Modulating gene expression based on the engineering of the mRNA-rRNA interaction landscape of an E. coli transcript

Based on computational modeling we first show that in prokaryotes the interactions between the rRNA (ribosomal RNA) and the mRNA both UTRs and coding regions affect all the mRNA translation steps. These computational models enable modulating the translation rate of an mRNA via the modification of each nucleotide composition.

To demonstrate our models we computationally designed nine variants of a GFP gene with different model-based mutations in its 5`UTR and ORF regions.

Our analysis indeed demonstrates that large variability in the protein levels of the variants which are correlated with our design. Thus, our approach suggests a new set of rules for gene expression designing in prokaryotes.