Emergence of switch-like behavior in a large family of simple biochemical networks

TL;DR

This study uses chemical reaction network theory to systematically analyze over 40,000 simple gene regulatory networks, revealing that bistability and switch-like behavior are common and can arise without complex cooperativity, with implications for understanding biological switches.

Contribution

It provides a comprehensive in silico survey of bistability in simple GRNs, identifying numerous previously unknown bistable topologies and demonstrating the widespread capacity for switch-like behavior.

Findings

Approximately 90% of networks can exhibit bistability with suitable parameters.

Many bistable networks lack traditional cooperative features.

Identified minimal bistable network topologies.

Abstract

Bistability plays a central role in the gene regulatory networks (GRNs) controlling many essential biological functions, including cellular differentiation and cell cycle control. However, establishing the network topologies that can exhibit bistability remains a challenge, in part due to the exceedingly large variety of GRNs that exist for even a small number of components. We begin to address this problem by employing chemical reaction network theory in a comprehensive in silico survey to determine the capacity for bistability of more than 40,000 simple networks that can be formed by two transcription factor-coding genes and their associated proteins (assuming only the most elementary biochemical processes). We find that there exist reaction rate constants leading to bistability in ~90% of these GRN models, including several circuits that do not contain any of the TF cooperativity commonly associated with bistable systems, and the majority of which could only be identified as bistable through an original subnetwork-based analysis. A topological sorting of the two-gene family of networks based on the presence or absence of biochemical reactions reveals eleven minimal bistable networks (i.e., bistable networks that do not contain within them a smaller bistable subnetwork). The large number of previously unknown bistable network topologies suggests that the capacity for switch-like behavior in GRNs arises with relative ease and is not easily lost through network evolution. To highlight the relevance of the systematic application of CRNT to bistable network identification in real biological systems, we integrated publicly available protein-protein interaction, protein-DNA interaction, and gene expression data from Saccharomyces cerevisiae, and identified several GRNs predicted to behave in a bistable fashion.