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Appl Environ Microbiol. 2015 Mar;81(5):1622-33. doi: 10.1128/AEM.03279-14. Epub 2014 Dec 19.

Using a genome-scale metabolic model of Enterococcus faecalis V583 to assess amino acid uptake and its impact on central metabolism.

Author information

1
Department of Modeling Biological Processes, Center for Organismal Studies/Bioquant, Heidelberg University, Heidelberg, Germany nadine.veith@bioquant.uni-heidelberg.de.
2
Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway.
3
Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam and Netherlands Institute of Systems Biology, Amsterdam, The Netherlands.
4
Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines, and Systems, VU University of Amsterdam, Amsterdam, The Netherlands.
5
Department of Modeling Biological Processes, Center for Organismal Studies/Bioquant, Heidelberg University, Heidelberg, Germany.

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.

PMID:
25527553
PMCID:
PMC4325170
DOI:
10.1128/AEM.03279-14
[Indexed for MEDLINE]
Free PMC Article

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