a comprehensive, quantitative, and genome-wide model of translation一个全面、定量和全基因组的翻译模式.pdfVIP

A Comprehensive, Quantitative, and Genome-Wide Model of Translation 1 1,2 Marlena Siwiak , Piotr Zielenkiewicz * 1 Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland, 2 Laboratory of Plant Molecular Biology, Faculty of Biology, Warsaw University, Warsaw, Poland Abstract Translation is still poorly characterised at the level of individual proteins and its role in regulation of gene expression has been constantly underestimated. To better understand the process of protein synthesis we developed a comprehensive and quantitative model of translation, characterising protein synthesis separately for individual genes. The main advantage of the model is that basing it on only a few datasets and general assumptions allows the calculation of many important translational parameters, which are extremely difficult to measure experimentally. In the model, each gene is attributed with a set of translational parameters, namely the absolute number of transcripts, ribosome density, mean codon translation time, total transcript translation time, total time required for translation initiation and elongation, translation initiation rate, mean mRNA lifetime, and absolute number of proteins produced by gene transcripts. Most parameters were calculated based on only one experimental dataset of genome-wide ribosome profiling. The model was implemented in Saccharomyces cerevisiae, and its results were compared with available data, yielding reasonably good correlations. The calculated coefficients were used to perform a global analysis of translation in yeast, revealing some interesting aspects of the process. We have shown that two commonly used measures of translation efficiency – ribosome