Unifying synthetic small regulatory RNAs

统一合成小调控RNA

• 批准号: 2001743
• 负责人: Tae Seok Moon
• 金额: $ 66.45万
• 依托单位: Washington University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-06-01 至 2025-05-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2001743&HistoricalAwards=false
• 关键词: Unifying; synthetic; small; regulatory; RNAs

RNA is generally known as a messenger to carry genetic instructions from DNA, however, many small RNAs act as regulators controlling gene expression. Over the past two decades, researchers have engineered such regulatory RNAs and have built simple RNA-based genetic circuits in bacteria, nevertheless, the construction of complex RNA-based genetic circuits remains challenging. This project involves developing generalizable design principles by which simple RNA-based genetic circuits can be combined to generate complex genetic circuits. The utility of these complex circuits is demonstrated by engineering bacteria that produce valuable chemicals that contribute to the bioeconomy. In addition, this project provides unique interdisciplinary training opportunities for students, involving biophysics, biochemistry, molecular biology and engineering. An outreach program provides K-12 teachers with the materials to lead their students through lab activities, broadening student participation in science and engineering.The past two decades have witnessed remarkable progress in understanding complex gene regulatory networks by building simpler genetic circuits from the bottom-up. However, RNA-based genetic circuits have seldom been built by integrating different types of RNA regulators that control multiple steps of gene expression (e.g., both transcription and translation). Consequently, RNA-based circuit complexity is limited. In this project, the investigators first build RNA-based gene expression controllers (GECs) that demonstrate consistently predictable behaviors regardless of connected genetic parts. Mathematical modeling is combined with experimental characterization in order to systematically connect different sensors to RNA regulators. Next, insights into the circuit integration rule are obtained first by quantitatively characterizing both integrated genetic programs and individual GECs then by comparing their behaviors before and after integration. Finally, based on the gathered design rules, dynamic pathway controllers are created to autonomously modulate metabolic pathways, demonstrating enhanced biochemical production. This interdisciplinary project provides the research community with a unified, standardized RNA regulator toolbox for fundamental research and biotechnological applications.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.

RNA通常被认为是携带DNA遗传指令的信使，然而，许多小RNA充当控制基因表达的调节器。在过去的二十年里，研究人员已经设计出了这样的调控rna，并在细菌中建立了简单的基于rna的遗传电路，然而，基于rna的复杂遗传电路的构建仍然具有挑战性。该项目涉及开发可通用的设计原则，通过这些原则，简单的基于rna的遗传电路可以组合成复杂的遗传电路。这些复杂电路的效用是通过工程细菌来证明的，这些细菌可以产生对生物经济有贡献的有价值的化学物质。此外，该项目还为学生提供了独特的跨学科培训机会，涉及生物物理学、生物化学、分子生物学和工程学。一项拓展计划为K-12教师提供指导学生进行实验活动的材料，扩大学生对科学和工程的参与。在过去的二十年里，通过自下而上构建更简单的基因回路，在理解复杂的基因调控网络方面取得了显著进展。然而，基于RNA的遗传电路很少通过整合不同类型的RNA调节因子来控制基因表达的多个步骤（例如，转录和翻译）。因此，基于rna的电路复杂性是有限的。在这个项目中，研究人员首先构建了基于rna的基因表达控制器（GECs），无论连接的遗传部分如何，它都能表现出一致的可预测行为。数学建模与实验表征相结合，以便系统地将不同的传感器连接到RNA调节因子。接下来，首先通过定量表征集成遗传程序和单个gec，然后通过比较它们在集成前后的行为，获得对电路集成规则的见解。最后，基于收集到的设计规则，创建动态路径控制器来自主调节代谢路径，展示增强的生化生产。这个跨学科项目为基础研究和生物技术应用提供了一个统一的、标准化的RNA调控工具箱。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。

项目成果

Making Security Viral: Shifting Engineering Biology Culture and Publishing

让安全病毒式传播：改变工程生物学文化和出版

• DOI: 10.1021/acssynbio.1c00324
• 发表时间: 2022
• 期刊: ACS Synthetic Biology
• 影响因子: 4.7
• 作者: Mackelprang, Rebecca;Adamala, Katarzyna P.;Aurand, Emily R.;Diggans, James C.;Ellington, Andrew D.;Evans, Samuel Weiss;Fortman, J. L.;Hillson, Nathan J.;Hinman, Albert W.;Isaacs, Farren J.
• 通讯作者: Isaacs, Farren J.

Duplex Structure of Double-Stranded RNA Provides Stability against Hydrolysis Relative to Single-Stranded RNA

• DOI: 10.1021/acs.est.1c01255
• 发表时间: 2021-05-25
• 期刊: ENVIRONMENTAL SCIENCE & TECHNOLOGY
• 影响因子: 11.4
• 作者: Zhang，Ke;Hodge，Joseph;Parker，Kimberly M.
• 通讯作者: Parker，Kimberly M.

Engineering the Future through Synthetic Biology

通过合成生物学设计未来

• DOI: 10.1007/s12257-022-0191-9
• 发表时间: 2023
• 期刊: Biotechnology and Bioprocess Engineering
• 影响因子: 3.2
• 作者: Moon, Tae Seok

Model-based design of synthetic antisense RNA for predictable gene repression

基于模型的合成反义 RNA 设计，用于可预测的基因抑制

• 发表时间: 2022
• 期刊: Methods in molecular biology
• 作者: Moon, Tae Seok