Curtiss W C, Vournakis J N
J Mol Evol. 1984;20(3-4):351-61. doi: 10.1007/BF02104741.
Eukaryotic 5S rRNA sequences from 34 diverse species were compared by the following method: (1) The sequences were aligned; (2) the positions of substitutions were located by comparison of all possible pairs of sequences; (3) the substitution sites were mapped to an assumed general base pairing model; and (4) the R-Y model of base stacking was used to study stacking pattern relationships in the structure. An analysis of the sequence and structure variability in each region of the molecule is presented. It was found that the degree of base substitution varies over a wide range, from absolute conservation to occurrence of over 90% of the possible observable substitutions. The substitutions are located primarily in stem regions of the 5S rRNA secondary structure. More than 88% of the substitutions in helical regions maintain base pairing. The disruptive substitutions are primarily located at the edges of helical regions, resulting in shortening of the helical regions and lengthening of the adjacent nonpaired regions. Base stacking patterns determined by the R-Y model are mapped onto the general secondary structure. Intrastrand and interstrand stacking could stabilize alternative coaxial structures and limit the conformational flexibility of nonpaired regions. Two short contiguous regions are 100% conserved in all species. This may reflect evolutionary constraints imposed at the DNA level by the requirement for binding of a 5S gene transcription initiation factor during gene expression.
采用以下方法对来自34个不同物种的真核生物5S rRNA序列进行了比较：(1) 对序列进行比对；(2) 通过比较所有可能的序列对来确定替换位点；(3) 将替换位点映射到假定的通用碱基配对模型上；(4) 使用碱基堆积的R-Y模型来研究结构中的堆积模式关系。本文对分子每个区域的序列和结构变异性进行了分析。结果发现，碱基替换程度在很大范围内变化，从绝对保守到出现超过90%的可能可观察到的替换。替换主要位于5S rRNA二级结构的茎区。螺旋区域中超过88%的替换保持碱基配对。破坏性替换主要位于螺旋区域的边缘，导致螺旋区域缩短和相邻非配对区域延长。由R-Y模型确定的碱基堆积模式被映射到通用二级结构上。链内和链间堆积可以稳定替代的同轴结构，并限制非配对区域的构象灵活性。两个短的连续区域在所有物种中100%保守。这可能反映了基因表达过程中5S基因转录起始因子结合需求在DNA水平上施加的进化限制。
