RNA-Binding moonlighting function of metabolic enzymes reveals deep evolutionary roots in Cyanobacteria

Abstract

RNA-binding proteins (RBPs) have emerged as key regulators of diverse physiological and metabolic processes in cells. Notably, many metabolic enzymes exhibit moonlighting RNA-binding functions, and a substantial fraction localize to chloroplasts, the primary hub of photosynthesis and cellular metabolic homeostasis. Since chloroplasts originated from free-living cyanobacteria, understanding the RBP repertoire in these ancient phototrophs holds particular evolutionary and functional significance. A comprehensive characterization of the cyanobacterial RBPome is still lacking. Here, we employed Synechococcus elongatus PCC 7942, a model cyanobacterium, to define its RBPome using an RNA-interactome capture approach. We identified 136 RBPs, of which nearly 30% are associated with metabolic pathways, a proportion notably higher than that observed in bacteria, algae, plants, flies, worms, or animals. Strikingly, several enzymes from core metabolic pathways, including glycolysis/gluconeogenesis, the TCA cycle, and the pentose phosphate pathway, that are known RNA binders in humans are also conserved as RBPs in cyanobacteria. We identified a wide array of proteins from the photosynthetic apparatus exhibiting RNA-binding activity, many of which are conserved across the green lineage. In silico structural alignments of RNA-binding metabolic enzymes with their NAD(P)-binding pockets, a potential site for RNA-binding, suggests a broad conservation of RNA-binding capacity of core metabolic enzymes across species. Recent discoveries have revealed that RNA-binding can modulate enzymatic activity. In this context, our findings suggest that RNA-mediated control of core cellular metabolic processes may be widespread in cyanobacteria and riboregulation might be an evolutionarily ancient mechanism, potentially tracing its origins back to cyanobacteria.