Hsiao Chiaolong, Mohan Srividya, Kalahar Benson K, Williams Loren Dean
School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA.
Mol Biol Evol. 2009 Nov;26(11):2415-25. doi: 10.1093/molbev/msp163. Epub 2009 Jul 23.
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 Mg(2+)-mediated assembly of at least 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.
我们描述了一种建立古代核糖体进化时间线的方法。该方法利用了盐沼盐杆菌（Haloarcula marismortui）和嗜热栖热菌（Thermus thermophilus）大亚基（LSU）基于结构和基于序列的比较。这些是目前分辨率最高的核糖体结构，代表了进化树中不同的区域。我们已将叠加的LSU分割成同心壳层，就像洋葱一样，以肽基转移位点作为原点（PT原点）。这种球形近似与逐层比较相结合，沿着进化时间线捕捉到了重要信息，例如，23S rRNA的序列和构象相似性在PT原点附近最大，并随着与它的距离而平滑地发散。结果表明，RNA和蛋白质的构象及相互作用在进化时间内都可以以可观察的方式发生变化。大分子呈现规则二级结构元件（如具有沃森-克里克碱基对的A-型螺旋（RNA）以及α-螺旋和β-折叠（蛋白质））的趋势在早期时间点较低，但随着时间的推移而增加。PT原点附近核糖体蛋白质组分的构象表明，它们可能是核糖体蛋白质肽祖先的分子化石。它们缩短的长度可能限制了二级结构的形成，在LSU最靠近PT原点的区域确实几乎没有二级结构。早期PT中心的形成和进化可能涉及至少部分单链RNA寡聚物或聚合物的镁离子介导组装。当从中心向外围移动时，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。这里分析的嗜热栖热菌LSU是完全组装好的核糖体的一部分，而这里分析的盐沼盐杆菌LSU则与其他核糖体组分解离。从叠加中可以明显看出23S rRNA存在大规模的构象差异，这使得rRNA的某些部分（包括L1茎）无法进行结构比对。
