Chemical fidelity of an RNA polymerase ribozyme
Chemical fidelity of an RNA polymerase ribozyme
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DOI：
10.1039/c3sc50574j
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发表时间：
2013-01-01
期刊：
影响因子：
8.4
通讯作者：
Holliger, Philipp
中科院分区：
文献类型：
--
作者：
Attwater, James;Tagami, Shunsuke;Holliger, Philipp
具有催化活性的RNA酶（核酶）的出现被广泛认为是生命起源中的一个重要转变。在一个可能的异质性化学环境的背景下，底物特异性和选择性的这些原始酶的功能将是至关重要的。在这里，我们探讨了化学保真度，即底物的选择性和特异性的单一和多个催化步骤的Z RNA聚合酶核酶的原始RNA复制酶的现代类似物。使用广泛的核苷酸类似物和离子条件下，我们观察到强大的能量，但弱的几何歧视在掺入步骤，表明一个开放的活性位点。相比之下，通过与3 '-末端核苷以及新生产物和模板链的特异性下游和上游相互作用，在延伸步骤中发挥严格的选择性。我们的研究结果表明，特异性机制，在天然聚合酶的功能类似的形式。它们还揭示了多个催化步骤的化学保真度水平，这对于从随机序列库从头开发的相对未优化的酶来说是显著的。在遗传学上不相关的蛋白质聚合酶和聚合酶核酶中特异性机制的趋同进化表明，化学和信息保真度是聚合酶的新兴特性。
The emergence of catalytically active RNA enzymes (ribozymes) is widely believed to have been an important transition in the origin of life. In the context of a likely heterogeneous chemical environment, substrate specificity and selectivity of these primordial enzymes would have been critical for function. Here we have explored the chemical fidelity, i.e. substrate selectivity and specificity for both single and multiple catalytic steps of the Z RNA polymerase ribozyme a modern day analogue of the primordial RNA replicase. Using a wide range of nucleotide analogues and ionic conditions, we observe strong energetic but weak geometric discrimination at the incorporation step, indicative of an open active site. In contrast, stringent selectivity is exerted at the extension steps through specific down and upstream interactions with the 3'-terminal nucleoside as well as nascent product and template strands. Our results indicate specificity mechanisms that are found in functionally analogous forms in natural polymerases. They also reveal a level of chemical fidelity over multiple catalytic steps that is remarkable for a comparatively unoptimized enzyme developed de novo from a random sequence pool. The convergent evolution of specificity mechanisms in phylogenetically unrelated proteinaceous polymerases and polymerase ribozymes suggests that chemical as well as informational fidelity are emergent properties of polymerase enzymes.