Real-Time Genetic Compensation Defines the Dynamic Demands of Feedback Control

Biological signaling networks use feedback control to dynamically adjust their operation in real time. Traditional static genetic methods such as gene knockouts or rescue experiments can often identify the existence of feedback interactions but are unable to determine what feedback dynamics are required. Here, we implement a new strategy, closed-loop optogenetic compensation (CLOC), to address this problem. Using a custom-built hardware and software infrastructure, CLOC monitors, in real time, the output of a pathway deleted for a feedback regulator. A minimal model uses these measurements to calculate and deliver—on the fly—an optogenetically enabled transcriptional input designed to compensate for the effects of the feedback deletion. Application of CLOC to the yeast pheromone response pathway revealed surprisingly distinct dynamic requirements for three well-studied feedback regulators. CLOC, a marriage of control theory and traditional genetics, presents a broadly applicable methodology for defining the dynamic function of biological feedback regulators. [Display omitted] •Classical genetic complementation tests do not reveal temporal requirements•Closed-loop optogenetic compensation (CLOC) defines such dynamic demands•CLOC dynamically complements a knockout mutant using real-time in silico feedback•Application to the yeast mating pathway illuminates transcriptional feedback control An optogenetics-based method is developed to explore the temporal requirements for a gene product to produce a dynamic phenotype.