon-centre stereochemistry. Lastly, we show the functionality of the pathway by its expression in an Escherichia coli strain and production of 1 g L-1 and 0.8 g L-1 DHB from, respectively, glycolaldehyde or ethylene glycol.
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Affiliation(s)
- Cláudio J R Frazão
- Institute of Natural Materials Technology, TU Dresden, 01062, Dresden, Germany
| | - Nils Wagner
- Institute of Natural Materials Technology, TU Dresden, 01062, Dresden, Germany
| | - Kenny Rabe
- Institute of Natural Materials Technology, TU Dresden, 01062, Dresden, Germany
| | - Thomas Walther
- Institute of Natural Materials Technology, TU Dresden, 01062, Dresden, Germany.
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2
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Yang X, Wu L, Li A, Ye L, Zhou J, Yu H. The engineering of decameric d-fructose-6-phosphate aldolase A by combinatorial modulation of inter- and intra-subunit interactions. Chem Commun (Camb) 2020; 56:7561-7564. [PMID: 32519699 DOI: 10.1039/d0cc02437f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The combinatorial modulation of inter- and intra-subunit interactions of decameric d-fructose-6-phosphate aldolase A (FSAA) generated a triple-site variant I31T/Q59T/I195Q FSAA with 27- to 278-fold improvement in activity towards target heteroaromatic aldehydes. X-ray crystallographic data and molecular dynamics simulations ascribed the enhanced activity to the pronounced flexibility of the interface region between subunits, the expanded substrate entrance and binding pocket, and enhanced proton transfer, unambiguously demonstrating the efficiency of this strategy for engineering multimeric enzymes.
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Affiliation(s)
- Xiaohong Yang
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China.
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Chemical and Metabolic Controls on Dihydroxyacetone Metabolism Lead to Suboptimal Growth of Escherichia coli. Appl Environ Microbiol 2019; 85:AEM.00768-19. [PMID: 31126940 PMCID: PMC6643234 DOI: 10.1128/aem.00768-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 05/11/2019] [Indexed: 12/26/2022] Open
Abstract
DHA is an attractive triose molecule with a wide range of applications, notably in cosmetics and the food and pharmaceutical industries. DHA is found in many species, from microorganisms to humans, and can be used by Escherichia coli as a growth substrate. However, knowledge about the mechanisms and regulation of this process is currently lacking, motivating our investigation of DHA metabolism in E. coli. We show that under aerobic conditions, E. coli growth on DHA is far from optimal and is hindered by chemical, hierarchical, and possibly allosteric constraints. We show that optimal growth on DHA can be restored by releasing the hierarchical constraint. These results improve our understanding of DHA metabolism and are likely to help unlock biotechnological applications involving DHA as an intermediate, such as the bioconversion of glycerol or C1 substrates into value-added chemicals. In this work, we shed light on the metabolism of dihydroxyacetone (DHA), a versatile, ubiquitous, and important intermediate for various chemicals in industry, by analyzing its metabolism at the system level in Escherichia coli. Using constraint-based modeling, we show that the growth of E. coli on DHA is suboptimal and identify the potential causes. Nuclear magnetic resonance analysis shows that DHA is degraded nonenzymatically into substrates known to be unfavorable to high growth rates. Transcriptomic analysis reveals that DHA promotes genes involved in biofilm formation, which may reduce the bacterial growth rate. Functional analysis of the genes involved in DHA metabolism proves that under the aerobic conditions used in this study, DHA is mainly assimilated via the dihydroxyacetone kinase pathway. In addition, these results show that the alternative routes of DHA assimilation (i.e., the glycerol and fructose-6-phosphate aldolase pathways) are not fully activated under our conditions because of anaerobically mediated hierarchical control. These pathways are therefore certainly unable to sustain fluxes as high as the ones predicted in silico for optimal aerobic growth on DHA. Overexpressing some of the genes in these pathways releases these constraints and restores the predicted optimal growth on DHA. IMPORTANCE DHA is an attractive triose molecule with a wide range of applications, notably in cosmetics and the food and pharmaceutical industries. DHA is found in many species, from microorganisms to humans, and can be used by Escherichia coli as a growth substrate. However, knowledge about the mechanisms and regulation of this process is currently lacking, motivating our investigation of DHA metabolism in E. coli. We show that under aerobic conditions, E. coli growth on DHA is far from optimal and is hindered by chemical, hierarchical, and possibly allosteric constraints. We show that optimal growth on DHA can be restored by releasing the hierarchical constraint. These results improve our understanding of DHA metabolism and are likely to help unlock biotechnological applications involving DHA as an intermediate, such as the bioconversion of glycerol or C1 substrates into value-added chemicals.
