Meta-analysis of rice phosphoproteomics data to understand variation in cell signaling across the rice pan-genome
Phosphorylation is the most studied post-translational modification, and has multiple biological functions. In this study, we have reanalyzed publicly available mass spectrometry proteomics data sets enriched for phosphopeptides from Asian rice (Oryza sativa). In total we identified 15,565 phosphosi...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
American Chemical Society
2024
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| Online Access: | https://hdl.handle.net/10568/163805 |
| _version_ | 1855522165207597056 |
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| author | Ramsbottom, Kerry A. Prakash, Ananth Perez-Riverol, Yasset Camacho, Oscar Martin Sun, Zhi Kundu, Deepti J. Bowler-Barnett, Emily Martin, Maria Fan, Jun Chebotarov, Dmytro McNally, Kenneth L. Deutsch, Eric W. Vizcaíno, Juan Antonio Jones, Andrew R. |
| author_browse | Bowler-Barnett, Emily Camacho, Oscar Martin Chebotarov, Dmytro Deutsch, Eric W. Fan, Jun Jones, Andrew R. Kundu, Deepti J. Martin, Maria McNally, Kenneth L. Perez-Riverol, Yasset Prakash, Ananth Ramsbottom, Kerry A. Sun, Zhi Vizcaíno, Juan Antonio |
| author_facet | Ramsbottom, Kerry A. Prakash, Ananth Perez-Riverol, Yasset Camacho, Oscar Martin Sun, Zhi Kundu, Deepti J. Bowler-Barnett, Emily Martin, Maria Fan, Jun Chebotarov, Dmytro McNally, Kenneth L. Deutsch, Eric W. Vizcaíno, Juan Antonio Jones, Andrew R. |
| author_sort | Ramsbottom, Kerry A. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Phosphorylation is the most studied post-translational modification, and has multiple biological functions. In this study, we have reanalyzed publicly available mass spectrometry proteomics data sets enriched for phosphopeptides from Asian rice (Oryza sativa). In total we identified 15,565 phosphosites on serine, threonine, and tyrosine residues on rice proteins. We identified sequence motifs for phosphosites, and link motifs to enrichment of different biological processes, indicating different downstream regulation likely caused by different kinase groups. We cross-referenced phosphosites against the rice 3,000 genomes, to identify single amino acid variations (SAAVs) within or proximal to phosphosites that could cause loss of a site in a given rice variety and clustered the data to identify groups of sites with similar patterns across rice family groups. The data has been loaded into UniProt Knowledge-Base─enabling researchers to visualize sites alongside other data on rice proteins, e.g., structural models from AlphaFold2, PeptideAtlas, and the PRIDE database─enabling visualization of source evidence, including scores and supporting mass spectra. |
| format | Journal Article |
| id | CGSpace163805 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | American Chemical Society |
| publisherStr | American Chemical Society |
| record_format | dspace |
| spelling | CGSpace1638052025-02-18T10:03:23Z Meta-analysis of rice phosphoproteomics data to understand variation in cell signaling across the rice pan-genome Ramsbottom, Kerry A. Prakash, Ananth Perez-Riverol, Yasset Camacho, Oscar Martin Sun, Zhi Kundu, Deepti J. Bowler-Barnett, Emily Martin, Maria Fan, Jun Chebotarov, Dmytro McNally, Kenneth L. Deutsch, Eric W. Vizcaíno, Juan Antonio Jones, Andrew R. Phosphorylation is the most studied post-translational modification, and has multiple biological functions. In this study, we have reanalyzed publicly available mass spectrometry proteomics data sets enriched for phosphopeptides from Asian rice (Oryza sativa). In total we identified 15,565 phosphosites on serine, threonine, and tyrosine residues on rice proteins. We identified sequence motifs for phosphosites, and link motifs to enrichment of different biological processes, indicating different downstream regulation likely caused by different kinase groups. We cross-referenced phosphosites against the rice 3,000 genomes, to identify single amino acid variations (SAAVs) within or proximal to phosphosites that could cause loss of a site in a given rice variety and clustered the data to identify groups of sites with similar patterns across rice family groups. The data has been loaded into UniProt Knowledge-Base─enabling researchers to visualize sites alongside other data on rice proteins, e.g., structural models from AlphaFold2, PeptideAtlas, and the PRIDE database─enabling visualization of source evidence, including scores and supporting mass spectra. 2024-07-05 2024-12-19T12:53:02Z 2024-12-19T12:53:02Z Journal Article https://hdl.handle.net/10568/163805 en Open Access American Chemical Society Ramsbottom, Kerry A.; Prakash, Ananth; Perez-Riverol, Yasset; Camacho, Oscar Martin; Sun, Zhi; Kundu, Deepti J.; Bowler-Barnett, Emily; Martin, Maria; Fan, Jun; Chebotarov, Dmytro; McNally, Kenneth L.; Deutsch, Eric W.; Vizcaíno, Juan Antonio and Jones, Andrew R. 2024. Meta-analysis of rice phosphoproteomics data to understand variation in cell signaling across the rice pan-genome. J. Proteome Res., Volume 23 no. 7 p. 2518-2531 |
| spellingShingle | Ramsbottom, Kerry A. Prakash, Ananth Perez-Riverol, Yasset Camacho, Oscar Martin Sun, Zhi Kundu, Deepti J. Bowler-Barnett, Emily Martin, Maria Fan, Jun Chebotarov, Dmytro McNally, Kenneth L. Deutsch, Eric W. Vizcaíno, Juan Antonio Jones, Andrew R. Meta-analysis of rice phosphoproteomics data to understand variation in cell signaling across the rice pan-genome |
| title | Meta-analysis of rice phosphoproteomics data to understand variation in cell signaling across the rice pan-genome |
| title_full | Meta-analysis of rice phosphoproteomics data to understand variation in cell signaling across the rice pan-genome |
| title_fullStr | Meta-analysis of rice phosphoproteomics data to understand variation in cell signaling across the rice pan-genome |
| title_full_unstemmed | Meta-analysis of rice phosphoproteomics data to understand variation in cell signaling across the rice pan-genome |
| title_short | Meta-analysis of rice phosphoproteomics data to understand variation in cell signaling across the rice pan-genome |
| title_sort | meta analysis of rice phosphoproteomics data to understand variation in cell signaling across the rice pan genome |
| url | https://hdl.handle.net/10568/163805 |
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