The Interactions between the rRNA and the mRNA in Prokaryotes are Involved in all Steps of the Translation Process and Shape the Transcripts of the Bacteria

The process of translation initiation in prokaryotes involves binding of the 16S rRNA component of the small ribosomal subunit to the mRNA ribosome-binding site. The known prokaryotic mRNA ribosome-binding site is the Shine – Dalgarno (SD) sequence that can be found upstream to start codon and enables the initiation of translation. The rRNA-mRNA interaction strength in the coding region may affect the process of translation elongation as it may cause pauses during translation elongation. Pausing of ribosomes may affect a variety of phenomena including ribosomal traffic jams, protein folding, protein targeting, and ribosomal abortion. Therefore, the prediction of such interactions along transcripts is expected to affect bacterial synthetic, endogenous gene expression, and bacterial growth rates. we developed a novel computational pipeline that can be used for inferring the strength of rRNA-mRNA interaction in various prokaryotes, evolutionary selection for such interactions across the transcriptome, and for understanding, modeling and engineering the translation process in prokaryotes. We analyzed 551 different bacteria across the tree of life and our preliminary analysis suggests that the rRNA-mRNA interactions shape the nucleotide composition and affect all translation steps (initiation, elongation, termination) and all translation sub-steps. Thus, modeling and predicting selection for rRNA-mRNA interaction are fundamental for understanding genomic evolution and the biophysics of translation in bacteria.