Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA

The relative substitution rate of each nucleotide site in bacterial small subunit rRNA, large subunit rRNA and 5S rRNA was calculated from sequence alignments for each molecule. Two-dimensional and three-dimensional variability maps of the rRNAs were obtained by plotting the substitution rates on secondary structure models and on the tertiary structure of the rRNAs available from X-ray diffraction results. This showed that the substitution rates are generally low near the centre of the ribosome, where the nucleotides essential for its function are situated, and that they increase towards the surface. An inventory was made of insertions characteristic of the Archaea, Bacteria and Eucarya domains, and for additional insertions present in specific eukaryotic taxa. All these insertions occur at the ribosome surface. The taxon-specific insertions seem to arise randomly in the eukaryotic evolutionary tree, without any phylogenetic relatedness between the taxa possessing them.

针对细菌小亚基核糖体RNA（small subunit rRNA）、大亚基核糖体RNA（large subunit rRNA）以及5S核糖体RNA（5S rRNA），研究人员通过各分子的序列比对，计算得到每个核苷酸位点的相对替换率。研究人员将替换率映射至已通过X射线衍射解析得到的核糖体RNA二级结构模型与三级结构上，由此获得了三类rRNA的二维与三维变异图谱。分析结果表明，核糖体功能必需的核苷酸位点集中于核糖体核心区域，该区域的替换率普遍较低，而替换率随着向核糖体表面趋近而逐渐升高。研究人员对古菌域（Archaea）、细菌域（Bacteria）以及真核域（Eucarya）所特有的插入序列，以及特定真核类群中存在的额外插入序列进行了整理编目。所有上述插入序列均位于核糖体表面。类群特异性插入序列似乎在真核生物进化树中随机出现，拥有此类插入序列的类群之间不存在系统发育相关性。