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Trichez D, Auriol C, Baylac A, Irague R, Dressaire C, Carnicer-Heras M, Heux S, François JM, Walther T. Engineering of Escherichia coli for Krebs cycle-dependent production of malic acid. Microb Cell Fact 2018; 17:113. [PMID: 30012131 PMCID: PMC6048880 DOI: 10.1186/s12934-018-0959-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 07/06/2018] [Indexed: 11/27/2022] Open
Abstract
Background Malate is a C4-dicarboxylic acid widely used as an acidulant in the food and beverage industry. Rational engineering has been performed in the past for the development of microbial strains capable of efficient production of this metabolite. However, as malate can be a precursor for specialty chemicals, such as 2,4-dihydroxybutyric acid, that require additional cofactors NADP(H) and ATP, we set out to reengineer Escherichia coli for Krebs cycle-dependent production of malic acid that can satisfy these requirements. Results We found that significant malate production required at least simultaneous deletion of all malic enzymes and dehydrogenases, and concomitant expression of a malate-insensitive PEP carboxylase. Metabolic flux analysis using 13C-labeled glucose indicated that malate-producing strains had a very high flux over the glyoxylate shunt with almost no flux passing through the isocitrate dehydrogenase reaction. The highest malate yield of 0.82 mol/mol was obtained with E. coli Δmdh Δmqo ΔmaeAB ΔiclR ΔarcA which expressed malate-insensitive PEP carboxylase PpcK620S and NADH-insensitive citrate synthase GltAR164L. We also showed that inactivation of the dicarboxylic acid transporter DcuA strongly reduced malate production arguing for a pivotal role of this permease in malate export. Conclusions Since more NAD(P)H and ATP cofactors are generated in the Krebs cycle-dependent malate production when compared to pathways which depend on the function of anaplerotic PEP carboxylase or PEP carboxykinase enzymes, the engineered strain developed in this study can serve as a platform to increase biosynthesis of malate-derived metabolites such as 2,4-dihydroxybutyric acid. Electronic supplementary material The online version of this article (10.1186/s12934-018-0959-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Debora Trichez
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Clément Auriol
- TWB, 3 rue Ariane, 31520, Ramonville-St. Agnes, France.,Cinabio, Cinabio-Adisseo France S.A.S., 31077, Toulouse, France
| | - Audrey Baylac
- TWB, 3 rue Ariane, 31520, Ramonville-St. Agnes, France
| | - Romain Irague
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | | | | | - Stéphanie Heux
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Jean Marie François
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France. .,TWB, 3 rue Ariane, 31520, Ramonville-St. Agnes, France.
| | - Thomas Walther
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.,TWB, 3 rue Ariane, 31520, Ramonville-St. Agnes, France.,Institute of Natural Materials Technology, Technische Universität Dresden, 01062, Dresden, Germany
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Irague R, Topham CM, Martineau N, Baylac A, Auriol C, Walther T, François JM, André I, Remaud-Siméon M. A generic HTS assay for kinase screening: Validation for the isolation of an engineered malate kinase. PLoS One 2018; 13:e0193036. [PMID: 29462203 PMCID: PMC5819781 DOI: 10.1371/journal.pone.0193036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 02/03/2018] [Indexed: 01/17/2023] Open
Abstract
An end-point ADP/NAD+ acid/alkali assay procedure, directly applicable to library screening of any type of ATP-utilising/ADP producing enzyme activity, was implemented. Typically, ADP production is coupled to NAD+ co-enzyme formation by the conventional addition of pyruvate kinase and lactate dehydrogenase. Transformation of enzymatically generated NAD+ into a photometrically active alkali derivative product is then achieved through the successive application of acidic/alkali treatment steps. The assay was successfully miniaturized to search for malate kinase activity in a structurally-guided library of LysC aspartate kinase variants comprising 6,700 clones. The screening procedure enabled the isolation of nine positive variants showing novel kinase activity on (L)-malate, the best mutant, LysC V115A:E119S:E434V exhibited strong substrate selectivity for (L)-malate compared to (L)-aspartate with a (kcat/Km)malate/(kcat/Km)aspartate ratio of 86. Double mutants V115A:E119S, V115A:E119C and E119S:E434V were constructed to further probe the origins of stabilising substrate binding energy gains for (L)-malate due to mutation. The introduction of less sterically hindering side-chains in engineered enzymes carrying E119S and V115A mutations increases the effective volume available for substrate binding in the catalytic pocket. Improved binding of the (L)-malate substrate may be assisted by less hindered movement of the Phe184 aromatic side-chain. Additional favourable long-range electostatic effects on binding arising from the E434V surface mutation are conditionally dependent upon the presence of the V115A mutation close to Phe184 in the active-site.
