A photoconversion model for full spectral programming and multiplexing of optogenetic systems

Abstract

Optogenetics combines externally applied light signals and genetically engineered photoreceptors to control cellular processes with unmatched precision. Here, we develop a mathematical model of wavelength‐ and intensity‐dependent photoconversion, signaling, and output gene expression for our two previously engineered light‐sensing Escherichia coli two‐component systems. To parameterize the model, we develop a simple set of spectral and dynamical calibration experiments using our recent open‐source “Light Plate Apparatus” device. In principle, the parameterized model should predict the gene expression response to any time‐varying signal from any mixture of light sources with known spectra. We validate this capability experimentally using a suite of challenging light sources and signals very different from those used during the parameterization process. Furthermore, we use the model to compensate for significant spectral cross‐reactivity inherent to the two sensors in order to develop a new method for programming two simultaneous and independent gene expression signals within the same cell. Our optogenetic multiplexing method will enable powerful new interrogations of how metabolic, signaling, and decision‐making pathways integrate multiple input signals. image A predictive model of the time, wavelength, and intensity dependence of optogenetic tool output is developed. It allows compensating for spectral cross‐talk between two bacterial optogenetic tools and programs two simultaneous, independent gene expression signals in the same cell. An in vitro photoconversion model is extended to describe the in vivo signaling of optogenetic systems. The model is parameterized using high‐resolution spectral and dynamic characterization of engineered Cca SR and Cph8‐OmpR optogenetic systems. The model accurately predicts the gene expression response to spectrally and temporally challenging light input signals, including mixtures of two light sources. Multichannel light signals are computationally designed in order to program two simultaneous and independent gene expression signals in the same cell.