Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA.
Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China.
Mol Biol Evol. 2024 Nov 1;41(11). doi: 10.1093/molbev/msae228.
Functional innovation at the protein level is a key source of evolutionary novelties. The constraints on functional innovations are likely to be highly specific in different proteins, which are shaped by their unique histories and the extent of global epistasis that arises from their structures and biochemistries. These contextual nuances in the sequence-function relationship have implications both for a basic understanding of the evolutionary process and for engineering proteins with desirable properties. Here, we have investigated the molecular basis of novel function in a model member of an ancient, conserved, and biotechnologically relevant protein family. These Major Facilitator Superfamily sugar porters are a functionally diverse group of proteins that are thought to be highly plastic and evolvable. By dissecting a recent evolutionary innovation in an α-glucoside transporter from the yeast Saccharomyces eubayanus, we show that the ability to transport a novel substrate requires high-order interactions between many protein regions and numerous specific residues proximal to the transport channel. To reconcile the functional diversity of this family with the constrained evolution of this model protein, we generated new, state-of-the-art genome annotations for 332 Saccharomycotina yeast species spanning ∼400 My of evolution. By integrating phylogenetic and phenotypic analyses across these species, we show that the model yeast α-glucoside transporters likely evolved from a multifunctional ancestor and became subfunctionalized. The accumulation of additive and epistatic substitutions likely entrenched this subfunction, which made the simultaneous acquisition of multiple interacting substitutions the only reasonably accessible path to novelty.
蛋白质水平的功能创新是进化新颖性的主要来源。功能创新的限制在不同的蛋白质中可能是高度特定的，这些限制是由它们独特的历史和由它们的结构和生物化学产生的全局上位性的程度所决定的。这些序列-功能关系中的上下文细微差别对进化过程的基本理解以及对具有理想性质的蛋白质的工程设计都有影响。在这里，我们研究了一个古老、保守且具有生物技术相关性的蛋白质家族的模型成员中新型功能的分子基础。这些主要易化剂超家族糖转运蛋白是一组功能多样的蛋白质，被认为具有高度的可塑性和可进化性。通过剖析来自酿酒酵母 Saccharomyces eubayanus 的α-葡糖苷转运蛋白的一个近期进化创新，我们表明，运输新底物的能力需要许多蛋白质区域之间的高阶相互作用以及靠近运输通道的许多特定残基。为了使这个家族的功能多样性与这个模型蛋白的约束进化相协调，我们为跨越约 4000 万年进化的 332 个酿酒酵母物种生成了新的、最先进的基因组注释。通过在这些物种中整合系统发育和表型分析，我们表明，模型酵母α-葡糖苷转运蛋白可能是从一个多功能祖先进化而来的，并发生了亚功能化。累加和上位性取代的积累可能使这种亚功能固定下来，这使得同时获得多个相互作用的取代成为唯一合理的新颖途径。
