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Assembly factors chaperone rRNA folding by isolating helical junctions that are prone to misfolding

While RNAs are known to misfold, the underlying molecular causes remain unclear, and focused on alternative secondary structures. Conversely, how RNA chaperones function in a biological context to promote folding beyond duplex annealing, remains unknown. Here we show in a combination of DMS-MaPseq, structural analyses, biochemical experiments, and yeast genetics that three-way junctions are prone to misfolding during assembly of the small ribosomal subunit in vivo. We identify ubiquitous roles for ribosome assembly factors in chaperoning their folding by preventing the formation of tertiary interactions. In the absence of these assembly factors, tertiary interactions kinetically trap misfolded three-way junctions, thereby blocking further progress in the assembly cascade. While these protein chaperones act indirectly by binding the interaction partners, our analyses also suggest direct roles for snoRNAs in binding and chaperoning three-way junctions during transcription. This work furthermore shows that the dissociation of assembly factors renders reversible folding steps irreversible, thereby setting up a timer that regulates not just the flux of assembly but also dictates the propensity of misfolded intermediates to escape quality control. Finally, the data demonstrate how RNA chaperones act locally to unfold specific tertiary interactions, in contrast to protein chaperones, which globally unfold misfolded proteins.