PXD044239-2

PXD044239 is an original dataset announced via ProteomeXchange.

Title	Parallel proteomics and phosphoproteomics defines starvation signal specific processes in cell quiescence
Description	Cells arrest growth and enter a quiescent state upon nutrient deprivation. However, the molecular processes by which cells respond to different starvation signals to regulate exit from the cell division cycle and initiation of quiescence remains poorly understood. To study the role of protein expression and signaling in quiescence we combined temporal profiling of the proteome and phosphoproteome using stable isotope labeling with amino acids in cell culture (SILAC) in Saccharomyces cerevisiae (budding yeast). We find that carbon and phosphorus starvation signals activate quiescence through largely distinct proteome and phosphoproteome remodeling. However, increased expression of mitochondrial proteins is essential for quiescence establishment in response to both starvation signals. Whereas the quiescent proteome is established within 6 hours of starvation the quiescent phosphoproteome undergoes continuous changes for at least 30 hours following initial starvation. Deletion of the putative quiescence regulator RIM15, which encodes a serine-threonine kinase, results in reduced survival of cells starved for phosphorus and nitrogen, but not carbon. However, we identified common protein phosphorylation roles for RIM15 in quiescence that are enriched for RNA metabolism and translation. We also find evidence for RIM15-mediated phosphorylation of some targets, including IGO1, prior to starvation consistent with a functional role for RIM15 beyond quiescence regulation. Finally, we find evidence for widespread catabolism of amino acids in response to nitrogen starvation, indicating widespread amino acid recycling via salvage pathways in conditions lacking environmental nitrogen. Our study defines an expanded quiescent proteome and phosphoproteome in yeast, and highlights the multiple coordinated molecular processes at the level of protein expression that are required for quiescence.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:13:40.107.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	David Gresham
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	phosphorylated residue; monohydroxylated residue
Instrument	LTQ

Revision	Datetime	Status	ChangeLog Entry
0	2023-07-31 14:22:46	ID requested
1	2023-11-02 15:34:56	announced
⏵ 2	2024-10-22 06:13:40	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: Yeast, quiescence, starvation

David Gresham
contact affiliation	Department of Biology New York University New York NY
contact email	dgresham@nyu.edu
lab head
David Gresham
contact affiliation	New York University
contact email	dgresham@nyu.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD044239
     1. Label: PRIDE project
     2. Name: Parallel proteomics and phosphoproteomics defines starvation signal specific processes in cell quiescence