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

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.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.Gene translation is a central biological process in all living organisms by which an mRNA sequence is decoded by the ribosome to synthesize a specific protein. During the elongation stage of this process, each codon is iteratively translated by the ribosome to an amino acid. Translation elongation is known to be conserved in all living organisms (Bacteria, Archaea, and eukaryotes [1]); thus, understanding this process and the determinants related to it have important ramifications for human health [2-4], biotechnology [5-10], and evolution [4,8,11].Indeed, gene translation has been the topic of an increasing number of studies in recent years (see, for example, [5,7,8,12-20]). Specifically, it was recently discovered that the efficiency of translation can be controlled by the codon order in the coding sequence [8,17]. This is partially achieved by a 'ramp' at the beginning of the coding sequences composed of less efficient codons. This