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

Highlights

• Cryo-EM structure of an E. coli 6S RNA/RNA polymerase complex at 3.8 Å resolution

• Duplex RNA segments have A-form sugar puckers, but overall architecture mimics B-form

• 6S RNA specificity for σ⁷⁰-holo over σ^S-holo is largely determined by two amino acids

• 6S RNA mimics B-form DNA to directly regulate transcription by the DNA-dependent RNAP

Summary

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.