Retracing Evolution of Red Fluorescence in GFP-Like Proteins from Faviina Corals
Retracing Evolution of Red Fluorescence in GFP-Like Proteins from Faviina Corals
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DOI：
10.1093/molbev/msp230
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发表时间：
2010-02-01
影响因子：
10.7
通讯作者：
Matz, Mikhail V.
中科院分区：
文献类型：
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作者：
Field, Steven F.;Matz, Mikhail V.
绿色荧光蛋白家族的蛋白质代表了一种在分子水平上研究新颖性进化的便捷实验模型。在这里，我们专注于Faviina亚目珊瑚特征的kaede样红色荧光蛋白的起源。我们证明，使用一种涉及复活和分析可能的进化中间体库的原始方法，它需要12个突变的顺序，其中一些强相互作用，以完全概括祖先绿色的红色荧光表型的进化。如果没有祖先重建的帮助，其中5个已确定的突变是不可能被发现的，因为相应的位点状态在现存的红色和绿色蛋白质之间是共享的，这是由于它们最近从具有双重功能的共同祖先那里继承而来。12个突变中有7个影响与发色团不密切接触的残基，因此必须通过调整整个蛋白质折叠来间接发挥作用；这些突变的相关性无法从蛋白质结构的纯理论分析中预测出来。我们的研究结果为在明显上位性的情况下比较分析蛋白质家族的功能特异性提供了强有力的实验方法，为详细研究导致新颖性和复杂性的进化轨迹提供了基础，并将有助于合理修改现有的荧光标记。
Proteins of the green fluorescent protein family represent a convenient experimental model to study evolution of novelty at the molecular level. Here, we focus on the origin of Kaede-like red fluorescent proteins characteristic of the corals of the Faviina suborder. We demonstrate, using an original approach involving resurrection and analysis of the library of possible evolutionary intermediates, that it takes on the order of 12 mutations, some of which strongly interact epistatically, to fully recapitulate the evolution of a red fluorescent phenotype from the ancestral green. Five of the identified mutations would not have been found without the help of ancestral reconstruction, because the corresponding site states are shared between extant red and green proteins due to their recent descent from a dual-function common ancestor. Seven of the 12 mutations affect residues that are not in close contact with the chromophore and thus must exert their effect indirectly through adjustments of the overall protein fold; the relevance of these mutations could not have been anticipated from the purely theoretical analysis of the protein's structure. Our results introduce a powerful experimental approach for comparative analysis of functional specificity in protein families even in the cases of pronounced epistasis, provide foundation for the detailed studies of evolutionary trajectories leading to novelty and complexity, and will help rational modification of existing fluorescent labels.