Regulation of the ThiM riboswitch is facilitated by the trapped structure formed during transcription of the wild‐type sequence

Abstract

The ThiM riboswitch from Escherichia coli is a typical mRNA device that modulates downstream gene expression by sensing TPP. The helix‐based RNA folding theory is used to investigate its detailed regulatory behaviors in cells. This RNA molecule is transcriptionally trapped in a state with the unstructured SD sequence in the absence of TPP, which induces downstream gene expression. As a key step to turn on gene expression, formation of this trapped state (the genetic ON state) highly depends on the co‐transcriptional folding of its wild‐type sequence. Instead of stabilities of the genetic ON and OFF states, the transcription rate, pause, and ligand levels are combined to affect the ThiM riboswitch‐mediated gene regulation, which is consistent with a kinetic control model.