Reversible long-term memory devices in bacteria inspired by mammalian chromatin modification circuits

受哺乳动物染色质修饰电路启发，细菌中的可逆长期记忆装置

• 批准号: 2313877
• 负责人: Domitilla Del Vecchio
• 金额: $ 48.12万
• 依托单位: Massachusetts Institute of Technology
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-07-01 至 2026-06-30
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2313877&HistoricalAwards=false
• 关键词: Reversible; long; term; memory; devices

Enabling bacterial cells to remember long time environmental cues is essential for numerous processes including, sensing pollutants in water or soil, for recording biomarkers of stress in the human gut, and for triggering cell death to avoid escape in the environment. At the same time, if scientists can build this capability, they will also understand its principles, and thereby potentially shed light on how human cells can remember their identity for the life-time of an organism, a critical property that is broken in some biological processes. The unique innovation of this project is the engineering of a circuit motif in bacteria that mimics processes associated with long-term memory of chromatin states in mammalian cells. This design is expected to enable long-term memory of gene states in bacteria. This project will enrich the curriculum of the Biomolecular Feedback Systems Course, which is taught every year at MIT. This research will train graduate students in Mechanical, Biological, and Electrical Engineering at MIT, as well as provide undergraduate research experience to both MIT and non-MIT undergraduate students who come to the MIT campus yearly through the MIT Summer Research Program and Undergraduate Opportunity Research Program. MIT undergraduate students will further obtain a training opportunity under this project through the New Engineering Transformation Education Program. Reversible memory devices in bacteria, which can be switched between two stable states with a transient input stimulus, have been engineered before. However, after the input stimulus is removed, memory of the stable state usually vanishes after only a few days. This limits the applicability of bacterial memory devices. More broadly, there is a lack of understanding of the molecular mechanisms that control the temporal duration of memory. Here, the investigators seek to establish this understanding, engineer long-term memory devices in bacteria, and demonstrate these devices’ application to a biocontainment test-bed. To this end, the investigators propose to implement with bacterial processes the circuit motifs that are implicated in the long-term maintenance of chromatin states in mammalian cells. The investigators will use DNA inversion through invertase enzymes as the core process of the design since, just like chromatin modification, DNA inversion is an enzymatic reaction. The key innovation, which mirrors mammalian chromatin modification circuits, is to introduce autocatalysis of DNA inversions by having the inverted DNA express an invertase enzyme that catalyzes the inversion itself. The investigators propose to first demonstrate that autocatalysis of DNA inversion is required to achieve stability of the inverted DNA state. They then propose to show that two antagonistic autocatalytic DNA inversions, sharing the same substrate, create a bistable memory switch, and that the duration of memory of each of the two states hinges on the strength of autocatalysis. They finally propose to demonstrate that they can extend memory to last several weeks, that they can quickly reverse it by small molecules, and that the design can be applied for biocontainment.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

使细菌细胞能够记住长时间的环境线索对于许多过程至关重要，包括感知水或土壤中的污染物，记录人类肠道中的压力生物标志物，以及触发细胞死亡以避免在环境中逃逸。与此同时，如果科学家能够建立这种能力，他们也将了解其原理，从而有可能揭示人类细胞如何在生物体的一生中记住自己的身份，这是一个在某些生物过程中被破坏的关键特性。该项目的独特创新是在细菌中设计一个电路基序，模拟哺乳动物细胞中与染色质状态长期记忆相关的过程。这种设计有望实现细菌基因状态的长期记忆。这个项目将丰富麻省理工学院每年教授的生物分子反馈系统课程。这项研究将在麻省理工学院培养机械，生物和电气工程的研究生，并通过麻省理工学院夏季研究计划和本科生机会研究计划每年向麻省理工学院和非麻省理工学院的本科生提供本科生研究经验。麻省理工学院的本科生将通过新工程转型教育计划进一步获得该项目下的培训机会。细菌中的可逆记忆装置，可以通过瞬时输入刺激在两个稳定状态之间切换，以前已经被设计过。然而，在输入刺激被移除后，稳定状态的记忆通常在几天后消失。这限制了细菌记忆装置的适用性。更广泛地说，人们对控制记忆持续时间的分子机制缺乏了解。在这里，研究人员试图建立这种理解，在细菌中设计长期记忆装置，并展示这些装置在生物防护试验台上的应用。为此，研究人员建议用细菌过程实现与哺乳动物细胞中染色质状态的长期维持有关的电路基序。研究人员将使用通过转化酶的DNA反转作为设计的核心过程，因为就像染色质修饰一样，DNA反转是一种酶促反应。反映哺乳动物染色质修饰电路的关键创新是通过使倒置的DNA表达催化倒置本身的转化酶来引入DNA倒置的自催化。研究人员建议首先证明DNA反转的自催化是实现反转DNA状态稳定所必需的。然后，他们提出，两个拮抗性的自催化DNA倒位，共享相同的底物，创建一个记忆开关，两个状态中的每一个的记忆持续时间取决于自催化的强度。他们最终提出证明他们可以延长记忆持续数周，他们可以迅速扭转它的小分子，并设计可以应用于生物遏制。这个奖项反映了NSF的法定使命，并已被认为是值得支持的评估使用基金会的智力价值和更广泛的影响审查标准。