Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants.
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.
Nakagami
Hirofumi
H
RIKEN Plant Science Center, Tsurumi-ku, Yokohama 230-0045, Japan.
Sugiyama
Naoyuki
N
Mochida
Keiichi
K
Daudi
Arsalan
A
Yoshida
Yuko
Y
Toyoda
Tetsuro
T
Tomita
Masaru
M
Ishihama
Yasushi
Y
Shirasu
Ken
K
D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000378:metabolism*; D017124:Conserved Sequence; D008969:Molecular Sequence Data; D009711:Nucleotides / Q000378:metabolism; D012275:Oryza / Q000378:metabolism*; D010750:Phosphoproteins / Q000737:chemistry* / Q000145:classification / Q000378:metabolism*; D010766:Phosphorylation; D010940:Plant Proteins / Q000737:chemistry / Q000145:classification / Q000378:metabolism*; D011485:Protein Binding; D020543:Proteome / Q000737:chemistry / Q000378:metabolism; D040901:Proteomics / Q000379:methods*
D009711:Nucleotides; D010750:Phosphoproteins; D010940:Plant Proteins; D020543:Proteome
Annu Rev Plant Biol. 2009;60:139-64
19014346
Plant Physiol. 2007 Feb;143(2):661-9
17142480
J Proteome Res. 2006 Apr;5(4):988-94
16602707
Proteomics. 2009 Feb;9(4):964-88
19212952
Mol Cell Proteomics. 2005 Dec;4(12):2010-21
16249172
Genome Res. 2003 Sep;13(9):2178-89
12952885
Nucleic Acids Res. 2010 Jan;38(Database issue):D828-34
19880383
Cell. 2006 Nov 3;127(3):635-48
17081983
Plant J. 2002 Oct;32(2):195-204
12383085
Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14789-94
11121079
EMBO J. 2001 Jul 2;20(13):3596-607
11432846
Mol Plant Microbe Interact. 2005 Jun;18(6):570-82
15986927
BMC Res Notes. 2008 Jun 23;1:30
18710483
Plant Physiol. 2009 Jun;150(2):889-903
19376835
Plant Cell. 2002 Feb;14(2):435-50
11884685
PLoS One. 2007 Apr 18;2(4):e383
17440619
Mol Cell Proteomics. 2004 Jun;3(6):608-14
15034119
Science. 2003 Jul 18;301(5631):376-9
12869764
Plant Cell. 2004 Sep;16(9):2394-405
15308754
Nat Rev Genet. 2002 Nov;3(11):883-9
12415318
Bioinformatics. 2006 Jul 1;22(13):1600-7
16606683
Science. 2007 Oct 19;318(5849):453-6
17947581
Science. 2002 Apr 5;296(5565):92-100
11935018
Mol Cell Proteomics. 2007 Jul;6(7):1198-214
17317660
Plant Physiol. 2004 Jun;135(2):622-9
15208410
Mol Syst Biol. 2008;4:193
18463617
J Biol Chem. 2006 Dec 15;281(50):38697-704
17043356
Plant Cell. 2008 Mar;20(3):739-51
18344282
Proc Natl Acad Sci U S A. 2009 Jan 27;106(4):995-1000
19144917
J Chromatogr A. 2002 Dec 6;979(1-2):233-9
12498253
Theor Appl Genet. 2004 Nov;109(7):1434-47
15309302
Plant Cell Physiol. 2006 Nov;47(11):1530-40
17018557
Proteomics. 2009 May;9(10):2764-75
19405024
Bioinformatics. 2009 May 1;25(9):1189-91
19151095
Mol Cell Proteomics. 2007 Nov;6(11):2032-42
17675664
Immunity. 2009 Jan 16;30(1):143-54
19144319
Cell. 2006 Feb 24;124(4):803-14
16497589
J Proteome Res. 2006 Jul;5(7):1803-7
16823989
Plant Physiol. 2010 Jan;152(1):19-28
19923235
Trends Plant Sci. 2009 Feb;14(2):71-6
19162527
Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9528-33
15210983
Mol Cell Proteomics. 2007 Apr;6(4):601-10
17272265
Nature. 2006 Nov 16;444(7117):323-9
17108957
Anal Chem. 1994 Dec 15;66(24):4390-9
7847635
Mol Cell Proteomics. 2008 Jan;7(1):145-62
17934212
Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
7984417
Anal Chem. 2003 Feb 1;75(3):663-70
12585499
Curr Opin Plant Biol. 2006 Aug;9(4):383-90
16713729
J Biol Chem. 2006 Dec 1;281(48):36969-76
17023433