PMID: 2499685Apr 1, 1989Paper

Nucleic acid composition, codon usage, and the rate of synonymous substitution in protein-coding genes

Journal of Molecular Evolution
A Ticher, D Graur

Abstract

Based on the rates of synonymous substitution in 42 protein-coding gene pairs from rat and human, a correlation is shown to exist between the frequency of the nucleotides in all positions of the codon and the synonymous substitution rate. The correlation coefficients were positive for A and T and negative for C and G. This means that AT-rich genes accumulate more synonymous substitutions than GC-rich genes. Biased patterns of mutation could not account for this phenomenon. Thus, the variation in synonymous substitution rates and the resulting unequal codon usage must be the consequence of selection against A and T in synonymous positions. Most of the variation in rates of synonymous substitution can be explained by the nucleotide composition in synonymous positions. Codon-anticodon interactions, dinucleotide frequencies, and contextual factors influence neither the rates of synonymous substitution nor codon usage. Interestingly, the nucleotide in the second position of codons (always a nonsynonymous position) was found to affect the rate of synonymous substitution. This finding links the rate of nonsynonymous substitution with the synonymous rate. Consequently, highly conservative proteins are expected to be encoded by genes th...Continue Reading

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Citations

Sep 1, 1994·Journal of Molecular Evolution·H BurgerL C Dorssers
Apr 1, 1989·Journal of Molecular Evolution·D GraurW H Li
Aug 1, 1990·Journal of Molecular Evolution·D Mouchiroud, C Gautier
Nov 16, 2002·Current Opinion in Genetics & Development·Wen Hsiung LiKateryna Makova
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Jun 30, 2012·Gene·Andrés IriarteHéctor Musto
Mar 24, 2017·The Plant Journal : for Cell and Molecular Biology·Yue GuoJianchang Du
Jun 7, 2006·Molecular Biology and Evolution·Joshua B PlotkinHunter B Fraser
Jul 26, 2002·Molecular Biology and Evolution·Alex Mira, Howard Ochman
Jul 26, 2002·Molecular Biology and Evolution·John A Novembre
Oct 14, 2017·Nature Communications·Alexander BrandtJens Bast

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