Structure modulation of helix 69 from Escherichia coli 23S ribosomal RNA by pseudouridylations

Abstract

Helix 69 (H69) is a 19-nt stem-loop region from the large subunit ribosomal RNA. Three pseudouridine ()) modifications clustered in H69 are conserved across phylogeny and known to affect ribosome function. To explore the effects of ) on the conformations of Escherichia coli H69 in solution, nuclear magnetic resonance spectroscopy was used to reveal the structural differences between H69 with ()))) and without (UUU) ) modifications. Comparison of the two structures shows that H69 ))) has the following unique features: (i) the loop region is closed by a Watson-Crick base pair between )1911 and A1919, which is potentially reinforced by interactions involving )1911N1H and (ii) ) modifications at loop residues 1915 and 1917 promote base stacking from )1915 to A1918. In contrast, the H69 UUU loop region, which lacks ) modifications, is less organized. Structure modulation by ) leads to alteration in conformational behavior of the 5' half of the H69 loop region, observed as broadening of C1914 non-exchangeable base proton resonances in the H69 ))) nuclear magnetic resonance spectra, and plays an important biological role in establishing the ribosomal intersubunit bridge B2a and mediating translational fidelity. © The Author(s) 2013. Published by Oxford University Press.