Influence of the putative transcription factor ClbR and the thioesterase ClbQ on colibactin synthesis regulation and characterization of critical transcription start sites in Escherichia coli

By comparing the transcriptome profile upon deletion or overexpression of ClbR or ClbQ, we addressed the role of these proteins in regulation of colibactin expression. Our global screen indicates that ClbR is the key transcriptional activator of colibactin expression. In addition, we further investigated potential transcription start sites of the colibactin determinant. Bacterial cultures with an OD600nm of 0.4 (three biological triplicates with eight technical replicates, 140µl each), were pooled. The pools of five different samples (wildtype reference strain, and four different mutants) were included into RNA-seq analysis. In addition, a sample of the reference strain was TEX-treated for transcription start mapping by differential RNA-seq.