A synthetic gene circuit for imaging-free detection of signaling pulses

Cells employ intracellular signaling pathways to sense and respond to changes in their external environment. In recent years, live-cell biosensors have revealed complex pulsatile dynamics in many pathways, but studies of these signaling dynamics are limited by the necessity of live-cell imaging at high spatiotemporal resolution. Here, we describe an approach to infer pulsatile signaling dynamics from a single measurement in fixed cells using a pulse-detecting gene circuit. We computationally screened for circuits with the capability to selectively detect signaling pulses, revealing an incoherent feedforward topology that robustly performs this computation. We implemented the motif experimentally for the Erk signaling pathway using a single engineered transcription factor and fluorescent protein reporter. Our “recorder of Erk activity dynamics” (READer) responds sensitively to spontaneous and stimulus-driven Erk pulses. READer circuits open the door to permanently labeling transient, dynamic cell populations to elucidate the mechanistic underpinnings and biological consequences of signaling dynamics. [Display omitted] •A computational screen identifies an incoherent feedforward motif for pulse detection•A two-gene synthetic “READer” circuit implements pulse detection for the Erk pathway•READer acts as a bandpass filter for spontaneous and externally supplied Erk pulses•The READer circuit provides distinct dynamic information from the Erk target gene Fos Signaling pathways often exhibit discrete pulses of activity whose sources and functions remain poorly understood. Ravindran et al. discovered a network motif that selectively responds to signaling pulses, rather than constant high or low signaling states. They implemented this motif in a synthetic gene circuit for the Erk signaling pathway and characterized pulse detection in response to spontaneous and externally applied dynamics.