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Al-Smadi D, Enugala TR, Kessler V, Mhashal AR, Lynn Kamerlin SC, Kihlberg J, Norberg T, Widersten M. Chemical and Biochemical Approaches for the Synthesis of Substituted Dihydroxybutanones and Di- and Tri-Hydroxypentanones. J Org Chem 2019; 84:6982-6991. [PMID: 31066559 DOI: 10.1021/acs.joc.9b00742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polyhydroxylated compounds are building blocks for the synthesis of carbohydrates and other natural products. Their synthesis is mainly achieved by different synthetic versions of aldol-coupling reactions, catalyzed either by organocatalysts, enzymes, or metal-organic catalysts. We have investigated the formation of 1,4-substituted 2,3-dihydroxybutan-1-one derivatives from para- and meta-substituted phenylacetaldehydes by three distinctly different strategies. The first involved a direct aldol reaction with hydroxyacetone, dihydroxyacetone, or 2-hydroxyacetophenone, catalyzed by the cinchona derivative cinchonine. The second was reductive cross-coupling with methyl- or phenylglyoxal promoted by SmI2, resulting in either 5-substituted 3,4-dihydroxypentan-2-ones or 1,4 bis-phenyl-substituted butanones, respectively. Finally, in the third case, aldolase catalysis was employed for synthesis of the corresponding 1,3,4-trihydroxylated pentan-2-one derivatives. The organocatalytic route with cinchonine generated distereomerically enriched syn-products (de = 60-99%), with moderate enantiomeric excesses (ee = 43-56%) but did not produce aldols with either hydroxyacetone or dihydroxyacetone as donor ketones. The SmI2-promoted reductive cross-coupling generated product mixtures with diastereomeric and enantiomeric ratios close to unity. This route allowed for the production of both 1-methyl- and 1-phenyl-substituted 2,3-dihydroxybutanones at yields between 40-60%. Finally, the biocatalytic approach resulted in enantiopure syn-(3 R,4 S) 1,3,4-trihydroxypentan-2-ones.
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Affiliation(s)
- Derar Al-Smadi
- Department of Chemistry-BMC , Uppsala University , Box 576, SE-751 23 Uppsala , Sweden
| | - Thilak Reddy Enugala
- Department of Chemistry-BMC , Uppsala University , Box 576, SE-751 23 Uppsala , Sweden
| | - Vadim Kessler
- Department of Molecular Sciences , Swedish University of Agricultural Sciences , Box 7015, SE-750 07 Uppsala , Sweden
| | - Anil Ranu Mhashal
- Department of Chemistry-BMC , Uppsala University , Box 576, SE-751 23 Uppsala , Sweden
| | | | - Jan Kihlberg
- Department of Chemistry-BMC , Uppsala University , Box 576, SE-751 23 Uppsala , Sweden
| | - Thomas Norberg
- Department of Chemistry-BMC , Uppsala University , Box 576, SE-751 23 Uppsala , Sweden
| | - Mikael Widersten
- Department of Chemistry-BMC , Uppsala University , Box 576, SE-751 23 Uppsala , Sweden
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Ma H, Engel S, Enugala TR, Al-Smadi D, Gautier C, Widersten M. New Stereoselective Biocatalysts for Carboligation and Retro-Aldol Cleavage Reactions Derived from d-Fructose 6-Phosphate Aldolase. Biochemistry 2018; 57:5877-5885. [DOI: 10.1021/acs.biochem.8b00814] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Huan Ma
- Department of Chemistry-BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Sarah Engel
- Department of Chemistry-BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Thilak Reddy Enugala
- Department of Chemistry-BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Derar Al-Smadi
- Department of Chemistry-BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Candice Gautier
- Department of Chemistry-BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Mikael Widersten
- Department of Chemistry-BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
