The codon information index: a quantitative measure of the information provided by the codon bias

Abstract

The genetic code is redundant, as there are about three times more codons than amino acids. Because of this redundancy, a given amino acid can be specified by different codons, which are therefore considered synonymous. Despite being synonymous, however, such codons are used with different frequencies, a phenomenon known as codon bias. The origin and roles of the codon bias have not yet been fully clarified, although it is clear that it can affect the efficiency, accuracy and regulation of the translation process. In order to provide a tool to address these issues, we introduce here the codon information index (CII), which represents a measure of the amount of information stored in mRNA sequences through the codon bias. The calculation of the CII requires solely the knowledge of the mRNA sequences, without any other additional information. We found that the CII is highly correlated with the tRNA adaptation index (tAI), even if the latter requires the knowledge of the tRNA pool of an organism. We anticipate that the CII will represent a useful tool to study quantitatively the relationship between the information provided by the codon bias and various aspects of the translation process, thus identifying those aspects that are most influenced by it.