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

基于细胞的生物生产(在工程细胞或合成细胞内)的进展有望以可持续的方式解决燃料、食品、化妆品和药品的生产等全球性挑战。然而，扩大细胞生物产量受到这可能给宿主细胞造成的负担的限制。这项研究将开发可调的、低负担的RNA分子，以控制有用分子的基因表达。实验将得到计算模型的支持，以了解细胞负荷的动力学并优化生物生产性能。该项目是加州大学洛杉矶分校(美国)和伦敦帝国理工学院(英国)的研究人员合作的，将为几名研究生和本科生提供培训和指导。结果和方法将通过出版物、档案文件和数据储存库与科学界分享；首席调查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。这项研究将被整合到研究生课程和冷泉港实验室合成生物学夏季课程中。佛朗哥博士将在加利福尼亚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外展演讲。合成生物学已经使改变细胞的用途成为可能，使其成为微型工厂、能源甚至计算机。然而，引入可调性差且非宿主固有的途径往往会导致不希望看到的交叉相互作用和不可预测的反应，而可靠的细胞工程仍然是一个挑战。特别是，外源途径的引入耗尽了宿主的细胞资源，引发了生理变化、生长缓慢和电路性能差，这一系列现象统称为细胞负荷。这项研究将通过开发基于合成RNA的调节器来解决与稳健电路工程和负担减轻相关的挑战，合成RNA调节器是一个对主机施加低负担的可编程平台。该项目将集中于系统地筛选和调整两类RNA调节剂的反应函数，然后将用于表征细胞负荷反应的动力学，其起始和恢复速度尚未阐明。对负荷动力学的改进将能够产生健壮的基于RNA的反馈环来管理在大肠杆菌中甲伐他酸的生物生产。在每个阶段，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。这一美英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委员会的支持。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。

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.