Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655 [RNA-seq]

A transcription factor (TF), OmpR, plays a critical role in transcriptional regulation of the defense system for osmotic stress in bacteria. However, its full genome-wide regulatory potential is unknown. Here, we perform a genome-scale reconstruction of the OmpR regulon in Escherichia coli K-12 MG1655. Integrative data analysis reveals that a total of 37 genes in 24 transcription units (TUs) belong to OmpR regulon. Among them, 26 genes show more than two-fold changes in expression level under OmpR knock-out condition. We find that OmpR tends to regulate mostly membrane-located gene products of diverse fundamental biological processes, such as narU, ompX, and nuoN. Investigating co-regulation of entire set of genes regulated by other stress-response TFs unveils that they are surprisingly independently regulated by TF(s) responding to each stress. Additionally, detailed investigation of physiological roles of newly discovered OmpR regulon reveals that activation of narU encoding nitrate/nitrite transporter is a relatively unique strategy of E. coli K-12 MG1655 to significantly improve cellular tolerance toward osmotic stress. Overall design: A total of four samples were analyzed. WT and ?ompR mutant cells were cultured in M9 minimal media with 0.2% glucose. Then cells were treated with 0.3 M of NaCl at mid-log pahse for 30 min with agitation.