Synonymous codons, i.e., DNA nucleotide triplets coding for the same amino
acid, are used differently across the variety of living organisms. The
biological meaning of this phenomenon, known as codon usage bias, is still
controversial. In order to shed light on this point, we propose a new codon
bias index, CompAI, that is based on the competition between cognate and
near-cognate tRNAs during translation, without being tuned to the usage bias of
highly expressed genes. We perform a genome-wide evaluation of codon bias for
E.coli, comparing CompAI with other widely used indices: tAI, CAI, and
Nc. We show that CompAI and tAI capture similar information by being
positively correlated with gene conservation, measured by ERI, and
essentiality, whereas, CAI and Nc appear to be less sensitive to
evolutionary-functional parameters. Notably, the rate of variation of tAI and
CompAI with ERI allows to obtain sets of genes that consistently belong to
specific clusters of orthologous genes (COGs). We also investigate the
correlation of codon bias at the genomic level with the network features of
protein-protein interactions in E.coli. We find that the most densely
connected communities of the network share a similar level of codon bias (as
measured by CompAI and tAI). Conversely, a small difference in codon bias
between two genes is, statistically, a prerequisite for the corresponding
proteins to interact. Importantly, among all codon bias indices, CompAI turns
out to have the most coherent distribution over the communities of the
interactome, pointing to the significance of competition among cognate and
near-cognate tRNAs for explaining codon usage adaptation