Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants

Hirofumi Nakagami, Naoyuki Sugiyama, Keiichi Mochida, Arsalan Daudi, Yuko Yoshida, Tetsuro Toyoda, Masaru Tomita, Yasushi Ishihama, Ken Shirasu

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267 Citations (Scopus)

Abstract

Knowledge of phosphorylation events and their regulation is crucial to understand the functional biology of plants. Here, we report a large-scale phosphoproteome analysis in the model monocot rice (Oryza sativa japonica 'Nipponbare'), an economically important crop. Using unfractionated whole-cell lysates of rice cells, we identified 6,919 phosphopeptides from 3,393 proteins. To investigate the conservation of phosphoproteomes between plant species, we developed a novel phosphorylation-site evaluation method and performed a comparative analysis of rice and Arabidopsis (Arabidopsis thaliana). The ratio of tyrosine phosphorylation in the phosphoresidues of rice was equivalent to those in Arabidopsis and human. Furthermore, despite the phylogenetic distance and the use of different cell types, more than 50% of the phosphoproteins identified in rice and Arabidopsis, which possessed ortholog(s), had an orthologous phosphoprotein in the other species. Moreover, nearly half of the phosphorylated orthologous pairs were phosphorylated at equivalent sites. Further comparative analyses against the Medicago phosphoproteome also showed similar results. These data provide direct evidence for conserved regulatory mechanisms based on phosphorylation in plants. We also assessed the phosphorylation sites on nucleotide-binding leucine-rich repeat proteins and identified novel conserved phosphorylation sites that may regulate this class of proteins.

Original languageEnglish
Pages (from-to)1161-1174
Number of pages14
JournalPlant Physiology
Volume153
Issue number3
DOIs
Publication statusPublished - 2010 Jul

ASJC Scopus subject areas

  • Physiology
  • Genetics
  • Plant Science

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    Nakagami, H., Sugiyama, N., Mochida, K., Daudi, A., Yoshida, Y., Toyoda, T., Tomita, M., Ishihama, Y., & Shirasu, K. (2010). Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants. Plant Physiology, 153(3), 1161-1174. https://doi.org/10.1104/pp.110.157347