RNA-seq analyzes the effect of ptsI on transcriptome in Escherichia coli during ciprofloxacin treatment.

A deficiency in ptsI, encoding a cytoplasmic protein that serves as the gateway for the phosphoenolpyruvate:sugar phosphotransferase system, was found to confer tolerance to diverse types of disinfectants and antimicrobials. To understand the molecular basis of the increased tolerance, we performed RNA-seq analysis to compare the transcriptional profiles of the wild-type and the ?ptsI mutant strains before and after ciprofloxacin treatment. The data showed that cirpofloxacin treatment drastically increased the exprerssion of genes encoding enzymes in the TCA cycle and that the ptsI mutation suppressed the expression of most TCA genes and all ATP synthase genes, but elevated some of the genes involved in glycolysis and the pentose phosphate pathway (PPP) genes. Such transcriptomic alteration reduced stress-induced surge in respiration and accumutaion of toxic reaactive oxygen species, thereby conferring bacterial tolerance to diverse lethal stressors. Overall design: Mid-log-phase cultures of E. coli K-12 were treated with ciprofloxacin (5 MIC) for 0 min and 90 min. Cells were collected for total RNA extraction and subsequent RNA-seq. Differential expression of various conditions was analyzed.