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 language | English |
|---|---|
| Pages (from-to) | 1161-1174 |
| Number of pages | 14 |
| Journal | Plant Physiology |
| Volume | 153 |
| Issue number | 3 |
| DOIs | |
| Publication status | Published - 2010 Jul |
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ASJC Scopus subject areas
- Plant Science
- Genetics
- Physiology
- Medicine(all)
Cite this
Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants. / Nakagami, Hirofumi; Sugiyama, Naoyuki; Mochida, Keiichi; Daudi, Arsalan; Yoshida, Yuko; Toyoda, Tetsuro; Tomita, Masaru; Ishihama, Yasushi; Shirasu, Ken.
In: Plant Physiology, Vol. 153, No. 3, 07.2010, p. 1161-1174.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants
AU - Nakagami, Hirofumi
AU - Sugiyama, Naoyuki
AU - Mochida, Keiichi
AU - Daudi, Arsalan
AU - Yoshida, Yuko
AU - Toyoda, Tetsuro
AU - Tomita, Masaru
AU - Ishihama, Yasushi
AU - Shirasu, Ken
PY - 2010/7
Y1 - 2010/7
N2 - 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.
AB - 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.
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UR - http://www.scopus.com/inward/citedby.url?scp=77954247252&partnerID=8YFLogxK
U2 - 10.1104/pp.110.157347
DO - 10.1104/pp.110.157347
M3 - Article
C2 - 20466843
AN - SCOPUS:77954247252
VL - 153
SP - 1161
EP - 1174
JO - Plant Physiology
JF - Plant Physiology
SN - 0032-0889
IS - 3
ER -