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 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.