Bains W
Department of Biochemistry, University of Bath, Claverton Down, England.
J Mol Biol. 1987 Oct 5;197(3):379-88. doi: 10.1016/0022-2836(87)90551-1.
I have analysed the coding regions of 96 eukaryotic genes for their use of iso-coding codons. Specific codons occur more frequently in specific positions in all members of some gene families than would be expected if codon choice was determined solely by the frequency of codon usage. In the absence of evidence a priori for selection for particular codons at particular positions, I term such co-occurring codons "coincident codons". Coincident codons are not confined to particular regions of genes, and their occurrence is not detectably linked with the location of introns in the genomic sequence. Their presence is partly but not completely explained by the exchange of sequence between similar functional genes within a species: homologous genes from different organisms also possess the same codons at some sites with greater than expected frequencies. The relative excess of coincident codons correlates well with the overall length of the genes analysed, but not with the length of mRNA or coding regions, or with qualitative features of gene structure or expression. This, and the unusual sequence environment of coincident codons, suggests that they are a feature of the overall secondary structure of the heterogeneous nuclear RNA. Such considerations suggest approaches for optimizing the expression of exogenous genes in eukaryotic systems, and for predicting the structure of genes for which only partial sequence data is available.
我分析了96个真核基因的编码区，以研究它们对同义密码子的使用情况。在某些基因家族的所有成员中，特定密码子在特定位置出现的频率高于仅由密码子使用频率决定密码子选择时的预期频率。在没有先验证据表明在特定位置选择特定密码子的情况下，我将这种共现密码子称为“重合密码子”。重合密码子并不局限于基因的特定区域，其出现与基因组序列中内含子的位置没有明显关联。它们的存在部分但并非完全可以通过物种内相似功能基因之间的序列交换来解释：来自不同生物体的同源基因在某些位点也具有高于预期频率的相同密码子。重合密码子的相对过量与所分析基因的总长度密切相关，但与mRNA或编码区的长度、基因结构或表达的定性特征无关。这一点，以及重合密码子不寻常的序列环境，表明它们是异质核RNA整体二级结构的一个特征。这些考虑为优化真核系统中外源基因的表达以及预测仅获得部分序列数据的基因结构提供了方法。
