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A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors

Mathieu Larocque, Thierry Chénard, View ORCID ProfileRafael Najmanovich
doi: https://doi.org/10.1101/006932
Mathieu Larocque
Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke. Sherbrooke, J1H 5N4, Canada.
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Thierry Chénard
Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke. Sherbrooke, J1H 5N4, Canada.
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Rafael Najmanovich
Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke. Sherbrooke, J1H 5N4, Canada.
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  • ORCID record for Rafael Najmanovich
  • For correspondence: rafael.najmanovich@usherbrooke.ca
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ABSTRACT

Clostridium difficile is the leading cause of hospital-borne infections occurring when the natural intestinal flora is depleted following antibiotic treatment. We present iMLTC804cdf, an extensively curated reconstructed metabolic network for the C. difficile pathogenic strain 630. iMLTC804cdf contains 804 genes, 705 metabolites and 766 metabolic, 145 exchange and 118 transport reactions. iMLTC804cdf is the most complete and accurate metabolic reconstruction of a gram-positive anaerobic bacteria to date. We validate the model with simulated growth assays in different media and carbon sources and use it to predict essential genes. We obtain 88.8% accuracy in the prediction of gene essentiality when compared to experimental data for B. subtilis homologs. We predict the existence of 83 essential genes and 68 essential gene pairs, a number of which are unique to C. difficile and have non-existing or predicted non-essential human homologs. For 19 of these potential therapeutic targets, we find 72 inhibitors of homologous proteins that could serve as starting points in the development of new antibiotics, including approved drugs with the potential for drug repositioning.

Systems & Synthetic Biology Subject Category: Genome Scale & Integrative Biology

Molecular & Cell Biology Subject Category: Pharmacology & Drug Discovery

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted July 25, 2014.
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A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors
Mathieu Larocque, Thierry Chénard, Rafael Najmanovich
bioRxiv 006932; doi: https://doi.org/10.1101/006932
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A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors
Mathieu Larocque, Thierry Chénard, Rafael Najmanovich
bioRxiv 006932; doi: https://doi.org/10.1101/006932

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