AbstractThe well-established Shine-Dalgarno model suggests that translation initiation in bacteria is regulated via base-pairing between ribosomal RNA (rRNA) and mRNA. However, little is currently known about the contribution of such interactions to the rest of the translation process and to the way bacterial transcript evolve. We used novel computational analyses and modelling of 823 bacterial genomes coupled with experiments to demonstrate that rRNA-mRNA interactions are diverse and regulate not only initiation, but all translation steps from pre-initiation to termination across the many bacterial phyla that have the Shine-Dalgarno sequence. As these interactions dictate translation efficiency, they serve as a driving evolutionary force for shaping transcripts in bacteria. We observed selection for strong rRNA-mRNA interactions in regions where such interactions are likely to enhance initiation, regulate early elongation and ensure the fidelity of translation termination. We discovered selection against strong interactions and for intermediate interactions in coding regions and present evidence that these interactions maximize elongation efficiency while also enhancing initiation by ‘guiding’ free ribosomal units to the start codon.ImportancePrevious research has reported the significant influence of rRNA-mRNA interactions mainly in the initiation phase of translation. The results reported in this paper suggest that, in addition to the rRNA-mRNA interactions near the start codon that trigger initiation in bacteria, rRNA-mRNA interactions affect all sub-stages of the translation process (pre-initiation, initiation, elongation, termination). In addition, these interactions affect the way evolutionary forces shape the bacterial transcripts while considering trade-offs between the effects of different interactions across different transcript regions on translation efficacy and efficiency. Due to the centrality of the translation process, these findings are relevant to all biomedical disciplines.