Chen Swaine L, Lee William, Hottes Alison K, Shapiro Lucy, McAdams Harley H
Department of Developmental Biology, Stanford University School of Medicine, Beckman Center, B300, Stanford, CA 94304, USA.
Proc Natl Acad Sci U S A. 2004 Mar 9;101(10):3480-5. doi: 10.1073/pnas.0307827100. Epub 2004 Feb 27.
Analysis of genome-wide codon bias shows that only two parameters effectively differentiate the genome-wide codon bias of 100 eubacterial and archaeal organisms. The first parameter correlates with genome GC content, and the second parameter correlates with context-dependent nucleotide bias. Both of these parameters may be calculated from intergenic sequences. Therefore, genome-wide codon bias in eubacteria and archaea may be predicted from intergenic sequences that are not translated. When these two parameters are calculated for genes from nonmammalian eukaryotic organisms, genes from the same organism again have similar values, and genome-wide codon bias may also be predicted from intergenic sequences. In mammals, genes from the same organism are similar only in the second parameter, because GC content varies widely among isochores. Our results suggest that, in general, genome-wide codon bias is determined primarily by mutational processes that act throughout the genome, and only secondarily by selective forces acting on translated sequences.
全基因组密码子偏好性分析表明，只有两个参数能有效区分100种真细菌和古细菌的全基因组密码子偏好性。第一个参数与基因组GC含量相关，第二个参数与上下文依赖的核苷酸偏好性相关。这两个参数均可从基因间序列计算得出。因此，真细菌和古细菌的全基因组密码子偏好性可从未翻译的基因间序列中预测。当针对非哺乳动物真核生物的基因计算这两个参数时，同一生物体的基因再次具有相似的值，并且全基因组密码子偏好性也可从基因间序列中预测。在哺乳动物中，同一生物体的基因仅在第二个参数上相似，因为等密度区之间的GC含量差异很大。我们的结果表明，一般来说，全基因组密码子偏好性主要由作用于整个基因组的突变过程决定，其次才由作用于翻译序列的选择力决定。
