Entangled gene regulatory networks with cooperative expression endow robust adaptive responses to unforeseen environmental changes

TL;DR

This paper demonstrates that complex entangled gene regulatory networks with cooperative expression can provide robust, adaptive responses to unforeseen environmental changes, outperforming simple unidirectional networks in noise resilience and adaptability.

Contribution

The study reveals that entangled gene regulatory networks with cooperative interactions enable robust and adaptive responses to unforeseen challenges, introducing a novel design principle for cellular networks.

Findings

Entangled networks function effectively with low Hill coefficient reactions.

Network detours average out to enhance robustness against noise and mutations.

Genes exhibit similar dynamic responses regardless of inputs, aiding adaptation.

Abstract

Living organisms must respond to environmental changes. Generally, accurate and rapid responses are provided by simple, unidirectional networks that connect inputs with outputs. Besides accuracy and speed, biological responses should also be robust to environmental or intracellular noise and mutations. Furthermore, cells must also respond to unforeseen environmental changes that have not previously been experienced, to avoid extinction prior to the evolutionary rewiring of their networks, which takes numerous generations. We have investigated gene regulatory networks that mutually activate or inhibit, and have demonstrated that complex entangled networks can make appropriate input-output relationships that satisfy the robust and adaptive responses required for unforeseen challenges. Such entangled networks function for sloppy and unreliable responses with low Hill coefficient reactions for the expression of each gene. To compensate for such sloppiness, several detours in the regulatory network exist. By taking advantage of the averaging over such detours, the network shows a higher robustness to environmental and intracellular noise as well as to mutations in the network, when compared to simple unidirectional circuits. Furthermore, the appropriate response to unforeseen challenges, allowing for functional outputs, is achieved as many genes exhibit similar dynamic expression responses, irrespective of inputs, as confirmed by applying dynamic time warping and dynamic mode decomposition. As complex entangled networks are common in gene regulatory networks and global gene expression responses are observed in microbial experiments, the present results provide a novel design principle for cellular networks.