Control of translation by mRNA secondary structure in Escherichia coli. A quantitative analysis of literature data

J Mol Biol. 1994 Nov 25;244(2):144-50. doi: 10.1006/jmbi.1994.1714.


Translational efficiency in Escherichia coli is strongly controlled by the secondary structure of the mRNA in the translational initiation region. We have previously shown that protein production from the coat-protein gene of RNA bacteriophage MS2 is directly related to the fraction of mRNA molecules in which the ribosome binding site is unfolded. This fraction is dictated by the free energy (delta Gf0) of the local secondary structure. We now present a similar analysis of published data on four other ribosome binding sites. The results conform quantitatively to the same relationship as found for the MS2 coat-protein gene. The efficiency of translation is determined by the overall stability of the structure at the ribosome binding site, whether the initiation codon itself is base-paired or not. Structures weaker than -6 kcal/mol usually do not reduce translational efficiency. Below this threshold, all systems show a tenfold decrease in expression for every -1.4 kcal/mol, as predicted from theory.

MeSH terms

  • Bacteriophage mu / genetics
  • Base Sequence
  • Binding Sites
  • Capsid / genetics
  • DNA Transposable Elements / genetics
  • Escherichia coli / genetics*
  • Gene Expression Regulation*
  • Genes, Bacterial*
  • Genes, Viral
  • Insulin-Like Growth Factor I / genetics
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Nucleotidyltransferases / genetics
  • Peptide Chain Initiation, Translational
  • Protein Biosynthesis*
  • RNA, Messenger / chemistry*
  • Ribosomes / metabolism
  • Transposases


  • DNA Transposable Elements
  • RNA, Messenger
  • Insulin-Like Growth Factor I
  • Nucleotidyltransferases
  • Transposases