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

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JALALI P.; RAHIMI MIANJI GH.; GHOLIZADEH M.; PAKDIN PARIZI A.

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Journal: JOURNAL OF RUMINANT RESEARCH Year:2018 | Volume:6 | Issue:3 Page(s): 12-26

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Title

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

Author(s)

JALALI P. | RAHIMI MIANJI GH. | GHOLIZADEH M. | PAKDIN PARIZI A. | Issue Writer Certificate

Keywords

MammalsQ1

CalpastatinQ1

Bioinformatics analysisQ1

Codon biasQ1

spatial structureQ1

Abstract

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 mammalian species (human, rat, cattle, yak, sheep and goat) 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 Clustal Ω and Mega7 softwares. 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 locus. Results: Codon adaptation index (CAI) had the highest value for yak (0. 256) and lowest value for sheep (0. 236). Analysis by bioinformatic software for better understanding of protein structure of CAST showed that, in all sequences, lysine amino acid was the most frequent by 623 observations and tryptophan was the least with 5 repeats 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 maximum PI and Capra hircus species 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 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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APA: Copy

JALALI, P., RAHIMI MIANJI, GH., GHOLIZADEH, M., & PAKDIN PARIZI, A.. (2018). Codon usage deviations and bioinformatics analysis of encoding sequence of Calpastatin gene in some mammalian species. JOURNAL OF RUMINANT RESEARCH, 6(3 ), 12-26. SID. https://sid.ir/paper/244020/en

Vancouver: Copy

JALALI P., RAHIMI MIANJI GH., GHOLIZADEH M., PAKDIN PARIZI A.. Codon usage deviations and bioinformatics analysis of encoding sequence of Calpastatin gene in some mammalian species. JOURNAL OF RUMINANT RESEARCH[Internet]. 2018;6(3 ):12-26. Available from: https://sid.ir/paper/244020/en

IEEE: Copy

P. JALALI, GH. RAHIMI MIANJI, M. GHOLIZADEH, and A. PAKDIN PARIZI, “Codon usage deviations and bioinformatics analysis of encoding sequence of Calpastatin gene in some mammalian species,” JOURNAL OF RUMINANT RESEARCH, vol. 6, no. 3 , pp. 12–26, 2018, [Online]. Available: https://sid.ir/paper/244020/en

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