Prokaryotic rRNA-mRNA Interactions are Involved in all Translation Steps and Shape Bacterial Transcripts

The well-established Shine-Dalgarno model suggests that translation initiation in bacteria is regulated via base-pairing between the ribosomal RNA (rRNA) and mRNA. Indeed, it is well known that prokaryotic transcripts tend to include a ribosomal binding site around 8-10 bases upstream of the start codon AUG. In this study, based on novel computational analyses and modeling of 823 bacterial genomes across the tree of life coupled with relevant experiments, we demonstrate that rRNA-mRNA interactions regulate all translation steps from pre-initiation to termination. As these interactions dictate translation efficiency, they serve as a driving evolutionary force for shaping transcript sequences in bacteria. As expected, the reported signals are very weak or non-existent in bacteria with no canonical anti Shine-Dalgarno sequence in their 16S rRNA, and correlate with gene expression and growth rate. Due to the importance and centrality of the translation process, these findings are fundamental to all biomedical disciplines.