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

TitleAn ensemble-guided approach identifies ClpP as a major regulator of transcript levels in nitric oxide-stressed Escherichia coli.
Publication TypeJournal Article
Year of Publication2015
AuthorsRobinson, JL, Brynildsen, MP
JournalMetab Eng
Volume31
Pagination22-34
Date Published2015 09 01
ISSN1096-7184
KeywordsBiocatalysis, Dihydropteridine Reductase, Endopeptidase Clp, Escherichia coli, Escherichia coli Proteins, Hemeproteins, NADH, NADPH Oxidoreductases, Nitric Oxide, Promoter Regions, Genetic, RNA, Messenger, Sequence Analysis, RNA, Stress, Physiological, Transcription, Genetic
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(∙).

DOI10.1016/j.ymben.2015.06.005
Alternate JournalMetab. Eng.
PubMed ID26112956