Translation initiation modeling and mutational analysis based on the 3(')-end of the Escherichia coli 16S rRNA sequence

Biosystems. 2009 Apr;96(1):58-64. doi: 10.1016/j.biosystems.2008.11.008. Epub 2008 Nov 25.


A model for the process of translation in gene expression is proposed. The model is based on the assumption that the ribosome decodes the mRNA sequences using consecutive subsequences of the 3(')-end of its 16S rRNA subunit. The biological consistency of the model is validated by successful detection of the Shine-Dalgarno signal and the start codon. Furthermore, implications on the role of the 3(')-end in the complete process of prokaryotic translation are presented and discussed. Interestingly, the results obtained support the possibility of an involvement of this part of the ribosome in the process of translation termination. Subsequently, results obtained via the proposed model are compared with published experimental results for different mutations of the last 13 bases of the 16S rRNA molecule. Agreement between predictions and experimental results validate the biological relevance of the proposed model. By means of simulated nucleotide mutations, a global analysis of this part of the ribosome in the process of translation is conducted.

MeSH terms

  • Base Sequence
  • Codon, Initiator / genetics*
  • Computer Simulation
  • DNA Mutational Analysis / methods
  • Escherichia coli / genetics*
  • Models, Genetic*
  • Molecular Sequence Data
  • Mutation
  • Protein Biosynthesis / genetics*
  • RNA, Bacterial / genetics*
  • RNA, Ribosomal, 16S / genetics*
  • Sequence Analysis, RNA / methods*


  • Codon, Initiator
  • RNA, Bacterial
  • RNA, Ribosomal, 16S