Automatic Predictions of Novel rRNA-mRNA Interactions

Translation initiation in prokaryotes is commonly initiated by the base-pairings between the mRNA and the rRNA of the small subunit of the ribosome. The common binding sequence is called the Shine Dalgarno sequence (SD), that can be found upstream to start codon in many prokaryotes.

Hence, this base-pairing affects the step in translation that is considered to be a major determinant of gene expression level.

The widespread assumption is that the SD that can be found in the mRNA and its complementary sequence aSD that can be found in the rRNA, are usually the canonical sequences. In our research, we examine the hypothesis that there might be more than one binding sequence that can initiate translation in prokaryotes.

Therefore, we developed a novel computational pipeline that can be used for inferring the optimal SD and aSD sequences, based on rRNA-mRNA interaction strength.

We analyzed 551 different bacteria across the tree of life, and our preliminary analysis suggests that for 64 of the analyzed bacteria the optimal SD sequence is not the canonical SD. Due to the fact that the interactions between the mRNA (SD) and the rRNA (aSD) are crucial to initiate translation, the prediction of the optimal sequences is expected to promote efficient engineering of bacterial synthetic, endogenous gene expression, and bacterial growth rates.