Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution
Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution
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DOI：
10.1126/sciadv.abq4632
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发表时间：
2023-02-24
期刊：
影响因子：
13.6
通讯作者：
Eren, A. Murat
中科院分区：
文献类型：
--
作者：
Kiefl, Evan;Esen, Ozcan C.;Eren, A. Murat
利用宏基因组学对自然遗传多样性进行全面采样，使我们能够深入了解生态与进化之间的相互作用。然而，从种群内基因组变异中解决适应性、中性或净化进化过程仍然是一个挑战，部分原因是仅依赖基因序列来解释变异。在这里，我们描述了一种在预测蛋白质结构的背景下分析遗传变异的方法，并将其应用于SAR11亚枝1a中的海洋微生物种群。V，它支配着低纬度的表层海洋。我们的分析揭示了遗传变异和蛋白质结构之间的紧密联系。在氮代谢的中心基因中，我们观察到来自配体结合位点的非同义性变异的减少是硝酸盐浓度的函数，揭示了由营养可用性维持的不同进化压力的遗传目标。我们的工作产生了对进化的支配原则的见解，并使微生物种群遗传学的结构意识调查成为可能。
Comprehensive sampling of natural genetic diversity with metagenomics enables highly resolved insights into the interplay between ecology and evolution. However, resolving adaptive, neutral, or purifying processes of evolution from intrapopulation genomic variation remains a challenge, partly due to the sole reliance on gene sequences to interpret variants. Here, we describe an approach to analyze genetic variation in the context of predicted protein structures and apply it to a marine microbial population within the SAR11 subclade 1a.3.V, which dominates low-latitude surface oceans. Our analyses reveal a tight association between genetic variation and protein structure. In a central gene in nitrogen metabolism, we observe decreased occurrence of nonsynon- ymous variants from ligand-binding sites as a function of nitrate concentrations, revealing genetic targets of distinct evolutionary pressures maintained by nutrient availability. Our work yields insights into the governing principles of evolution and enables structure-aware investigations of microbial population genetics.