Synonymous Codon Usage Based on Codon-Anticodon Interaction Energy and Gene Expression Level

In unicellular organisms, synonymous codon bias is correlated with the level of gene expression [1]. The codon bias becomes stronger in genes with higher expression levels. It becomes weaker but still remains in genes with lower expression levels. The bias means that synonymous codons are not used at random. In highly expressed genes, the synonymous codon usage is mainly determined by an abundance of iso-accepting tRNAs [2]. In weakly expressed genes, on the other hand, constraints imposed by base composition mainly affect the codon usage. We have hypothesized that independently of the iso-accepting tRNA abundance and base composition, codon-anticodon interaction energy affects the synonymous codon usage. To verify this hypothesis, we investigated 1664 function-known genes in E. coli genome and 2575 function-known genes in S. cerevisiae genome.