Pausing guides RNA folding to populate transiently stable RNA structures for riboswitch-based transcription regulation

Elife. 2017 May 25:6:e21297. doi: 10.7554/eLife.21297.

Abstract

In bacteria, the regulation of gene expression by cis-acting transcriptional riboswitches located in the 5'-untranslated regions of messenger RNA requires the temporal synchronization of RNA synthesis and ligand binding-dependent conformational refolding. Ligand binding to the aptamer domain of the riboswitch induces premature termination of the mRNA synthesis of ligand-associated genes due to the coupled formation of 3'-structural elements acting as terminators. To date, there has been no high resolution structural description of the concerted process of synthesis and ligand-induced restructuring of the regulatory RNA element. Here, we show that for the guanine-sensing xpt-pbuX riboswitch from Bacillus subtilis, the conformation of the full-length transcripts is static: it exclusively populates the functional off-state but cannot switch to the on-state, regardless of the presence or absence of ligand. We show that only the combined matching of transcription rates and ligand binding enables transcription intermediates to undergo ligand-dependent conformational refolding.

Keywords: B. subtilis; E. coli; RNA; biochemistry; biophysics; folding; kinetics; meta-stable structures; riboswitches; structural biology; transcription.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacillus subtilis / genetics*
  • Gene Expression Regulation, Bacterial*
  • Magnetic Resonance Spectroscopy
  • Models, Biological
  • Models, Molecular
  • Nucleic Acid Conformation
  • RNA Folding*
  • RNA, Bacterial / chemistry*
  • RNA, Bacterial / metabolism*
  • Riboswitch*
  • Transcription, Genetic*

Substances

  • RNA, Bacterial
  • Riboswitch

Grants and funding

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.