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Open Access Research

Composite effects of gene determinants on the translation speed and density of ribosomes

Tamir Tuller1*, Isana Veksler-Lublinsky2, Nir Gazit3, Martin Kupiec4, Eytan Ruppin35 and Michal Ziv-Ukelson2

Author Affiliations

1 Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Ramat Aviv 69978, Israel

2 Department of Computer Science, Ben Gurion University of the Negev, Beer-Sheva 84105, Israel

3 Blavatnik School of Computer Science, Tel Aviv University, Ramat Aviv 69978, Israel

4 Department of Molecular Microbiology and Biotechnology Tel Aviv University, Ramat Aviv 69978, Israel

5 School of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel

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Genome Biology 2011, 12:R110  doi:10.1186/gb-2011-12-11-r110

Published: 3 November 2011

Abstract

Background

Translation is a central process of life, and its regulation is crucial for cell growth. In this article, focusing on two model organisms, Escherichia coli and Saccharomyces cerevisiae, we study how three major local features of a gene's coding sequence (its adaptation to the tRNA pool, its amino acid charge, and its mRNA folding energy) affect its translation elongation.

Results

We find that each of these three different features has a non-negligible distinct correlation with the speed of translation elongation. In addition, each of these features might contribute independently to slowing down ribosomal speed at the beginning of genes, which was suggested in previous studies to improve ribosomal allocation and the cost of translation, and to decrease ribosomal jamming. Remarkably, a model of ribosomal translation based on these three basic features highly correlated with the genomic profile of ribosomal density. The robustness to transcription errors in terms of the values of these features is higher at the beginnings of genes, suggesting that this region is important for translation.

Conclusions

The reported results support the conjecture that translation elongation speed is affected by the three coding sequence determinants mentioned above, and not only by adaptation to the tRNA pool; thus, evolution shapes all these determinants along the coding sequences and across genes to improve the organism's translation efficiency.