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

Marcin Luzarowski (1) , Rubén Vicente (2) , Andrei Kiselev (1, 3) , Mateusz Wagner (1, 4) , Dennis Schlossarek (1) , Alexander Erban (1) , Leonardo Perez de Souza (1) , Dorothee Childs (5) , Izabela Wojciechowska (1) , Urszula Luzarowska (1, 6) , Michał Górka (1) , Ewelina M Sokołowska (1) , Monika Kosmacz (1, 7) , Juan C Moreno (1, 7) , Aleksandra Brzezińska (1) , Bhavana Vegesna (1) , Joachim Kopka (1) , Alisdair R Fernie (1) , Lothar Willmitzer (1) , Jennifer C Ewald (8) , Aleksandra Skirycz (1, 9)

1 Department of Molecular Physiology [Potsdam-Golm]
2 MPI-MP - Max Planck Institute of Molecular Plant Physiology
3 LRSV - Laboratoire de Recherche en Sciences Végétales
4 UWr - University of Wrocław [Poland]
5 EMBL - European Molecular Biology Laboratory [Heidelberg]
6 BGU - Ben-Gurion University of the Negev
7 KAUST - King Abdullah University of Science and Technology [Saudi Arabia]
8 Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen
9 Boyce Thompson Institute [Ithaca]

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.

Mots clés: Enzymes; Mass spectrometry; Metabolomics; Proteins

Domaines: Biologie végétale

Marcin Luzarowski, Rubén Vicente, Andrei Kiselev, Mateusz Wagner, Dennis Schlossarek, et al.. Global mapping of protein–metabolite interactions in Saccharomyces cerevisiae reveals that Ser-Leu dipeptide regulates phosphoglycerate kinase activity. Communications Biology, 2021, 4 (1), 15 p. ⟨10.1038/s42003-021-01684-3⟩. ⟨hal-03407664⟩