Initial mutations direct alternative pathways of protein evolution.
Initial mutations direct alternative pathways of protein evolution.
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DOI：
10.1371/journal.pgen.1001321
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发表时间：
2011-03
期刊：
影响因子：
4.5
通讯作者：
de Visser JA
中科院分区：
文献类型：
--
作者：
Salverda ML;Dellus E;Gorter FA;Debets AJ;van der Oost J;Hoekstra RF;Tawfik DS;de Visser JA
进化是由于随机的历史细节而不稳定的，还是由于某些限制而重复地沿着相似的路径进行，目前还不清楚。上位性（即影响适应度的突变之间的非加性相互作用）是一种可以促成这两种情况的机制。上位性可以限制选择突变的类型和顺序，但它也可以使适应轨迹取决于第一次随机替代。这种效应在符号上位性下尤为明显，即突变的适应度效应的符号取决于其遗传背景。在目前的研究中，我们研究突变之间的上位相互作用如何决定替代的进化途径，使用抗生素抗性酶TEM-1 β-内酰胺酶的体外进化。首先，我们描述了在对一种新型抗生素（头孢噻肟）产生耐药性的进化过程中，复制系之间适应途径的多样性。与上位性约束的预测一致，大多数品系通过以固定顺序获得三个突变来增加抗性。然而，有几条线偏离了这种模式。接下来，为了测试备选初始替换之间的负相互作用是否驱动了这种分化，在相同的条件下进化了包含偏离系初始替换的等位基因。事实上，这些替代性的初始取代始终导致较低的适应峰值，涉及比在共同途径中观察到的更多和其他取代。我们发现，酶活性的降低和较低的折叠协同性的组合是在共同系和偏离系（分别为Gly238Ser和Arg164Ser）的关键突变冲突中的负符号优势的基础。我们的研究结果表明，上位性通过放大随机突变的选择性后果，有助于蛋白质进化中的偶然性。进化生物学的一个长期目标是了解控制进化结果的因素。上位性（即突变的适应性效应取决于其遗传背景的情况）就是这样一个因素。上位性不仅影响进化的动力学，还可能通过影响选择突变的类型和顺序来指导进化的结果。这种效应在符号上位性下尤为明显，即突变的适应度效应取决于其遗传背景。在这里，我们展示了上位性如何导致抗生素抗性酶TEM-1 β-内酰胺酶突变途径的分歧。首先，我们使用体外诱变，然后选择头孢噻肟抗性，以证明除了先前描述的主要途径外，还存在高抗性变异的替代突变途径。接下来，为了测试替代初始替换之间的负相互作用是否控制了这种多样化，我们开始了包含偏离系初始替换的等位基因的相同进化实验。这些等位基因不断进化到较低的适应峰值，并获得与主途径不同的突变。我们的研究结果表明，替代初始替代之间的符号上位可能迫使进化遵循不同的突变途径。
Whether evolution is erratic due to random historical details, or is repeatedly directed along similar paths by certain constraints, remains unclear. Epistasis (i.e. non-additive interaction between mutations that affect fitness) is a mechanism that can contribute to both scenarios. Epistasis can constrain the type and order of selected mutations, but it can also make adaptive trajectories contingent upon the first random substitution. This effect is particularly strong under sign epistasis, when the sign of the fitness effects of a mutation depends on its genetic background. In the current study, we examine how epistatic interactions between mutations determine alternative evolutionary pathways, using in vitro evolution of the antibiotic resistance enzyme TEM-1 β-lactamase. First, we describe the diversity of adaptive pathways among replicate lines during evolution for resistance to a novel antibiotic (cefotaxime). Consistent with the prediction of epistatic constraints, most lines increased resistance by acquiring three mutations in a fixed order. However, a few lines deviated from this pattern. Next, to test whether negative interactions between alternative initial substitutions drive this divergence, alleles containing initial substitutions from the deviating lines were evolved under identical conditions. Indeed, these alternative initial substitutions consistently led to lower adaptive peaks, involving more and other substitutions than those observed in the common pathway. We found that a combination of decreased enzymatic activity and lower folding cooperativity underlies negative sign epistasis in the clash between key mutations in the common and deviating lines (Gly238Ser and Arg164Ser, respectively). Our results demonstrate that epistasis contributes to contingency in protein evolution by amplifying the selective consequences of random mutations. A long-term goal of evolutionary biology is to understand the factors that govern the outcome of evolution. Epistasis (i.e. the situation in which the fitness effect of a mutation depends on its genetic background) is one such factor. Epistasis not only affects the dynamics of evolution, it may also direct its outcome by affecting the type and order of selected mutations. This effect is particularly strong under sign epistasis, which occurs when the sign of a mutation's fitness effect depends on its genetic background. Here, we demonstrate how epistasis causes divergence of mutational pathways of an antibiotic resistance enzyme, TEM-1 β-lactamase. First, we use in vitro mutagenesis followed by selection for cefotaxime resistance to demonstrate that alternative mutational pathways towards highly resistant variants exist in addition to the main pathway that was previously described. Next, to test whether negative interactions between alternative initial substitutions govern this diversification, we start identical evolution experiments with alleles containing initial substitutions from the deviating lines. These alleles consistently evolve to lower adaptive peaks and acquire different mutations than those in the main pathway. Our results demonstrate that sign epistasis between alternative initial substitutions may force evolution to follow different mutational pathways.