A phospho-dawn of protein modification anticipates light onset in the picoeukaryote Ostreococcus tauri.

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Here, we compare transcriptome data under light-dark cycles with partial proteome and phosphoproteome data, assayed using shotgun MS, from the alga Ostreococcus tauri, the smallest free-living eukaryote. A total of 10% of quantified proteins but two-thirds of phosphoproteins were rhythmic. Mathematical modelling showed that light-stimulated protein synthesis can account for the observed clustering of protein peaks in the daytime. Prompted by night-peaking and apparently dark-stable proteins, we also tested cultures under prolonged darkness, where the proteome changed less than under the diel cycle. Among the dark-stable proteins were prasinophyte-specific sequences that were also reported to accumulate when O. tauri formed lipid droplets. In the phosphoproteome, 39% of rhythmic phospho-sites reached peak levels just before dawn. This anticipatory phosphorylation suggests that a clock-regulated phospho-dawn prepares green cells for daytime functions. Acid-directed and proline-directed protein phosphorylation sites were regulated in antiphase, implicating the clock-related casein kinases 1 and 2 in phase-specific regulation, alternating with the CMGC protein kinase family. Understanding the dynamic phosphoprotein network should be facilitated by the minimal kinome and proteome of O. tauri. The data are available from ProteomeXchange, with identifiers PXD001734, PXD001735, and PXD002909.", "claims": [{"id": "claim-method", "statement": "For analysing the significance of changing protein and peptide abundance over time, non-linear response of expression using polynomial regression was modelled using the R Stats Package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37481465", "locator": "sections[16] \"P-value calculation and false discovery rate\" paragraph 2", "quote": "For analysing the significance of changing protein and peptide abundance over time, non-linear response of expression using polynomial regression was modelled using the R Stats Package."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 10% of quantified proteins but two-thirds of phosphoproteins were rhythmic.", "kind": "quantitative", "target": {"value": 10.0, "unit": "per cent", "tolerance": null, "source": "A total of 10% of quantified proteins but two-thirds of phosphoproteins were rhythmic."}, "evidence": [{"asset": "source:pmid:37481465", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 10% of quantified proteins but two-thirds of phosphoproteins were rhythmic."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "A total of 10% of quantified proteins but two-thirds of phosphoproteins were rhythmic.", "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:37481465"], "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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