The close proximity of Escherichia coli genes: Consequences for stop codon and synonymous codon use
The close proximity of Escherichia coli genes: Consequences for stop codon and synonymous codon use
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DOI：
10.1007/bf02198830
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发表时间：
1996-02-01
影响因子：
3.9
通讯作者：
EyreWalker, A
中科院分区：
文献类型：
--
作者：
EyreWalker, A
结果表明，同义密码子的使用不那么偏向于大肠杆菌基因末端高表达基因偏爱的密码子。这似乎是由于许多大肠杆菌基因非常接近所致。结果表明，有相当数量的基因与Shine-Dalgarno序列或染色体上下一个基因的编码序列重叠，并且重叠的密码子比不重叠的密码子具有更低的同义密码子偏好性。研究还表明，在靠近另一个基因的大肠杆菌基因末端，A-末端密码子的频率增加，而G-末端密码子的频率降低。这些成分的变化趋势可能与在染色体上下一个基因的起始处附近不形成mRNA二级结构的选择有关。终止密码子的使用也受到基因接近的影响；许多基因被迫使用TGA和标记终止密码子，因为它们要么终止于Shine-Dalgarno，要么终止于染色体上下一个基因的编码序列。讨论了这些结果对同义密码子使用的进化的影响。
It is shown that synonymous codon usage is less biased in favor of those codons preferred by highly expressed genes at the end of Escherichia coli genes than in the middle. This appears to be due to the close proximity of many E. coli genes. It is shown that a substantial number of genes overlap either the Shine-Dalgarno sequence or the coding sequence of the next gene on the chromosome and that the codons that overlap have lower synonymous codon bias than those which do not. It is also shown that there is an increase in the frequency of A-ending codons, and a decrease in the frequency of G-ending codons at the end of E. coli genes that lie close to another gene. It is suggested that these trends in composition could be associated with selection against the formation of mRNA secondary structure near the start of the next gene on the chromosome. Stop codon use is also affected by the close proximity of genes; many genes are forced to use TGA and TAG stop codons because they terminate either within the Shine-Dalgarno or coding sequence of the next gene on the chromosome. The implications these results have for the evolution of synonymous codon use are discussed.