Data from: Core genes evolve rapidly in the long-term evolution experiment with Escherichia coli

Bacteria can evolve rapidly under positive selection owing to their vast numbers, allowing their genes to diversify by adapting to different environments. We asked whether the same genes that evolve rapidly in the long-term evolution experiment with Escherichia coli (LTEE) have also diversified extensively in nature. To make this comparison, we identified ~2000 core genes shared among 60 E. coli strains. During the LTEE, core genes accumulated significantly more nonsynonymous mutations than flexible (i.e., noncore) genes. Furthermore, core genes under positive selection in the LTEE are more conserved in nature than the average core gene. In some cases, adaptive mutations appear to modify protein functions, rather than merely knocking them out. The LTEE conditions are novel for E. coli, at least in relation to its evolutionary history in nature. The constancy and simplicity of the environment likely favor the complete loss of some unused functions and the fine-tuning of others.

细菌因其种群规模庞大，可在正向选择（positive selection）作用下快速演化，使其基因通过适应不同环境实现多样化。我们探究了：在大肠杆菌（Escherichia coli）的长期进化实验（Long-Term Evolution Experiment, LTEE）中快速演化的基因，是否也在自然环境中发生了广泛的多样化。为开展此类对比研究，我们从60株大肠杆菌中鉴定出约2000个共有核心基因（core genes）。在LTEE实验中，核心基因所积累的错义突变（nonsynonymous mutations）数量显著多于柔性基因（即非核心基因，flexible (noncore) genes）。此外，在LTEE中受正向选择作用的核心基因，在自然环境中的保守性要高于普通核心基因。在部分情形中，适应性突变似乎会修饰蛋白质功能，而非仅仅使其功能失活。LTEE的实验环境对于大肠杆菌而言是全新的，至少相较于其在自然环境中的演化历史而言如此。该环境的恒定性与极简性，可能更有利于部分闲置功能的完全丢失，以及其余功能的精细调控。