title: Using a genome-scale metabolic model of Enterococcus faecalis V583 to assess amino acid uptake and its impact on central metabolism.
abstract: Increasing antibiotic resistance in pathogenic bacteria necessitates the development of new medication strategies. Interfering with the metabolic network of the pathogen can provide novel drug targets but simultaneously requires a deeper and more detailed organism-specific understanding of the metabolism, which is often surprisingly sparse. In light of this, we reconstructed a genome-scale metabolic model of the pathogen Enterococcus faecalis V583. The manually curated metabolic network comprises 642 metabolites and 706 reactions. We experimentally determined metabolic profiles of E. faecalis grown in chemically defined medium in an anaerobic chemostat setup at different dilution rates and calculated the net uptake and product fluxes to constrain the model. We computed growth-associated energy and maintenance parameters and studied flux distributions through the metabolic network. Amino acid auxotrophies were identified experimentally for model validation and revealed seven essential amino acids. In addition, the important metabolic hub of glutamine/glutamate was altered by constructing a glutamine synthetase knockout mutant. The metabolic profile showed a slight shift in the fermentation pattern toward ethanol production and increased uptake rates of multiple amino acids, especially l-glutamine and l-glutamate. The model was used to understand the altered flux distributions in the mutant and provided an explanation for the experimentally observed redirection of the metabolic flux. We further highlighted the importance of gene-regulatory effects on the redirection of the metabolic fluxes upon perturbation. The genome-scale metabolic model presented here includes gene-protein-reaction associations, allowing a further use for biotechnological applications, for studying essential genes, proteins, or reactions, and the search for novel drug targets.
authors.affiliation: Department of Modeling Biological Processes, Center for Organismal Studies/Bioquant, Heidelberg University, Heidelberg, Germany nadine.veith@bioquant.uni-heidelberg.de.
authors.forename: Nadine
authors.initials: N
authors.lastname: Veith
authors.affiliation: Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway.
authors.forename: Margrete
authors.initials: M
authors.lastname: Solheim
authors.affiliation: Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam and Netherlands Institute of Systems Biology, Amsterdam, The Netherlands.
authors.forename: Koen W A
authors.initials: KW
authors.lastname: van Grinsven
authors.affiliation: Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines, and Systems, VU University of Amsterdam, Amsterdam, The Netherlands.
authors.forename: Brett G
authors.initials: BG
authors.lastname: Olivier
authors.affiliation: Department of Modeling Biological Processes, Center for Organismal Studies/Bioquant, Heidelberg University, Heidelberg, Germany.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Levering
authors.affiliation: Department of Modeling Biological Processes, Center for Organismal Studies/Bioquant, Heidelberg University, Heidelberg, Germany.
authors.forename: Ruth
authors.initials: R
authors.lastname: Grosseholz
authors.affiliation: Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam and Netherlands Institute of Systems Biology, Amsterdam, The Netherlands.
authors.forename: Jeroen
authors.initials: J
authors.lastname: Hugenholtz
authors.affiliation: Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway.
authors.forename: Helge
authors.initials: H
authors.lastname: Holo
authors.affiliation: Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway.
authors.forename: Ingolf
authors.initials: I
authors.lastname: Nes
authors.affiliation: Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines, and Systems, VU University of Amsterdam, Amsterdam, The Netherlands.
authors.forename: Bas
authors.initials: B
authors.lastname: Teusink
authors.affiliation: Department of Modeling Biological Processes, Center for Organismal Studies/Bioquant, Heidelberg University, Heidelberg, Germany.
authors.forename: Ursula
authors.initials: U
authors.lastname: Kummer
mesh_terms: D000596:Amino Acids / Q000378:metabolism*; D003198:Computer Simulation; D004734:Energy Metabolism; D013293:Enterococcus faecalis / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D064688:Metabolic Flux Analysis; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D008954:Models, Biological
chemical_list: D000596:Amino Acids