The question of how (intermediary) metabolism and the regulation of gene expression are inter-connected represents one of the central challenges for the next decade of research. This proposal aims to take a decisive stab at this question, exploiting hidden gems from the literature and modern day technologies.
Some metabolic enzymes have been caught “moonlighting” as RNA-binding proteins and, intriguingly, their RNA-binding activities appear to be under the control of metabolites and/or cofactors of these enzymes. Moonlighting enzymes could thus act as metabolite-controlled RNA regulators in RNA-enzyme-metabolite, or “REM” networks, imposing post-transcriptional influence on gene expression in metabolite-dependent ways. The riboswitches found in bacteria offer a precedent for how metabolites can have a direct effect on RNA metabolism.
Within this proposal, we describe how we plan to uncover “all” the mRNA-binding proteins (the mRNA interactomes) of eukaryotic cells in vivo, a feat which would have been impossible until recently. Following the determination of the mRNA interactomes of yeast and three strategically chosen mammalian cell lines, we will focus our follow-up analyses on the RNA-binding enzymes of intermediary metabolism of these interactomes: decipher their bound RNA targets, learn how different metabolic states and metabolites affect the RNA-enzyme interactions and, most importantly, establish the physiological importance of the studied REM networks.
The determination of mRNA interactomes will generate an unprecedented resource for the RNA biology community. We undertake this work with the motivation to uncover a key principle of how metabolism and gene expression may be connected, opening a new field of investigation for different disciplines in biomedical research, and unveiling a level of cellular regulation that would have broad implications for our understanding of basic biology and disease.
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