Proteomic and phosphoproteomic analyses of yeast reveal the global cellular response to sphingolipid depletion.

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How sphingolipid homeostasis is achieved is not yet well understood. Studies performed primarily in yeast showed that the phosphorylation states of several enzymes and regulators of sphingolipid synthesis are important, although a global understanding for such regulation is lacking. Here, we used high-resolution MS-based proteomics and phosphoproteomics to analyze the cellular response to sphingolipid synthesis inhibition. Our dataset reveals that changes in protein phosphorylation, rather than protein abundance, dominate the response to blocking sphingolipid synthesis. We identified Ypk signaling as a pathway likely to be activated under these conditions, and we identified potential Ypk1 target proteins. Our data provide a rich resource for on-going mechanistic studies of key elements of the cellular response to the depletion of sphingolipid levels and the maintenance of sphingolipid homeostasis. All MS data have been deposited in the ProteomeXchange with identifier PXD003854 (http://proteomecentral.proteomexchange.org/dataset/PXD003854).", "claims": [{"id": "claim-target-result", "statement": "Changes in protein phosphorylation, rather than protein abundance, dominate the response to blocking sphingolipid synthesis; significance was assessed using MaxQuant’s significance A value, with a moderated t-test and Benjamini-Hochberg correction as an alternative, and the source data are available through ProteomeXchange’s PRIDE partner repository under dataset identifier PXD003854.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:27717283", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Our dataset reveals that changes in protein phosphorylation, rather than protein abundance, dominate the response to blocking sphingolipid synthesis."}, {"asset": "source:pmid:27717283", "locator": "sections[7] \"p\" paragraph 1", "quote": "the abundance of 399 proteins and 579 phosphorylation sites on 370 proteins were significantly changed according to MaxQuant’s significance A value"}, {"asset": "source:pmid:27717283", "locator": "sections[8] \"p\" paragraph 1", "quote": "we calculated the p-values with a moderated t-test, Benjamini-Hochberg corrected them for multiple hypothesis testing"}, {"asset": "source:pmid:27717283", "locator": "sections[20] \"fn-group\" paragraph 1", "quote": "The mass spectrometry proteomics data are deposited at ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD003854"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Changes in protein phosphorylation, rather than protein abundance, dominate the response to blocking sphingolipid synthesis; significance was assessed using MaxQuant’s significance A value, with a moderated t-test and Benjamini-Hochberg correction as an alternative, and the source data are available through ProteomeXchange’s PRIDE partner repository under dataset identifier PXD003854.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:27717283"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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