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

Mazumder, Tarikul Huda; Chakraborty, Supriyo

We analyzed the nucleotide composition of coding sequences from TP53 genes ( Table 1 ) which revealed that mean value of C (361.50) was the highest followed by G (306.75), A (270.88) and T (227.50) among all the selected mammals. The mean percentage of GC and AT compositions was 57.3% and 42.7% respectively. Thus, the overall nucleotide composition suggested that the nucleotide C and G occurred more frequently compared to A and T in the coding sequences of TP53 gene across the mammalian species. The nucleotide composition at the third position of codon (A 3 ,T 3 ,G 3 ,C 3 ) showed that the mean values of C 3 and G 3 were the highest followed by T 3 and A 3 . The GC 3 values (ranged from 58.7%-70.6%, mean = 65.1%, SD = 0.040) was compared with that of AT 3 values (ranged from 29.4%-41.3%, mean = 34.9%, SD = 0.040) in the coding sequences of TP53 genes. The average percentage of GC contents at the first and second codon positions (GC 12 ) was found in the range of 52.6% to 54.9% with a mean value of 53.4% and a standard deviation (SD) of 0.008. Therefore, nucleotide composition analysis suggested that GC-ending codons might be preferred over AT-ending codons in the coding sequences of TP53 genes across the selected mammalian species. Further, we calculated the occurrence of frequently used optimal codons (Fop) for each amino acid as suggested by Lavner and Kotler (2005) [14] . The frequency was allied with statistical analysis to find out the highest and lowest frequently used codon. Our results showed that the most frequently used codons were G/C-ending for the corresponding amino acid (Fig. 2) in TP53 genes across mammalian species.