Scossa Federico, Fernie Alisdair R
Max-Planck-Institute of Molecular Plant Physiology (MPI-MP), 14476 Potsdam-Golm, Germany.
Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), Rome, Italy.
Comput Struct Biotechnol J. 2021 Mar 16;19:1579-1594. doi: 10.1016/j.csbj.2021.03.008. eCollection 2021.
Whilst substantial research effort has been placed on understanding the interactions of plant proteins with their molecular partners, relatively few studies in plants - by contrast to work in other organisms - address how these interactions evolve. It is thought that ancestral proteins were more promiscuous than modern proteins and that specificity often evolved following gene duplication and subsequent functional refining. However, ancestral protein resurrection studies have found that some modern proteins have evolved from ancestors lacking those functions. Intriguingly, the new interactions evolved as a consequence of just a few mutations and, as such, acquisition of new functions appears to be neither difficult nor rare, however, only a few of them are incorporated into biological processes before they are lost to subsequent mutations. Here, we detail the approach of ancestral sequence reconstruction (ASR), providing a primer to reconstruct the sequence of an ancestral gene. We will present case studies from a range of different eukaryotes before discussing the few instances where ancestral reconstructions have been used in plants. As ASR is used to dig into the remote evolutionary past, we will also present some alternative genetic approaches to investigate molecular evolution on shorter timescales. We argue that the study of plant secondary metabolism is particularly well suited for ancestral reconstruction studies. Indeed, its ancient evolutionary roots and highly diverse landscape provide an ideal context in which to address the focal issue around the emergence of evolutionary novelties and how this affects the chemical diversification of plant metabolism.
虽然已经投入了大量的研究精力来理解植物蛋白与其分子伴侣之间的相互作用，但与其他生物的研究相比，植物中研究这些相互作用如何进化的相对较少。人们认为，祖先蛋白比现代蛋白更具多配性，特异性通常在基因复制和随后的功能细化后进化而来。然而，祖先蛋白复活研究发现，一些现代蛋白是从缺乏这些功能的祖先进化而来的。有趣的是，新的相互作用是由少数几个突变产生的，因此，新功能的获得似乎既不困难也不罕见，然而，只有少数新功能在被后续突变丢失之前被纳入生物过程。在这里，我们详细介绍祖先序列重建（ASR）的方法，提供一个重建祖先基因序列的入门指南。在讨论植物中使用祖先重建的少数情况之前，我们将展示一系列不同真核生物的案例研究。由于ASR用于深入研究遥远的进化历史，我们还将介绍一些替代遗传方法，以研究较短时间尺度上的分子进化。我们认为，植物次生代谢的研究特别适合进行祖先重建研究。事实上，它古老的进化根源和高度多样的格局为解决围绕进化新奇性的出现以及这如何影响植物代谢的化学多样化这一核心问题提供了理想的背景。
