Synthetic Genome Defenses against Selfish DNA Elements Stabilize Engineered Bacteria against Evolutionary Failure
Synthetic Genome Defenses against Selfish DNA Elements Stabilize Engineered Bacteria against Evolutionary Failure
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DOI：
10.1021/acssynbio.8b00426
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发表时间：
2019-03-01
影响因子：
4.7
通讯作者：
Barrick, Jeffrey E.
中科院分区：
文献类型：
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作者：
Geng, Peng;Leonard, Sean P.;Barrick, Jeffrey E.
移动遗传元件通过破坏基因和重新排列基因组来驱动进化。真核生物已经进化出表观遗传机制，包括 DNA 甲基化和 RNA 干扰，这些机制可以沉默移动元件，从而保持其基因组的完整性。我们创建了一个基于 CRISPR 干扰的人工可重编程表观遗传系统，为工程细菌提供了类似的防线，抵御转座子和基因组中其他自私的元素。我们证明，这种针对移动元件的 CRISPR 干扰 (CRISPRi-ME) 方法可用于同时抑制大肠杆菌中两个不同的转座子家族，从而提高昂贵的蛋白质表达的进化稳定性。我们进一步表明，沉默 Acinetobacter baylyi ADP1 中的转座子可将突变率降低 5 倍，几乎相当于从其基因组中删除该元件的所有副本。通过在广泛宿主范围的载体上部署 CRISPRi-ME，我们创建了一个通用平台，用于稳定工程细菌细胞的基因组，以应用于代谢工程和合成生物学。
Mobile genetic elements drive evolution by disrupting genes and rearranging genomes. Eukaryotes have evolved epigenetic mechanisms, including DNA methylation and RNA interference, that silence mobile elements and thereby preserve the integrity of their genomes. We created an artificial reprogrammable epigenetic system based on CRISPR interference to give engineered bacteria a similar line of defense against transposons and other selfish elements in their genomes. We demonstrate that this CRISPR interference against mobile elements (CRISPRi-ME) approach can be used to simultaneously repress two different transposon families in Escherichia coli, thereby increasing the evolutionary stability of costly protein expression. We further show that silencing a transposon in Acinetobacter baylyi ADP1 reduces mutation rates by a factor of 5, nearly as much as deleting all copies of this element from its genome. By deploying CRISPRi-ME on a broad-host-range vector, we have created a generalizable platform for stabilizing the genomes of engineered bacterial cells for applications in metabolic engineering and synthetic biology.