Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)

Escherichia coli use two-component systems (TCSs) to respond to environmental signals. TCSs affect gene expression and are parts of E. coli's global transcriptional regulatory network (TRN). Here, we identified the regulons of five TCSs in E. coli MG1655: BaeSR and CpxAR, which were stimulated by ethanol stress, and KdpDE, PhoRB, and ZraSR, which were stimulated by potassium, phosphate, and zinc, respectively. We analyzed RNA-seq data using independent component analysis (ICA). ChIP-exo data was used to validate condition-specific target gene binding sites. Based on this data we (1) identify the target genes for each TCS; (2) show how the target genes are transcribed in response to stimulus; and (3) reveal novel relationships between TCSs, which indicate non-cognate inducers for various response regulators, such as BaeR to iron starvation, CpxR to phosphate limitation, and PhoB and ZraR to cell envelope stress. Our understanding of the TRN in E. coli is thus notably expanded. Overall design: Expression profiling data for five two-component system deletion strains and wild type were generated by RNA-seq, in duplicate