Screening Potential Substrates for E. coli Growth

To determine the carbon, nitrogen, phosphorus and sulfur sources that could support simulated growth, we screened all of the metabolites that could be exchanged with the environment (i.e., exchange reactions) in the iAF1260 and iJR904 models. The identified metabolites formed the potential substrate sets (Table IV). Through subsequent simulations, we set an arbitrary maximum flux of 20 mmol substrate gDW⁻¹ h⁻¹ for each potential substrate tested (consistent with maximum observed substrate uptake rates in vivo) and optimized for flux through the BOF_CORE using FBA and either iAF1260 or iJR904. An OUR of 18.5 mmol gDW⁻¹ h⁻¹, the BOF_CORE, a NGAM of 8.39 mmol ATP gDW⁻¹ h⁻¹, a GAM of 59.81 mmol ATP gDW⁻¹ and no regulatory constrains were used during the growth condition analysis of iAF1260 (for iJR904, see Reed et al, 2003 (link)). During the analysis, the reactions CAT, SPODM and SPODMpp were constrained to zero to prevent generation of cellular energy equivalents through reactions involved in E. coli's response to oxidative stress. If a positive flux could be generated through the BOF_CORE reaction (v_BOFcore>0), then the substrate was considered a viable source. Experimental data used in the comparison were provided by Biolog (http://www.biolog.com) and both ‘weak' and ‘positive' readings from the biolog data were considered as a positive growth condition.