MUTATION PRESSURE AND NATURAL SELECTION AFFECT PATTERN OF CODON USAGE BIAS IN MITOCHONDRIAL ATPASE 6 AND ATPASE 8 GENES IN DIFFERENT MAMMALIAN SPECIES

A. UDDIN¹, S. CHAKRABORTY²*
¹Department of Biotechnology, Assam University, Silchar- 788 011, Assam, India.
²Department of Biotechnology, Assam University, Silchar- 788 011, Assam, India.
* Corresponding Author : supriyoch_2008@rediffmail.com

Received : 03-05-2014     Accepted : 06-11-2014     Published : 10-11-2014
Volume : 5     Issue : 1       Pages : 68 - 75
Int J Comput Biol 5.1 (2014):68-75

Keywords : Codon, Codon usage, Synonymous codon, Mitochondrial genome, Mammals
Academic Editor : Dr Lei Zhang
Conflict of Interest : None declared
Acknowledgements/Funding : We are thankful to the Department of Biotechnology, Assam University, Silchar for providing lab facility. AU is also thankful to the University Grant Commission, India for SRF-MANF (Maulana Azad National Fellowship).

Background: The non uniform usage of synonymous codons during translation makes codon usage bias i.e some codons are used more frequently than others. However the synonymous codon usage pattern differs among the genes of an organism and also among different organisms. Mitochondrial genome is small, highly conserved and maternally inherited with high mutation rate. The study of codon usage bias pattern is useful for better understanding the process of evolution in terms of molecular biology. Methods and Result: In this study we analyzed codon usage pattern of genes encoding mitochondrial ATPase 6 and ATPase 8 in different species of mammals. From our study it was evident that leucine is the most frequent amino acid in both genes in the mammalian species. ENC value ranged from 57 to 60 with a mean of 59.25 in ATPase 6. In ATPase 8, ENC value ranged from 42 to 60 with a mean of 54.1. In ATPase 6, a significant positive correlation was observed between overall A and A3% (r =0.9065, p<0.001), C and C3% (r = 0.9238, p< 0.001), GC and GC3% (r = 0.9244, p<0.001). ENC showed a highly significant positive correlation with overall GC content (r =0.9479, p<0.001) and GC3 (r = 0.9387, p<0.001) in ATPase 6. But in ATPase 8, significant positive correlations were observed between A% and A3% (r=0.6502, p<0.05), C% and C3% (r =0.9804, p< 0.001), GC% and GC3% (r =0.9732, p<0.001). In addition, a highly positive correlation was found between ENC and GC (r = 0.9333 p<0.001), ENC and GC3 (r = 0.9811, p<0.001) in ATPase 8. Conclusion: In our findings, we observed the codon usage bias in ATPase 6 and ATPase 8 in mammalian species is not remarkable. However in both the genes, the frequent codons favour A or C at the 3rd codon position. Our results supported that mutation pressure plays a major role in the codon usage pattern in mitochondrial ATPase 6 and ATPase 8 in addition to natural selection in some mammalian species.