Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
Swiss Institute of Bioinformatics, Lausanne, Switzerland.
PLoS Comput Biol. 2020 Nov 30;16(11):e1008433. doi: 10.1371/journal.pcbi.1008433. eCollection 2020 Nov.
The evolution of cross-feeding among individuals of the same species can help generate genetic and phenotypic diversity even in completely homogeneous environments. Cross-feeding Escherichia coli strains, where one strain feeds on a carbon source excreted by another strain, rapidly emerge during experimental evolution in a chemically minimal environment containing glucose as the sole carbon source. Genome-scale metabolic modeling predicts that cross-feeding of 58 carbon sources can emerge in the same environment, but only cross-feeding of acetate and glycerol has been experimentally observed. Here we use metabolic modeling to ask whether acetate and glycerol cross-feeding are especially likely to evolve, perhaps because they require less metabolic change, and thus perhaps also less genetic change than other cross-feeding interactions. However, this is not the case. The minimally required metabolic changes required for acetate and glycerol cross feeding affect dozens of chemical reactions, multiple biochemical pathways, as well as multiple operons or regulons. The complexity of these changes is consistent with experimental observations, where cross-feeding strains harbor multiple mutations. The required metabolic changes are also no less complex than those observed for multiple other of the 56 cross feeding interactions we study. We discuss possible reasons why only two cross-feeding interactions have been discovered during experimental evolution and argue that multiple new cross-feeding interactions may await discovery.
同种个体之间的交叉喂养的进化有助于在完全同质的环境中产生遗传和表型多样性。在含有葡萄糖作为唯一碳源的化学最小环境中进行实验进化时，大肠杆菌菌株之间的交叉喂养会迅速出现，其中一种菌株以另一种菌株分泌的碳源为食。基于基因组规模的代谢模型预测，在相同环境中可能会出现 58 种碳源的交叉喂养，但仅观察到乙酸盐和甘油的交叉喂养。在这里，我们使用代谢建模来询问乙酸盐和甘油的交叉喂养是否特别容易进化，也许是因为它们需要较少的代谢变化，因此也许比其他交叉喂养相互作用需要更少的遗传变化。然而，事实并非如此。乙酸盐和甘油交叉喂养所需的最小代谢变化会影响数十个化学反应、多个生化途径以及多个操纵子或调节子。这些变化的复杂性与实验观察结果一致，其中交叉喂养菌株携带有多个突变。所需的代谢变化也不比我们研究的 56 种交叉喂养相互作用中的其他几种观察到的变化复杂。我们讨论了在实验进化中仅发现两种交叉喂养相互作用的可能原因，并认为可能还需要发现多种新的交叉喂养相互作用。
