Temporal dynamics of RNA metabolic enzyme interactome lay the foundation for riboregulation mediated circadian metabolism

Abstract

The temporal regulation of the RNA-binding to metabolic enzymes offers a compelling framework to address the open question of whether circadian control of metabolism can be mediated through riboregulation. To advance this understanding, we investigated the time-of-the-day dependent dynamics of RNA-enzymes interactome using a time-resolved RIC approach. 70% of the captured RBPs exhibit differential RNA-binding between subjective day and night, with 27% associated to metabolic pathways, suggesting temporal riboregulation of metabolic enzymes can be widespread. Intriguingly, 63 metabolic enzymes displayed circadian RNA-binding uncoupled from their protein abundance dynamics. This observation suggests that the temporal regulation of their RNA-binding "moonlighting" functions is likely mediated by alternative mechanisms, such as post-translational modifications. Our study presents a catalog of metabolic enzymes localized in mitochondria and chloroplast that exhibit dynamic RNA binding across circadian time, providing a valuable testbed to explore the mechanistic role of riboregulation in driving daily metabolic rhythms across species.