Fig. 8: Model of the co-transcriptional folding pathways of the yybp riboswitch class.

Transcription can follow two different pathways depending on the presence of a saturating concentration of Mn²⁺ in the cellular environment. The G104 pause constitutes a transcriptional checkpoint at which NusA is either stabilized or released from the EC. In the absence ofMn²⁺ (Upper), NusA remains bound to the EC assisting the initial nucleation of P1.1 switching helix. The pre-organized P1.1 helix remains in place to sense Mn²⁺ at the latest stage of riboswitch transcription, allowing a fast response to environmental changes and efficiently regulate gene expression. Co-transcriptional folding of the riboswitch in the ligand-bound state (Lower), by contrast, promotes NusA release from the EC. Mn²⁺ binding favors downstream stabilization of P1.1 to ultimately promote transcription readthrough.