A spectrum of modularity in multi‐functional gene circuits

TLDR

Understanding how a circuit’s structure relates to its function is a major challenge, especially when the circuit must perform multiple distinct functions in the same organism. The authors investigate the extent to which multi‑functional circuits contain modules that correspond to their distinct functions. They computationally surveyed bi‑functional circuits lacking simple structural modularity, noting that both functions depend on all genes in the circuit. Analysis revealed two classes—hybrid circuits that overlay two mono‑functional sub‑circuits and emergent circuits that cannot be decomposed into modules—both of which are equally robust, suggesting that a bias toward modular systems may obscure real biological circuit behavior.

Abstract

Abstract A major challenge in systems biology is to understand the relationship between a circuit's structure and its function, but how is this relationship affected if the circuit must perform multiple distinct functions within the same organism? In particular, to what extent do multi‐functional circuits contain modules which reflect the different functions? Here, we computationally survey a range of bi‐functional circuits which show no simple structural modularity: They can switch between two qualitatively distinct functions, while both functions depend on all genes of the circuit. Our analysis reveals two distinct classes: hybrid circuits which overlay two simpler mono‐functional sub‐circuits within their circuitry, and emergent circuits, which do not. In this second class, the bi‐functionality emerges from more complex designs which are not fully decomposable into distinct modules and are consequently less intuitive to predict or understand. These non‐intuitive emergent circuits are just as robust as their hybrid counterparts, and we therefore suggest that the common bias toward studying modular systems may hinder our understanding of real biological circuits.