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A new kinetic model reveals the synergistic effect of E-, P- and A-sites on +1 ribosomal frameshifting

Pei-Yu Liao1, Prateek Gupta, Alexey N Petrov

  • 1School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA.

Nucleic Acids Research
|March 18, 2008
PubMed

Insights

Programmed ribosomal frameshifting (+1 PRF) models reveal P-site tRNA slippage drives frameshifting. Destabilization in the E-site and a

Area of Science:

  • Molecular Biology
  • Biophysics
  • Genetics

Background:

  • Programmed ribosomal frameshifting (PRF) allows ribosomes to synthesize multiple proteins from a single mRNA.
  • Ribosome dynamics and tRNA interactions are crucial for regulating translation fidelity and efficiency.

Purpose of the Study:

  • To develop and validate kinetic models for +1 PRF in Escherichia coli.
  • To elucidate the roles of ribosomal E-, P-, and A-sites in promoting efficient +1 PRF.
  • To investigate the impact of tRNA dynamics and codon-anticodon interactions on frameshifting efficiency.

Main Methods:

  • Development of three kinetic models for +1 PRF.
  • Mathematical modeling using established kinetic rate constants.
  • Experimental validation using a dual fluorescence reporter construct to examine E-site codon:anticodon interactions.
  • Estimation of the rate constant for P-site tRNA slippage (k(s)).

Main Results:

  • Kinetic models demonstrate synergistic effects of E-site tRNA dissociation, P-site peptidyl-tRNA rearrangement, and A-site aa-tRNA availability in promoting +1 PRF.
  • Experimental data confirmed the influence of E-site codon:anticodon interactions.
  • The rate constant for P-site tRNA slippage (k(s)) was estimated at approximately 1.9 s(-1) for the RF2 frameshifting sequence.

Conclusions:

  • P-site tRNA slippage is identified as the primary driver of +1 PRF.
  • A 'hungry codon' in the A-site and E-site destabilization act as enhancers for +1 PRF in E. coli.
  • The interplay between ribosomal sites and tRNA dynamics governs efficient programmed ribosomal frameshifting.

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