A nascent riboswitch helix orchestrates robust transcriptional regulation through signal integration

TL;DR

This paper explains how a specific RNA structure in bacteria helps regulate gene activity by integrating signals during transcription.

Contribution

The study reveals how a riboswitch helix coordinates ligand binding and transcription events for precise gene regulation.

Findings

The riboswitch helix P1.1 coordinates Mn2+ and RNA polymerase to stabilize RNA structure.

The helix enables a semi-docked RNA conformation and extends RNA polymerase pauses.

This mechanism enforces transcription readthrough and integrates signals for gene control.

Abstract

Widespread manganese-sensing transcriptional riboswitches effect the dependable gene regulation needed for bacterial manganese homeostasis in changing environments. Riboswitches – like most structured RNAs – are believed to fold co-transcriptionally, subject to both ligand binding and transcription events; yet how these processes are orchestrated for robust regulation is poorly understood. Through a combination of single molecule and bulk approaches, we discovered how a single Mn
2+
ion and the transcribing RNA polymerase (RNAP), paused immediately downstream by a DNA template sequence, are coordinated by the bridging switch helix P1.1 in the paradigmatic
Lactococcus lactis
riboswitch. This coordination achieves a heretofore-overlooked semi-docked global conformation of the nascent RNA, P1.1 base pair stabilization, transcription factor NusA ejection, and RNAP pause extension, thereby enforcing transcription readthrough. Our work demonstrates how a central, adaptable RNA helix functions analogous to a molecular fulcrum of a first-class lever system to integrate disparate signals for finely balanced gene expression control.