Access Type

Open Access Dissertation

Date of Award

January 2012

Degree Type


Degree Name




First Advisor

John SantaLucia, Jr.



"Fine-tuning" of ribosomal structure and functions by pseudouridylation and RNA-protein interactions




Advisor: Prof. John SantaLucia Jr.

Major: Chemistry (Biochemistry)

Degree: Doctor of Philosophy

Ribosomal structure and functions appear to be "fine-tuned" by pseudouridylation and RNA-protein interactions. Pseudouridylation may promote base stacking interactions by mediating the base stacking between residues on both sides. In the RNA duplex region, this enhanced stacking interaction contributes to stabilization of duplex folding. In the loop region, enhanced stacking in one structural motif may destabilize the conformation of adjacent structural residues. This hypothesis is supported by both UV-melting experiments, where pseudouridylation significantly stabilized H69 stem duplex folding, while destabilize the loop conformation. In addition, NMR also supports this hypothesis. The NMR structure of H69UUU shows that the U1915, A1916, and U1917 form a local sheared stacking, instead of participating in an extensive stacking which extends to C1924. The NMR structure and crystal structures of H69ΨΨΨ shows that Ψ1915 and Ψ1917 (E. coli numbering) mediate the extensive stacking. The dynamic property was also revealed in the NMR spectrum of H69ΨΨΨ (C1914), which suggests that the enhanced stacking interactions from Ψ1915 to C1924 may contribute to the destabilization of the loop conformation of H69ΨΨΨ and pre-organization of the stem-loop structure of H69ΨΨΨ for ribosomal subunits association. RNA-protein interactions are another method to regulate ribosome biogenesis and activity. An ambient dissociation constant between the ribosomal RNA and ribosomal protein is required for the optimal ribosome biogenesis and activity (77nM for the E. coli cognate pair and 198 nM for the P. aeruginosa cognate pair). Either a too weak (dissociation constants of 77 nM vs. 312 nM for Ech9 - EcS20/PaS20) or a too strong interaction (dissociation constants of 198 nM vs. 51 nM for Pah9 - PaS20/EcS20) could affect the ability of S20 ribosomal protein to coordinate the correct folding of 16S rRNA.