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Abstract：
A protein\'s genetic architecture - the set of causal rules by which its sequence produces its functions - also determines its possible evolutionary trajectories. Prior research has proposed that the genetic architecture of proteins is very complex, with pervasive epistatic interactions that constrain evolution and make function difficult to predict from sequence. Most of this work has analyzed only the direct paths between two proteins of interest - excluding the vast majority of possible genotypes and evolutionary trajectories - and has considered only a single protein function, leaving unaddressed the genetic architecture of functional specificity and its impact on the evolution of new functions. Here, we develop a new method based on ordinal logistic regression to directly characterize the global genetic determinants of multiple protein functions from 20-state combinatorial deep mutational scanning (DMS) experiments. We use it to dissect the genetic architecture and evolution of a transcription factor\'s specificity for DNA, using data from a combinatorial DMS of an ancient steroid hormone receptor\'s capacity to activate transcription from two biologically relevant DNA elements. We show that the genetic architecture of DNA recognition consists of a dense set of main and pairwise effects that involve virtually every possible amino acid state in the protein-DNA interface, but higher-order epistasis plays only a tiny role. Pairwise interactions enlarge the set of functional sequences and are the primary determinants of specificity for different DNA elements. They also massively expand the number of opportunities for single-residue mutations to switch specificity from one DNA target to another. By bringing variants with different functions close together in sequence space, pairwise epistasis therefore facilitates rather than constrains the evolution of new functions.
摘要：
蛋白质的遗传结构——其序列产生其功能的一组因果规则——也决定了其可能的进化轨迹。先前的研究表明，蛋白质的遗传结构非常复杂，具有普遍的上位性相互作用，限制了进化并使功能难以从序列中预测。大多数这项工作只分析了两种感兴趣的蛋白质之间的直接路径-排除了绝大多数可能的基因型和进化轨迹-并且只考虑了单一的蛋白质功能。未解决功能特异性的遗传结构及其对新功能进化的影响。这里,我们开发了一种基于序数逻辑回归的新方法，可以从20态组合深度突变扫描（DMS）实验中直接表征多种蛋白质功能的全局遗传决定因素。我们用它来剖析转录因子对DNA特异性的遗传结构和进化，使用来自古代类固醇激素受体的组合DMS的数据激活两个生物相关DNA元件的转录能力。我们表明，DNA识别的遗传结构由一组密集的主要和配对效应组成，这些效应涉及蛋白质-DNA界面中几乎所有可能的氨基酸状态，但是高阶上位只起到很小的作用。成对相互作用扩大了功能序列集，并且是不同DNA元件特异性的主要决定因素。他们还大量扩大了单残基突变将特异性从一个DNA靶标切换到另一个的机会。通过将具有不同功能的变体在序列空间中靠近在一起，因此，成对上位促进而不是限制新功能的发展。
