Fast decisions with biophysically constrained gene promoter architectures

TL;DR

This paper investigates how biophysical constraints shape gene promoter architectures for rapid decision-making, revealing that temporal gene activity trajectories enable faster responses and that architecture topology influences response cooperativity and speed.

Contribution

It introduces an optimization framework to analyze promoter architectures under time constraints, highlighting the role of rate-limiting steps and non-equilibrium effects in rapid gene regulation.

Findings

Temporal trajectories enable faster decision-making than integrated activity.

Low, shallow, non-cooperative responses at low TF concentrations.

High, cooperative responses at high TF concentrations.

Abstract

Cells integrate signals and make decisions about their future state in short amounts of time. A lot of theoretical effort has gone into asking how to best design gene regulatory circuits that fulfill a given function, yet little is known about the constraints that performing that function in a small amount of time imposes on circuit architectures. Using an optimization framework, we explore the properties of a class of promoter architectures that distinguish small differences in transcription factor concentrations under time constraints. We show that the full temporal trajectory of gene activity allows for faster decisions than its integrated activity represented by the total number of transcribed mRNA. The topology of promoter architectures that allow for rapidly distinguishing low transcription factor concentrations result in a low, shallow, and non cooperative response, while at high concentrations, the response is high and cooperative. In the presence of non-cognate ligands, networks with fast and accurate decision times need not be optimally selective, especially if discrimination is difficult. While optimal networks are generically out of equilibrium, the energy associated with that irreversibility is only modest, and negligible at small concentrations. Instead, our results highlight the crucial role of rate-limiting steps imposed by biophysical constraints.