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Research Paper | Biotechnology | India | Volume 3 Issue 6, June 2014
Mutation Pressure Dictates Codon Usage Pattern in Mitochondrial Atpase8 in Some Mammalian Species
Arif Uddin | Supriyo Chakraborty
Abstract: Background: Codon usage bias is the phenomenon of unequal use of synonymous codons in a gene; some codons are more preferred than others. However codon usage pattern is different in different genes and organisms and is mainly caused by mutation and selection pressure. Codon usage bias is mostly found in highly expressed genes. Mammals are the highly evolved organisms in animal kingdom. Study of codon usage bias helps in better understanding of molecular biology; genetics and evolution of genes. Methods and Result: We used bioinformatics approach to understand the pattern of codon usage bias of mitochondrial atpase8 gene in ten species of mammals. We have found that GC content varies from 27.5 to 46.4 % with a mean of 37.495.12 and GC content at 3rd codon position varies from 16.2 to 47.8 % with a mean of 34.119.76. ENC values are much higher and range from 42 to 60 with a mean of 54.15.93. 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) and between GC12 and GC3 (r=0.8270 p<0.01). A significant positive correlation was 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) and significant negative correlation was found for most other nucleotides comparisons. We performed linear regression analysis between observed ENC and base composition at third codon position (Wobble codon position) and observed that the effective numbers of codons are negatively affected by A3 and T3 but positively affected by G3 and C3. Conclusion: It was found that the nucleotide A would occur more frequently at the 3rd codon position. The pattern of codon bias for atpase8 gene is not remarkable. Our results suggest that mutation pressure is the major force in shaping the evolution of codon usage bias in mitochondrial atpase8 gene in mammalian species.
Keywords: Codon usage, mutation pressure, mitochondria, mammals
Edition: Volume 3 Issue 6, June 2014,
Pages: 2206 - 2212
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