PXD003463

PXD003463 is an original dataset announced via ProteomeXchange.

Title	Combining deep-sequencing, proteomics, phosphoproteomics and functional screens to discover novel regulators of sphingolipids homeostasis.
Description	Sphingolipids (SLs) are essential components of cell membranes and broad-range bioactive signaling molecules. SL levels must be tightly regulated as imbalances affect cellular function and contribute to pathologies ranging from neurodegenerative and metabolic disorders to cancer and aging. Deciphering how SL homeostasis is maintained and uncovering new regulators are two key aspects for understanding lipid biology and defining opportunities for therapeutic interventions. Here we combine multiple systematic technologies to identify the changes of the transcriptome, proteome and phosphoproteome in the yeast Saccharomyces cerevisiae upon SL depletion by myriocin. Surprisingly we find that SL depletion triggers only small changes on the expression and steady-state levels of regulatory proteins of SL homeostasis. However dramatic regulation occurs at level of the phosphoproteome suggesting that maintaining SL homeostasis demands rapid responses that cannot occur at the transcriptional level. To discover which of the phosphoproteomic changes are required for the cell’s first-line response to SL depletion and which are the bi-product of the cellular changes occurring following SL alterations, we combined the results with systematic growth screens for genes required during growth in myriocin when either mutated or overexpressed. By following the rate of SL biosynthesis in those candidates that are both essential for growth during myriocin and are phosphorylated in response to the drug we uncovered new regulators of SL homeostasis.
HostingRepository	PRIDE
AnnounceDate	2017-05-04
AnnouncementXML	Submission_2017-05-04_04:02:27.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nicolas Lebesgue
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	phosphorylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-01-14 01:56:40	ID requested
⏵ 1	2017-05-04 04:02:28	announced

Lebesgue N, Megyeri M, Cristobal A, Scholten A, Chuartzman SG, Voichek Y, Scheltema RA, Mohammed S, Futerman AH, Schuldiner M, Heck AJ, Lemeer S, Combining Deep Sequencing, Proteomics, Phosphoproteomics, and Functional Screens To Discover Novel Regulators of Sphingolipid Homeostasis. J Proteome Res, 16(2):571-582(2017) [pubmed]

curator keyword: Biological

submitter keyword: sphingolipid metabolism, Saccharomyces Cerevisiae, LC-MS/MS, label-free quantification, myriocin

Albert J.R Heck
contact affiliation	Biomolecular Mass Spectrometry and Proteomics Bijvoet Center for Biomolecular Reseach and Utrecht Institute of Pharmaceutical Sciences Utrecht University Padualaan 8, 3584 CH Utrecht, The Netherland
contact email	A.J.R.Heck@uu.nl
lab head
Nicolas Lebesgue
contact affiliation	Utrecht University
contact email	n.f.m.lebesgue@uu.nl
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD003463
     1. Label: PRIDE project
     2. Name: Combining deep-sequencing, proteomics, phosphoproteomics and functional screens to discover novel regulators of sphingolipids homeostasis.