Abstract
Protein–metabolite interactions are of crucial importance for all cellular processes but remain understudied. Here, we applied a biochemical approach named PROMIS, to address the complexity of the protein–small molecule interactome in the model yeast Saccharomyces cerevisiae. By doing so, we provide a unique dataset, which can be queried for interactions between 74 small molecules and 3982 proteins using a user-friendly interface available at https://promis.mpimp-golm.mpg.de/yeastpmi/. By interpolating PROMIS with the list of predicted protein–metabolite interactions, we provided experimental validation for 225 binding events. Remarkably, of the 74 small molecules co-eluting with proteins, 36 were proteogenic dipeptides. Targeted analysis of a representative dipeptide, Ser-Leu, revealed numerous protein interactors comprising chaperones, proteasomal subunits, and metabolic enzymes. We could further demonstrate that Ser-Leu binding increases activity of a glycolytic enzyme phosphoglycerate kinase (Pgk1). Consistent with the binding analysis, Ser-Leu supplementation leads to the acute metabolic changes and delays timing of a diauxic shift. Supported by the dipeptide accumulation analysis our work attests to the role of Ser-Leu as a metabolic regulator at the interface of protein degradation and central metabolism.
Highlights
Protein–metabolite interactions are of crucial importance for all cellular processes but remain understudied
Discussion we used PROMIS to chart a map of protein–small molecule interactions (PMIs) in the model yeast Saccharomyces cerevisiae
Our most remarkable observation relates to the wealth of small molecules present in the protein complexes; this attests to the complexity of the protein–small molecule interactome and highlights an important but severely understudied role of small molecules as protein regulators
Summary
Protein–metabolite interactions are of crucial importance for all cellular processes but remain understudied. Powerful approaches that enable PMI studies at the cell-wide scale have been recently reported[14] These technologies include affinity purification[15], thermal proteome profiling[16], drug affinity responsive target stability[17], small molecule limited proteolysis[18], tandem affinity purification[19,20] and capture compound mass spectrometry[21]. These are conceptually very different strategies, but they all share a common characteristic: namely, they require a predefined protein or metabolite as a bait. They are ideal for studying interactions of a single metabolite or protein
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