PXD000940

PXD000940 is an original dataset announced via ProteomeXchange.

Title	Dynamic phosphoproteomics yeast rapamycin-induced shift
Description	To resolve the temporal sequence of phosphorylation events responding to nutritional and chemically induced up and downshifts of TORC1 signaling in S. cerevisiae wildtype, we performed quantitative MS phosphoproteomics upon nitrogen-quality up and downshifts and rapamycin treatment. We generated a high quality dataset byapplying a high resolution sampling, parallel sample processing and a dedicated data analysis pipeline that allowed us to select significant transient dynamics. By exploiting the temporal resolution of our data and the complementary of the shift experiments, we identified early phosphorylation changes regulated directly by TORC1 or by its proximal substrate kinases, and found both established and novel candidate TORC1 targets. Among the candidateTORC1 targets were the metabolic enzymes Amd1, Hom3, Nth1 and Tsl1, involved in nucleotide, amino acid and storage carbohydrate metabolism. Functional assessment of the role of phosphorylation for these and other enzymes was achieved by correlating phosphopeptide with the corresponding enzyme-associated metabolite dynamics. Candidate kinases regulating these enzymes were identified by establishing TORC1-proximity and differential kinase activity criteria. Our work provides first evidence of TORC1-dependent regulation of the metabolic enzymes Amd1and Hom3 by the kinases Sch9 and Atg1, respectively, providing mechanistic insights into on how TORC1 controls nucleotide and amino acid metabolism in response to the quality of the nitrogen source.
HostingRepository	PRIDE
AnnounceDate	2022-02-22
AnnouncementXML	Submission_2022-02-22_03:42:08.002.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christina Ludwig
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	phosphorylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2014-04-29 08:50:20	ID requested
⏵ 1	2022-02-22 03:42:08	announced

Oliveira AP, Ludwig C, Zampieri M, Weisser H, Aebersold R, Sauer U, Dynamic phosphoproteomics reveals TORC1-dependent regulation of yeast nucleotide and amino acid biosynthesis. Sci Signal, 8(374):rs4(2015) [pubmed]

curator keyword: Biological

submitter keyword: dynamic phosphoproteomics, nitrogen shift, glutamine, Rapamycin, Saccharomyces cerevisiae, yeast

Ruedi Aebersold
contact affiliation	Institute of Molecular Systems Biology, ETH Zürich, Switzerland
contact email	aebersold@imsb.biol.ethz.ch
lab head
Christina Ludwig
contact affiliation	ETH Zürich
contact email	ludwig@imsb.biol.ethz.ch
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/2022/02/PXD000940

PRIDE project URI

• PRIDE
  1. PXD000940
     1. Label: PRIDE project
     2. Name: Dynamic phosphoproteomics yeast rapamycin-induced shift