The route to transcription initiation determines the mode of transcriptional bursting in E. coli

Transcription is fundamentally noisy, leading to significant heterogeneity across bacterial populations. Noise is often attributed to burstiness, but the underlying mechanisms and their dependence on the mode of promotor regulation remain unclear. Here, we measure E. coli single cell mRNA levels for two stress responses that depend on bacterial sigma factors with different mode of transcription initiation (σ(70) and σ(54)). By fitting a stochastic model to the observed mRNA distributions, we show that the transition from low to high expression of the σ(70)-controlled stress response is regulated via the burst size, while that of the σ(54)-controlled stress response is regulated via the burst frequency. Therefore, transcription initiation involving σ(54) differs from other bacterial systems, and yields bursting kinetics characteristic of eukaryotic systems.