Laboratory evolution of Escherichia coli enables life based on fluorinated amino acids

Organofluorine compounds are toxic to various living beings in different habitats. This usher the development of strategies based on the metabolic capacity of various fast-growing microbial strains to evolve an effective adaptation strategy for efficient environmental cleaning. We tackle this problem by trying to answer an essential question: can fluorinated amino acids be used as xenobiotics in general to build up biomass, or do large amounts of fluorine in the cells render them nonviable? To gain information about the effect of long-term exposure of a cellular proteome to fluorine, we constructed an experimental model based on bacterial adaptation in artificial fluorinated habitats. In particular, we propagated Escherichia coli (E. coli) in the presence of either 4- or 5-fluoroindole as essential precursors for the in situ synthesis of tryptophan (Trp) analogues. We found that full adaptation requires astonishingly few genetic mutations but is accompanied by large rearrangements in regulatory networks, membrane integrity and quality control of protein folding. These findings highlight the cellular mechanisms of the evolutionary adaption process and provide the molecular foundation for novel and innovative bioengineering of microbial strains potentially useful in bioaugmentation in fluorine-contaminated areas.

有机氟化合物对不同生境中的各类生物均具有毒性，这推动了基于各类快速生长微生物菌株代谢能力、用于高效环境净化的适应性策略的研发。本研究通过解答一个核心问题来攻克该难题：含氟氨基酸能否普遍作为外源性物质（xenobiotics）用于生物量合成，抑或是细胞内大量氟元素会导致菌体失活？为探明细胞蛋白质组长期暴露于氟环境的影响，我们构建了基于人工氟污染生境中细菌适应性演化的实验模型。具体而言，我们以4-氟吲哚或5-氟吲哚作为色氨酸（tryptophan, Trp）类似物原位合成的必需前体，对大肠杆菌（Escherichia coli, E. coli）进行传代培养。研究结果显示，菌株实现完全适应性演化仅需极少量的基因突变，但同时伴随调控网络、膜完整性以及蛋白质折叠质控机制的大规模重排。本研究结果阐明了演化适应性过程中的细胞机制，同时为可应用于氟污染区域生物强化修复的新型微生物菌株工程改造提供了分子基础。