Abstract
Long stretches of "rare" codons are known to severely inhibit the efficiency of translation. Understanding the distribution of such rare codons is of critical importance in improving the efficiency of heterologous gene expression systems. Accurate estimates of codon usage take the abundance of each protein into consideration. In this paper, we analyze the correlation between approximate measures of codon usage and the availability of tRNA at various growth rates in E coli. We show that the computationally derived estimates of tRNA isoacceptor concentration enable the finding of poorly translated codons.
Highlights
The translation of codons to amino acids takes place via charged tRNA molecules that can recognize and bind to each codon while carrying the corresponding amino acid [1]
The tRNA-codon recognition pattern is known to vary across eubacterial species and even across different strains of the same species
Note that the list T needs to be re-calculated for each growth rate, since the concentration of tRNA isoacceptors varies across growth rates
Summary
The translation of codons to amino acids takes place via charged tRNA molecules that can recognize and bind to each codon while carrying the corresponding amino acid [1]. The rate at which the ribosome translates codons in a eubacterial mRNA sequence is shown to depend on the availability or abundance of the corresponding tRNA isoacceptors [10]. Extensive studies have been conducted to understand the distribution of poorly-translated codons, i.e. codons whose tRNA isoacceptors are in low concentration in the cell, and to investigate if they serve any functional roles [13]. Such investigations have led to quite a few interesting findings, such as the effect of rare codons on modulating gene expression [14] and in attenuating viruses [15]. It has been shown that the presence of rare codons serves to pause the ribosome and gives protein domains time to fold [16]
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