Transient Protein-RNA Interactions Guide Nascent Ribosomal RNA Folding

Abstract

Ribosome assembly is an efficient, but complex and heterogeneous process during which ribosomal proteins assemble on the nascent ribosomal RNA (rRNA) during transcription. Understanding how the interplay between nascent RNA folding and protein binding determines the fate of transcripts remains a major challenge. Here, using single-molecule fluorescence-microscopy, we follow assembly of the entire 3’domain of the bacterial small ribosomal subunit in real-time. We find that co-transcriptional rRNA folding is complicated by the formation of long-range RNA interactions, and that r-proteins self-chaperone the rRNA folding process prior to stable incorporation into a ribonucleoprotein complex (RNP). Assembly is initiated by transient rather than stable protein binding, and the protein-RNA binding dynamics gradually decrease during assembly. This work questions the paradigm of strictly sequential and cooperative ribosome assembly and proposes that transient binding of RNA binding proteins to cellular RNAs could provide a general mechanism to shape nascent RNA folding during RNP assembly.

Keywords: ribosome assembly, co-transcriptional RNA folding, single-molecule fluorescence microscopy, ribonucleoprotein assembly, protein-RNA dynamics, RNA chaperones, cooperativity, RNA misfolding, RNA biology, protein-RNA interactions