Dynamics of bacterial operons during genome-wide stresses is influenced by premature terminations and internal promoters

Bacterial gene networks have many operons, each coordinating the kinetics of a few genes in time and strength. In E. coli, nearly half of these operons also have internal promoters, which allow regulating the downstream genes, independently from upstream genes. We studied their role during genome-wide stresses targeting a few key elements of the transcription machinery, namely, RNAP and Gyrase. We show that absolute differences in response strength between genes in the same operon follow a sinusoidal function of the distance between them. This results from the combined effect of elongation fall-offs and internal promoters. The frequency of this function is regulated by the positioning of internal promoters, while its amplitude differs with the perturbation strength. Moreover, we find that positive supercoiling buildup partially explains the RNAP fall-off rates. Finally, we report similar sinusoidal patterns in Escherichia coli cells subject to other stresses, as well as in Bacillus subtilis, Corynebacterium glutamicum, and Helicobacter pylori. Overall, our results suggest that the strength, number, and positioning of internal promoters in operons are influenced by a genome-wide need to compensate for RNAP fall-offs and provide distal genes in the operon with similar response strength as genes proximal to the primary promoter. Examination of genome-wide responses under Antibiotics (Novobiocin and Rifampicin) ------------- GENEWIZ, Inc. (Leipzig, Germany)