Dynamic Acclimation to High Light in Arabidopsis thaliana Involves Widespread Reengineering of the Leaf Proteome.

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A mutant, gpt2, lacking a chloroplast glucose-6-phosphate/phosphate translocator, is deficient in its ability to acclimate to increased light. Here, we have used a label-free proteomics approach, to perform relative quantitation of 1993 proteins from Arabidopsis wild type and gpt2 leaves exposed to increased light. Data are available via ProteomeXchange with identifier PXD006598. Acclimation to light is shown to involve increases in electron transport and carbon metabolism but no change in the abundance of photosynthetic reaction centers. The gpt2 mutant shows a similar increase in total protein content to wild type but differences in the extent of change of certain proteins, including in the relative abundance of the cytochrome b6f complex and plastocyanin, the thylakoid ATPase and selected Benson-Calvin cycle enzymes. Changes in leaf metabolite content as plants acclimate can be explained by changes in the abundance of enzymes involved in metabolism, which were reduced in gpt2 in some cases. Plants of gpt2 invest more in stress-related proteins, suggesting that their reduced ability to acclimate photosynthetic capacity results in increased stress.", "claims": [{"id": "claim-method", "statement": "When a comparison of two conditions was made, a t-test was used, using the constraints detailed in the figure legends. When a comparison of more than two conditions was made, an ANOVA was used.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28775726", "locator": "sections[5] \"Label-Free Proteomics\" paragraph 6", "quote": "When a comparison of two conditions was made, a t-test was used, using the constraints detailed in the figure legends. When a comparison of more than two conditions was made, an ANOVA was used."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (Vizcaino et al., 2016) partner repository with the dataset identifier PXD006598 and 10.6019/PXD006598.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28775726", "locator": "sections[5] \"Label-Free Proteomics\" paragraph 9", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (Vizcaino et al., 2016) partner repository with the dataset identifier PXD006598 and 10.6019/PXD006598."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Label-free proteomics with t-tests for two-condition comparisons and ANOVA for comparisons of more than two conditions quantified 1993 proteins and showed that high-light acclimation in WT involves increased electron transport and carbon metabolism without a change in photosynthetic reaction-center abundance, while gpt2 fails to increase several relevant proteins to WT levels; source data are available through ProteomeXchange/PRIDE under PXD006598.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28775726", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here, we have used a label-free proteomics approach, to perform relative quantitation of 1993 proteins from Arabidopsis wild type and gpt2 leaves exposed to increased light."}, {"asset": "source:pmid:28775726", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD006598."}, {"asset": "source:pmid:28775726", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Acclimation to light is shown to involve increases in electron transport and carbon metabolism but no change in the abundance of photosynthetic reaction centers."}, {"asset": "source:pmid:28775726", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The gpt2 mutant shows a similar increase in total protein content to wild type but differences in the extent of change of certain proteins, including in the relative abundance of the cytochrome b6f complex and plastocyanin, the thylakoid ATPase and selected Benson-Calvin cycle enzymes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Label-free proteomics with t-tests for two-condition comparisons and ANOVA for comparisons of more than two conditions quantified 1993 proteins and showed that high-light acclimation in WT involves increased electron transport and carbon metabolism without a change in photosynthetic reaction-center abundance, while gpt2 fails to increase several relevant proteins to WT levels; source data are available through ProteomeXchange/PRIDE under PXD006598.", "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:28775726"], "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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