title: Composite effects of gene determinants on the translation speed and density of ribosomes.
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.
authors: Department of Biomedical Engineering, Tel Aviv University, Israel. tamirtul@post.tau.ac.il
authors: Tamir
authors: T
authors: Tuller
authors: Isana
authors: I
authors: Veksler-Lublinsky
authors: Nir
authors: N
authors: Gazit
authors: Martin
authors: M
authors: Kupiec
authors: Eytan
authors: E
authors: Ruppin
authors: Michal
authors: M
authors: Ziv-Ukelson
mesh_terms: D000596:Amino Acids / Q000235:genetics; D005075:Biological Evolution; D003062:Codon / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D008957:Models, Genetic; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames / Q000235:genetics; D010441:Peptide Chain Elongation, Translational; D012329:RNA, Bacterial / Q000235:genetics*; D012331:RNA, Fungal / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics*; D012343:RNA, Transfer / Q000235:genetics*; D012270:Ribosomes / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D055672:Static Electricity; D013816:Thermodynamics
chemical_list: D000596:Amino Acids; D003062:Codon; D012329:RNA, Bacterial; D012331:RNA, Fungal; D012333:RNA, Messenger; D012343:RNA, Transfer