title: Translational resistivity/conductivity of coding sequences during exponential growth of Escherichia coli.
abstract: Codon adaptation index (CAI) has been widely used for prediction of expression of recombinant genes in Escherichia coli and other organisms. However, CAI has no mechanistic basis that rationalizes its application to estimation of translational efficiency. Here, I propose a model based on which we could consider how codon usage is related to the level of expression during exponential growth of bacteria. In this model, translation of a gene is considered as an analog of electric current, and an analog of electric resistance corresponding to each gene is considered. "Translational resistance" is dependent on the steady-state concentration and the sequence of the mRNA species, and "translational resistivity" is dependent only on the mRNA sequence. The latter is the sum of two parts: one is the resistivity for the elongation reaction (coding sequence resistivity), and the other comes from all of the other steps of the decoding reaction. This electric circuit model clearly shows that some conditions should be met for codon composition of a coding sequence to correlate well with its expression level. On the other hand, I calculated relative frequency of each of the 61 sense codon triplets translated during exponential growth of E. coli from a proteomic dataset covering over 2600 proteins. A tentative method for estimating relative coding sequence resistivity based on the data is presented.
authors.affiliation: Department of Materials Sciences and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan. Electronic address: takai.kazuyuki.mz@ehime-u.ac.jp.
authors.forename: Kazuyuki
authors.initials: K
authors.lastname: Takai
mesh_terms: D003062:Codon / Q000235:genetics; D017097:Electric Impedance; D004926:Escherichia coli / Q000254:growth & development* / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000378:metabolism; D016366:Open Reading Frames / Q000235:genetics*; D014176:Protein Biosynthesis
chemical_list: D003062:Codon; D029968:Escherichia coli Proteins
keywords: Codon adaptation index; Electric circuit model; Relative codon usage; Steady state