Dynamic competition between a ligand and transcription factor NusA governs riboswitch-mediated transcription regulation

Abstract

Co-transcriptional RNA folding is widely assumed to influence the timely control of gene expression, but our understanding remains limited. In bacteria, the fluoride (F-) sensing riboswitch is a transcriptional control element essential to defend against toxic F- levels. Using this model riboswitch, we find that its ligand F- and essential bacterial transcription factor NusA compete for binding the co-transcriptionally folding RNA, opposing each other’s modulation of downstream pausing and termination by RNA polymerase. Single molecule fluorescence assays probing active transcription elongation complexes discover that NusA unexpectedly binds highly reversibly, frequently interrogating the complex for emerging, co-transcriptionally folding RNA duplexes. NusA thus fine-tunes the transcription rate in dependence of the ligand-responsive higher order structure of the riboswitch. At the high NusA concentrations found intracellularly, this dynamic modulation is expected to lead to adaptive bacterial transcription regulation with fast response times.