A nascent riboswitch helix orchestrates robust transcriptional regulation through signal integration

• Published in: Nature communications 2024-05, Vol.15 (1), p.3955-18, Article 3955
• Main Authors: Chauvier, Adrien, Dandpat, Shiba S., Romero, Rosa, Walter, Nils G.
• Format: Article
• Language: English
• Subjects: 631/337/2179; 631/45/500; 631/57/2265; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Changing environments; Conformation; DNA-directed RNA polymerase; DNA-Directed RNA Polymerases - genetics; DNA-Directed RNA Polymerases - metabolism; Environmental changes; Gene expression; Gene Expression Regulation, Bacterial; Gene regulation; Homeostasis; Humanities and Social Sciences; Lactococcus lactis - genetics; Lactococcus lactis - metabolism; Manganese; Manganese - metabolism; Manganese ions; multidisciplinary; Nucleic Acid Conformation; Nucleotide sequence; Ribonucleic acid; Riboswitch - genetics; Riboswitches; RNA; RNA polymerase; RNA, Bacterial - chemistry; RNA, Bacterial - genetics; RNA, Bacterial - metabolism; Robustness; Science; Science (multidisciplinary); Single Molecule Imaging; Transcription factors; Transcription Factors - genetics; Transcription Factors - metabolism; Transcription, Genetic
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-48409-8

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 discover 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 representative 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. Here the authors unveil an intermediate state during the folding of the manganese riboswitch from L. lactis . This transient state allows the integration of multiple cellular signals including RNA polymerase pausing and transcription factor NusA.