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 σ⁷⁰-holoenzyme (Eσ⁷⁰) 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 Eσ⁷⁰ 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 Eσ⁷⁰ and show how an ncRNA can mimic B-form DNA to directly regulate transcription by the DNA-dependent RNAP.

非编码RNA（ncRNA）调节所有生物体中的基因表达。细菌6S RNA通过结合RNA聚合酶（RNAP）全酶并与启动子DNA竞争来全局调节转录。大肠杆菌（生态）6S RNA相互作用特异性地与管家σ ⁷⁰ -holoenzyme（Eσ ⁷⁰）和起着转录重编程时指数和固定相之间移了关键作用。6S RNA模板RNA合成后，抑制作用得以缓解。我们在这里报告6S RNA和Eσ之间的复杂的3.8的决议结构⁷⁰通过单粒子低温电子显微镜确定，并使用覆盖和交联方法验证结构。双链RNA片段具有A型C3'内糖折叠，但主要沟宽加宽，使RNA具有模仿B型启动子DNA的整体结构。我们的研究结果有助于解释特异性生态6S RNA为Eσ ⁷⁰，并展示如何在非编码RNA可以模仿B型DNA直接通过DNA依赖的RNA聚合酶调节转录。