Nucleotide bias causes a genomewide bias in the amino acid composition of proteins

We analyzed the nucleotide contents of several completely sequenced genomes, and we show that nucleotide bias can have a dramatic effect on the amino acid composition of the encoded proteins. By surveying the genes in 21 completely sequenced eubacterial and archaeal genomes, along with the entire Sa...

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Bibliographic Details
Published in:Molecular biology and evolution 2000-11, Vol.17 (11), p.1581-1588
Main Authors: Singer, G A, Hickey, D A
Format: Article
Language:English
Subjects:
Amino Acids - genetics
Animals
Base Composition
Codon - genetics
Eukaryotic Cells - metabolism
Genetic Variation
Genome
Genome, Archaeal
Genome, Bacterial
Humans
Nucleotides - genetics
Phylogeny
Plasmodium falciparum
Proteins - genetics
Saccharomyces cerevisiae
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Summary:We analyzed the nucleotide contents of several completely sequenced genomes, and we show that nucleotide bias can have a dramatic effect on the amino acid composition of the encoded proteins. By surveying the genes in 21 completely sequenced eubacterial and archaeal genomes, along with the entire Saccharomyces cerevisiae genome and two Plasmodium falciparum chromosomes, we show that biased DNA encodes biased proteins on a genomewide scale. The predicted bias affects virtually all genes within the genome, and it could be clearly seen even when we limited the analysis to sets of homologous gene sequences. Parallel patterns of compositional bias were found within the archaea and the eubacteria. We also found a positive correlation between the degree of amino acid bias and the magnitude of protein sequence divergence. We conclude that mutational bias can have a major effect on the molecular evolution of proteins. These results could have important implications for the interpretation of protein-based molecular phylogenies and for the inference of functional protein adaptation from comparative sequence data.
ISSN:0737-4038
DOI:10.1093/oxfordjournals.molbev.a026257