Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
Nat Commun. 2019 Feb 25;10(1):935. doi: 10.1038/s41467-019-08888-6.
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.
合成生物学旨在设计和构建携带自我复制生命所需的最少基因的细菌基因组。然而，在实验室条件下，减少基因组的细菌通常表现出生长受损的情况，而这不能仅根据去除的基因来理解。这些出乎意料的表型凸显了我们对细菌基因组的有限理解。在这里，我们部署适应性实验室进化 (ALE) 来重新优化基因组减少菌株的生长性能。生长表现不佳的基础是 ALE 过程中代谢失衡。代谢重布线是由 rpoD 中的突变全局协调的，这些突变改变了 RNA 聚合酶的启动子结合。最后，进化后的菌株没有翻译缓冲能力，从而能够有效地翻译丰富的 mRNA。对进化菌株的多组学分析揭示了转录组和翻译组的广泛重塑，这些重塑协调了代谢和生长。这些结果表明，预测失败可能不是由于对单个基因的理解不足，而是由于对菌株系统生物学的理解不足。
