Modeling σ E biochemical network reveals context-dependent feedback control and kinetic constraints in the envelope...

The bacterial cell envelope is essential for mechanical stability, barrier function, defining cell size and shape, and supporting cellular processes. Because external or internal stressors can challenge its integrity, bacteria have evolved stress response systems to maintain envelope homeostasis. For example, under stress, E. coli activates ${\sigma }^{\text{E}}$ to induce a regulon that restores envelope homeostasis. The molecular mechanisms underlying the transcriptional and post-translational regulation of ${\sigma }^{\text{E}}$ and its anti-sigma factor RseA have been well-mapped. However, how these regulatory layers function at the systems level to regulate ${\sigma }^{\text{E}}$ activity remains unclear. Here, we combine mathematical modeling with quantitative gene expression measurements to determine how the interplay of transcription and post-translational regulation affects the dynamics of the ${\sigma }^{\text{E}}$ response. The results suggest that the ${\sigma }^{\text{E}}$ activity is determined by the balance between the release from RseA, resulting from its degradation, and slow binding of free ${\sigma }^{\text{E}}$ to the intact RseA. Notably, the combined action of transcriptional and post-translational regulation reveals that autoregulation, traditionally assumed to be a positive feedback, transitions from negative to positive feedback under extreme stress, enabling a finely tuned response that prevents premature activation while ensuring a robust response under severe envelope stress. In summary, our findings elucidate the mechanisms of ${\sigma }^{\text{E}}$ regulation, thereby advancing our understanding of how alternative sigma factor bacterial networks control stress-response pathways.