Bacterial operons response dynamics to genome-wide stresses.

Bacterial gene networks rely on operons to coordinate activities involving multiple genes. In Escherichia coli, operons have internal promoters that allow regulating downstream genes, independently from upstream genes. We studied genome-wide stress responses in this organism targeting two global transcription regulators. We show that premature terminations of transcription elongation and internal promoters play a major role in operons, causing differences between gene response strengths to follow sinusoidal patterns that are influenced by positive supercoiling buildup. We further observe the same using data on E. coli cells subject to other stresses, as well as in Bacillus subtilis, Corynebacterium glutamicum, and Helicobacter pylori. Overall, our results suggest that internal promoters assist operons by compensating for premature terminations. This finding further opens new avenues by suggesting a new means to achieve complex dynamical behaviors in synthetic genetic circuits.