CAREER: Uncovering Quantitative Design Principles of RNA Regulators For Synthetic Biology

职业：揭示合成生物学 RNA 调节剂的定量设计原理

• 批准号: 1452441
• 负责人: Julius Lucks
• 金额: $ 75万
• 依托单位: Cornell University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-02-01 至 2016-10-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1452441&HistoricalAwards=false
• 关键词: CAREER; Uncovering; Quantitative; Design; Principles

Nontechnical Description: Cells have an amazing ability to process information, make decisions, and change their state in response to changing environments. This ability is encoded within the cellular DNA genome, which is converted into RNA and protein molecules through the basic processes of gene expression. Among the many functions these RNAs and proteins perform is regulating their own expression. In fact RNAs are now known to regulate almost all aspects of gene expression, and play central roles in controlling some of life's most basic processes. A key question in biotechnology and synthetic biology is then: How can RNA molecules be designed to control the expression of target genes inside cells to facilitate applications ranging from using cells as chemical factories all the way to using them as environmental sensors? As with many biomolecules, RNA function is intimately related to its structure. In this work, the investigator builds off of his development of a new small synthetic RNA mechanism called Small Transcription Activating RNAs, or STARs. STARs are hypothesized to allow the construction of unique gene expression control techniques since they represent a brand new function for sRNAs. This project seeks to use STARs as a test-bed for uncovering the principles for engineering RNA molecules to precisely control gene expression inside cells. This work will help realize the potential of RNA as a powerful substrate for cellular engineering. It will also shed new light on our scientific understanding of the fundamental sequence/structure/function relationship that underlies RNA's central role in natural biological systems. The projected studies and research training activities are thus expected to have a broad impact on society, ranging from the science of cellular gene regulation and the engineering science of RNA gene regulation that can directly connect to a broad array of biotechnological applications. This project will also cultivate the next generation of highly trained graduate students and teachers of synthetic biology who will be introduced to the broad, interdisciplinary nature of biotechnology research. Moreover, this program will actively engage the broader community to help create an informed public that is equipped to make important decisions about the future of synthetic biology.Technical Description: The overall goal of this project is to build an integrated research and education program focused on uncovering quantitative design principles that link small RNA sequence, structure, and function, and to use these principles to design synthetic RNAs that can precisely regulate gene expression. The education plan focuses on integrating research into the training of the next generation of synthetic biology students and teachers, and informing and exciting the broader public about synthetic biology.Trans-acting bacterial small RNAs (sRNA) exert regulation via direct RNA-RNA interactions with target messenger RNAs (mRNAs) that cause structural changes in the target. These changes in turn regulate many aspects of gene expression including transcription, translation and mRNA degradation. The central hypotheses of this project are that: 1) quantitative sRNA structure/function design principles can be discovered and used to rationally optimize and expand the functionality of RNA regulators, and 2) circuit-level design rules can be discovered and used to engineer new synthetic RNA genetic modules that control the timing and pattern of gene expression. The central goal of this CAREER project is to use Small Transcription Activating RNAs (STARs) as a test-bed for uncovering the quantitative design principles of RNA regulators for synthetic biology. This will be pursued using a multi-faceted approach that includes using cutting-edge RNA structure measurement technologies to elucidate the molecular level design principles of STARs. Once molecular-level principles are learned, the project will focus on using these techniques to learn the design rules for integrating STARs into decision making regulatory networks. In addition, new experiments and computational tools that can quantitatively model the kinetics of gene expression mediated by STARs will be used to understand how different aspects of STAR function propagate through RNA networks. Successful completion of these studies will forward the broader goal of creating a quantitative discipline of biological design that can be used to program cellular systems to solve important problems in sustainable energy, and biomanufacturing. In addition, the work may provide insight to mechanisms of native small RNA regulation of naturally occurring biological systems.Educational activities include developing a long term plan for the continuation of the Cold Spring Harbor Synthetic Biology summer course as a training center for a broad range of students and teachers across the globe; developing quantitative curricular materials for training future generations of synthetic biologists; and performing hands-on activities aimed towards families with school-age children to excite and inform them about synthetic biology.

