Engineering autoregulation of the epitranscriptome to track and control stress responses

生物系统的环境应激源是高度复杂的。有人推测，环境应激源可以导致生物细胞的RNA修饰。对这种修饰的研究被称为表位转录组学。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，正在使用表位转录组学来研究如何利用化学诱导的生物细胞内RNA分子的变化来记录环境压力。这项研究利用了计算工具、生化特征、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、记录和对其环境做出反应的总体理解，并对理解如何设计早期预警系统进行病毒检测等方面具有重要意义。该项目通过德克萨斯大学奥斯汀分校的“培养未来科学家”计划，为来自低收入、代表性不足社区的学生提供研究机会。重点是促进本科生的参与，作为鼓励他们对科学和工程研究生课程感兴趣的一种方式。该项目还促进了公立学校合成生物学课程的发展。这项提议使用表位转录组作为一种机制来感知、记录和回应环境的复杂性。我们的目标是在新型模块化设备中利用RNA修饰，这种设备将称为“RNA传感器”的感觉RNA基序与激活的蛋白质结构域或“蛋白质执行器”相结合，以实现对细胞反应的工程化调节。这项研究结合了包括计算工具、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活体下一代测序的工具的综合系统方法来完成三个目标：(I)建立表位转录组作为细菌中的感觉模块，(Ii)合理地重新设计8-OG识别蛋白作为执行模块，以及(Iii)将表位转录组的感知和激活与CRISPR系统耦合，以实现信号、记忆和应激反应控制能力。这项研究的结果广泛适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。该提案由分子和细胞生物科学部的系统和合成生物学项目以及化学生物工程环境和运输系统部门的细胞和生化工程项目联合资助。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势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.