Investigation of network flexibility and identification of reaction essentiality of human host cells infected by S. flexneri.
We have developed a consistently reduced core model for HeLa based on the genome scale human reconstruction. This reduced model includes the central carbon pathways, the electron transport chains, all the necessary transport and exchange reactions and the essential compartments for HeLa. In addition, the pyruvate/glutamate metabolism and the purine/pyrimidine catabolism for HeLa were incorporated based on available experimental observations. The core HeLa model consists of 273 reactions and 202 metabolites. The tFBA analysis of the resulting model, where we integrated experimental information about the metabolites concentrations and fluxes, allowed us to: (i) identify the thermodynamically feasible direction profiles of the system; (ii) classify the reactions according to how close (or far) they operate from their thermodynamic equilibrium. This analysis also shed light on the flexibility of the network in terms of the feasible ranges of the metabolite levels and Gibbs energies of reactions. Furthermore, we used the ORACLE (Optimization and Risk Analysis of Complex Living Entities) framework to develop sets of mechanistic kinetics models. ORACLE allows us, despite incomplete information about kinetic properties of the network, to integrate thermodynamics, and available omics and kinetic data. Using these models, we identified and ranked the metabolites according to their impact on the HeLa physiology when drained from the system. This analysis allowed us to uncover the ‘weak’ and ‘strong’ links in host-pathogen interactions. The identification of such links of the metabolic interface between host and pathogen networks could potentially be validated in vitro and can help us understand the mechanisms of infection and provide insights in the fight against intracellular pathogens.