Analysis of base-pairing potentials between 16S rRNA and 5 ' UTR for translation initiation in various prokaryotes

Motivation: It is well accepted that the 3' end of 16S rRNA is directly inv olved in prokaryotic translation initiation by pairing with the Shine-Dalga rno (SD) sequence, which is located in the ribosome-binding site of mRNA. A ccording to Shine and Dalgarno, Escherichia coli's 5' UTR has the pattern o f 'AGGAGG' (SD sequence), which is complementary to the 3' end sequence of 16S rRNA. In this work, we systematically calculated free-energy values of the base pairing between the 3' end of 16S rRNA and the 5' UTR of mRNA, in order to analyze the base-pairing potentials in various prokaryotes. The fr ee-energy values were then plotted over distances from the start codon to v isualize the free-energy pattern of 5' UTRs. Results: The average free-ener gy values fell sharply before the start codon in E. coli, which is consiste nt with the model that the 3' end of 16S rRNA base pairs with the SD sequen ce. Haemophilus influenzae, Bacillus subtilis and Helicobacter pylori show a similar pattern, suggesting that the organisms have basically the same me chanism of translation initiation as E. coli. Other eubacteria, such as Syn cechocystis PCC6803, Mycoplasma genialium, Mycoplasma Pneumoniae and Borrel ia burgdorferi also show decreases in their free-energy values, although th ey are less evident. We also did the same analysis with a eukaryote genome as a control; no fall in free-energy values was observed between the 3' end of 18S rRNA and 5' UTRs of Saccharomyces cerevisiae, suggesting that this organism does not base pair in translation initiation. The three archaebact eria A. fulgidus, M. jannaschii and M. thermoautotrophicum show patterns si milar to eubacteria, but not to S. cerevisiae, indicating that archaebacter ia are closer to eubacteria than to eukaryotes with respect to the mechanis m of translation initiation. From these observation, it appears that the sh ape of the curve produced by the algorthim can be used to predict the mecha nism of translation initiation.