A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types
Fig 4
Condition-specific GEM validation and evaluation.
(A) Quantitative exo-metabolomics measurements (for both CDM and CDMG) were used to build two condition specific GEMs. Growth was simulated using flux balance analysis and cross-checked against experimentally observed growth rates. See S1 Appendix for comparison of predicted and measured relative growth rate across the two media types. (B) We compared the measured and simulated relative oxygen consumption as well as the relative intracellular ATP concentration between the two condition-specific GEMs (Methods). (C) Growth phenotype predictions for 28 CDM-specific mutant GEMs were compared against experimentally observed transposon mutant growth phenotypes. Two genes (ackA and gudB) were classified as false positives due to the presence of alternative pathways. (D) We simulated single reaction knockouts and compared essential reactions across conditions. The Venn diagram highlights the differences in reaction essentiality between the CDM-specific GEM and the CDMG-specific GEM.