Smit S, Widmann J, Knight R
Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA.
Nucleic Acids Res. 2007;35(10):3339-54. doi: 10.1093/nar/gkm101. Epub 2007 Apr 27.
Understanding patterns of rRNA evolution is critical for a number of fields, including structure prediction and phylogeny. The standard model of RNA evolution is that compensatory mutations in stems make up the bulk of the changes between homologous sequences, while unpaired regions are relatively homogeneous. We show that considerable heterogeneity exists in the relative rates of evolution of different secondary structure categories (stems, loops, bulges, etc.) within the rRNA, and that in eukaryotes, loops actually evolve much faster than stems. Both rates of evolution and abundance of different structural categories vary with distance from functionally important parts of the ribosome such as the tRNA path and the peptidyl transferase center. For example, fast-evolving residues are mainly found at the surface; stems are enriched at the subunit interface, and junctions near the peptidyl transferase center. However, different secondary structure categories evolve at different rates even when these effects are accounted for. The results demonstrate that relative rates and patterns of evolution are lineage specific, suggesting that phylogenetically and structurally specific models will improve evolutionary and structural predictions.
了解rRNA的进化模式对于包括结构预测和系统发育在内的许多领域都至关重要。RNA进化的标准模型是，茎中的补偿性突变构成了同源序列之间变化的主要部分，而未配对区域相对较为均匀。我们发现，rRNA内不同二级结构类别（茎、环、凸起等）的相对进化速率存在相当大的异质性，并且在真核生物中，环的进化实际上比茎快得多。进化速率和不同结构类别的丰度都随与核糖体功能重要部分（如tRNA路径和肽基转移酶中心）的距离而变化。例如，快速进化的残基主要位于表面；茎在亚基界面以及肽基转移酶中心附近的连接处富集。然而，即使考虑到这些影响，不同的二级结构类别仍以不同的速率进化。结果表明，进化的相对速率和模式具有谱系特异性，这表明系统发育和结构特异性模型将改善进化和结构预测。
