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Improving Translational Accuracy

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...

Coordination of Gene Expression Processes in Bacteria

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Related Experiment Video

Updated: Jul 3, 2026

Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling

Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling

Published on: December 21, 2017

Ribosome collisions and translation efficiency: optimization by codon usage and mRNA destabilization.

Namiko Mitarai¹, Kim Sneppen, Steen Pedersen

¹Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark.

Journal of Molecular Biology

|July 16, 2008

Summary

Ribosome collisions and queuing are inevitable during mRNA translation, significantly reducing efficiency. Cells minimize these issues through mRNA instability and optimized codon usage, balancing breakdown costs with translation gains.

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Area of Science:

Molecular Biology
Systems Biology
Biophysics

Background:

Multiple ribosomes translate individual messenger RNAs (mRNAs) with a few-second interval between initiations.
Ribosome speed is codon-dependent, and ribosome queuing is a proposed mechanism for in vivo translation data.
Understanding ribosome traffic dynamics is crucial for explaining mRNA translation efficiency.

Purpose of the Study:

To model the stochastic translation process as a traffic problem to analyze ribosome collisions and queuing.
To determine the initiation on-rate and ribosome occlusion time for Escherichia coli lacZ mRNA in vivo.
To investigate the consequences of ribosome collisions and queuing on natural mRNA translation efficiency.

Main Methods:

Stochastic modeling of the translation process, conceptualized as a traffic problem.
In vivo analysis of Escherichia coli lacZ mRNA translation dynamics.
Quantitative determination of ribosome initiation rates and occlusion periods.

Main Results:

Ribosome collisions and queuing are inevitable outcomes of stochastic translation, substantially reducing translation efficiency on natural mRNAs.
The initiation on-rate for Escherichia coli lacZ mRNA was determined to be 0.8 to 1.1 initiations/s.
A preceding ribosome was found to occlude initiation for 1 second.

Conclusions:

Cells employ strategies such as mRNA instability and selected codon usage at the mRNA start to minimize ribosome collisions.
The cost of mRNA breakdown is compensated by increased translation efficiency resulting from collision mitigation.
Stochastic translation mechanisms inherently lead to inefficiencies that cellular strategies aim to overcome.