Codons as fragments of the genetic code articulate both nucleotidic and proteic constraints.
If codon usage bias is now admitted to be mainly influenced by GC content, codon
frequencies in general may display a more subtle compromise between base composition and
selection at proteic level. In order to investigate the existing ...»»»»
Codons as fragments of the genetic code articulate both nucleotidic and proteic constraints.
If codon usage bias is now admitted to be mainly influenced by GC content, codon
frequencies in general may display a more subtle compromise between base composition and
selection at proteic level. In order to investigate the existing non-GC content factors of codon
frequencies, we compared coding sequences (CDS) of 280 Archaea plus S. cerevisiae genomes
to their randomized version (same base-composition and same length). Through dedicated
counts we identified several CDS vs random patterns in Archaea some of which reflecting
probable or evident proteic constraint : in particular, the systematic enrichment of CDS in
negatively charged amino acids, and the strong constraint existing on codons having a T in
second position, which, on the basis of hydrophobic cluster analysis attests a folding
constraint. The sum of these patterns constitutes a coding profile that enables to accurately
classify about 99% of individual archaea sequences between CDS and randomized CDS. In
S. cerevisiae, whose coding profile shares similarities with Archeae of close GC content,
phylostratigraphic methods allowed to investigate the coding profile of CDS based on their
relative age. This analysis reveals that contrary to other genes, the youngest genes (only
found in S. cerevisiae) as a whole do not have a strong coding profile. This can be explained
by their relative shortness in comparison with other genes. But even when taking length
into account, a clear enrichment of misclassified sequences appears in the youngest S.
cerevisiae genes. This enrichment may reflect an insufficient proteic optimization operated
by selection.^^^^