Codon usage deviations and bioinformatics analysis of encoding sequence of Calpastatin gene in some mammalian species

Abstract

Abstract2
Background and Object: Calpastatin (CAST) is one of the enzymes of Calpine proteolytic system. The proteolytic protein complex contains Ca+2 dependent proteases which contributes in construction, degradation and muscle tissue compression after slaughter, and is also regarded a candidate gene associated with growth efficacy and quality of meat.
Materials and Methods: In this study, gene and protein coding sequences region of CAST in six species of mammals (human, rat, cow, Bos grunniens, sheep and goats) were examined. Gene and protein sequences were retrieved from gene bank and then analyzed. Homology analysis and alignment, phylogenetic and nucleotide diversity and variation in coding region and stop codon were carried out using the softwares Clustal Ω and Mega7. SOPMA and Protparam programs were used for homology and alignment analyses, and to investigate the atoms diversity in protein structure, amino acid and terminal amino acid diversity in sequences retrieved from the NCBI database. Preferred codon sequences were obtained using CodonW software to explore the codon usage status.
Results: Codon adaptation index (CAI) had the highest value for Bos grunniens (0.256) and lowest value for Ovisaries (0.236). Using bioinformatics software for better understanding of protein structure of CAST showed that, in all sequences, the amino acid lysine was the most frequent by 623 observations and amino acid tryptophan was the least with 5 repeat in the structure of the protein. The ration of Polar amino acids to non-polar amino acids in the protein was 2. The relative efficiency of synonymous codons (RSCU) for the amino acids serine and aspartic acid as the terminal amino acid in different species were, respectively, (AGC =1/38) and (GAU =1/01). Ovisaries species showed the maximumn PI and The species Capra hircus had the highest value of effective number of codons index (ENC) .
Conclusion: hydrophobic amino acids constitute the main part of the amino acid sequence of Calpastatin protein. Given the role of inhibition of Calpastatin protein for the activity of the enzyme calpain in muscle and considering that the most sequences of calpain are captured by hydrophilic amino acids, the explore of amino acid sequence in Calpastatin and the role of these hydrophobic amino acids against the hydrophilic amino acids in calpain is important. Calpastatin protein, is much more tolerant in humans rather than ruminants. The codon bias analysis of the studied species showed that, in the evolution, Bos grunniens protein species had higher phenotype appearance for preferred codons than other species and function of the optimal codons were shown to be stronger than others.

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References

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Journal of Ruminant Research
Volume 6, Issue 3
December 2018
Pages 12-26

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