Protein-guided RNA dynamics during early ribosome assembly

The assembly of 30S ribosomes requires the precise addition of 20 proteins to the 16S ribosomal RNA. How early binding proteins change the ribosomal RNA structure so that later proteins may join the complex is poorly understood. Here we use single-molecule fluorescence resonance energy transfer (FRET) to observe real-time encounters between Escherichia coli ribosomal protein S4 and the 16S 5′ domain RNA at an early stage of 30S assembly. Dynamic initial S4–RNA complexes pass through a stable non-native intermediate before converting to the native complex, showing that non-native structures can offer a low free-energy path to protein–RNA recognition. Three-colour FRET and molecular dynamics simulations reveal how S4 changes the frequency and direction of RNA helix motions, guiding a conformational switch that enforces the hierarchy of protein addition. These protein-guided dynamics offer an alternative explanation for induced fit in RNA–protein complexes. Three-colour fluorescence resonance energy transfer and molecular dynamics simulations are used to study the events occurring early in assembly of the 30S ribosome; within a non-native intermediate S4 ribosomal protein–16S RNA structure, S4 is capable of altering the RNA helix dynamics to facilitate conformation changes that enable subsequent protein binding. The assembly of protein–RNA complexes can involve the sculpting of RNA structure as proteins are sequentially bound, but direct demonstration of the details of these changes has been difficult. Sarah Woodson and colleagues have used sophisticated three-colour fluorescence resonance energy transfer (FRET) and modelling to look at the events occurring early in the assembly of the 30S ribosome. They find that when the S4 ribosomal protein interacts with the 16S rRNA, there is a stable, on-path, non-native intermediate, and that the S4 protein can alter the RNA helix dynamics to facilitate conformational changes that enable subsequent protein binding.