Adaptive laboratory evolution of a genome-reduced Escherichia coli
Adaptive laboratory evolution of a genome-reduced Escherichia coli
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DOI：
10.1038/s41467-019-08888-6
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发表时间：
2019-02-25
影响因子：
16.6
通讯作者：
Cho, Byung-Kwan
中科院分区：
文献类型：
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作者：
Choe, Donghui;Lee, Jun Hyoung;Cho, Byung-Kwan
合成生物学的目标是设计和构建细菌基因组，这些基因组含有自我复制生命所需的最低数量的基因。然而，基因组减少的细菌在实验室条件下往往表现出生长受损，而根据移除的基因无法理解这些条件。意想不到的表型突显了我们对细菌基因组有限的理解。在这里，我们采用适应性实验室进化(ALE)来重新优化基因组减少菌株的生长性能。次优生长的基础是在ALE期间重新连接的不平衡新陈代谢。RpoD的突变改变了RNA聚合酶的启动子结合，从而在全球范围内协调了代谢重排。最后，进化的菌株没有翻译缓冲能力，使丰富的mRNAs能够有效翻译。对进化菌株的多组学分析揭示了转录组和翻译组范围内协调新陈代谢和生长的重塑。这些结果表明，预测的失败可能与了解单个基因无关，而是因为对菌株的系统生物学了解不足。
Synthetic biology aims to design and construct bacterial genomes harboring the minimum number of genes required for self-replicable life. However, the genome-reduced bacteria often show impaired growth under laboratory conditions that cannot be understood based on the removed genes. The unexpected phenotypes highlight our limited understanding of bacterial genomes. Here, we deploy adaptive laboratory evolution (ALE) to re-optimize growth performance of a genome-reduced strain. The basis for suboptimal growth is the imbalanced metabolism that is rewired during ALE. The metabolic rewiring is globally orchestrated by mutations in rpoD altering promoter binding of RNA polymerase. Lastly, the evolved strain has no translational buffering capacity, enabling effective translation of abundant mRNAs. Multi-omic analysis of the evolved strain reveals transcriptome- and translatome-wide remodeling that orchestrate metabolism and growth. These results reveal that failure of prediction may not be associated with understanding individual genes, but rather from insufficient understanding of the strain's systems biology.