Systematic identification and characterization of uncharacterized transcription factors in Escherichia coli K-12 MG1655

Bacteria regulate gene expression to adapt to changing environments through transcriptional regulatory networks (TRNs). Although extensively studied, TRNs are not fully characterized since we do not know the identity of all the transcriptional regulators that comprise a TRN. Here, we experimentally evaluate 40 uncharacterized proteins in the model organisms Escherichia coli K-12 MG1655, which were previously predicted to be transcription factors (TFs). First, we used myc-tagging and a multiplexed ChIP-exo assay to characterize genome-wide binding sites for the 40 candidate TFs. Then, we compared those binding sites with those of RNA polymerase and sigma factors to increase the confidence in the measured DNA-binding events. Finally, we used these data to infer potential functional annotation for 13 candidate TFs. As a result, we characterized 570 new binding sites for 34 of 40 candidate TFs. Taken together, the study; 1) expands the number of confirmed TFs from 249 to 278, that is close to the estimated total of about 280 TFs in E. coli K-12 MG1655, 2) it provides a roadmap for  functional characterization of the 34 discovered TFs, and 3) it enables the elucidation of the first comprehensive TRN. Expression profiling data for wild type E. coli and their yTFs deletion strains were generated by RNA-seq, in duplicate