Understanding and stimulating cellular resource transactions for robust cell growth and genetic circuit performance

Thesis: S.M., Massachusetts Institute of Technology, Department of Mechanical Engineering, 2018.Cataloged from PDF version of thesis.Includes bibliographical references (pages 133-138).A premier challenge facing synthetic biology is achieving robust performance of synthetic circuits as they share transcription and translational resource amongst each other and the host-cell. It is important to model the full physics of cellular-resource sharing when designing genetic circuits to ensure robustness. Current models used in synthetic and systems biology lack the ability to account for the nontrivial spatial distribution of resources and genes that has been experimentally observed. The first part of this thesis introduces a model consisting of a set of partial differential equitations (PDE's) that captures the experimentally observed spatial information in the cell and it is framed in a resource sharing context. A comparison of gene expression, circuit-circuit and circuit-host-cell interactions between the proposed model and the commonly used well-mixed ordinary differential equations (ODE's) model is provided. An efficient numerical method to solve the PDE's is given and regimes where the set of PDE's can be simplified to ODE's by simply adjusting the effective ribosome binding strength (RBS) of each genetic circuit is discussed. It is envisioned that a centralized controller which regulates resource production can be implemented to ensure robust circuit performance. The second half of this thesis introduces an actuator which can be used to regulate resource production in the centralized controller. By tapping into the endogenous circuitry of the cell responsible for adjusting resource levels in the cell based on environmental conditions, we provide a proof-of-concept for this actuator. Theoretical and experimental results are provided to characterize the actuator performance. The actuator is then applied in an engineering context to rescue the cellular growth rate defects arising from overexpression of an exogenous protein. Finally, the actuator is also shown to minimize the coupling that arises between synthetic circuits due to resource sharing."This work is supported by National Science Foundation (NSF) Graduate Research Fellowships Program (GRFP), the Ford Foundation Fellowship, and Health (NIH) grant P50 GM098792"--Page 5.by Carlos Barajas.S.M