Abstract：
Transversion and transition mutations have variable effects on the stability of RNA secondary structure considering that the former destabilizes the double helix geometry to a greater extent by introducing purine:purine (R:R) or pyrimidine:pyrimidine (Y:Y) base pairs. Therefore, transversion frequency is likely to be lower than that of transition in the secondary structure regions of RNA genes. Here, we performed an analysis of transition and transversion frequencies in tRNA genes defined well with secondary structure and compared with the intergenic regions in five bacterial species namely Escherichia coli, Klebsiella pneumoniae, Salmonella enterica, Staphylococcus aureus and Streptococcus pneumoniae using a large genome sequence data set. In general, the transversion frequency was observed to be lower than that of transition in both tRNA genes and intergenic regions. The transition to transversion ratio was observed to be greater in tRNA genes than that in the intergenic regions in all the five bacteria that we studied. Interestingly, the intraspecies base substitution analysis in tRNA genes revealed that non-compensatory substitutions were more frequent than compensatory substitutions in the stem region. Further, transition to transversion ratio in the loop region was observed to be significantly lesser than that among the non-compensatory substitutions in the stem region. This indicated that the transversion is more deleterious than transition in the stem regions. In addition, substitutions from amino bases (A/C) to keto bases (G/T) were also observed to be more than the reverse substitutions in the stem region. Substitution from amino bases to keto bases are likely to facilitate the stable G:U pairing unlike the reverse substitution that facilitates the unstable A:C pairing in the stem region of tRNA. This work provides additional support that the secondary structure of tRNA molecule is what drives the different substitutions in its gene sequence.
摘要：
考虑到前者通过引入嘌呤:嘌呤(R:R)或嘧啶:嘧啶(Y:Y)碱基对在更大程度上使双螺旋几何结构不稳定,因此转化和转换突变对RNA二级结构的稳定性具有可变的影响。因此,在RNA基因的二级结构区域中，颠倒频率可能低于转变频率。这里,我们进行了转换和颠换频率的分析，在tRNA基因定义良好的二级结构，并与基因间区域在五个细菌物种，即大肠杆菌，肺炎克雷伯菌,肠沙门氏菌,使用大基因组序列数据集的金黄色葡萄球菌和肺炎链球菌。总的来说,在tRNA基因和基因间区域中，颠倒频率均低于转变频率。在我们研究的所有五种细菌中，tRNA基因中的转化转化比在基因间区域中的转化比更大。有趣的是,tRNA基因的种内碱基置换分析显示,在茎区,非代偿性置换比代偿性置换更为频繁.Further,观察到环区的转换到颠换的比率明显低于茎区的非代偿性置换。这表明在茎区域中的颠换比过渡更有害。此外,还观察到从氨基碱基(A/C)到酮碱基(G/T)的取代多于茎区的反向取代。从氨基碱基到酮碱基的取代可能促进稳定的G:U配对,这与促进tRNA的茎区域中的不稳定的A:C配对的反向取代不同。这项工作提供了额外的支持，即tRNA分子的二级结构是驱动其基因序列中不同取代的原因。
