Shine-Dalgarno Anti-Shine-Dalgarno Sequence Interactions and Their Functional Role in Translational Efficiency of Bacteria and Archaea

Akram Abolbaghaei, Université D'Ottawa / University Of Ottawa, Université D'Ottawa / University Of Ottawa
Translation is a crucial factor in determining the rate of protein biosynthesis; for this reason, bacterial species typically evolve features to improve translation efficiency. Biosynthesis is a finely tuned cellular process aimed at providing the cell with an appropriate amount of proteins and RNAs to fulfill all of its metabolic functions. A key bacterial feature for faster recognition of the start codon on mRNA is the binding between the anti-Shine-Dalgarno (aSD) sequence on prokaryotic
more » ... omes at the 3' end of the small subunit (SSU) 16S rRNA and Shine-Dalgarno (SD) sequence, a purine-rich sequence located upstream of the start codon in the mRNA. This binding helps to facilitate positioning of initiation codon at the ribosomal P site. This pairing, as well as factors such as the location of aSD binding relative to the start codon and the sequence of the aSD motif can heavily influence translation efficiency. The objective of this thesis is to understand the SD-aSD interactions and how changes in aSD sequences can affect SD sequences in addition to the underlying impact these changes have on the translational efficiency of prokaryotes. In chapter two, we hypothesized that differences in the prevalence of SD motifs between B. subtilis and E. coli arise as a result of changes in the free 3' end of 16S rRNA which may have led B. subtilis and E. coli to evolve differently. E. coli is expected to be more amenable to the acquisition of SD motifs that do not perfectly correspond with its free 3' 16S rRNA end than B. subtilis. Further, we proposed that the evolutionary divergence of these upstream sequences may be exacerbated in B. subtilis by the absence of a functional S1 protein. Based on the differences between E. coli and B. subtilis, we were able to identify SD motifs that can only perfectly base pair in one of the two species and are expected to work well in one species, but not the other. Furthermore, we determine the frequency and proportion of these specific SD motifs that are expected to be preferentially [...]
doi:10.20381/ruor-212 fatcat:kxcyjsyl3fdadhospevy66b6ey