Gene Regulation by a Kinetic Riboswitch with Negative Feedback Loop.

Understanding the folding behaviors and cellular roles is important to fully illuminate functions of riboswitches in vivo. Since riboswitches act without the need for protein factors, RNA structure prediction methods are ideally suited for computationally analyzing their cellular activities. Here, a helix-based RNA folding theory is used to predict the cotranscriptional folding pathways of the flavin mononucleotide (FMN)-binding riboswitch from Bacillus subtilis (B. subtilis) under different conditions. The results show that the efficient function is determined by a balance between the transcription speed, pausing, and the binding rates of the metabolite. According to the predicted behaviors, a general kinetic model is established to investigate how the riboswitch couples sensing and regulatory functions to help bacteria respond to environmental changes at the system levels.