Codon usage and tRNA genes in eukaryotes: Correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis
Codon usage and tRNA genes in eukaryotes: Correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis
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DOI：
10.1007/s002390010219
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发表时间：
2001-10-01
影响因子：
3.9
通讯作者：
Ikemura, T
中科院分区：
文献类型：
--
作者：
Kanaya, S;Yamada, Y;Ikemura, T
采用主成分分析法研究了粟酒裂殖酵母、秀丽隐杆线虫、黑腹果蝇、非洲爪蟾和智人5种真核生物的密码子使用多样性。根据tRNA基因拷贝数预测翻译的最佳密码子。高表达的基因，如编码核糖体蛋白和组蛋白的基因在S。pombe，C. elegans和D.黑腹动物具有在广泛的单细胞生物中观察到的密码子使用的偏向模式。In S.在pombe和C elegans中，对主成分贡献最大的密码子（Z（1）-参数）对应于根据tRNA基因数预测的最佳密码子。In D.在黑腹鱼中，这种相关性不太明显，并且对Z（1）参数有正贡献的密码子主要对应于密码子第三位具有C或G的密码子。在X. laevis和H.在智人中，编码核糖体蛋白和组蛋白的基因中的密码子使用没有显著偏倚，这表明影响这些物种中密码子使用多样性的主要因素不是翻译效率。这些物种的密码子使用多样性主要反映了等容线结构。在本研究中，第二个额外的因素被解释的密码子含有CG-二核苷酸的使用水平，这是讨论相对于通过甲基化的CG-二核苷酸，这是在哺乳动物基因组中观察到的转录调控。
The species-specific diversity of codon usage in five eukaryotes (Schizosaccharomyces pombe, Caenorhabditis elegans, Drosophila melanogaster, Xenopus laevis, and Homo sapiens) was investigated with principal component analysis. Optimal codons for translation were predicted on the basis of tRNA-gene copy numbers. Highly expressed genes, such as those encoding ribosomal proteins and histones in S. pombe, C. elegans, and D. melanogaster have biased patterns of codon usage which have been observed in a wide range of unicellular organisms. In S. pombe and C elegans, codons contributing positively to the principal component with the largest variance (Z(1)-parameter) corresponded to the optimal codons which were predicted on the basis of tRNA gene numbers. In D. melanogaster, this correlation was less evident, and the codons contributing positively to the Z(1)-parameter corresponded primarily to codons with a C or G in the codon third position. In X. laevis and H. sapiens, codon usage in the genes encoding ribosomal proteins and histones was not significantly biased, suggesting that the primary factor influencing codon-usage diversity in these species is not translation efficiency. Codon-usage diversity in these species is known to reflect primarily isochore structures. In the present study, the second additional factor was explained by the level of use of codons containing CG-dinucleotides, and this is discussed with respect to transcription regulation via methylation of CG-dinucleotides, which is observed in mammalian genomes.