PMID: 28988932

Authors:

Chen J, Wassarman KM, Feng S, Leon K, Feklistov A, Winkelman JT, Li Z, Walz T, Campbell EA, Darst SA

Title:

6S RNA Mimics B-Form DNA to Regulate Escherichia coli RNA Polymerase.

Journal:

Mol Cell. 2017 Oct 19;68(2):388-397.e6. doi: 10.1016/j.molcel.2017.09.006. Epub, 2017 Oct 5.

Abstract:

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 sigma70-holoenzyme (Esigma70) 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 A resolution structure of a complex between 6S RNA and Esigma70 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 Esigma70 and show how an ncRNA can mimic B-form DNA to directly regulate transcription by the DNA-dependent RNAP.