title: Stable isotope metabolic labeling-based quantitative phosphoproteomic analysis of Arabidopsis mutants reveals ethylene-regulated time-dependent phosphoproteins and putative substrates of constitutive triple response 1 kinase.
abstract: Ethylene is an important plant hormone that regulates numerous cellular processes and stress responses. The mode of action of ethylene is both dose- and time-dependent. Protein phosphorylation plays a key role in ethylene signaling, which is mediated by the activities of ethylene receptors, constitutive triple response 1 (CTR1) kinase, and phosphatase. To address how ethylene alters the cellular protein phosphorylation profile in a time-dependent manner, differential and quantitative phosphoproteomics based on (15)N stable isotope labeling in Arabidopsis was performed on both one-minute ethylene-treated Arabidopsis ethylene-overly-sensitive loss-of-function mutant rcn1-1, deficient in PP2A phosphatase activity, and a pair of long-term ethylene-treated wild-type and loss-of-function ethylene signaling ctr1-1 mutants, deficient in mitogen-activated kinase kinase kinase activity. In total, 1079 phosphopeptides were identified, among which 44 were novel. Several one-minute ethylene-regulated phosphoproteins were found from the rcn1-1. Bioinformatic analysis of the rcn1-1 phosphoproteome predicted nine phosphoproteins as the putative substrates for PP2A phosphatase. In addition, from CTR1 kinase-enhanced phosphosites, we also found putative CTR1 kinase substrates including plastid transcriptionally active protein and calcium-sensing receptor. These regulatory proteins are phosphorylated in the presence of ethylene. Analysis of ethylene-regulated phosphosites using the group-based prediction system with a protein-protein interaction filter revealed a total of 14 kinase-substrate relationships that may function in both CTR1 kinase- and PP2A phosphatase-mediated phosphor-relay pathways. Finally, several ethylene-regulated post-translational modification network models have been built using molecular systems biology tools. It is proposed that ethylene regulates the phosphorylation of arginine/serine-rich splicing factor 41, plasma membrane intrinsic protein 2A, light harvesting chlorophyll A/B binding protein 1.1, and flowering bHLH 3 proteins in a dual-and-opposing fashion.
authors.affiliation: Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China;
authors.forename: Zhu
authors.initials: Z
authors.lastname: Yang
authors.forename: Guangyu
authors.initials: G
authors.lastname: Guo
authors.forename: Manyu
authors.initials: M
authors.lastname: Zhang
authors.forename: Claire Y
authors.initials: CY
authors.lastname: Liu
authors.forename: Qin
authors.initials: Q
authors.lastname: Hu
authors.forename: Henry
authors.initials: H
authors.lastname: Lam
authors.forename: Han
authors.initials: H
authors.lastname: Cheng
authors.forename: Yu
authors.initials: Y
authors.lastname: Xue
authors.forename: Jiayang
authors.initials: J
authors.lastname: Li
authors.forename: Ning
authors.initials: N
authors.lastname: Li
mesh_terms: D020816:Amino Acid Motifs; D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D002135:Calcium-Binding Proteins / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology; D005030:Ethylenes / Q000378:metabolism / Q000494:pharmacology*; D018506:Gene Expression Regulation, Plant; D007553:Isotope Labeling; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D009154:Mutation; D009587:Nitrogen Isotopes; D010750:Phosphoproteins / Q000235:genetics / Q000378:metabolism*; D010766:Phosphorylation; D010937:Plant Growth Regulators / Q000378:metabolism / Q000494:pharmacology*; D054730:Protein Interaction Domains and Motifs; D025941:Protein Interaction Mapping; D011494:Protein Kinases / Q000235:genetics / Q000378:metabolism*; D054648:Protein Phosphatase 2 / Q000235:genetics / Q000378:metabolism*; D011499:Protein Processing, Post-Translational; D015398:Signal Transduction; D013379:Substrate Specificity; D013997:Time Factors
chemical_list: D029681:Arabidopsis Proteins; C532740:CAS protein, Arabidopsis; D002135:Calcium-Binding Proteins; D005030:Ethylenes; D009587:Nitrogen Isotopes; D010750:Phosphoproteins; D010937:Plant Growth Regulators; C036216:ethylene; D011494:Protein Kinases; C477753:CTR1 protein, Arabidopsis; D054648:Protein Phosphatase 2; C478612:RCN1 protein, Arabidopsis
