Protein-free ribosomal RNA folds to a near-native state in the presence of Mg2+

Abstract

The assembled bacterial ribosome contains around 50 proteins and many counterions. Here, focusing on rRNA from the large ribosomal subunit, we demonstrate that Mg²⁺ causes structural collapse in the absence of ribosomal proteins. The collapsed rRNA forms many native-like RNA–RNA interactions, similar to those observed in the assembled ribosome. We assayed rRNA structure by chemical footprinting in the presence and absence of Mg²⁺. Our results indicate that Mg²⁺-dependent conformational change is focused in non-helical regions, consistent with tertiary interactions. In the presence of Mg²⁺, the large subunit rRNA adopts a state that includes the core inter-domain architecture of the assembled ribosome. We infer that the rRNA–Mg²⁺ state represents the core architecture of the LSU which, while not catalytically active, positions the residues of the LSU rRNA in such a way as to promote native interactions with rProteins to ultimately form a functional LSU.