title: Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals.
abstract: 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' method for programming tailor-made gene expression signals in live bacterial cells. We designed precomputed light sequences based on experimentally calibrated mathematical models of light-switchable two-component systems and used them to drive intracellular protein levels to match user-defined reference time courses. We used this approach to generate 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 dynamical analyses of synthetic and natural gene circuits, providing an essential step toward the predictive design and rigorous understanding of biological systems.
authors.affiliation: Graduate Program in Applied Physics, Rice University, Houston, Texas, USA.
authors.forename: Evan J
authors.initials: EJ
authors.lastname: Olson
authors.affiliation: Department of Bioengineering, Rice University, Houston, Texas, USA.
authors.forename: Lucas A
authors.initials: LA
authors.lastname: Hartsough
authors.affiliation: Department of Bioengineering, Rice University, Houston, Texas, USA.
authors.forename: Brian P
authors.initials: BP
authors.lastname: Landry
authors.affiliation: Department of Bioengineering, Rice University, Houston, Texas, USA.
authors.forename: Raghav
authors.initials: R
authors.lastname: Shroff
authors.affiliation: 1] Department of Bioengineering, Rice University, Houston, Texas, USA. [2] Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, USA.
authors.forename: Jeffrey J
authors.initials: JJ
authors.lastname: Tabor
mesh_terms: D004926:Escherichia coli / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology*; D053263:Gene Regulatory Networks; D017930:Genes, Reporter; D008164:Luminescent Proteins / Q000235:genetics / Q000378:metabolism; D008954:Models, Biological
chemical_list: D008164:Luminescent Proteins