Mechanisms shaping the transcriptome of E. coli to non-lethal rifampicin stress

Rifampicin, by hampering transcription, perturbs bacteria even at non-lethal concentrations. In response, Escherichia coli adapts its phenotype to minimize mortality, which is followed by beneficial mutations. Most genome-wide transcriptional regulatory mechanisms controlling the adaptations remain unidentified. We studied the genome-wide, time-resolved, transcriptional program of susceptible E. coli cells under non-lethal rifampicin stress. Dynamically, the transcriptome widely diverged from the control, but later partially realigned. The mechanisms were changes in RNAP and Gyrase levels, promoter sequences, transcription factor network, intergenic distance, sensitivity to DNA supercoiling buildup, {sigma} factor specificity, (p)ppGpp, and a few global regulators. These results show that the genome-wide response dynamics to rifampicin is influenced by the structure of the gene regulatory network. Next, we compared the evolutionarily distant pathogen Mycobacterium tuberculosis. In both species, adjacent genes on the DNA exhibited similar response strengths. Also, the response strengths of orthologous genes were correlated, suggesting that both species implement similar (likely beneficial) phenotypic adaptations. In support, E. coli orthologs were enriched in the mechanisms identified as influential. Overall, E. coli, and likely other bacteria, have mechanisms influencing specific gene cohort responses to non-lethal rifampicin stress, which likely enhances survivability, thus facilitating the emergence of resistance.