On Base-Pairing Potential Between 16S rRNA and 5’ UTR in Archaebacterial Genomes

The Shine-Dalgarno (SD) sequence [4] of E. coli is known to be a signal to initiate translation. The widely accepted model is that the 3’ end of 16S rRNA base-pairs with the SD sequence in the first step of ribosome binding to mRNA. However, archaebacteria have been supposed to have systems of translation different from those of eubacteria and eucaryotes. Further, some eubacteria, such as M. genitalium, do not seem to have SD-like sequences. Rather than directly displaying consensus sequences using software such as Sequence Logos [3], we have developed a method to systematically analyze base-pairing potentials between the 3’ end of 16S rRNA and the 5’ UTRs of all genes. The base-pairing potentials between the two sequences are calculated as free-energy values, and those values at each position in the 5’ UTR are averaged over all of the genes, in order to visualize the base-pairing trend of the organism as a whole.