mRNA secondary-structure-stability regulates bacterial translation insulation and reinitiation

Translation reinitiation in bacteria is essential to utilize polycistronic mRNAs, yet the mechanisms which regulate it are insufficiently understood. Herein, we report the discovery of a ribosome termination sequence (RTS), which is an evolutionarily conserved feature, of precisely localized predicted stable mRNA secondary structures around stop codons. This feature functions as a ribosomal insulator which regulates translation reinitiation in bacteria. We experimentally demonstrate that RTS is the main governing factor of reinitiation efficiency in an Escherichia coli synthetic construct (R2=0.8). By analyzing over 150 genomes, we reveal that in all bacterial phyla, these structures are thermodynamically depleted when reinitiation is advantageous and enriched in order to insulate translation when reinitiation is not beneficial.