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

Mazumder, Tarikul Huda; Chakraborty, Supriyo

Codon usage patterns in TP53 genes across mammalian species Correlation coefficient between codon usage and GC bias was analyzed using heat map ( Fig. 1 ) in order to find out the relationship between the codon usage variation and the GC constraints among the selected coding sequences of TP53 genes. In our analysis, nearly all codons ending with G/C base showed positive correlation with GC bias and nearly all A/T-ending codons showed negative correlation with GC bias. But, 8 G/C-ending codons (ATC, ACG, TAC, TTG, TCC, CAC, GTG, GGG) showed negative correlation with GC bias whereas 6 A/T-ending codons (AAT, ATT, TGT, CGA, GTA, GGA) showed positive correlation with AT bias although statistically not significant (p>0.05). Two G-ending codons i.e. TCG for serine and CTG for leucine amino acid showed strong positive correlation (p<0.01) with GC 3s , indicating that codon usage has been influenced by GC bias due to GC 3s . Interestingly, we observed that the codon ATA encoding isoleucine amino acid was not favored by natural selection in TP53 genes across mammalian species during the course of evolution. Thus, scanning the codon usage pattern provides the basis of the mechanism for synonymous codon usage bias and has both practical as well as theoretical significance in gaining clues of understanding molecular biology [34] .