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

The importance of NO∙ to immunity is highlighted by the diversity of pathogens that require NO∙-defensive systems to establish infections. Proteases have been identified to aid pathogens in surviving macrophage attack, inspiring us to investigate their role during NO∙ stress in Escherichia coli. We discovered that the elimination of ClpP largely impaired NO∙ detoxification by E. coli. Using a quantitative model of NO∙ 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∙ dioxygenase. Interestingly, the defect was not confined to hmp, as ΔclpP imparted widespread perturbations to the expression of NO∙-responsive genes. This work identified a target for anti-infective therapies based on disabling NO∙ defenses, and demonstrated the utility of model-based approaches for exploring the complex, systems-level stress exerted by NO∙.