Synthetic gene networks recapitulate dynamic signal decoding and differential gene expression

Abstract

Cells live in constantly changing environments and employ dynamic signaling pathways to transduce information about the signals they encounter. However, the mechanisms by which dynamic signals are decoded into appropriate gene expression patterns remain poorly understood. Here, we devise networked optogenetic pathways that achieve novel dynamic signal processing functions that recapitulate cellular information processing. Exploiting light-responsive transcriptional regulators with differing response kinetics, we build a falling-edge pulse-detector and show that this circuit can be employed to demultiplex dynamically encoded signals. We combine this demultiplexer with dCas9-based gene networks to construct pulsatile-signal filters and decoders. Applying information theory, we show that dynamic multiplexing significantly increases the information transmission capacity from signal to gene expression state. Finally, we use dynamic multiplexing for precise multidimensional regulation of a heterologous metabolic pathway. Our results elucidate design principles of dynamic information processing and provide original synthetic systems capable of decoding complex signals for biotechnological applications.

Temperature-responsive optogenetic probes of cell signaling

“…In addition to shaping long-term activation dynamics, BcLOV4 temperature sensitivity can be leveraged to allow multiplexing of blue-light sensitive tools in single cells, allowing control of 3 or 4 distinct cell states using a single blue light channel. Our approach is complementary to a recent report wherein distinct transcriptional targets were activated using blue light with different temporal patterns 42 . Our method provides similar capability but at the post-translational level, for example for the study of how multiple signals (e.g.…”

Toward Multiplexed Optogenetic Circuits

“…Multiplexing then could take two ways: 1) the orthogonal way: using different lights to trigger the corresponding sensors, 2) a dynamic way: take advantage of receptors sensing the same wavelength but harboring different photocycle periods (e.g., one fast dark dissociated coupled to a slow one). For example, incoherent feed-forward loop has been generated by combining the positive and negative regulations in yeast ( Benzinger et al, 2021 ). This could lead to a unique type of light to sequential signal processing.…”