Peeling the Onion: Ribosomes Are Ancient Molecular Fossils
Peeling the Onion: Ribosomes Are Ancient Molecular Fossils
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DOI：
10.1093/molbev/msp163
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发表时间：
2009-11-01
影响因子：
10.7
通讯作者：
Williams, Loren Dean
中科院分区：
文献类型：
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作者：
Hsiao, Chiaolong;Mohan, Srividya;Williams, Loren Dean
我们描述了一种方法来建立古代核糖体进化年表。该方法使用基于结构和基于序列的比较的大亚基（LSU）的海死盐蚌和嗜热栖热菌。这些是最高分辨率的核糖体结构，代表了进化树的不同区域。我们已经将叠加的LSU分成同心壳，像洋葱一样，使用肽基转移的位点作为起点（PT起点）。这种球形近似与逐壳比较相结合的方法沿着进化时间线捕获了重要的信息，例如，揭示了23 S rRNA的序列和构象相似性在PT起点附近最大，并且随着距离的增加而平滑地发散。结果表明，RNA和蛋白质的构象和相互作用可以被描述为以可观察的方式变化，随着进化时间的推移。大分子呈现规则二级结构元件的趋势，例如具有沃森-克里克碱基对（RNA）的A型螺旋以及α螺旋和β折叠（蛋白质）在早期时间点较低，但随着时间的推移而增加。PT-原点附近的核糖体蛋白组分的构象表明，它们可能是核糖体蛋白的肽祖先的分子化石。其缩短的长度可能有被禁止的二级结构的形成，这实际上是几乎不存在的区域的LSU最接近PT的起源。早期PT中心的形成和演变可能涉及Mg 2+介导的至少部分单链RNA寡聚体或聚合物的组装。当一个人从中心移动到外围时，蛋白质似乎取代了镁离子。已知LSU在组装时经历了大规模的构象变化。霸王这里分析的嗜热菌LSU是完全组装的核糖体的一部分，而嗜热菌LSU是完全组装的核糖体的一部分。这里分析的marismortui LSU与其他核糖体组分分离。23 S rRNA的大规模构象差异从重叠中显而易见，并阻止了rRNA的某些部分（包括L1茎）的结构对齐。
We describe a method to establish chronologies of ancient ribosomal evolution. The method uses structure-based and sequence-based comparison of the large subunits (LSUs) of Haloarcula marismortui and Thermus thermophilus. These are the highest resolution ribosome structures available and represent disparate regions of the evolutionary tree. We have sectioned the superimposed LSUs into concentric shells, like an onion, using the site of peptidyl transfer as the origin (the PT-origin). This spherical approximation combined with a shell-by-shell comparison captures significant information along the evolutionary time line revealing, for example, that sequence and conformational similarity of the 23S rRNAs are greatest near the PT-origin and diverge smoothly with distance from it. The results suggest that the conformation and interactions of both RNA and protein can be described as changing, in an observable manner, over evolutionary time. The tendency of macromolecules to assume regular secondary Structural elements such as A-form helices with Watson-Crick base pairs (RNA) and alpha-helices and beta-sheets (protein) is low at early time points but increases as time progresses. The conformations of ribosomal protein components near the PT-origin suggest that they may be molecular fossils of the peptide ancestors of ribosomal proteins. Their abbreviated length may have proscribed formation of secondary structure, which is indeed nearly absent from the region of the LSU nearest the PT-origin. Formation and evolution of the early PT center may have involved Mg2+-mediated assembly of atleast partially single-stranded RNA oligomers or polymers. As one moves from center to periphery, proteins appear to replace magnesium ions. The LSU is known to have undergone large-scale conformation changes upon assembly. The T. thermophilus LSU analyzed here is part of a fully assembled ribosome, whereas the H. marismortui LSU analyzed here is dissociated from other ribosomal components. Large-scale conformational differences in the 23S rRNAs are evident from superimposition and prevent structural alignment of some portions of the rRNAs, including the L1 stalk.