The Solution Structure of Spinach Chloroplast and of Xenopus Laevis Oocyte 5S rRNAs

Abstract

Detailed atomic models of a eubacterial 5S rRNA (from spinach chloroplast) and of a eukaryotic 5S rRNA (from Xenopus laevis oocyte) were built using computer graphic modeling. These models integrate the experimental data on the accessibility of bases and phosphates towards several structure-specific probes and the stereochemical constraints. The proposed 3-dimensional models adopt a Y-shaped structure with no tertiary interactions between the different domains of the RNA. The models have been corroborated by footprinting experiments with ribosomal proteins and by the analysis of various mutant 5S rRNAs. From these studies, several conclusions can be reached: (i) the two 5S rRNA molecules adopt a Y-shape structure with no long range tertiary interactions between the different helical domains, (ii) The internal loops, in particular region E, contain several non canonical base pairs of A-A, A-G and U-U types. The intrinsic structure of these loops are strictly sequence-dependent, (iii) The hinge nucleotides in loop A govern the relative orientation of the three helical domains.