SHF: Small: Evolvability and Robustness of Synthetic Gene Circuits in Bacteria

智能价值合成生物学这一新兴领域的主要目标之一是在活细胞中设计合成遗传‘电路’，对人工功能进行编程。这种程序化细胞可以作为有价值的药物、化学品和生物燃料的高效细胞工厂，或者可以植入患者体内的智能生物传感器或治疗工具。今天，基因程序员组装合成遗传电路的方式类似于工程师设计和制造电子电路的方式，通过将许多“部件”连接到一个复杂的电路中？以细胞可以解释的形式合成(即DNA)。然而，就像有许多不同的电路可以作为无线电一样，也有许多总体电路设计来实现特定的蜂窝功能。拟议研究的主要目标是问：在生物学背景下实现更好(如果不是最好的)电路设计的最佳策略是什么？这不是一个微不足道的问题，因为基因电路必须在复杂的生物环境中发挥作用。当合成电路在细胞内部运行时，细胞生长、适应、死亡，甚至发生突变。理想情况下，基因工程电路应该在这种动态且相当不可预测的环境中强健地发挥作用。我们建议采用自然界一直用来“设计”自己的电路的策略：进化。首先，我们将通过基因操作在细菌中产生大量(数百万)不同的电路。然后，这些电路在受控环境中经历涉及选择和突变的实验室进化过程。我们期望最好的电路设计能够在活细胞中稳健地发挥作用，这是从实验室进化过程中产生的。我们还将研究进化的电路种群如何获得新的功能，这也是进化的一个重要方面。这些研究有望增强我们编程具有复杂和有用功能的活细胞的能力，并加深我们对进化如何塑造自然界中观察到的复杂遗传电路的理解。广泛的影响通过拟议的研究获得的工具和见解应该会提高我们为未来的实际应用编程活细胞的能力。通过拟议的项目开发的基因部分将提供给研究界。此外，拟议的研究将积极吸引国内外本科生作为研究实习生和暑期研究员。高中生也将通过加州大学戴维斯分校管理的暑期项目参与这项研究。拟议的项目将通过尖端研究活动促进不同背景的年轻学生之间的互动。

Intellectual meritOne of the major goals of the emerging field of synthetic biology is to design synthetic genetic 'circuits' in living cells to program artificial functions. Such programmed cells may serve as efficient cell factories for valuable drugs, chemicals, and biofuels, or intelligent biosensors or therapeutic vehicles that can be implanted in patients. Today, genetic programmers assemble synthetic genetic circuits in a manner similar to how engineers design and build electronic circuits, by connecting a number of 'parts' into a complex ?circuit? synthesized in the form that the cells can interpret (i.e. DNA). However, just as there are many different circuits that can function as a radio, there are many overall circuit designs to achieve a certain cellular function. The main goal of the proposed research is to ask: what is the best strategy to arrive at better (if not the best) circuit designs in the biological context? This is not a trivial question because genetic circuits must function in the complex biological environment. Cells grow, adapt, die, and even mutate while the synthetic circuits run inside them. Ideally, engineered genetic circuits should function robustly in such dynamic and rather unpredictable environment. We propose to adapt the strategy that nature has been using to 'design' its own circuits: evolution. First, we will generate a large number (millions) of different circuits in bacteria through genetic manipulation. The circuits are then subjected to the laboratory evolution process that involves selection and mutation in the controlled environment. We expect that the best circuit designs that robustly function in the living cells emerge from the laboratory evolution process. We will also study how the evolving circuit populations acquire new functions, which is also an important aspect of evolution. These studies are expected to enhance our ability to program living cells with complex and useful functions, as well as to deepen our understanding of how evolution shapes the complex genetic circuits observed in nature.Broader impactsThe tools and insights gained through the proposed research should advance our ability to program living cells for the future practical applications. Genetic parts that are developed through the proposed project will be made available to the research community. Furthermore, the proposed research will actively engage domestic and international undergraduate students as research interns and summer researchers. High school students will also participate in the research through a summer program administered at UC Davis. The proposed project will foster interactions among the young students with diverse backgrounds through cutting-edge research activities.