Identification of proteins enriched in rice egg or sperm cells by single-cell proteomics.

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Despite their importance in plant reproduction and development, how the egg cell is specialized, fuses with the sperm cell, and converts into an active zygote for early embryogenesis remains unclear. This lack of knowledge is partly attributable to the difficulty of direct analyses of gametes in angiosperms. In the present study, proteins from egg and sperm cells obtained from rice flowers were separated by one-dimensional polyacrylamide gel electrophoresis and globally identified by highly sensitive liquid chromatography coupled with tandem mass spectroscopy. Proteome analyses were also conducted for seedlings, callus, and pollen grains to compare their protein expression profiles to those of gametes. The proteomics data have been deposited to the ProteomeXchange with identifier PXD000265. A total of 2,138 and 2,179 expressed proteins were detected in egg and sperm cells, respectively, and 102 and 77 proteins were identified as preferentially expressed in egg and sperm cells, respectively. Moreover, several rice or Arabidopsis lines with mutations in genes encoding the putative gamete-enriched proteins showed clear phenotypic defects in seed set or seed development. These results suggested that the proteomic data presented in this study are foundational information toward understanding the mechanisms of reproduction and early development in angiosperms.", "claims": [{"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [31] with the dataset identifier PXD000265 and DOI 10.6019/PXD000265.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:23936051", "locator": "sections[7] \"Identification of Proteins by Tandem Mass Spectrometry\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [31] with the dataset identifier PXD000265 and DOI 10.6019/PXD000265."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The headline proteomic result was that 2,138 and 2,179 expressed proteins were detected in rice egg and sperm cells, respectively, with 102 and 77 proteins identified as preferentially expressed in egg and sperm cells; no formal statistical method is explicitly stated, while protein identification used Mascot software and the source data were deposited through PRIDE with dataset identifier PXD000265.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:23936051", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 2,138 and 2,179 expressed proteins were detected in egg and sperm cells, respectively, and 102 and 77 proteins were identified as preferentially expressed in egg and sperm cells, respectively."}, {"asset": "source:pmid:23936051", "locator": "sections[7] \"Identification of Proteins by Tandem Mass Spectrometry\" paragraph 2", "quote": "Dataset of protein sequences obtained from the Rice Annotation Project Database (Tsukuba, Japan; http://rapdb.dna.affrc.go.jp/download/irgsp1.html) was searched using Mascot software (ver. 2.2.1, Matrix Science, MA, USA) with the following parameters."}, {"asset": "source:pmid:23936051", "locator": "sections[7] \"Identification of Proteins by Tandem Mass Spectrometry\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [31] with the dataset identifier PXD000265 and DOI 10.6019/PXD000265."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The headline proteomic result was that 2,138 and 2,179 expressed proteins were detected in rice egg and sperm cells, respectively, with 102 and 77 proteins identified as preferentially expressed in egg and sperm cells; no formal statistical method is explicitly stated, while protein identification used Mascot software and the source data were deposited through PRIDE with dataset identifier PXD000265.", "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:23936051"], "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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