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Rodrigo G, Fares MA. Intrinsic adaptive value and early fate of gene duplication revealed by a bottom-up approach. eLife 2018; 7:29739. [PMID: 29303479 PMCID: PMC5771667 DOI: 10.7554/elife.29739] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 01/04/2018] [Indexed: 02/06/2023] Open
Abstract
The population genetic mechanisms governing the preservation of gene duplicates, especially in the critical very initial phase, have remained largely unknown. Here, we demonstrate that gene duplication confers per se a weak selective advantage in scenarios of fitness trade-offs. Through a precise quantitative description of a model system, we show that a second gene copy serves to reduce gene expression inaccuracies derived from pervasive molecular noise and suboptimal gene regulation. We then reveal that such an accuracy in the phenotype yields a selective advantage in the order of 0.1% on average, which would allow the positive selection of gene duplication in populations with moderate/large sizes. This advantage is greater at higher noise levels and intermediate concentrations of the environmental molecule, when fitness trade-offs become more evident. Moreover, we discuss how the genome rearrangement rates greatly condition the eventual fixation of duplicates. Overall, our theoretical results highlight an original adaptive value for cells carrying new-born duplicates, broadly analyze the selective conditions that determine their early fates in different organisms, and reconcile population genetics with evolution by gene duplication.
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Affiliation(s)
- Guillermo Rodrigo
- Instituto de Biología Molecular y Celular de Plantas, CSIC - UPV, Valencia, Spain.,Instituto de Biología Integrativa y de Sistemas, CSIC - UV, Paterna, Spain
| | - Mario A Fares
- Instituto de Biología Molecular y Celular de Plantas, CSIC - UPV, Valencia, Spain.,Instituto de Biología Integrativa y de Sistemas, CSIC - UV, Paterna, Spain.,Trinity College Dublin, University of Dublin, Dublin, Ireland
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Stellmacher L, Sandalova T, Schneider S, Schneider G, Sprenger GA, Samland AK. Novel mode of inhibition by D-tagatose 6-phosphate through a Heyns rearrangement in the active site of transaldolase B variants. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:467-76. [PMID: 27050126 DOI: 10.1107/s2059798316001170] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 01/19/2016] [Indexed: 01/06/2023]
Abstract
Transaldolase B (TalB) and D-fructose-6-phosphate aldolase A (FSAA) from Escherichia coli are C-C bond-forming enzymes. Using kinetic inhibition studies and mass spectrometry, it is shown that enzyme variants of FSAA and TalB that exhibit D-fructose-6-phosphate aldolase activity are inhibited covalently and irreversibly by D-tagatose 6-phosphate (D-T6P), whereas no inhibition was observed for wild-type transaldolase B from E. coli. The crystal structure of the variant TalB(F178Y) with bound sugar phosphate was solved to a resolution of 1.46 Å and revealed a novel mode of covalent inhibition. The sugar is bound covalently via its C2 atom to the ℇ-NH2 group of the active-site residue Lys132. It is neither bound in the open-chain form nor as the closed-ring form of D-T6P, but has been converted to β-D-galactofuranose 6-phosphate (D-G6P), a five-membered ring structure. The furanose ring of the covalent adduct is formed via a Heyns rearrangement and subsequent hemiacetal formation. This reaction is facilitated by Tyr178, which is proposed to act as acid-base catalyst. The crystal structure of the inhibitor complex is compared with the structure of the Schiff-base intermediate of TalB(E96Q) formed with the substrate D-fructose 6-phosphate determined to a resolution of 2.20 Å. This comparison highlights the differences in stereochemistry at the C4 atom of the ligand as an essential determinant for the formation of the inhibitor adduct in the active site of the enzyme.
