Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA.
Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
Mol Cell. 2017 Oct 19;68(2):388-397.e6. doi: 10.1016/j.molcel.2017.09.006. Epub 2017 Oct 5.
Noncoding RNAs (ncRNAs) regulate gene expression in all organisms. Bacterial 6S RNAs globally regulate transcription by binding RNA polymerase (RNAP) holoenzyme and competing with promoter DNA. Escherichia coli (Eco) 6S RNA interacts specifically with the housekeeping σ-holoenzyme (Eσ) and plays a key role in the transcriptional reprogramming upon shifts between exponential and stationary phase. Inhibition is relieved upon 6S RNA-templated RNA synthesis. We report here the 3.8 Å resolution structure of a complex between 6S RNA and Eσ determined by single-particle cryo-electron microscopy and validation of the structure using footprinting and crosslinking approaches. Duplex RNA segments have A-form C3' endo sugar puckers but widened major groove widths, giving the RNA an overall architecture that mimics B-form promoter DNA. Our results help explain the specificity of Eco 6S RNA for Eσ and show how an ncRNA can mimic B-form DNA to directly regulate transcription by the DNA-dependent RNAP.
非编码 RNA（ncRNA）在所有生物体中都能调节基因表达。细菌 6S RNA 通过与 RNA 聚合酶（RNAP）全酶结合并与启动子 DNA 竞争，从而在全球范围内调节转录。大肠杆菌（Eco）6S RNA 与管家 σ-全酶（Eσ）特异性相互作用，并在指数期和静止期之间的转变过程中在转录重编程中发挥关键作用。当 6S RNA 模板指导 RNA 合成时，抑制作用得到缓解。我们通过单颗粒冷冻电镜确定了 6S RNA 与 Eσ 之间复合物的 3.8Å 分辨率结构，并通过足迹法和交联法验证了结构的准确性。双链 RNA 片段具有 A 型 C3' 内式糖 puckers，但拓宽了大沟宽度，使 RNA 具有整体结构，模拟 B 型启动子 DNA。我们的结果有助于解释 Eco 6S RNA 对 Eσ 的特异性，并展示了 ncRNA 如何模拟 B 型 DNA 直接通过依赖 DNA 的 RNAP 调节转录。