非技术描述：细胞具有处理信息、做出决策以及根据不断变化的环境改变其状态的惊人能力。这种能力被编码在细胞 DNA 基因组中，通过基因表达的基本过程转化为 RNA 和蛋白质分子。这些 RNA 和蛋白质执行的众多功能之一是调节它们自身的表达。事实上，现在人们知道RNA可以调节基因表达的几乎所有方面，并在控制生命的一些最基本过程中发挥核心作用。那么生物技术和合成生物学的一个关键问题是：如何设计RNA分子来控制细胞内靶基因的表达，以促进从将细胞用作化工厂一直到将它们用作环境传感器的应用？与许多生物分子一样，RNA 功能与其结构密切相关。在这项工作中，研究人员以他开发的一种新的小合成 RNA 机制为基础，称为小转录激活 RNA（STAR）。 STAR 被假设允许构建独特的基因表达控制技术，因为它们代表了 sRNA 的全新功能。该项目旨在利用 STAR 作为试验台，揭示工程 RNA 分子以精确控制细胞内基因表达的原理。这项工作将有助于实现 RNA 作为细胞工程强大底物的潜力。它还将为我们对 RNA 在自然生物系统中核心作用的基本序列/结构/功能关系的科学理解提供新的线索。因此，预计的研究和研究培训活动预计将对社会产生广泛的影响，范围从细胞基因调控科学到可直接与广泛的生物技术应用相关的 RNA 基因调控工程科学。该项目还将培养下一代训练有素的合成生物学研究生和教师，他们将了解生物技术研究的广泛、跨学科性质。此外，该计划将积极吸引更广泛的社区参与，帮助创建一个知情公众，有能力就合成生物学的未来做出重要决策。 技术描述：该项目的总体目标是建立一个综合研究和教育计划，重点关注揭示连接小RNA序列、结构和功能的定量设计原理，并利用这些原理设计能够精确调节基因表达的合成RNA。该教育计划的重点是将研究整合到下一代合成生物学学生和教师的培训中，并向更广泛的公众宣传合成生物学并激发他们的兴趣。反式作用细菌小 RNA (sRNA) 通过直接 RNA-RNA 相互作用发挥调节作用。引起靶标结构变化的靶标信使 RNA (mRNA)。这些变化反过来调节基因表达的许多方面，包括转录、翻译和 mRNA 降解。该项目的中心假设是：1）可以发现定量的sRNA结构/功能设计原​​理并用于合理优化和扩展RNA调节器的功能，2）可以发现并用于设计新的电路级设计规则控制基因表达的时间和模式的合成RNA遗传模块。该 CAREER 项目的中心目标是使用小转录激活 RNA (STAR) 作为试验台，揭示合成生物学 RNA 调节因子的定量设计原理。这将通过多方面的方法来实现，包括使用尖端的 RNA 结构测量技术来阐明 STAR 的分子水平设计原理。一旦了解了分子水平的原理，该项目将专注于使用这些技术来学习将 STAR 集成到决策监管网络中的设计规则。此外，可以定量模拟 STAR 介导的基因表达动力学的新实验和计算工具将用于了解 STAR 功能的不同方面如何通过 RNA 网络传播。这些研究的成功完成将推动创建生物设计定量学科的更广泛目标，该学科可用于对细胞系统进行编程，以解决可持续能源和生物制造中的重要问题。 此外，这项工作还可以深入了解天然存在的生物系统的天然小RNA调节机制。教育活动包括制定一项长期计划，以继续冷泉港合成生物学夏季课程作为广泛的培训中心全球各地的学生和教师；开发定量课程材料以培训下一代合成生物学家；针对有学龄儿童的家庭开展实践活动，激发他们的兴趣并让他们了解合成生物学。