Department of Molecular and Cell Biology, University of Arizona, Tucson, AZ, 85721, USA.
Department of Molecular and Cell Biology, University of Arizona, Tucson, AZ, 85721, USA; Department of Astronomy and Steward Observatory, University of Arizona, Tucson, AZ, 85721, USA.
Free Radic Biol Med. 2019 Aug 20;140:260-269. doi: 10.1016/j.freeradbiomed.2019.03.033. Epub 2019 Apr 2.
Throughout the history of life, enzymes have served as the primary molecular mediators of biogeochemical cycles by catalyzing the metabolic pathways that interact with geochemical substrates. The byproducts of enzymatic activities have been preserved as chemical and isotopic signatures in the geologic record. However, interpretations of these signatures are limited by the assumption that such enzymes have remained functionally conserved over billions of years of molecular evolution. By reconstructing ancient genetic sequences in conjunction with laboratory enzyme resurrection, preserved biogeochemical signatures can instead be related to experimentally constrained, ancestral enzymatic properties. We may thereby investigate instances within molecular evolutionary trajectories potentially tied to significant biogeochemical transitions evidenced in the geologic record. Here, we survey recent enzyme resurrection studies to provide a reasoned assessment of areas of success and common pitfalls relevant to ancient biogeochemical applications. We conclude by considering the Great Oxidation Event, which provides a constructive example of a significant biogeochemical transition that warrants investigation with ancestral enzyme resurrection. This event also serves to highlight the pitfalls of facile interpretation of paleophenotype models and data, as applied to two examples of enzymes that likely both influenced and were influenced by the rise of atmospheric oxygen - RuBisCO and nitrogenase.
纵观生命历史，酶一直是生物地球化学循环的主要分子介体，通过催化与地球化学底物相互作用的代谢途径。酶活性的副产物作为化学和同位素特征保存在地质记录中。然而，这些特征的解释受到这样的酶在数十亿年的分子进化中保持功能保守的假设的限制。通过与实验室酶复活相结合重建古代遗传序列，保存的生物地球化学特征可以与实验约束的、祖先的酶特性相关联。因此，我们可以研究分子进化轨迹中可能与地质记录中明显的生物地球化学转变相关的实例。在这里，我们调查了最近的酶复活研究，以合理评估与古代生物地球化学应用相关的成功领域和常见陷阱。最后，我们以大氧化事件为例，该事件为一个重要的生物地球化学转变提供了一个建设性的例子，值得通过祖先酶复活进行研究。该事件还突出了在应用于可能同时影响和受大气氧上升影响的两种酶（RuBisCO 和固氮酶）的古表型模型和数据时，对其进行简单解释的陷阱。
