Analysis of factors affecting codon usage bias in human papillomavirus
Published: Jan. 31, 2018
Indices of codon usage pattern of human papillomavirus (HPV) were analyzed to understand the key determinants of synonymous codon usage in the HPV genome. The complete sequences of 39 HPV genomes were downloaded from the website of the National Center for Biotechnology Information. The relative synonymous codon usage values, effective number of codons, GC content, percentage of GCs at the third position of synonymous codons (GC3s), codon adaptation index, hydrophobicity, aromaticity of conceptually translated gene products were calculated using the Codon W 1.4.2 program. HPV preferentially used codons ending with A/U. By comparing relative synonymous codon usage of the HPV genome and human genome, the codon usage of HPV was almost entirely different from that of humans. Statistical significant of the separation between codons ending with A/U and G/C on the first axis was shown by the principal component analysis. The greater number of the effective number of codon values against the value of GC3s was below the expected values. The correlation between effective number of codon values and both aromaticity and hydrophobicity showed significant high negative correlation. These results showed that composition constraint is likely the key element for codon usage in the HPV genome.
Principal component analysis, codon usage., composition constraints, papilloma virus
Where, N is the number of amino acids and ki is the hydrophobic index of the ith amino acid.
The aromaticity index (Peden, 1999) is calculated as:
Correlation analysis was calculated using Spearman’s rank correlation method of the R package (R Development Core Team, 2011).
Comparison of the genomes of HPV and humans revealed that the codon usage pattern of the virus was different from that of the host (Figure 1). There were only few similar synonymous codon usage patterns between HPV and humans; these similarities were found in Ala (GGU), Pro (CCA and CCU), Arg (AGA), and Ser (UCU) (Table 2).
We also investigated whether other factors could explain the codon usage bias seen in the HPV genome. Significant high negative correlation was observed in between ENC and both aromaticity (Figure 4b) (Spearman, r = -0.71464, p < 0.001) and GRAVY (Figure 4c) (Spearman, r = -0.4391, p < 0.001).
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