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Affiliation(s)
- Lena Stellmacher
- Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, 70550 Stuttgart, Germany
| | - Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institutet, 17 165 Stockholm, Sweden
| | - Sarah Schneider
- Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, 70550 Stuttgart, Germany
| | - Gunter Schneider
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17 177 Stockholm, Sweden
| | - Georg A Sprenger
- Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, 70550 Stuttgart, Germany
| | - Anne K Samland
- Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, 70550 Stuttgart, Germany
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Mahdi R, Guérard-Hélaine C, Laroche C, Michaud P, Prévot V, Forano C, Lemaire M. Polysaccharide-layered double hydroxide–aldolase biohybrid beads for biocatalysed CC bond formation. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2015.07.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Calleja D, Kavanagh J, de Mas C, López-Santín J. Simulation and prediction of protein production in fed-batch E. coli cultures: An engineering approach. Biotechnol Bioeng 2015; 113:772-82. [PMID: 26416399 DOI: 10.1002/bit.25842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/22/2015] [Accepted: 09/24/2015] [Indexed: 12/17/2022]
Abstract
An overall model describing the dynamic behavior of fed-batch E. coli processes for protein production has been built, calibrated and validated. Using a macroscopic approach, the model consists of three interconnected blocks allowing simulation of biomass, inducer and protein concentration profiles with time. The model incorporates calculation of the extra and intracellular inducer concentration, as well as repressor-inducer dynamics leading to a successful prediction of the product concentration. The parameters of the model were estimated using experimental data of a rhamnulose-1-phosphate aldolase-producer strain, grown under a wide range of experimental conditions. After validation, the model has successfully predicted the behavior of different strains producing two different proteins: fructose-6-phosphate aldolase and ω-transaminase. In summary, the presented approach represents a powerful tool for E. coli production process simulation and control.
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Affiliation(s)
- Daniel Calleja
- Departament d'Enginyeria Química, Escola d'Enginyeria, Edifici Q, Universitat Autònoma de Barcelona, 08193 Bellaterra, Catalunya, Spain
| | - John Kavanagh
- School of Chemical and Biomolecular Engineering, Chemical Engineering Building, The University of Sydney, New South Wales, Australia
| | - Carles de Mas
- Departament d'Enginyeria Química, Escola d'Enginyeria, Edifici Q, Universitat Autònoma de Barcelona, 08193 Bellaterra, Catalunya, Spain
| | - Josep López-Santín
- Departament d'Enginyeria Química, Escola d'Enginyeria, Edifici Q, Universitat Autònoma de Barcelona, 08193 Bellaterra, Catalunya, Spain.
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Stellmacher L, Sandalova T, Leptihn S, Schneider G, Sprenger GA, Samland AK. Acid-Base Catalyst Discriminates between a Fructose 6-Phosphate Aldolase and a Transaldolase. ChemCatChem 2015. [DOI: 10.1002/cctc.201500478] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Lena Stellmacher
- Institut für Mikrobiologie; Universität Stuttgart; Allmandring 31 70550 Stuttgart Germany
| | - Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine, Solna; Karolinska Institutet; 17165 Stockholm Sweden
| | - Sebastian Leptihn
- Institut für Mikrobiologie; Universität Hohenheim; Garbenstrasse 30 70599 Stuttgart Germany
| | - Gunter Schneider
- Department of Medical Biochemistry and Biophysics; Karolinska Institutet; 17177 Stockholm Sweden
| | - Georg A. Sprenger
- Institut für Mikrobiologie; Universität Stuttgart; Allmandring 31 70550 Stuttgart Germany
| | - Anne K. Samland
- Institut für Mikrobiologie; Universität Stuttgart; Allmandring 31 70550 Stuttgart Germany
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Guérard-Hélaine C, de Berardinis V, Besnard-Gonnet M, Darii E, Debacker M, Debard A, Fernandes C, Hélaine V, Mariage A, Pellouin V, Perret A, Petit JL, Sancelme M, Lemaire M, Salanoubat M. Genome Mining for Innovative Biocatalysts: New Dihydroxyacetone Aldolases for the Chemist’s Toolbox. ChemCatChem 2015. [DOI: 10.1002/cctc.201500014] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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12
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DHAP-dependent aldolases from (hyper)thermophiles: biochemistry and applications. Extremophiles 2013; 18:1-13. [DOI: 10.1007/s00792-013-0593-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Accepted: 10/10/2013] [Indexed: 12/20/2022]
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