The effective number of codons for individual amino acids: some codons are more optimal than others.

The aim of this study was to evaluate the codon bias using the effective number of codons for individual amino acids (N(c)(AA)) and to assess the codon bias in relation to the definition of optimal codons, using Escherichia coli as a model organism. We show that a general correlation exists between the effective number of codons (Ncirc(c)) or codon adaptation index (CAI) and N(c)(AA), but that this correlation is not equally strong for all amino acids within a degeneracy group. For example, leucine codons contribute more to Ncirc(c) and the codon adaptation index than serine codons. A possible explanation is that some optimal codons are more optimal than others, in terms of the selectional advantage they offer. This hypothesis is confirmed by further analysis on the correlations that exist between values for relative synonymous codon usage (RSCU), N(c)(AA), and the codon adaptation index.