Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment
Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment
复制标题
DOI：
10.1186/s12862-016-0733-x
复制
发表时间：
2016-08-20
影响因子：
3.4
通讯作者：
Schneider, Dominique
中科院分区：
文献类型：
--
作者：
Grosskopf, Tobias;Consuegra, Jessika;Schneider, Dominique
背景：预测适应性轨迹是进化生物学的一个主要目标，对实际应用很有用。系统生物学使基因组规模的代谢模型的发展成为可能。然而，通过通量平衡分析（FBA）分析这些模型不能预测许多进化结果，包括适应性多样化，即祖先谱系分叉以填补多个生态位。在这里，我们结合联合收割机在硅片进化与FBA和应用此建模框架，evoFBA，一个长期的进化实验与Escherichia coli.Results：模拟预测的适应性多样化，发生在一个实验种群和产生的假说的机制，促进共存的分歧谱系。我们实验测试，并在平衡，验证这些机制，表明多样化涉及生态位建设和字符位移通过差异养分吸收和改变代谢regulation.Conclusion：evoFBA框架是一个有前途的新方法来模拟生化进化，一个可以产生可测试的预测进化和生态系统水平的结果。
Background: Predicting adaptive trajectories is a major goal of evolutionary biology and useful for practical applications. Systems biology has enabled the development of genome-scale metabolic models. However, analysing these models via flux balance analysis (FBA) cannot predict many evolutionary outcomes including adaptive diversification, whereby an ancestral lineage diverges to fill multiple niches. Here we combine in silico evolution with FBA and apply this modelling framework, evoFBA, to a long-term evolution experiment with Escherichia coli.Results: Simulations predicted the adaptive diversification that occurred in one experimental population and generated hypotheses about the mechanisms that promoted coexistence of the diverged lineages. We experimentally tested and, on balance, verified these mechanisms, showing that diversification involved niche construction and character displacement through differential nutrient uptake and altered metabolic regulation.Conclusion: The evoFBA framework represents a promising new way to model biochemical evolution, one that can generate testable predictions about evolutionary and ecosystem-level outcomes.