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 Mg 2+ 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 Mg 2+. Our results indicate that Mg 2+ -dependent conformational change is focused in nonhelical regions, consistent with tertiary interactions. In the presence of Mg 2+ , the large subunit rRNA adopts a state that includes the core inter-domain architecture of the assembled ribosome. We infer that the rRNA-Mg 2+ 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.

Multiple prebiotic metals mediate translation

“…SHAPE provides quantitative, nucleotide-resolution information about RNA flexibility, base pairing, and 3D structure, and has previously been used to monitor the influence of cations, small molecules, or proteins on RNA structure (27–32). We previously used SHAPE to show that the LSU rRNA adopts a near-native state in the presence of Mg 2+ , with the core inter-domain architecture of the assembled ribosome and residues positioned for interactions with rProteins (33). Here, SHAPE experiments were performed in an anoxic chamber to maintain the oxidation state of the metals and to prevent Fenton cleavage.…”

“…SHAPE (28, 32, 33) was conducted on the ~2900 nt Thermus thermophilus 23 rRNA (LSU) in 250 mM monovalent cation (Na + or K + ) to favor formation of secondary structure, and in 250 mM Na + or K + plus various divalent cation (10 mM MgCl 2 , 2.5 mM FeCl 2 , or 2.5 mM MnCl 2 ) to favor tertiary interactions. These divalent cation concentrations are sufficient to fold rRNA.…”

RNA: packaged and protected by VLPs

“…RNA compaction may play a role in packaging efficiency. It has been shown that a-rRNA 38 and 23S rRNA 42,43 fold to compact secondary and tertiary structures. We compared Qb VLP packaging of mRNA GFP -hp to a-rRNA-hp and 23S rRNA-hp.…”

Cutting in-line with iron: ribosomal function and non-oxidative RNA cleavage

“…Under pre-GOE conditions, Fe 2+ would not have caused the oxidative damage to biomolecules that occurs today in the presence of O 2 , via Fenton chemistry (22). We recently reported that Fe 2+ can mediate in vitro translation under “pre-GOE” conditions: in the presence of abundant Fe 2+ and in the absence of O 2 (23,24). Based on these findings, we proposed that early ribosomal folding and catalysis used Fe 2+ instead of, or in combination with Mg 2+ and other M 2+ ions.…”