Bioinformatics, Vol 15, 578-581, Copyright © 1999 by Oxford University Press
Y Osada, R Saito and M Tomita
MOTIVATION: It is well accepted that the 3' end of 16S rRNA is directly
involved in prokaryotic translation initiation by pairing with the
Shine-Dalgarno (SD) sequence, which is located in the ribosome-binding site
of mRNA. According to Shine and Dalgarno, Escherichia coli 's 5' UTR has
the pattern of '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 free-energy values were then plotted over
distances from the start codon to visualize the free- energy pattern of
5'UTRs. RESULTS: The average free-energy values fell sharply before the
start codon in E. coli, which is consistent with the model that the 3' end
of 16S rRNA base pairs with the SD sequence. Haemophilus influenzae,
Bacillus subtilis and Helicobacter pylori show a similar pattern,
suggesting that the organisms have basically the same mechanism of
translation initiation as E. coli. Other eubacteria, such as Synechocystis
PCC6803, Mycoplasma genitalium, Mycoplasma pneumoniae and Borrelia
burgdorferi also show decreases in their free- energy values, although they
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
archaebacteria A. fulgidus, M. jannaschii and M. thermoautotrophicum show
patterns similar to eubacteria, but not to S. cerevisiae, indicating that
archaebacteria are closer to eubacteria than to eukaryotes with respect to
the mechanism of translation initiation. From these observations, it
appears that the shape of the curve produced by the algorithm can be used
to predict the mechanism of translation initiation. AVAILABILITY: The C
programs used in our analysis are available upon request.
ARTICLES
Analysis of base-pairing potentials between 16S rRNA and 5' UTR for translation initiation in various prokaryotes
Laboratory for Bioinformatics, Keio University, 5322 Endo, Fujisawa, 252, Japan.
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