Multiple Mechanisms Determine Translation Termination Outcome in Bacteria

Three outcomes are possible when a ribosome reaches a stop codon: translation termination, involving dissociation of the ribosome from the mRNA strand; read-through translation, where an amino-acid is incorporated and translation continues past the stop codon; and re-initiation, with the ribosome partially dissociating but continuing to scan nearby mRNA regions and possibly restarting translation of another coding sequence. The choice between these three outcomes is important for efficient and accurate translation, especially considering most genes in bacteria are translated from polycistronic transcripts. Cues from the sequence surrounding the stop codon are expected to tilt the balance toward the required outcome, but the details of this process are not understood well.

To identify how different elements of the mRNA sequence interact to affect the termination outcome, we analyzed the regions surrounding the stop codon in 183 species across the tree of life (including 128 diverse bacteria) for the presence of conserved features recently detected in this region. As termination and initiation frequently occur in close proximity in bacteria, we analyzed the presence of initiation-promoting signals, including start codons and anti-Shine Dalgarno hybridization energy. In addition, we looked for regions of increased or decreased local secondary structure in the mRNA on both sides of the stop codon, where different propensities for folding appear depending on operonic position and other factors. We propose a new model combining all previously found features and showing how they interact in different bacterial species. The combined model shows which elements are required in different contexts and may be applied to control the gene expression process of synthetic coding sequences.