Role of conserved residues for RNA binding and catalysis in two bacterial pseudouridine synthases

Abstract

Pseudouridine synthases are RNA modification enzymes targeting various forms of RNA in the cell. RluB and RluF are pseudouridine synthases modifying adjacent uridines in E. coli ribosomal RNA. These enzymes have a highly conserved RNA-binding loop, distinct between RluB and RluF, proposed to play a role in their specificity. This thesis provides preliminary insight into the importance of the eight-residue binding loops of RluB and RluF for RNA target recognition. I have shown that altering the residues of the binding loop decreases the enzyme’s affinity for RNA and effectively abolish the enzyme’s pseudouridylation activity. I conclude that the binding loops of RluB and RluF are critical for RNA binding and for positioning the target RNA for catalysis. Better understanding the requirements for specificity and target recognition of RluB and RluF will enhance our knowledge on ribosome formation and may aid in engineering new enzymes to pseudouridylate other functional RNAs.