Fig. 7
Integration of CsrA into E. coli regulatory networks. a Transcriptional regulators, two-component regulatory system (TCS) sensor kinases, and sRNAs that were differentially expressed in the csrA mutant and their target genes are shown. E. coli transcriptional and sRNA regulatory networks were extracted from RegulonDB4. Regulators associated with CLIP-seq peaks and differentially expressed are shown in green and those differentially expressed without an associated CLIP-seq peak are in purple. Those with CLIP-seq peaks that were not differentially expressed are shown in green and white. Regulators represented as squares are transcription factors, triangles are sRNAs, and diamonds are sigma factors. Sensor kinases that were differentially expressed are shown together with their cognate response regulators. b–e Electrophoretic mobility shift assays (EMSA) showing interaction of CsrA with transcripts of regulatory genes: b fliA (−30 to +165 nt relative to the start codon). c soxS (−40 to +87 relative to the start codon), d lrp (−318 to +45 nt relative to the start codon). e cra (−81 to +222 nt relative to the start codon)