references.citation: Genetics. 2009 Nov;183(3):979-1003
references.pmid: 19752216
references.citation: Phytochemistry. 2011 Jul;72(10):1028-39
references.pmid: 21315391
references.citation: Plant Cell. 1998 Mar;10(3):451-9
references.pmid: 9501117
references.citation: Biochem Biophys Res Commun. 1982 Aug;107(3):1104-9
references.pmid: 6291515
references.citation: J Plant Physiol. 2003 Nov;160(11):1335-40
references.pmid: 14658386
references.citation: Plant Cell. 2007 Jul;19(7):2186-96
references.pmid: 17630275
references.citation: Eur J Cell Biol. 2010 Feb-Mar;89(2-3):145-51
references.pmid: 20034701
references.citation: Mol Cell Proteomics. 2007 May;6(5):860-81
references.pmid: 17293592
references.citation: FASEB J. 1995 May;9(8):576-96
references.pmid: 7768349
references.citation: Plant Cell. 1996 Jul;8(7):1181-91
references.pmid: 8768376
references.citation: Science. 2002 Dec 6;298(5600):1912-34
references.pmid: 12471243
references.citation: Plant Physiol. 2008 Feb;146(2):351-67
references.pmid: 18156295
references.citation: EMBO J. 2003 Mar 17;22(6):1282-8
references.pmid: 12628921
references.citation: Plant Mol Biol. 2003 Sep;53(1-2):117-31
references.pmid: 14756311
references.citation: Cell. 1993 Feb 12;72(3):427-41
references.pmid: 8431946
references.citation: Plant Physiol. 2002 Apr;128(4):1428-38
references.pmid: 11950991
references.citation: Plant Cell. 2010 Jul;22(7):2384-401
references.pmid: 20647342
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D449-51
references.pmid: 14681454
references.citation: Plant Cell. 1993 May;5(5):523-530
references.pmid: 12271074
references.citation: Nature. 2008 Feb 14;451(7180):789-95
references.pmid: 18273012
references.citation: J Proteome Res. 2008 Jan;7(1):47-50
references.pmid: 18067251
references.citation: Plant Physiol. 2004 Oct;136(2):2921-7
references.pmid: 15466219
references.citation: Plant Cell. 1990 Jun;2(6):513-23
references.pmid: 2152173
references.citation: Proc Natl Acad Sci U S A. 2003 Jan 7;100(1):352-7
references.pmid: 12509505
references.citation: Proc Natl Acad Sci U S A. 2007 Apr 10;104(15):6484-9
references.pmid: 17389366
references.citation: Science. 2011 Jun 10;332(6035):1322-6
references.pmid: 21659605
references.citation: Chem Soc Rev. 2012 May 21;41(10):3912-28
references.pmid: 22498958
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D572-4
references.pmid: 17135203
references.citation: Proc Natl Acad Sci U S A. 2012 Feb 28;109(9):3582-7
references.pmid: 22334645
references.citation: Curr Opin Plant Biol. 2008 Oct;11(5):479-85
references.pmid: 18692429
references.citation: J Exp Bot. 2012 Feb;63(3):1095-106
references.pmid: 22143917
references.citation: BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S22
references.pmid: 21342552
references.citation: Proc Natl Acad Sci U S A. 2010 Sep 7;107(36):15986-91
references.pmid: 20733066
references.citation: Mol Cell Proteomics. 2008 Sep;7(9):1598-608
references.pmid: 18463090
references.citation: J Proteome Res. 2009 Apr;8(4):1782-91
references.pmid: 19714810
references.citation: Science. 2012 Oct 19;338(6105):390-3
references.pmid: 22936567
references.citation: Biochemistry. 2003 Apr 1;42(12):3503-8
references.pmid: 12653554
references.citation: Mol Cell Proteomics. 2012 Aug;11(8):272-85
references.pmid: 22442259
references.citation: Annu Rev Biophys. 2010;39:291-308
references.pmid: 20462376
references.citation: Plant Mol Biol. 1998 May;37(2):235-41
references.pmid: 9617797
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D525-31
references.pmid: 19850723
references.citation: Nat Biotechnol. 2001 Mar;19(3):242-7
references.pmid: 11231557
references.citation: Phytochemistry. 2004 Jun;65(11):1507-15
references.pmid: 15276448
references.citation: Cell. 2003 Dec 12;115(6):667-77
references.pmid: 14675532
references.citation: Proteomics. 2009 Mar;9(6):1646-61
references.pmid: 19253305
references.citation: Plant J. 2003 Jan;33(2):221-33
references.pmid: 12535337
references.citation: FEBS Lett. 2012 May 7;586(9):1265-71
references.pmid: 22616989
references.citation: Proc Natl Acad Sci U S A. 2012 Nov 20;109(47):19486-91
references.pmid: 23132950
references.citation: Science. 1999 Feb 12;283(5404):996-8
references.pmid: 9974395
references.citation: Mol Cell Proteomics. 2008 Jun;7(6):1019-30
references.pmid: 18234664
