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Global mapping of protein–metabolite interactions in Saccharomyces cerevisiae reveals that Ser-Leu dipeptide regulates phosphoglycerate kinase activity

MPS-Authors
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Luzarowski,  M.
Small Molecules, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Vicente,  R.
System Regulation, Department Stitt, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Kiselev,  A.
Small-Molecule Signalling, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Wagner,  M.
Small-Molecule Signalling, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Schlossarek,  D.
Small-Molecule Signalling, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Erban,  A.
Applied Metabolome Analysis, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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de Souza,  L. P.
Central Metabolism, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Wojciechowska,  I.
Small Molecules, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Luzarowska,  U.
Genetics of Metabolic Traits, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Gorka,  M.
Small-Molecule Signalling, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Sokolowska,  E.
Small Molecules, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Kosmacz,  M.
Small Molecules, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Moreno,  J.C.
Small Molecules, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Brzezinska,  A.
Small-Molecule Signalling, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Vegesna,  B.
Small-Molecule Signalling, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Kopka,  J.
Applied Metabolome Analysis, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Fernie,  A. R.
Central Metabolism, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Willmitzer,  L.
Small Molecules, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Skirycz,  A.
Small-Molecule Signalling, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Citation

Luzarowski, M., Vicente, R., Kiselev, A., Wagner, M., Schlossarek, D., Erban, A., et al. (2021). Global mapping of protein–metabolite interactions in Saccharomyces cerevisiae reveals that Ser-Leu dipeptide regulates phosphoglycerate kinase activity. Communications Biology, 4(1): 181. doi:10.1038/s42003-021-01684-3.


Cite as: http://hdl.handle.net/21.11116/0000-0007-F787-A
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.