Singer G A, Hickey D A
Department of Biology, University of Ottawa, Ottawa, Ontario, Canada.
Mol Biol Evol. 2000 Nov;17(11):1581-8. doi: 10.1093/oxfordjournals.molbev.a026257.
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.
我们分析了几个全序列测定基因组的核苷酸含量，结果表明核苷酸偏向性会对所编码蛋白质的氨基酸组成产生显著影响。通过对21个全序列测定的真细菌和古细菌基因组中的基因，以及整个酿酒酵母基因组和两条恶性疟原虫染色体进行研究，我们发现偏向性DNA在全基因组范围内编码偏向性蛋白质。这种预测的偏向性几乎影响基因组内的所有基因，即使我们将分析限定于同源基因序列集时也能清晰地看到。在古细菌和真细菌中发现了组成偏向性的平行模式。我们还发现氨基酸偏向程度与蛋白质序列分歧程度之间存在正相关。我们得出结论，突变偏向性可能对蛋白质的分子进化产生重大影响。这些结果可能对基于蛋白质的分子系统发育解释以及从比较序列数据推断功能性蛋白质适应性具有重要意义。
