title: Modelling the efficiency of codon-tRNA interactions based on codon usage bias.
abstract: The tRNA adaptation index (tAI) is a widely used measure of the efficiency by which a coding sequence is recognized by the intra-cellular tRNA pool. This index includes among others weights that represent wobble interactions between codons and tRNA molecules. Currently, these weights are based only on the gene expression in Saccharomyces cerevisiae. However, the efficiencies of the different codon-tRNA interactions are expected to vary among different organisms. In this study, we suggest a new approach for adjusting the tAI weights to any target model organism without the need for gene expression measurements. Our method is based on optimizing the correlation between the tAI and a measure of codon usage bias. Here, we show that in non-fungal the new tAI weights predict protein abundance significantly better than the traditional tAI weights. The unique tRNA-codon adaptation weights computed for 100 different organisms exhibit a significant correlation with evolutionary distance. The reported results demonstrate the usefulness of the new measure in future genomic studies.
authors.affiliation: Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel.
authors.forename: Renana
authors.initials: R
authors.lastname: Sabi
authors.affiliation: Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel The Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel tamirtul@post.tau.ac.il.
authors.forename: Tamir
authors.initials: T
authors.lastname: Tuller
mesh_terms: D003062:Codon; D019295:Computational Biology; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D012343:RNA, Transfer / Q000235:genetics* / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D013045:Species Specificity
chemical_list: D003062:Codon; D012343:RNA, Transfer
keywords: codon usage bias; protein levels; ribosome; tRNA adaptation index; wobble interactions