Systems approach for identification of the Escherichia coli K-12 LysR-type transcriptional regulators function.

It is now possible to discover the physiological function of LysR-family transcription factors (LLTF) in E. coli using ChIP-Exo (in vivo DNA-binding), growth phenotype, conserved gene clustering, and transcriptional analysis (RNA-seq deletion mutants). The LysR-family regulator phenotype microarray has been detected for YbdO, YbeF, YcaN, YiaU, and YgfI deletion mutants and for the isogenic E. coli BW25113 strain in minimal medium at carbon/nitrogen starvation or L-threonine supplement conditions. The LLTF YbdO and YgfI regulation is important for bacterial growth adaptation to low pH with citrate supplementation or glycerol as the carbon source, respectively. A systems analysis approach allows for the identification of the YneJ (putrescine utilization), YgfI, and YbdO transcription factor regulated genes in Escherichia coli. YgfI regulates DhaKLM, the phosphotransferase system involved in glycerol and dihydroxyacetone utilization. YbdO is a repressor for ybdMN and is likely involved in citrate lyase regulation. YneJ, re-named PtrR, directly controls the expression of the succinate-semialdehyde dehydrogenase Sad (YneI) and is important for bacterial growth in the presence of L-glutamate as a nitrogen source. The sad promoter is repressed by PtrR. PtrR is also a repressor of the fnrS gene, encoding a small regulatory RNA involved in the regulation of the sodB gene, as shown by RNA-seq data. A 15-bp palindromic PtrR-binding site was identified in the upstream regions of the sad / ptrR and fnrS genes and confirmed by ChIP-Exo and fluorescent polarization assays. The PtrR-dependent regulation of fnrS likely leads to a regulatory cascade induced by this small RNA. Ribosomal RNA removed RNA prepared from cell cultures of Escherichia coli at the exponential phase