Global Regulation of Transcription by a Small RNA: A Quantitative View

Small RNAs are integral regulators of bacterial gene expression, the majority of which act posttranscriptionally by basepairing with target mRNAs, altering translation or mRNA stability. 6S RNA, however, is a small RNA that is a transcriptional regulator, acting by binding directly to σ70-RNA polymerase (σ70-RNAP) and preventing its binding to gene promoters. At the transition from exponential to stationary phase, 6S RNA accumulates and globally downregulates the transcription of hundreds of genes. At the transition from stationary to exponential phase (outgrowth), 6S RNA is released from σ70-RNAP, resulting in a fast increase in free σ70-RNAP and transcription of many genes. The transition from stationary to exponential phase is sharp, and is thus accessible for experimental study. However, the transition from exponential to stationary phase is gradual and complicated by changes in other factors, making it more difficult to isolate 6S RNA effects experimentally at this transition. Here, we use mathematical modeling and simulation to study the dynamics of 6S RNA-dependent regulation, focusing on transitions in growth mediated by altered nutrient availability. We first show that our model reproduces the sharp increase in σ70-RNAP at outgrowth, as well as the behavior of two experimentally tested mutants, thus justifying its use for characterizing the less accessible dynamics of the transition from exponential to stationary phase. We characterize the dynamics of the two transitions for Escherichia coli wild-type, as well as for mutants with various 6S RNA-RNAP affinities, demonstrating that the 6S RNA regulation mechanism is generally robust to a wide range of such mutations, although the level of regulation at single promoters and their resulting expression fold change will be altered with changes in affinity. Our results provide insight into the potential advantage of transcription regulation by 6S RNA, as it enables storage and efficient release of σ70-RNAP during transitions in nutrient availability, which is likely to give a competitive advantage to cells encountering diverse environmental conditions.