Nitzan Mor, Wassarman Karen M, Biham Ofer, Margalit Hanah
Racah Institute of Physics, The Hebrew University, Jerusalem, Israel; Faculty of Medicine, The Hebrew University, Jerusalem, Israel.
Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin.
Biophys J. 2014 Mar 4;106(5):1205-14. doi: 10.1016/j.bpj.2014.01.025.
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 σ(70)-RNA polymerase (σ(70)-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 σ(70)-RNAP, resulting in a fast increase in free σ(70)-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 σ(70)-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 σ(70)-RNAP during transitions in nutrient availability, which is likely to give a competitive advantage to cells encountering diverse environmental conditions.
小RNA是细菌基因表达的重要调节因子，其中大多数通过与靶mRNA碱基配对在转录后发挥作用，改变翻译或mRNA稳定性。然而，6S RNA是一种作为转录调节因子的小RNA，它通过直接结合σ(70)-RNA聚合酶(σ(70)-RNAP)并阻止其与基因启动子结合来发挥作用。在从指数生长期到稳定期的转变过程中，6S RNA积累并全局下调数百个基因的转录。在从稳定期到指数生长期（复苏）的转变过程中，6S RNA从σ(70)-RNAP释放，导致游离σ(70)-RNAP快速增加和许多基因的转录。从稳定期到指数生长期的转变很突然，因此便于进行实验研究。然而，从指数生长期到稳定期的转变是渐进的，并且受到其他因素变化的影响而变得复杂，使得在此转变过程中通过实验分离6S RNA的作用更加困难。在这里，我们使用数学建模和模拟来研究6S RNA依赖性调节的动力学，重点关注由营养可用性改变介导的生长转变。我们首先表明，我们的模型再现了复苏时σ(70)-RNAP的急剧增加以及两个经过实验测试的突变体的行为，从而证明其可用于表征从指数生长期到稳定期较难研究的转变动力学。我们表征了大肠杆菌野生型以及具有各种6S RNA-RNAP亲和力的突变体的两个转变的动力学，表明6S RNA调节机制通常对广泛的此类突变具有鲁棒性，尽管单个启动子的调节水平及其产生的表达倍数变化会随着亲和力的变化而改变。我们的结果深入了解了6S RNA转录调节的潜在优势，因为它能够在营养可用性转变期间储存和有效释放σ(70)-RNAP，这可能会给遇到不同环境条件的细胞带来竞争优势。
