Evolution of the ribosome at atomic resolution
Evolution of the ribosome at atomic resolution
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DOI：
10.1073/pnas.1407205111
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发表时间：
2014-07-15
影响因子：
11.1
通讯作者：
Williams, Loren Dean
中科院分区：
文献类型：
--
作者：
Petrov, Anton S.;Bernier, Chad R.;Williams, Loren Dean
30 - 40亿年前，核糖体的起源和进化仍然印刻在现存生命的生物化学和核糖体的结构中。核糖体RNA（rRNA）扩增的过程可以通过比较细菌（小）、酵母（中）和后生动物（大）的3D rRNA结构来“观察”。rRNA的大小与物种的复杂性密切相关。不同物种间核糖体的差异表明，rRNA扩展片段已被添加到rRNA中，而不会干扰预先存在的核心。在这里，我们表明，rRNA的增长发生的过程，包括插入一个分支螺旋到一个预先存在的主干螺旋和延长的螺旋数量有限。rRNA扩增可以留下独特的原子分辨率指纹，我们称之为“插入指纹”。“观察核糖体共同核心中的插入指纹可以识别可能的祖先扩展片段。从概念上逆转这些扩展允许外推时间向后生成原始核糖体的模型。这里提出的方法提供了洞察前最后的通用共同祖先rRNA的结构和随后的扩展，形成的肽基转移酶中心和保守的核心。我们推断不同阶段的核糖体进化，通过核糖体颗粒的发展，获得编码和易位，并延长和阐述出口隧道。
The origins and evolution of the ribosome, 3-4 billion years ago, remain imprinted in the biochemistry of extant life and in the structure of the ribosome. Processes of ribosomal RNA (rRNA) expansion can be "observed" by comparing 3D rRNA structures of bacteria (small), yeast (medium), and metazoans (large). rRNA size correlates well with species complexity. Differences in ribosomes across species reveal that rRNA expansion segments have been added to rRNAs without perturbing the preexisting core. Here we show that rRNA growth occurs by a limited number of processes that include inserting a branch helix onto a preexisting trunk helix and elongation of a helix. rRNA expansions can leave distinctive atomic resolution fingerprints, which we call "insertion fingerprints." Observation of insertion fingerprints in the ribosomal common core allows identification of probable ancestral expansion segments. Conceptually reversing these expansions allows extrapolation backward in time to generate models of primordial ribosomes. The approach presented here provides insight to the structure of pre-last universal common ancestor rRNAs and the subsequent expansions that shaped the peptidyl transferase center and the conserved core. We infer distinct phases of ribosomal evolution through which ribosomal particles evolve, acquiring coding and translocation, and extending and elaborating the exit tunnel.