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Affiliation(s)
- Romain Irague
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- Toulouse White Biotechnology, Parc technologique du canal, Bâtiment NAPA CENTER B, Toulouse, France
| | - Christopher M. Topham
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- Toulouse White Biotechnology, Parc technologique du canal, Bâtiment NAPA CENTER B, Toulouse, France
| | - Nelly Martineau
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- Toulouse White Biotechnology, Parc technologique du canal, Bâtiment NAPA CENTER B, Toulouse, France
| | - Audrey Baylac
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- Toulouse White Biotechnology, Parc technologique du canal, Bâtiment NAPA CENTER B, Toulouse, France
| | - Clément Auriol
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- Toulouse White Biotechnology, Parc technologique du canal, Bâtiment NAPA CENTER B, Toulouse, France
| | - Thomas Walther
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- Toulouse White Biotechnology, Parc technologique du canal, Bâtiment NAPA CENTER B, Toulouse, France
| | - Jean-Marie François
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- Toulouse White Biotechnology, Parc technologique du canal, Bâtiment NAPA CENTER B, Toulouse, France
| | - Isabelle André
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- Toulouse White Biotechnology, Parc technologique du canal, Bâtiment NAPA CENTER B, Toulouse, France
| | - Magali Remaud-Siméon
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- Toulouse White Biotechnology, Parc technologique du canal, Bâtiment NAPA CENTER B, Toulouse, France
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Serino M, Luche E, Gres S, Baylac A, Bergé M, Cenac C, Waget A, Klopp P, Iacovoni J, Klopp C, Mariette J, Bouchez O, Lluch J, Ouarné F, Monsan P, Valet P, Roques C, Amar J, Bouloumié A, Théodorou V, Burcelin R. Metabolic adaptation to a high-fat diet is associated with a change in the gut microbiota. Gut 2012; 61:543-53. [PMID: 22110050 PMCID: PMC3292714 DOI: 10.1136/gutjnl-2011-301012] [Citation(s) in RCA: 443] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE The gut microbiota, which is considered a causal factor in metabolic diseases as shown best in animals, is under the dual influence of the host genome and nutritional environment. This study investigated whether the gut microbiota per se, aside from changes in genetic background and diet, could sign different metabolic phenotypes in mice. METHODS The unique animal model of metabolic adaptation was used, whereby C57Bl/6 male mice fed a high-fat carbohydrate-free diet (HFD) became either diabetic (HFD diabetic, HFD-D) or resisted diabetes (HFD diabetes-resistant, HFD-DR). Pyrosequencing of the gut microbiota was carried out to profile the gut microbial community of different metabolic phenotypes. Inflammation, gut permeability, features of white adipose tissue, liver and skeletal muscle were studied. Furthermore, to modify the gut microbiota directly, an additional group of mice was given a gluco-oligosaccharide (GOS)-supplemented HFD (HFD+GOS). RESULTS Despite the mice having the same genetic background and nutritional status, a gut microbial profile specific to each metabolic phenotype was identified. The HFD-D gut microbial profile was associated with increased gut permeability linked to increased endotoxaemia and to a dramatic increase in cell number in the stroma vascular fraction from visceral white adipose tissue. Most of the physiological characteristics of the HFD-fed mice were modulated when gut microbiota was intentionally modified by GOS dietary fibres. CONCLUSIONS The gut microbiota is a signature of the metabolic phenotypes independent of differences in host genetic background and diet.
