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Translational initiation on structured messengers. Another role for the Shine-Dalgarno interaction

M H de Smit1, J van Duin

  • 1Department of Biochemistry, Gorlaeus Laboratories, University of Leiden, The Netherlands.

Journal of Molecular Biology
|January 7, 1994
PubMed
Summary

A strong Shine-Dalgarno (SD) interaction can enhance translation efficiency by outcompeting messenger RNA secondary structures for ribosomal binding. This compensates for reduced SD complementarity, highlighting the interplay between RNA structure and protein synthesis.

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Area of Science:

  • Molecular Biology
  • Bacterial Genetics
  • Protein Synthesis

Background:

  • Translational efficiency in Escherichia coli is influenced by the Shine-Dalgarno (SD) interaction, a base-pairing event between 16S rRNA and mRNA.
  • Previous studies lacked quantitative relationships between SD complementarity and translational efficiency, likely due to uncharacterized messenger RNA secondary structures.
  • mRNA secondary structures near the ribosome binding site can significantly impact translational efficiency.

Purpose of the Study:

  • To investigate the quantitative relationship between Shine-Dalgarno (SD) complementarity and translational efficiency in bacteriophage MS2 coat-protein gene.
  • To determine how messenger RNA secondary structure stability affects the role of SD interaction in translation initiation.
  • To elucidate the compensatory role of strong SD interactions in overcoming inhibitory mRNA structures.

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Main Methods:

  • Site-directed mutagenesis was employed to alter the Shine-Dalgarno (SD) sequence complementarity in the bacteriophage MS2 coat-protein gene.
  • Mutations were introduced to modify the stability of the messenger RNA hairpin structure at the ribosome binding site.
  • Translational efficiency was measured for various mutant and wild-type sequences, correlating SD complementarity with mRNA structure.

Main Results:

  • Mutations reducing SD complementarity by one or two nucleotides only decreased translational efficiency when the messenger RNA structure impeded ribosome binding.
  • In the absence of inhibitory secondary structures, these minor reductions in SD complementarity had no significant effect on translation.
  • A strong SD interaction can effectively compensate for a structured initiation region, enhancing ribosome binding affinity.

Conclusions:

  • The Shine-Dalgarno (SD) interaction's strength is crucial for overcoming inhibitory messenger RNA secondary structures during translation initiation.
  • Translational initiation involves a competition between mRNA intramolecular base-pairing and binding to the 30S ribosomal subunit, influenced by SD affinity.
  • The contribution of SD base-pairs to ribosome-mRNA affinity correlates well with theoretical base-pairing stabilities.