Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome.
J Proteome Res
; 23(7): 2518-2531, 2024 Jul 05.
Article
in En
| MEDLINE
| ID: mdl-38810119
ABSTRACT
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-Baseâenabling researchers to visualize sites alongside other data on rice proteins, e.g., structural models from AlphaFold2, PeptideAtlas, and the PRIDE databaseâenabling visualization of source evidence, including scores and supporting mass spectra.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Phosphoproteins
/
Plant Proteins
/
Oryza
/
Signal Transduction
/
Genome, Plant
/
Proteomics
Language:
En
Journal:
J Proteome Res
Journal subject:
BIOQUIMICA
Year:
2024
Document type:
Article
Affiliation country:
Reino Unido