WHICH EVOLUTIONARY FORCES DICTATE CODON USAGE IN HUMAN TESTIS SPECIFIC GENES?
Abstract
Objective: Unequal usage of synonymous codons encoding an amino acid is termed as codon usage bias. Synonymous codon usage bias is an inevitable phenomenon in organismic taxa across the three domains of life, i.e. plants, animals and microbes. Here we report the codon usage pattern in human testis-specific genes found in Y chromosome. Testis-specific genes are associated with several dysfunctions, such as gonadal sex reversion, infertility, gonadoblastoma and non-syndromic hearing impairment.
Methods: We used bioinformatics approaches to analyze codon usage bias in human testis-specific genes
Results: Highly significant negative correlation was found between ICDI and tAI (r=-0.939**, p<0.01). Moreover, highly significant positive correlation between A% and A3% (r =0.774*, p<0.05), T and T3% (r=0.894**, p<0.01), GC% and GC3% (r = 0.897**, p<0.01) suggest that mutation pressure played an important role in codon usage pattern of these genes. However, significant positive correlation between G and G3 % (r =0.936**, p<0.01), G and C3 (r=0.557, p>0.05) but negative correlation between GC and T3 % (r=-0.960**, p<0.01) indicate the role of natural selection on codon bias. Variation of codon usage pattern was also evident in different genes from principal component analysis (PCA).
Conclusion: Codon usage bias in human testis-specific genes is low. These genes are rich in GC content. Both natural selection and mutation pressure affect the codon usage bias in these genes.
Keywords: Codon usage bias, Mutation pressure, Natural selection
Downloads
References
Grantham R, Gautier C, Gouy M, Mercier R, Pave A. Codon catalog usage and the genome hypothesis. Nucleic Acids Res 1980;8:49–62.
Marin A, Bertranpetit J, Oliver JL, Medina JR. Variation in G+C-content and codon choice: differences among synonymous codon groups in vertebrate genes. Nucleic Acids Res 1989;17:6181–9.
Gu W, Zhou T, Ma J, Sun X, Lu Z. Analysis of synonymous codon usage in SARS coronavirus and other viruses in the Nidovirales. Virus Res 2004;101:155–61.
Liu YS, Zhou JH, Chen HT, Ma LN, Pejsak Z. The characteristics of the synonymous codon usage in enterovirus 71 virus and the effects of host on the virus in codon usage pattern. Infect Genet Evol 2011;11:1168–73.
Sharp PM, Li WH. Codon usage in regulatory genes in Escherichia coli does not reflect selection for ‘rare’ codons. Nucleic Acids Res 1986;14:7737–49.
Swerdloff RS, Wang C, Bhasin S. Developments in the control of the testicular function. Baillieres Clin Endocrinol Metab 1992;6:451-83.
Dufau ML, Tsai-Morris C, Tang Khanum A. Regulation of steroidogenic enzymes and a novel testicular RNA helicase. J Steroid Biochem Mol Biol 2001;76:187-97.
Walker WH. Molecular mechanisms of testosterone action in spermatogenesis. Steroids 2009;74:602-7.
Liu FJ, Jin SH, Li N, Liu X, Wang HY, Li JY. Comparative and functional analysis of testis-specific genes. Biol Pharm Bull 2011;34:28-35.
Sharp PM, Li WH. The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 1986;14:7749.
Wright F. The effective number of codons' used in a gene. Gene 1990;87:23.
Carbone A, Zinovyev A, Képès F. Codon adaptation index, as a measure of dominating codon bias. Bioinformatics 2003;19:2005-15.
Sur S, Sen A, Bothra AK. Mutational drift prevails over translational efficiency in Frankia nif operons. Indian J Biotechnol 2007;6:321-8.
Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of protein. J Mol Biol 1982;157:105-32.
Jenkins GM, Holmes EC. The extent of codon usage bias in human RNA viruses and its evolutionary origin. Virus Res 2003;92:1–7.
Butt AM, Nasrullah I, Tong Y. Genome-wide analysis of codon usage and influencing factors in chikungunya viruses. PloS One 2014;9:e90905. Doi:10.1371/journal.pone.0090905. [Article in Press]
Behura SK, Severson DW. Comparative analysis of codon usage bias and codon context patterns between dipteran and hymenopteran sequenced genomes. PloS One 2012;7:e43111. DOI: 10.1371/journal.pone.0043111. [Article in Press]
Wei L, He J, Jia X, Qi Q, Liang Z. Analysis of codon usage bias of mitochondrial genome in Bombyx mori and its relation to evolution. BMC Evol Biol 2014;14:262.
Aramouni M, Segalés J, Sibila M, Martin-Valls GE, Nieto D. Torque teno sus virus 1 and 2 viral loads in postweaning multisystemic wasting syndrome (PMWS) and porcine dermatitis and nephropathy syndrome (PDNS) affected pigs. Vet Microbiol 2011;153:377-81.
Powell JR, Sezzi E, Moriyama EN, Gleason JM, Caccone A. Analysis of a shift in codon usage in Drosophila. J Mol Evol 2003;57:214–25.
Wright F. The effective number of codons used in a gene. Gene 1990;87:23–9.
Sharp PM, Li WH. The codon adaptation index, a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 1987;15:1281-95.
Hoda Mirsafian, Adiratna MP, Singh A, Hwan PT, Merican AF, Mohamad SB. A comparative analysis of synonymous codon usage bias pattern in human albumin superfamily. Scientific World Journal 2014. Doi.org/10.1155/2014/639682. [Article in Press].