A two-state photoconversion model predicts the spectral response dynamics of optogenetic systems

In optogenetics, light signals are used to control genetically engineered photoreceptors, and in turn manipulate biological pathways with unmatched precision. Recently, evolved photoreceptors with diverse in vitro-measured wavelength and intensity-dependent photoswitching properties have been repurposed for synthetic control of gene expression, proteolysis, and numerous other cellular processes. However, the relationship between the input light spectrum and in vivo photoreceptor response dynamics is poorly understood, restricting the utility of these optogenetic tools. Here, we advance a classic in vitro two-state photoreceptor model to reflect the in vivo environment, and combine it with simplified mathematical descriptions of signal transduction and output gene expression through our previously engineered green/red and red/far red photoreversible bacterial two-component systems (TCSs). Additionally, we leverage our recent open-source optical instrument to develop a workflow of spectral and dynamical characterization experiments to parameterize the model for both TCSs. To validate our approach, we challenge the model to predict experimental responses to a series of complex light signals very different from those used during parameterization. We find that the model generalizes remarkably well, predicting the results of all categories of experiments with high quantitative accuracy for both systems. Finally, we exploit this predictive power to program two simultaneous and independent dynamical gene expression signals in bacteria expressing both TCSs. This multiplexed gene expression programming approach will enable entirely new studies of how metabolic, signaling, and decision-making pathways integrate multiple gene expression signals. Additionally, our approach should be compatible with a wide range of optogenetic tools and model organisms.\n\nSignificance statementLight-switchable signaling pathways (optogenetic tools) enable precision studies of how biochemical networks underlie cellular behaviors. We have developed a versatile mathematical model based on a two-state photoconversion mechanism that we have applied to the E. coli CcaSR and Cph8-OmpR optogenetic tools. This model enables accurate prediction of the gene expression response to virtually any light source or mixture of light sources. We express both optogenetic tools in the same cell and apply our model to program two simultaneous and independent gene expression signals in the same cell. This method can be used to study how biological pathways integrate multiple inputs and should be extensible to other optogenetic tools and host organisms.