Chronology of tRNA structural dynamics prior to and during interaction with a pseudouridine synthase

Transfer RNA has long served as an exemplar of a thermodynamically stable, structured RNA. Yet it undergoes significant structural changes upon binding and catalysis by diverse modification enzymes. We leveraged optical binding assays and single-molecule FRET to observe the structural dynamics of two yeast tRNAs, in isolation, and upon interaction with the conserved pseudouridine synthase Pus4/TruB. We show that unmodified and pseudouridylated tRNA^eMet(CAU) and tRNA^Thr(AGU) all sample open, compact and intermediate conformations, though tRNA^Thr(AGU) exhibits faster dynamics. Consistent with its role in modifying RNAs with different structural properties, Pus4 binds robustly to unmodified tRNA, tRNA that was pseudouridylated prior to engaging Pus4 ("pre-modified"), and even an unrelated riboswitch RNA. Pus4 binding to tRNA^eMet(CAU) leads to additional tRNA conformational states. The ensemble of conformations explored by Pus4-bound pre-modified tRNA resolved within minutes back into open, compact and intermediate states. tRNA^eMet(CAU) that is initially unmodified more gradually approached the ensemble of structures that were attained rapidly by pre-modified tRNA. Thus, Pus4 both catalyzes a lasting chemical change on tRNA and remodels it over time after catalysis, perhaps to promote subsequent steps of tRNA maturation.