PXD021530

PXD021530 is an original dataset announced via ProteomeXchange.

Title	A global map of protein–metabolite interactions in budding yeast reveals a novel role of a proteogenic dipeptide Ser-Leu in the regulation of a key glycolytic enzyme Pgk1.
Description	Protein-metabolite interactions (PMIs) are of crucial importance for all cellular processes but remain understudied. Here, we applied a novel 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 novel PMIs between 74 small molecules and 3982 proteins using a user-friendly interface. By interpolating PROMIS with the list of predicted PMIs, 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 switch at the interface of protein degradation and central metabolism.
HostingRepository	PRIDE
AnnounceDate	2021-04-26
AnnouncementXML	Submission_2021-04-25_22:06:33.848.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Marcin Luzarowski
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-09-17 00:52:03	ID requested
⏵ 1	2021-04-25 22:06:34	announced

Dataset with its publication pending

submitter keyword: PROMIS, yeast, complexes, dipeptide, protein–metabolite interaction, glycolysis, central metabolism, PGK1, purine degradation, ligand, small molecule

Aleksandra Skirycz
contact affiliation	Max-Planck-Institute of Molecular Plant Physiology, Golm, Germany
contact email	skirycz@mpimp-golm.mpg.de
lab head
Marcin Luzarowski
contact affiliation	Max Planck Institute of Molecular Plant Physiology
contact email	luzarowski@mpimp-golm.mpg.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/04/PXD021530

PRIDE project URI

• PRIDE
  1. PXD021530
     1. Label: PRIDE project
     2. Name: A global map of protein–metabolite interactions in budding yeast reveals a novel role of a proteogenic dipeptide Ser-Leu in the regulation of a key glycolytic enzyme Pgk1.