composite effects of gene determinants on the translation speed and density of ribosomes复合基因因素对翻译的影响速度和核糖体密度.pdfVIP

Tuller et al. Genome Biology 2011, 12:R110 /2011/12/11/R110 RESEARCH Open Access Composite effects of gene determinants on the translation speed and density of ribosomes 1*† 2† 3 4 3,5 2 Tamir Tuller , Isana Veksler-Lublinsky , Nir Gazit , Martin Kupiec , Eytan Ruppin and Michal Ziv-Ukelson 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 sequenc