Gaining Insights into the Codon Usage Patterns of TP53 Gene across Eight Mammalian Species

Mazumder, Tarikul Huda; Chakraborty, Supriyo

doi:10.1371/journal.pone.0121709.g002 a higher predominance of G/C-ending codons. It suggested that GC 3s values determined the codon usage pattern in the coding sequences of TP53 gene [33] . Nabiyouni et al., (2013) reported that eukaryotic organisms with very high GC-contents have high GC 3 -composition while organisms with low GC-content have low GC 3 -composition in the genome [37] . We also calculated GC 3 skew values which ranged from 0.000 to -0.094, indicating that GC 3 composition at the third position of codon might have played an important role in the codon usage bias [38] . Negative GC skew was observed in all the coding sequences of TP53 gene which revealed that the abundance of C over G [39] . In addition, lower values of the frequency of optimal codons (FOP) and the effective number of codons (ENC) along with higher GC contents suggested that a moderate bias exists in the usage of synonymous codons [33] for TP53 gene in different mammalian species. Predominant codon usage bias was observed in TP53 gene of M.unguiculatus compared to other mammalian species (Table 3) . RCBS value of a gene can be used as an effective measure of predicting gene expression and its value depends on the patterns of codon usage along with nucleotide compositional bias of a gene [20] . The distribution of RCBS values for TP53 gene across eight mammalian species is shown in figure below (Fig. 6) . The RCBS values ranged from 0.006 to 0.065 with a mean value of 0.039 and a standard deviation (SD) of 0.021. In our analysis, low mean RCBS value suggested that there exists a low codon bias for TP53 gene associated with low expression level [20] .