Fuglsang Anders
Danish University of Pharmaceutical Sciences, Institute of Pharmacology, Universitetsparken, Copenhagen, Denmark.
Mol Biol Evol. 2004 Jun;21(6):1152-9. doi: 10.1093/molbev/msh133. Epub 2004 Mar 24.
This study compared orthologous gene pairs from Escherichia coli K12, E. coli O157:H7 EDL933, Salmonella typhimurium LT2, and Yersinia pestis CO92 using only homologs of equal length, and differing nucleotides were counted and mapped. The data showed very clearly how the rates of divergence change with intragenic and extragenic position. The rate of synonymous mutation is lowest near start codons and near stop codons, and, a little surprisingly, the opposite seemed to be true for nonsynonymous substitutions. Analysis outside genes reveals that nucleotide divergences occur less frequently upstream of start codons than downstream of stop codons, and a remarkable drop in divergences is seen for two of the data sets around N = 9 nucleotides upstream of start codons; that is, the Shine-Dalgarno region changes at a lower rate. The explanation is likely to be the link between expressivity and sequence complementarity to the 3' end of 16S ribosomal rRNA. The latter is highly conserved across many bacterial and archaebacterial species.
本研究仅使用等长的同源物，比较了大肠杆菌K12、大肠杆菌O157:H7 EDL933、鼠伤寒沙门氏菌LT2和鼠疫耶尔森菌CO92的直系同源基因对，并对不同的核苷酸进行计数和定位。数据非常清楚地显示了分歧率如何随基因内和基因外位置而变化。同义突变率在起始密码子附近和终止密码子附近最低，而且，有点令人惊讶的是，非同义替换似乎正好相反。基因外分析表明，起始密码子上游的核苷酸分歧比终止密码子下游的频率更低，并且在两个数据集中，起始密码子上游约N = 9个核苷酸处的分歧显著下降；也就是说，Shine-Dalgarno区域的变化率较低。其解释可能是表达性与16S核糖体rRNA 3'端序列互补性之间的联系。后者在许多细菌和古细菌物种中高度保守。
