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PROMIS, global analysis of PROtein-Metabolite Interactions using Size separation in Arabidopsis thaliana

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PROMIS, global analysis of PROtein-Metabolite Interactions using Size separation in Arabidopsis thaliana

by Daniel Veyel, Ewelina Maria Sokolowska, Juan C Moreno, Sylwia Kierszniowska, Justyna Cichon, Izabela Wojciechowska, Marcin Luzarowski, Monika Kosmacz, Jagoda Szlachetko, Michal Gorka, Michael Meret, Alexander Graf, Etienne H Meyer, Lothar Willmitzer, Aleksandra Skirycz
Scientific Year: 2018 DOI: 10.1074/jbc.RA118.003351

Extra Information

Journal of Biological Chemistry 

Abstract

Small molecules not only represent cellular building blocks and metabolic intermediates, but also regulatory ligands and signaling molecules that interact with proteins. Although these interactions affect cellular metabolism, growth, and development, they have been largely understudied. Herein, we describe a method, which we named tein-etabolite nteractions using ize separation (PROMIS), that allows simultaneous, global analysis of endogenous protein-small molecule and of protein-protein complexes. To this end, a cell-free native lysate from Arabidopsis thaliana cell cultures was fractionated by size-exclusion chromatography, followed by quantitative metabolomic and proteomic analyses. Proteins and small molecules showing similar elution behavior, across protein-containing fractions, constituted putative interactors. Applying PROMIS to an A. thaliana extract, we ascertained known protein-protein (PPIs) and protein-metabolite (PMIs) interactions and reproduced binding between small-molecule protease inhibitors and their respective proteases. More importantly, we present examples of two experimental strategies that exploit the PROMIS dataset to identify novel PMIs. By looking for similar elution behavior of metabolites and enzymes belonging to the same biochemical pathways, we identified putative feedback and feed-forward regulations in pantothenate biosynthesis and the methionine salvage cycle, respectively. By combining PROMIS with an orthogonal affinity purification approach, we identified an interaction between the dipeptide Tyr-Asp and the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase. In summary, we present proof of concept for a powerful experimental tool that enables system-wide analysis of PMIs and PPIs across all biological systems. The dataset obtained here comprises nearly 140 metabolites and 5000 proteins, which can be mined for putative interactors.

Keywords

chromatography ligand-binding protein metabolomics protein-protein interactions protein-small molecule interactions proteomics size-exclusion chromatography systems biology
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