BBSRC-NSF/BIO: Characterizing efficiency and limitations of RNA regulators to achieve robust dynamic behaviors

BBSRC-NSF/BIO：表征 RNA 调节器的效率和局限性以实现稳健的动态行为

• 批准号: 2020039
• 负责人: Elisa Franco
• 金额: $ 72万
• 依托单位: University of California-Los Angeles
• 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: 2020-07-01 至 2024-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2020039&HistoricalAwards=false
• 关键词: BBSRC; NSF; BIO; Characterizing; efficiency

Advances in cell-based bioproduction (within engineered or synthetic cells) promises to solve global challenges such as production of fuel, food, cosmetics, and drugs in a sustainable manner. Scaling-up cellular bioproduction is however limited by the burdens this can cause to the host cell. This research will develop tunable, low-burden RNA molecules for control of gene expression of useful molecules. Experiments will be supported by computational models, to understand the dynamics of cellular burden and to optimize bioproduction performance. This project, which is a collaboration between researchers at the University of California-Los Angeles (US) and Imperial College London (UK), will provide training and mentorship to several graduate and undergraduate students. Results and methods will be shared with the scientific community via publications, archival documents, and data repositories; the Principal Investigators will also share their work within the World Economic Forum Expert Network and the Engineering Biology Research Consortium. This research will be integrated both in graduate courses and in the Cold Spring Harbor Laboratory Synthetic Biology summer course. Dr. Franco will deliver outreach talks at underserved schools in California’s Inland Empire as well as at international conferences supported by the IEEE Controls Systems Society. Synthetic biology has made it possible to repurpose cells to operate as microscale factories, energy sources, and even computers. However, the introduction of pathways that are poorly tunable and non-native to the host often causes undesired cross-interactions and unpredictable responses, and reliable engineering of cells remains a challenge. In particular, the introduction of exogenous pathways depletes cellular resources of the host, triggering physiological changes, lower growth, and poor circuit performance, a set of phenomena collectively known as cellular burden. This research will address the challenges related to robust circuit engineering and burden mitigation by developing synthetic RNA-based regulators, a programmable platform that imposes a low burden on the host. The project will focus on systematic screening and tuning of the response function of two classes of RNA regulators, which will then be used to characterize the kinetics of the cellular burden response, whose onset and recovery speed have not been elucidated. An improved knowledge of burden kinetics will enable the generation of robust RNA-based feedback loops to manage bioproduction of mevalonic-acid in E. coli. At every stage, experiments will be supported and guided by mathematical modeling and feedback control design principles.This collaborative US/UK project is supported by the US National Science Foundation and the UK Biotechnology and Biological Sciences Research Council.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.

基于细胞的生物生产（在工程或合成细胞内）的进展有望以可持续的方式解决燃料，食品，化妆品和药物生产等全球挑战。然而，扩大细胞生物生产受到这可能对宿主细胞造成的负担的限制。这项研究将开发可调的低负荷RNA分子，用于控制有用分子的基因表达。实验将由计算模型支持，以了解细胞负荷的动态并优化生物生产性能。该项目是加州大学洛杉矶分校（美国）和帝国理工学院伦敦（英国）的研究人员之间的合作，将为几名研究生和本科生提供培训和指导。研究结果和方法将通过出版物、档案文件和数据库与科学界分享;主要研究人员还将在世界经济论坛专家网络和工程生物学研究联盟内分享他们的工作。这项研究将被整合在研究生课程和冷泉港实验室合成生物学夏季课程。Franco博士将在加州内陆帝国服务不足的学校以及IEEE控制系统协会支持的国际会议上发表推广演讲。合成生物学已经使细胞的重新用途成为可能，可以作为微型工厂，能源甚至计算机。然而，引入对宿主来说可调性差且非天然的途径通常会导致不期望的交叉相互作用和不可预测的反应，并且细胞的可靠工程化仍然是一个挑战。特别是，外源性途径的引入会耗尽宿主的细胞资源，引发生理变化、生长减慢和电路性能差，这一系列现象统称为细胞负担。这项研究将通过开发基于RNA的合成调节器来解决与强大的电路工程和减轻负担相关的挑战，这是一种可编程的平台，对宿主造成低负担。该项目将侧重于系统筛选和调整两类RNA调节剂的响应功能，然后将其用于表征细胞负荷响应的动力学，其起始和恢复速度尚未阐明。对负荷动力学知识的改进将使基于RNA的反馈回路的产生能够管理E.杆菌在每一个阶段，实验都将得到数学建模和反馈控制设计原则的支持和指导。这个美国/英国合作项目得到了美国国家科学基金会和英国生物技术和生物科学研究理事会的支持。这个奖项反映了NSF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

Bistable State Switch Enables Ultrasensitive Feedback Control in Heterogeneous Microbial Populations

双稳态开关可实现异质微生物群体中的超灵敏反馈控制

• 发表时间: 2021
• 期刊: Proceedings of the American Control Conference
• 作者: Ren, X;Cuba Samaniego, C.;Murray, R.M.;Franco, E.
• 通讯作者: Franco, E.

Signaling-based neural networks for cellular computation

用于细胞计算的基于信号的神经网络

• DOI: 10.23919/acc50511.2021.9482800
• 发表时间: 2021
• 期刊: 2021 American Control Conference (ACC
• 作者: Samaniego, Christian Cuba;Moorman, Andrew;Giordano, Giulia;Franco, Elisa
• 通讯作者: Franco, Elisa

Ultrasensitive molecular controllers for quasi-integral feedback

• DOI: 10.1016/j.cels.2021.01.001
• 发表时间: 2021-03-17
• 期刊: CELL SYSTEMS
• 影响因子: 9.3
• 作者: Samaniego, Christian Cuba;Franco, Elisa
• 通讯作者: Franco, Elisa

RNA Compensation: A Positive Feedback Insulation Strategy for RNA-Based Transcription Networks

• DOI: 10.1021/acssynbio.1c00540
• 发表时间: 2022-03-18
• 期刊: ACS SYNTHETIC BIOLOGY
• 影响因子: 4.7
• 作者: Liu, Baiyang;Samaniego, Christian Cuba;Franco, Elisa
• 通讯作者: Franco, Elisa