Codon usage between genomes is constrained by genome-wide mutational processes
Codon usage between genomes is constrained by genome-wide mutational processes
复制标题
DOI：
10.1073/pnas.0307827100
复制
发表时间：
2004-03-09
影响因子：
11.1
通讯作者：
McAdams, HH
中科院分区：
文献类型：
--
作者：
Chen, SL;Lee, W;McAdams, HH
全基因组密码子偏倚分析表明，只有两个参数可以有效区分100种真细菌和古细菌的全基因组密码子偏倚。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差相关。这两个参数都可以从基因间序列中计算出来。因此，真细菌和古细菌的全基因组密码子偏倚可以通过未翻译的基因间序列来预测。当这两个参数计算来自非哺乳动物真核生物的基因时，来自同一生物的基因再次具有相似的值，并且基因间序列也可以预测全基因组密码子偏倚。在哺乳动物中，来自同一生物体的基因只有在第二个参数上是相似的，因为GC含量在各同工间差异很大。我们的研究结果表明，一般来说，全基因组密码子偏倚主要是由整个基因组的突变过程决定的，其次是作用于翻译序列的选择性力。
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 eubacterial 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.