Circadian clock genes perform dual roles as systemic oscillators and context-dependent regulators

The plant circadian clock aligns developmental processes with environmental cycles, a function traditionally attributed to a unified, systemic oscillator. However, this view is challenged by observations that mutations in specific clock genes can cause major developmental phenotypes without a proportional disruption to systemic rhythms. This Hypothesis proposes that clock genes perform dual roles: they act not only as components of the systemic oscillator that generates rhythmicity, but also as specific, context-dependent regulators that control the timing of key developmental events. We argue that this gene-centric perspective extends and refines the classical oscillator model, positing that the pleiotropic nature of clock genes reflects their evolutionary history, whereby transcription factors with pre-existing developmental roles were co-opted for timekeeping. Understanding this functional duality - how individual clock components are deployed in specific tissues and conditions - offers a new perspective for dissecting the complex interplay between timekeeping and development.