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Affiliation(s)
- Matteo Serino
- Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, France,Université Paul Sabatier (UPS), Unité Mixte de Recherche (UMR) 1048, Institut de Maladies Métaboliques et Cardiovasculaires (IMC), Toulouse Cedex 4, France
| | - Elodie Luche
- Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, France,Université Paul Sabatier (UPS), Unité Mixte de Recherche (UMR) 1048, Institut de Maladies Métaboliques et Cardiovasculaires (IMC), Toulouse Cedex 4, France
| | - Sandra Gres
- Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, France,Université Paul Sabatier (UPS), Unité Mixte de Recherche (UMR) 1048, Institut de Maladies Métaboliques et Cardiovasculaires (IMC), Toulouse Cedex 4, France
| | - Audrey Baylac
- Université de Toulouse III, UPS, LU49, Adhésion Bactérienne et Formation de Biofilms, Toulouse Cedex 9, France
| | - Mathieu Bergé
- Université de Toulouse III, UPS, LU49, Adhésion Bactérienne et Formation de Biofilms, Toulouse Cedex 9, France
| | - Claire Cenac
- Neuro-Gastroenterology and Nutrition Unit, UMR INRA/EI-Purpan, Toulouse Cedex 3, France
| | - Aurelie Waget
- Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, France,Université Paul Sabatier (UPS), Unité Mixte de Recherche (UMR) 1048, Institut de Maladies Métaboliques et Cardiovasculaires (IMC), Toulouse Cedex 4, France
| | - Pascale Klopp
- Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, France,Université Paul Sabatier (UPS), Unité Mixte de Recherche (UMR) 1048, Institut de Maladies Métaboliques et Cardiovasculaires (IMC), Toulouse Cedex 4, France
| | - Jason Iacovoni
- Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, France,Université Paul Sabatier (UPS), Unité Mixte de Recherche (UMR) 1048, Institut de Maladies Métaboliques et Cardiovasculaires (IMC), Toulouse Cedex 4, France
| | - Christophe Klopp
- Plateforme Bio-informatique Toulouse Genopole®, UBIA INRA, Castanet-Tolosan Cedex, France
| | - Jerome Mariette
- Plateforme Bio-informatique Toulouse Genopole®, UBIA INRA, Castanet-Tolosan Cedex, France
| | - Olivier Bouchez
- GENOTOUL Platform, INRA Chemin de Borde-Rouge, Auzeville, France
| | - Jerome Lluch
- GENOTOUL Platform, INRA Chemin de Borde-Rouge, Auzeville, France
| | - Francoise Ouarné
- Université de Toulouse III, INSA, UPS, INP, LISBP, Toulouse, France
| | - Pierre Monsan
- Université de Toulouse III, INSA, UPS, INP, LISBP, Toulouse, France,CNRS, UMR5504, Toulouse, France,INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France,Institut Universitaire de France, Paris, France
| | - Philippe Valet
- Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, France,Université Paul Sabatier (UPS), Unité Mixte de Recherche (UMR) 1048, Institut de Maladies Métaboliques et Cardiovasculaires (IMC), Toulouse Cedex 4, France
| | - Christine Roques
- Université de Toulouse III, UPS, LU49, Adhésion Bactérienne et Formation de Biofilms, Toulouse Cedex 9, France
| | - Jacques Amar
- Rangueil Hospital, Department of Therapeutics, Toulouse, France
| | - Anne Bouloumié
- Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, France,Université Paul Sabatier (UPS), Unité Mixte de Recherche (UMR) 1048, Institut de Maladies Métaboliques et Cardiovasculaires (IMC), Toulouse Cedex 4, France
| | - Vassilia Théodorou
- Neuro-Gastroenterology and Nutrition Unit, UMR INRA/EI-Purpan, Toulouse Cedex 3, France
| | - Remy Burcelin
- Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, France,Université Paul Sabatier (UPS), Unité Mixte de Recherche (UMR) 1048, Institut de Maladies Métaboliques et Cardiovasculaires (IMC), Toulouse Cedex 4, France
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