Figure 1. Adenoviral fiber usage of A/T ended codons results in low codon adaptation index to human cells.

(A) Principal Component analysis (PCA) of all Ad5 proteins: the left panel shows the loadings, which correspond to codons characterized by their usage frequency, the right panel shows the distribution of viral proteins in the two first principal components. The first principal component shows a separation between early regulatory proteins and proteins participating in replication or virion formation. This separation is related to their differential use of A/T ended codons (red and orange) or of G/C ended codons (cyan and blue). Adenoviral fiber, hexon and polymerase are highlighted in red, green and blue respectively. (B) Principal Component analysis (PCA) of 117 adenoviral fibers, 103 hexons and 105 polymerases using as loadings codons characterized by their usage frequency as in (A). (C) Codon Adaptation Index (CAI) analysis according to the human codon usage of all sequenced adenoviral fibers, hexons and polymerases (in red, green and blue respectively) in comparison with human proteins (in grey). The red vertical line corresponds to the CAI of the Ad5 adenoviral fiber. (D) Representation of the CAI values along the sequence of the Ad5 fiber and hexon structures in monomeric or trimeric models (with green corresponding to lowest CAI and red corresponding to maximum CAI).