Eyre-Walker A, Bulmer M
Department of Biological Sciences, Rutgers University, Piscataway, NJ 08855-1059.
Nucleic Acids Res. 1993 Sep 25;21(19):4599-603. doi: 10.1093/nar/21.19.4599.
Synonymous codon usage is less biased at the start of Escherichia coli genes than elsewhere. The rate of synonymous substitution between E.coli and Salmonella typhimurium is substantially reduced near the start of the gene, which suggests the presence of an additional selection pressure which competes with the selection for codons which are most rapidly translated. Possible competing sources of selection are the presence of secondary ribosome binding sites downstream from the start codon, the avoidance of mRNA secondary structure near the start of the gene and the use of sub-optimal codons to regulate gene expression. We provide evidence against the last of these possibilities. We also show that there is a decrease in the frequency of A, and an increase in the frequency of G along the E.coli genes at all three codon positions. We argue that these results are most consistent with selection to avoid mRNA secondary structure.
在大肠杆菌基因的起始位置，同义密码子的使用偏好性比其他位置更低。大肠杆菌和鼠伤寒沙门氏菌之间同义替换的速率在基因起始位置附近大幅降低，这表明存在一种额外的选择压力，它与对翻译速度最快的密码子的选择相互竞争。可能的竞争选择来源包括起始密码子下游二级核糖体结合位点的存在、避免基因起始位置附近的mRNA二级结构以及使用次优密码子来调节基因表达。我们提供了反对最后一种可能性的证据。我们还表明，在大肠杆菌基因的所有三个密码子位置上，A的频率都有所下降，而G的频率则有所增加。我们认为这些结果与为避免mRNA二级结构而进行的选择最为一致。
