Abstract
The three-tiered transcriptional cascade of flagellar genes in E. coli has long been used as a model system for the study of hierarchical transcriptional networks. In this cascade, master regulator genes (class I) drive the expression of two other groups of genes that mainly consists of the basal body of the motor (Class II) and the filament (Class III). An appealing inference based on this “simple” topology is that environmental cues that promote the master regulator transcription should deterministically “turn on” the rest of the flagellar cascade. Surprisingly, we find that in individual E. coli cells growing in a steady environment, constitutive transcription of the master regulator results in stochastic pulsatile activity of downstream (Class II and III) genes. These pulses alternate between periods of inactivity and strong flagellar gene transcription, each lasting multiple generations. We also find that while transcriptional pulses are simultaneous for genes within the same class, Class III pulses can sometimes skip Class II pulses. We demonstrate that this skipping behavior is governed by a checkpoint for the formation of the flagellar basal body. Finally, we discover that pulses arise from an underlying circuit with memory that controls the cellular commitment to flagellar synthesis. We speculate that this pulsating mode of regulation might allow individual cells to sample different phenotypes under “neutral” environments.