Luzarowski Marcin, Vicente Rubén, Kiselev Andrei, Wagner Mateusz, Schlossarek Dennis, Erban Alexander, de Souza Leonardo Perez, Childs Dorothee, Wojciechowska Izabela, Luzarowska Urszula, Górka Michał, Sokołowska Ewelina M, Kosmacz Monika, Moreno Juan C, Brzezińska Aleksandra, Vegesna Bhavana, Kopka Joachim, Fernie Alisdair R, Willmitzer Lothar, Ewald Jennifer C, Skirycz Aleksandra
Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.
Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.
Commun Biol. 2021 Feb 10;4(1):181. doi: 10.1038/s42003-021-01684-3.
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.
蛋白质-代谢物相互作用对所有细胞过程都至关重要，但仍未得到充分研究。在此，我们应用了一种名为PROMIS的生化方法，以解决模式酵母酿酒酵母中蛋白质-小分子相互作用组的复杂性问题。通过这样做，我们提供了一个独特的数据集，可使用https://promis.mpimp-golm.mpg.de/yeastpmi/上提供的用户友好界面查询74种小分子与3982种蛋白质之间的相互作用。通过将PROMIS与预测的蛋白质-代谢物相互作用列表进行比对，我们为225个结合事件提供了实验验证。值得注意的是，在与蛋白质共洗脱的74种小分子中，有36种是蛋白原性二肽。对代表性二肽Ser-Leu的靶向分析揭示了众多蛋白质相互作用分子，包括伴侣蛋白、蛋白酶体亚基和代谢酶。我们还能进一步证明，Ser-Leu的结合会增加糖酵解酶磷酸甘油酸激酶（Pgk1）的活性。与结合分析一致，补充Ser-Leu会导致急性代谢变化，并延迟二次生长转换的时间。在二肽积累分析的支持下，我们的工作证明了Ser-Leu作为蛋白质降解和中心代谢界面处的代谢调节剂的作用。
