ABSTRACT Much evidence has accumulated over the past several decades that metabolism does more than just provide the building blocks and energy to fuel biological functions. Instead, it is increasingly clear that metabolism has a profound effect in determining the behaviors of cells, tissues and organisms. We hypothesize that many of these effects are mediated by direct physical interactions whereby metabolites act on macromolecules, like proteins, to alter their functions. Unfortunately, the available methodologies for discovering such interactions are limited in scale, throughput and sensitivity. For this reason, we developed the MIDAS platform, which uses simple biophysical principles to discover interactions with very high sensitivity and selectivity. MIDAS has enabled the discovery of many novel metabolite-protein interactions, some of which we have shown to exert functionally important effects in cell models. We now propose to implement MIDAS in a much more systematic way, including collaborative efforts to define the metabolite interactions of the ubiquitin- proteasome system and the autophagy machinery. Metabolite interactions with RNA are known to be functionally important in bacteria, which use RNA elements known as riboswitches to couple direct metabolite binding to changes in RNA function. We have used MIDAS to identify metabolite ligands for some previously “orphan” riboswitches and will functionally characterize such interactions. More importantly, we hypothesized that RNA-metabolite interactions also exist and drive cellular behaviors in human cells. We used an integrated platform of transcriptome screening and RNA-adapted MIDAS to discover several intriguing putative interactions between metabolites and human mRNAs. We have validated and demonstrated the functionality of one of these interactions, with cAMP binding and stimulating the translation of the COX7B mRNA. We will collaboratively determine the structure and function of this interaction and it will serve as a model for the many such interactions that we propose are important in mediating metabolic signaling in human cells. We anticipate that these two modes of metabolite regulation, via proteins and RNA, are fundamental to the metabolic effects on cell behavior, and the understanding that we will gain over time will be transformative.