Label-free quantitative analysis of the casein kinase 2-responsive phosphoproteome of the marine minimal model species Ostreococcus tauri.

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CK2 is functionally conserved across eukaryotes, although the substrate proteins identified in a range of complex tissues are often different. The marine alga Ostreococcus tauri is a unicellular eukaryotic model organism ideally suited to efficiently study generic roles of CK2 in the cellular circadian clock. Overexpression of CK2 leads to a slow circadian rhythm, verifying functional conservation of CK2 in timekeeping. The proteome was analysed in wild-type and CK2-overexpressing algae at dawn and dusk, revealing that differential abundance of the global proteome across the day is largely unaffected by overexpression. However, CK2 activity contributed more strongly to timekeeping at dusk than at dawn. The phosphoproteome of a CK2 overexpression line and cells treated with CK2 inhibitor was therefore analysed and compared to control cells at dusk. We report an extensive catalogue of 447 unique CK2-responsive differential phosphopeptide motifs to inform future studies into CK2 activity in the circadian clock of more complex tissues. All MS data have been deposited in the ProteomeXchange with identifier PXD000975 (http://proteomecentral.proteomexchange.org/dataset/PXD000975).", "claims": [{"id": "claim-method", "statement": "Differences in protein quantities between the two lines and/or the two time points were analysed by pair‐wise t‐test (Supplemental Table 1).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25930153", "locator": "sections[12] \"The effect of CK2 overexpression on the global proteome\" paragraph 3", "quote": "Differences in protein quantities between the two lines and/or the two time points were analysed by pair‐wise t‐test (Supplemental Table 1)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All MS data have been deposited in the ProteomeXchange with identifier PXD000975 (http://proteomecentral.proteomexchange.org/dataset/PXD000975).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25930153", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "All MS data have been deposited in the ProteomeXchange with identifier PXD000975 (http://proteomecentral.proteomexchange.org/dataset/PXD000975)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used pairwise t-tests to analyze protein-abundance differences and reported 447 unique CK2-responsive differential phosphopeptide motifs; the underlying MS data are deposited in ProteomeXchange under identifier PXD000975.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:25930153", "locator": "sections[12] \"The effect of CK2 overexpression on the global proteome\" paragraph 3", "quote": "Differences in protein quantities between the two lines and/or the two time points were analysed by pair‐wise t‐test (Supplemental Table 1)."}, {"asset": "source:pmid:25930153", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We report an extensive catalogue of 447 unique CK2‐responsive differential phosphopeptide motifs to inform future studies into CK2 activity in the circadian clock of more complex tissues."}, {"asset": "source:pmid:25930153", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "All MS data have been deposited in the ProteomeXchange with identifier PXD000975 (http://proteomecentral.proteomexchange.org/dataset/PXD000975)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used pairwise t-tests to analyze protein-abundance differences and reported 447 unique CK2-responsive differential phosphopeptide motifs; the underlying MS data are deposited in ProteomeXchange under identifier PXD000975.", "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:25930153"], "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": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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