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

Pavithran T Ravindran; Sarah McFann; Richard H Thornton; Jared E Toettcher

doi:10.1016/j.cels.2021.10.002

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

Cell Syst. 2022 Feb 16;13(2):131-142.e13. doi: 10.1016/j.cels.2021.10.002. Epub 2021 Nov 4.

Authors

Pavithran T Ravindran¹, Sarah McFann², Richard H Thornton³, Jared E Toettcher⁴

Affiliations

¹ Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.
² Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
³ Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
⁴ Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA. Electronic address: toettcher@princeton.edu.

Abstract

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.

Keywords: cell signaling; network motifs; signaling dynamics; synthetic biology.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Gene Expression Regulation
Gene Regulatory Networks* / genetics
Genes, Synthetic*
MAP Kinase Signaling System
Signal Transduction / genetics

Abstract

Publication types

MeSH terms

Grants and funding