Engineering autoregulation of the epitranscriptome to track and control stress responses

生物系统的环境压力源是高度复杂的。据推测，环境压力因素可导致生物细胞中的RNA修饰。这种修饰的研究被称为表观转录组学。在这个项目中，一个跨学科的研究团队，包括研究生和本科生，正在使用表观转录组学来研究生物细胞内RNA分子的化学诱导变化如何被用来记录环境压力。该研究利用了计算工具、生化表征、传统遗传学方法以及下一代测序工具。这些研究有助于对细胞如何感知、记录和对环境作出反应的一般理解，并且对于理解如何设计诸如病毒检测的早期预警系统非常重要。该项目通过德克萨斯大学奥斯汀分校的“培养未来科学家”项目，为来自低收入群体的学生提供研究机会。重点是促进本科生的参与，以鼓励他们对科学和工程研究生课程的兴趣。该项目还促进了公立学校合成生物学课程的发展。该建议使用表转录组作为感知、记录和响应环境复杂性的机制。目标是在新型模块化设备中利用RNA修饰，将称为“RNA传感器”的感觉RNA基元与激活蛋白质结构域或“蛋白质致动器”相结合，以实现细胞反应的工程调节。该研究结合了集成系统方法，包括计算工具，分子rna -蛋白质生化表征策略，传统遗传学方法和新颖的基于体内下一代测序的工具，以实现三个目标：(i)将表转录组建立为细菌中的传感模块，（ii）合理地重新设计8-OG识别蛋白作为驱动模块，以及（iii）将表转录组的传感和驱动与crispr系统结合起来，以实现信号传导、记忆和应激反应控制能力。该研究结果可广泛应用于合成生物学领域，并可用于了解特定的环境暴露，以进行风险评估和干预。本提案由分子与细胞生物科学系的系统与合成生物学项目和化学生物工程、环境与运输系统系的细胞与生化工程项目共同资助。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Environmental stressors of biological systems are highly complex. It has been postulated that environmental stressors can result in RNA modifications in biological cells. The study of such modifications is known as epitranscriptomics. In this project, an interdisciplinary team of researchers, including graduate students and undergraduate students, are using epitranscriptomics to study how chemically induced changes in RNA molecules within biological cells could be used to record environmental stresses. The study makes use of computational tools, biochemical characterization, traditional genetics methods as well as tools in Next Generation Sequencing. These studies contribute to the general understanding of how cells sense, record and respond to their environments and are important for understanding how to design early warning systems for virus detection for example. The project provides research opportunities to students from low-income underrepresented communities through the “Raising Future Scientists” program at the University of Texas at Austin. Emphasis is given on promoting participation of undergraduate students as a way to encourage their interest in graduate programs in science and engineering. The project also contributes to the advancement of the public-school synthetic biology curriculum.This proposal uses the epitranscriptome as a mechanism to sense, record, and respond to the complexities of the environment. The goal is to utilize RNA modifications in new classes of modular devices that combine sensory RNA motifs, called “RNA Sensors,” with activating protein domains, or “Protein Actuators”, to enable engineered regulation of cellular responses. The research combines integrated systems approaches involving computational tools, molecular RNA-protein biochemical characterization strategies, traditional genetics methods, and novel, in vivo Next Generation Sequencing-based tools to accomplish three objectives: (i) establish the epitranscriptome as a sensory module in bacteria, (ii) rationally re-engineer 8-OG recognition proteins as actuating modules, and (iii) couple sensing and actuation of the epitranscriptome with CRISPR-systems for signaling, memory, and stress response control capabilities. Results from this research are broadly applicable in the field of synthetic biology and could be used for understanding specific environmental exposures for risk assessment and interventions.This proposal is jointly funded by the Systems and Synthetic Biology program in the Division of Molecular and Cellular Biosciences and the Cellular and Biochemical Engineering program in the Division of Chemical Bioengineering Environmental and Transport Systems.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.