Adaptive laboratory evolution (ALE) is a general and effective strategy for optimizing the design of engineered genetic circuits and upgrading metabolic phenotypes. However, the specific characteristics of each microorganism typically ask for exclusive conditions that need to be adjusted to the biological chassis at stake. In this work, we have adopted a do-it-yourself (DIY) approach to implement a flexible and automated framework for performing ALE experiments with the environmental bacterium and metabolic engineering platform Pseudomonas putida. The setup includes a dual-chamber semi-continuous log-phase bioreactor design combined with an anti-biofilm layout to manage specific traits of this bacterium in long-term cultivation experiments. As a way of validation, the prototype was instrumental for selecting fast-growing variants of a P. putida strain engineered to metabolize D-xylose as sole carbon and energy source after running an automated 42 days protocol of iterative regrowth. Several genomic changes were identified in the evolved population that pinpointed the role of RNA polymerase in controlling overall physiological conditions during metabolism of the new carbon source.

中文翻译：

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恶臭假单胞菌实验进化的自动化 DIY 框架

自适应实验室进化 (ALE) 是优化工程遗传回路设计和升级代谢表型的通用且有效的策略。然而，每种微生物的特定特征通常要求需要针对所涉及的生物底盘进行调整的专有条件。在这项工作中，我们采用了自己动手 (DIY) 的方法来实现一个灵活和自动化的框架，用于使用环境细菌和代谢工程平台恶臭假单胞菌进行 ALE 实验. 该设置包括双室半连续对数相生物反应器设计和抗生物膜布局，以管理这种细菌在长期培养实验中的特定性状。作为一种验证方式，该原型有助于选择快速生长的恶臭假单胞菌菌株变体，该菌株被设计用于在运行 42 天的自动迭代再生方案后代谢 D-木糖作为唯一的碳和能源。在进化种群中发现了一些基因组变化，这些变化确定了 RNA 聚合酶在新碳源代谢过程中控制整体生理条件的作用。