Comparative qualitative phosphoproteomics analysis identifies shared phosphorylation motifs and associated biological processes in evolutionary divergent plants

J Proteomics. 2018 Jun 15;181:152-159. doi: 10.1016/j.jprot.2018.04.011. Epub 2018 Apr 11.

Abstract

Phosphorylation is one of the most prevalent post-translational modifications and plays a key role in regulating cellular processes. We carried out a bioinformatics analysis of pre-existing phosphoproteomics data, to profile two model species representing the largest subclasses in flowering plants the dicot Arabidopsis thaliana and the monocot Oryza sativa, to understand the extent to which phosphorylation signaling and function is conserved across evolutionary divergent plants. We identified 6537 phosphopeptides from 3189 phosphoproteins in Arabidopsis and 2307 phosphopeptides from 1613 phosphoproteins in rice. We identified phosphorylation motifs, finding nineteen pS motifs and two pT motifs shared in rice and Arabidopsis. The majority of shared motif-containing proteins were mapped to the same biological processes with similar patterns of fold enrichment, indicating high functional conservation. We also identified shared patterns of crosstalk between phosphoserines with enrichment for motifs pSXpS, pSXXpS and pSXXXpS, where X is any amino acid. Lastly, our results identified several pairs of motifs that are significantly enriched to co-occur in Arabidopsis proteins, indicating cross-talk between different sites, but this was not observed in rice.

Significance: Our results demonstrate that there are evolutionary conserved mechanisms of phosphorylation-mediated signaling in plants, via analysis of high-throughput phosphorylation proteomics data from key monocot and dicot species: rice and Arabidposis thaliana. The results also suggest that there is increased crosstalk between phosphorylation sites in A. thaliana compared with rice. The results are important for our general understanding of cell signaling in plants, and the ability to use A. thaliana as a general model for plant biology.

Keywords: Bioinformatics; Evolutionary conservation; Motif identification; Pathway analysis; Phosphoproteomics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Arabidopsis / genetics
  • Arabidopsis / metabolism
  • Arabidopsis Proteins* / biosynthesis
  • Arabidopsis Proteins* / genetics
  • Evolution, Molecular*
  • Gene Expression Regulation, Plant / physiology*
  • Oryza* / genetics
  • Oryza* / metabolism
  • Phosphoproteins* / biosynthesis
  • Phosphoproteins* / genetics
  • Phosphorylation / physiology
  • Proteomics

Substances

  • Arabidopsis Proteins
  • Phosphoproteins