The rpsA gene and its product ribosomal protein S1: investigating the role of RNA structure in translation

Abstract

The rpsA gene contains a translation initiation region (TIR) which lacks a Shine-Dalgarno element, is highly structured, and which efficiently drives translation in bacteria. The rpsA gene is downregulated by its gene product, ribosomal protein S1. To investigate how the structure of the TIR facilitates function both in translation and downregulation, we employed a combined SAXS, SHAPE, and computational approach. The structure-function relationship reveals that the introduction of single nucleotide substitutions in the TIR alters its structure, corresponding to a modulated translation efficiency in vivo. The activity of the rpsA TIR in a minimal in vitro transcription/translation system was investigated to understand the TIR’s requirement for additional factors. We observed that S1 is strictly required for its translation, and that S1 specifically recognizes and binds to the TIR when in excess over ribosomes. The structure-driven mechanism of this TIR may represent a previously overlooked strategy of translation initiation in bacteria.