Adaptive siderophore repression and redox-metabolic remodeling limit E. coli Fenton-mediated cytotoxicity after H2O2 exposure

Abstract

Hydrogen peroxide imposes linked redox and metal stress on bacteria by promoting ferrous iron-dependent Fenton chemistry, generating reactive species that damage DNA, proteins, iron-sulfur cofactors, and membranes. Because siderophores expand iron acquisition, their continued production during peroxide exposure may increase cytotoxicity by enlarging the labile iron pool. Here, we identify an adaptive iron-restriction response that connects siderophore repression, envelope integrity, and metabolic remodeling during bacterial peroxide stress. Using Acinetobacter baumannii, Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus, we evaluated cellular oxidation kinetics, growth-normalized extracellular siderophore release, membrane permeabilization, and viability following sub-inhibitory H2O2 exposure. Acute peroxide treatment significantly elevated general fluorophore oxidation across all species (p < 0.0001), while prolonged exposure reduced biomass-normalized siderophore output, most strongly in E. coli and S. aureus. Membrane permeability accounted for a substantial fraction of extracellular siderophore variation, indicating that envelope alterations link peroxide-induced damage to iron-acquisition dynamics. We further integrated these physical phenotypes with differential transcriptomics, oxidation gene expression regression, E-Flux-constrained genome-scale metabolic modeling, flux variability analysis, shadow price analysis, and in silico gene-essentiality mapping in acute and 500-generation H2O2-adapted E. coli. Acute stress transiently co-activated iron uptake, efflux, NADPH regeneration, and stress-defense genes. In contrast, long-term adaptation systematically repressed enterobactin biosynthesis and uptake components (fepA, entE, fes, ryhB) while inducing persistent peroxide- and acid-resistance modules (ahpC, gadA, gadB). Genome-scale metabolic modeling independently verified that this evolutionary adaptation contracted flux variability, relieved envelope bottlenecks, and eliminated acute stress-specific single-gene vulnerabilities at the cost of reduced maximal growth capacity. Together, these results define siderophore repression as a system-level adaptive response that limits Fenton-reactive iron influx while reallocating metabolic resources toward redox buffering, membrane stabilization, and genetic robustness.