references.citation: Plant Physiol. 2010 Mar;152(3):1180-2
references.pmid: 20034964
references.citation: Cell. 1998 Jul 24;94(2):261-71
references.pmid: 9695954
references.citation: Anal Chem. 2001 Jul 1;73(13):2836-42
references.pmid: 11467524
references.citation: Proc Natl Acad Sci U S A. 1998 Apr 28;95(9):5401-6
references.pmid: 9560288
references.citation: PLoS Genet. 2011 Jan 06;7(1):e1001263
references.pmid: 21253566
references.citation: Annu Rev Plant Physiol Plant Mol Biol. 1997;48:277-96
references.pmid: 11541139
references.citation: Science. 1993 Oct 22;262(5133):539-44
references.pmid: 8211181
references.citation: Mol Plant. 2011 Jul;4(4):626-34
references.pmid: 21690206
references.citation: Mol Cell Proteomics. 2004 Dec;3(12):1154-69
references.pmid: 15385600
references.citation: Plant J. 2003 Jun;34(5):709-18
references.pmid: 12787251
references.citation: J Biol Chem. 2000 Dec 8;275(49):38467-73
references.pmid: 10952977
references.citation: Trends Cell Biol. 1994 Aug;4(8):287-91
references.pmid: 14731592
references.citation: J Biol Chem. 2003 Sep 5;278(36):34725-32
references.pmid: 12821658
references.citation: Nat Biotechnol. 1999 Oct;17(10):994-9
references.pmid: 10504701
references.citation: Plant Physiol. 2003 Apr;131(4):1705-17
references.pmid: 12692329
references.citation: J Biol Chem. 1995 May 26;270(21):12526-30
references.pmid: 7759498
references.citation: Mol Cell Proteomics. 2002 May;1(5):376-86
references.pmid: 12118079
references.citation: J Proteome Res. 2003 Mar-Apr;2(2):153-61
references.pmid: 12716129
references.citation: Plant J. 1999 Jun;18(6):589-600
references.pmid: 10417710
references.citation: Science. 2012 Sep 14;337(6100):1348-52
references.pmid: 22984071
references.citation: Nat Cell Biol. 2012 Oct;14(10):991-8
references.pmid: 22983115
references.citation: Plant Cell. 1995 Feb;7(2):173-82
references.pmid: 7756828
references.citation: EMBO J. 1996 May 1;15(9):2115-24
references.pmid: 8641277
references.citation: Plant Physiol. 2001 Feb;125(2):1061-73
references.pmid: 11161061
references.citation: Nat Chem Biol. 2005 Oct;1(5):252-62
references.pmid: 16408053
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3635-41
references.pmid: 12824383
references.citation: J Proteome Res. 2008 Jan;7(1):45-6
references.pmid: 18081243
references.citation: Plant J. 2004 Aug;39(4):537-59
references.pmid: 15272873
references.citation: Cell. 2003 Dec 12;115(6):679-89
references.pmid: 14675533
references.citation: J Exp Bot. 2009;60(12):3311-36
references.pmid: 19567479
references.citation: Science. 1999 Jun 25;284(5423):2148-52
references.pmid: 10381874
references.citation: Nature. 2005 Feb 24;433(7028):892-5
references.pmid: 15729347
references.citation: Pflugers Arch. 2009 Jan;457(3):645-55
references.pmid: 18228034
references.citation: Nature. 2006 Feb 9;439(7077):688-94
references.pmid: 16340961
references.citation: J Biol Chem. 1999 Jul 16;274(29):20116-22
references.pmid: 10400623
references.citation: Genes Dev. 2009 Feb 15;23(4):512-21
references.pmid: 19196655
references.citation: Nat Biotechnol. 2010 Jul;28(7):710-21
references.pmid: 20622845
references.citation: J Biol Chem. 1957 Feb;224(2):621-35
references.pmid: 13405892
references.citation: Mol Cell Proteomics. 2012 Oct;11(10):957-72
references.pmid: 22787273
references.citation: Plant Physiol. 2013 Feb;161(2):904-17
references.pmid: 23188807
references.citation: Plant J. 2006 Aug;47(4):532-46
references.pmid: 16813576
references.citation: J Proteome Res. 2003 Jan-Feb;2(1):43-50
references.pmid: 12643542
references.citation: Funct Plant Biol. 2002 Aug;29(8):989-999
references.pmid: 32689549
references.citation: Brief Funct Genomic Proteomic. 2005 Feb;3(4):372-81
references.pmid: 15814027
references.citation: Cell. 1997 Jun 27;89(7):1133-44
references.pmid: 9215635
references.citation: Expert Rev Proteomics. 2010 Feb;7(1):79-92
references.pmid: 20121478
references.citation: Annu Rev Plant Biol. 2010;61:491-516
references.pmid: 20192741
references.citation: J Am Soc Mass Spectrom. 2008 Dec;19(12):1867-74
references.pmid: 18818092
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D412-6
references.pmid: 18940858
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D637-40
references.pmid: 18000002
references.citation: Plant Physiol. 1999 Jul;120(3):897-906
references.pmid: 10398726