An ensemble-guided approach identifies ClpP as a major regulator of transcript levels in nitric oxide-stressed Escherichia coli

The importance of NO^{{bullet operator}} to immunity is highlighted by the diversity of pathogens that require NO^{{bullet operator}}-defensive systems to establish infections. Proteases have been identified to aid pathogens in surviving macrophage attack, inspiring us to investigate their role during NO^{{bullet operator}} stress in Escherichia coli. We discovered that the elimination of ClpP largely impaired NO^{{bullet operator}} detoxification by E. coli. Using a quantitative model of NO^{{bullet operator}} stress, we employed an ensemble-guided approach to identify the underlying mechanism. Iterations of in silico analyses and corresponding experiments identified the defect to result from deficient transcript levels of hmp, which encodes NO^{{bullet operator}} dioxygenase. Interestingly, the defect was not confined to hmp, as δclpP imparted widespread perturbations to the expression of NO^{{bullet operator}}-responsive genes. This work identified a target for anti-infective therapies based on disabling NO^{{bullet operator}} defenses, and demonstrated the utility of model-based approaches for exploring the complex, systems-level stress exerted by NO^{{bullet operator}}.