Guanine and Cytosine at the Second Codon Position Influence Gene Expression in Cereals

被引：1

作者：

Chakraborty S. ^{[1
]}

Paul P. ^{[1
]}

机构：

[1] Department of Biotechnology, Assam University, Silchar, 788011, Assam

来源：

Proceedings of the National Academy of Sciences, India Section B: Biological Sciences | 2015年 / 85卷 / 4期

关键词：

Codon usage bias; Gene expression; Selection; Synonymous codons; Translation;

D O I：

10.1007/s40011-015-0542-9

中图分类号：

学科分类号：

摘要：

The compositional variation and the codon usage bias of the coding sequences of genes were analyzed in five species of grass family i.e. Oryza sativa, Triticum aestivum, Sorghum bicolor, Hordeum vulgare and Zea mays along with two outlier species belonging to family Solanaceae viz. Lycopersicon esculentum and Nicotiana tabacum. Pyrimidine-skew and keto-skew values varied across the cereals. These two parameters showed moderate positive correlation with codon adaptation index which was used as a measure of gene expression and with the tRNA adaptation index commonly used as a measure of translational efficiency. These were further elucidated by regression analysis and adaptive codon enrichment analysis. The present analysis revealed that the guanine and cytosine content at second codon position influence the gene expression in cereal crops. Although the codon usage pattern in five cereals was similar but differed significantly from the outliers L. esculentum and N. tabacum. © 2015, The National Academy of Sciences, India.

引用

页码：1105 / 1115

页数：10

共 50 条

[1]

Akashi H., Eyre-Walker A., Translational selection and molecular evolution, Curr Opin Genet Dev, 8, 6, pp. 688-693, (1998)

[2]

Duret L., Mouchiroud D., Expression pattern and surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis, Proc Natl Acad Sci USA, 96, 8, pp. 4482-4487, (1999)

[3]

Li W.H., Models of nearly neutral mutations with particular implications for nonrandom usage of synonymous codons, J Mol Evol, 24, 4, pp. 337-345, (1987)

[4]

Behura S.K., Severson D.W., Comparative analysis of codon usage bias and codon context patterns between dipteran and hymenopteran sequenced genomes, PLoS One, 7, 8, (2012)

[5]

Kawabe A., Miyashita N.T., Patterns of codon usage bias in three dicot and four monocot plant species, Genes Genet Syst, 78, 5, pp. 343-352, (2003)

[6]

Lynn D.J., Singer G.A., Hickey D.A., Synonymous codon usage is subject to selection in thermophilic bacteria, Nucleic Acids Res, 30, 19, pp. 4272-4277, (2002)

[7]

Moriyama E.N., Hartl D.L., Codon usage bias and base composition of nuclear genes in Drosophila, Genetics, 134, 3, pp. 847-858, (1993)

[8]

Singer G.A., Hickey D.A., Thermophilic prokaryotes have characteristic patterns of codon usage, amino acid composition and nucleotide content, Gene, 317, 1-2, pp. 39-47, (2003)

[9]

Grantham R., Gautier C., Gouy M., Mercier R., Pave A., Codon catalog usage and the genome hypothesis, Nucleic Acids Res, 8, 1, pp. r49-r62, (1980)

[10]

Ikemura T., Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system, J Mol Biol, 151, 3, pp. 389-409, (1981)

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