Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA.
Methods Mol Biol. 2022;2569:267-281. doi: 10.1007/978-1-0716-2691-7_13.
Proteins have played a fundamental role throughout life's history on Earth. Despite their biological importance, ancient origin, early function, and evolution of proteins are seldom able to be directly studied because few of these attributes are preserved across geologic timescales. Ancestral sequence reconstruction (ASR) provides a method to infer ancestral amino acid sequences and determine the evolutionary predecessors of modern-day proteins using phylogenetic tools. Laboratory application of ASR allows ancient sequences to be deduced from genetic information available in extant organisms and then experimentally resurrected to elucidate ancestral characteristics. In this article, we provide a generalized, stepwise protocol that considers the major elements of a well-designed ASR study and details potential sources of reconstruction bias that can reduce the relevance of historical inferences. We underscore key stages in our approach so that it may be broadly utilized to reconstruct the evolutionary histories of proteins.
蛋白质在地球生命历史中一直发挥着重要作用。尽管它们具有重要的生物学意义，但由于这些特性在地质时间尺度上很少得到保存，因此很难直接研究蛋白质的古老起源、早期功能和进化。祖先序列重建 (ASR) 提供了一种使用系统发育工具推断祖先氨基酸序列和确定现代蛋白质进化前体的方法。ASR 的实验室应用允许从现存生物中可用的遗传信息推断古代序列，然后通过实验复活来阐明祖先特征。在本文中，我们提供了一个通用的、逐步的方案，该方案考虑了精心设计的 ASR 研究的主要要素，并详细介绍了可能降低历史推断相关性的重建偏差的潜在来源。我们强调了我们方法中的关键阶段，以便可以广泛用于重建蛋白质的进化历史。
