(291c) The E. coli Proteome and Metallome Under Oxidative Stress

How tolerant a cell is to oxidative stress is a function of many complex and interacting mechanisms. We reconstructed a multiscale constraint-based model (stressME) of metabolic, proteome, and metallome responses to oxidative stress in Escherichia coli. Oxidative stress induced a global metabolic shift from respiration toward respiro-fermentation. The global shifts were mediated by the sigma factor RpoS, which was correctly predicted to be up-regulated. Oxidative stress decreased the overall translational efficiency due to the mismetallation of peptide deformylase (Def). The model predicted a compensatory up-regulation of Def, which was confirmed by RNA-Seq. Oxidative stress damaged iron-sulfur clusters in enzymes catalyzing amino acid biosynthesis. Auxotrophies were correctly predicted for aromatic, branched-chain, and sulfur-containing amino acids under oxidative stress. We further identified 32 stress-associated genes, which were more conserved across bacteria and archaea. We then simulated macrophage-mediated killing of E. coli through the interaction of Zn(II) overloading and reactive oxygen species (ROS). We found that the combination of ROS and a constraint on translational efficiency sensitized E. coli to Zn(II) overloading. We expect stressME to be useful for investigating the interplay between reactive oxygen species, metal homeostasis, and cell physiology in the context of disease and metabolic engineering.