An all-optical biological function generator and oscilloscope framework for characterizing gene circuit dynamics
Olson, Evan James
Tabor, Jeffrey J.
Master of Science
Gene circuits are dynamical systems that regulate cellular behaviors, often using protein signals as inputs and outputs. Here we have developed an optogenetic ‘function generator’ for programming tailor-made gene expression signals in live E. coli. We designed light sequences with experimentally calibrated models of light-switchable two-component systems and used them to drive intracellular protein levels to match user-defined reference time-courses. This approach enabled generation of accelerated and linearized dynamics, sinusoidal oscillations with desired amplitudes and periods, and a complex waveform, all with unprecedented accuracy and precision. We also combined the function generator with a dual fluorescent protein reporter system, analogous to a dual-channel oscilloscope, to reveal that a synthetic repressible promoter linearly transforms repressor signals with an approximate 7-min delay. Our approach will enable a new generation of dynamic analyses of synthetic and natural gene circuits, providing an essential step toward the predictive design and rigorous understanding of biological systems.
Optogenetics; Synthetic biology; Bioengineering