Computer analysis of potential stem structures of rRNA operons in various procaryote genomes

Rintaro Saito, Yousuke Ozawa, Naoki Kuzuno, Masaru Tomita

Research output: Contribution to journalArticlepeer-review

7 Citations (Scopus)


The processing of 16S rRNA and 23S rRNA by RNase III in E.coli is known to involve stem structures formed by both ends of the rRNA. Indeed, complementary nucleotide sequences are usually found at both ends of 16S rRNA and 23S rRNA. However, whether or not this phenomenon exists in various other bacteria has not yet been adequately studied. We have conducted computer analyses of potential stem structures of rRNA operons in 12 bacterial and 3 archaeal genomes, and compared characteristics of the stem structures among these species. We systematically computed free energy values by exhaustively 'annealing' sequences around the 5′ end and sequences around the 3′ end of both 16S rRNA and 23S rRNA genes, in order to predict potential stem structures. The results suggest that rRNAs in most species form stem structures at both ends. Some species, such as A.aeolicus, seem to form unusually stable stem structures. On the other hand, some rRNAs, such as rRNAs of D.radiodurans, seem not to form solid stem structures. This suggests that rRNA processing in those species must employ a reliable targeting mechanism other than recognizing stem structures by RNase III.

Original languageEnglish
Pages (from-to)217-222
Number of pages6
Issue number1-2
Publication statusPublished - 2000 Dec 23


  • Free energy
  • Processing
  • RNase III
  • Ribonuclease

ASJC Scopus subject areas

  • Genetics


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