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

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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.