title: An ensemble-guided approach identifies ClpP as a major regulator of transcript levels in nitric oxide-stressed Escherichia coli.
abstract: 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(∙).
authors.affiliation: Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States.
authors.forename: Jonathan L
authors.initials: JL
authors.lastname: Robinson
authors.affiliation: Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States. Electronic address: mbrynild@princeton.edu.
authors.forename: Mark P
authors.initials: MP
authors.lastname: Brynildsen
mesh_terms: D055162:Biocatalysis; D004093:Dihydropteridine Reductase / Q000235:genetics*; D049071:Endopeptidase Clp / Q000502:physiology*; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics* / Q000502:physiology*; D006420:Hemeproteins / Q000235:genetics*; D009247:NADH, NADPH Oxidoreductases / Q000235:genetics*; D009569:Nitric Oxide / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D012333:RNA, Messenger / Q000032:analysis*; D017423:Sequence Analysis, RNA; D013312:Stress, Physiological; D014158:Transcription, Genetic
chemical_list: D029968:Escherichia coli Proteins; D006420:Hemeproteins; D012333:RNA, Messenger; D009569:Nitric Oxide; D004093:Dihydropteridine Reductase; C076538:hmp protein, E coli; D009247:NADH, NADPH Oxidoreductases; C483572:ClpP protease, E coli; D049071:Endopeptidase Clp
keywords: ClpP protease; Escherichia coli; Hmp; Kinetic modeling; Nitric oxide; Nitrosative stress