title: Analysis of base-pairing potentials between 16S rRNA and 5' UTR for translation initiation in various prokaryotes.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  The C programs used in our analysis are available upon request.
authors.affiliation: Laboratory for Bioinformatics, Keio University, 5322 Endo, Fujisawa, 252, Japan.
authors.forename: Y
authors.initials: Y
authors.lastname: Osada
authors.forename: R
authors.initials: R
authors.lastname: Saito
authors.forename: M
authors.initials: M
authors.lastname: Tomita
mesh_terms: D020121:5' Untranslated Regions; D001105:Archaea / Q000737:chemistry / Q000235:genetics; D001419:Bacteria / Q000737:chemistry / Q000235:genetics; D020029:Base Pairing; D001483:Base Sequence; D018387:Codon, Initiator / Q000737:chemistry / Q000235:genetics; D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics; D016678:Genome; D010442:Peptide Chain Initiation, Translational / Q000235:genetics*; D011387:Prokaryotic Cells; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000235:genetics; D013816:Thermodynamics
chemical_list: D020121:5' Untranslated Regions; D018387:Codon, Initiator; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S