Genome instability mediates the loss of key traits by Acinetobacter baylyi ADP1 during laboratory evolution.
Genome instability mediates the loss of key traits by Acinetobacter baylyi ADP1 during laboratory evolution.
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基因组不稳定性介导贝氏不动杆菌 ADP1 在实验室进化过程中关键性状的丧失。
DOI：
10.1128/jb.02263-14
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发表时间：
2015
影响因子：
3.2
通讯作者：
Barrick,JeffreyE
中科院分区：
文献类型：
--
作者：
Renda,BrianA;Dasgupta,Aurko;Leon,Dacia;Barrick,JeffreyE
贝氏不动杆菌 ADP1 有潜力成为合成生物学的多功能细菌宿主，因为它具有天然可转化性。为了检查这一理想性状的遗传可靠性并了解其他工程能力的潜在稳定性，我们将 ADP1 在丰富的营养肉汤中繁殖了 1,000 代，并通过全基因组测序分析了进化的遗传变化。在实验过程中，可变形性显着降低，细胞聚集增加。在大多数情况下，IS1236 转座元件的新插入和 IS1236 介导的缺失导致了这些表型，并且在选定的突变中总体上很常见。我们还观察到原噬菌体区域有一个 49 kb 的缺失，该区域从每个进化的基因组中删除了一个已用于基因组工程的整合位点。在减少选择的情况下繁殖 7,500 代的谱系中，这三类突变的发生率相对较低，表明它们在常见的实验室生长条件下提高了 ADP1 的适应性。我们的结果表明，消除影响关键生物性状的转座元件和其他遗传失败模式对于提高未驯化微生物宿主（例如贝氏不动杆菌 ADP1）中代谢工程和基因组编辑的可靠性至关重要。
Acinetobacter baylyi ADP1 has the potential to be a versatile bacterial host for synthetic biology because it is naturally transformable. To examine the genetic reliability of this desirable trait and to understand the potential stability of other engineered capabilities, we propagated ADP1 for 1,000 generations of growth in rich nutrient broth and analyzed the genetic changes that evolved by whole-genome sequencing. Substantially reduced transformability and increased cellular aggregation evolved during the experiment. New insertions of IS1236transposable elements and IS1236-mediated deletions led to these phenotypes in most cases and were common overall among the selected mutations. We also observed a 49-kb deletion of a prophage region that removed an integration site, which has been used for genome engineering, from every evolved genome. The comparatively low rates of these three classes of mutations in lineages that were propagated with reduced selection for 7,500 generations indicate that they increase ADP1 fitness under common laboratory growth conditions. Our results suggest that eliminating transposable elements and other genetic failure modes that affect key organismal traits is essential for improving the reliability of metabolic engineering and genome editing in undomesticated microbial hosts, such as Acinetobacter baylyi ADP1.