Antibiotic tolerance is associated with a broad and complex transcriptional response in E. coli
SummaryAntibiotic treatment kills a large portion of a population, while a small, tolerant subpopulation survives. Tolerant bacteria disrupt the efficacy of antibiotics and increase the likelihood that a population gains antibiotic resistance, a growing concern. Using a systems biology approach to, we examine how transcriptional networks respond to antibiotic stress to survive and recover from antibiotic treatment. We are the first to apply transcriptional regulatory network (TRN) analysis to antibiotic tolerance in E. coli, by comparing gene expression with and without lethal concentrations of ampicillin and leveraging existing knowledge of transcriptional regulation. TRN analysis shows that changes in gene expression specific to ampicillin treatment are likely caused by specific sigma and transcription factors typically regulated by proteolysis. These results demonstrate that altered activity of specific regulatory proteins cause an active and coordinated transcriptional response that leverages multiple gene systems to survive and recover from ampicillin treatment.