Plant protein-protein interaction network and interactome.
Protein-protein interaction network represents an important aspect of systems biology. The understanding of the plant protein-protein interaction network and interactome will provide crucial insights into the regulation of plant developmental, physiological, and pathological processes. In this review, we will first define the concept of plant interactome and the protein-protein interaction network. The significance of the plant interactome study will be discussed. We will then compare the pros and cons for different strategies for interactome mapping including yeast two-hybrid system (Y2H), affinity purification mass spectrometry (AP-MS), bimolecular fluorescence complementation (BiFC), and in silico prediction. The application of these platforms on specific plant biology questions will be further discussed. The recent advancements revealed the great potential for plant protein-protein interaction network and interactome to elucidate molecular mechanisms for signal transduction, stress responses, cell cycle control, pattern formation, and others. Mapping the plant interactome in model species will provide important guideline for the future study of plant biology.
Zhang
Yixiang
Y
Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA.
Gao
Peng
P
Yuan
Joshua S
JS
Nat Rev Genet. 2007 Sep;8(9):699-710
17703239
Proc Natl Acad Sci U S A. 1998 Apr 28;95(9):5187-92
9560251
Proteomics. 2002 Jun;2(6):611-23
12112840
Plant Physiol. 2007 Dec;145(4):1090-9
18056859
Nature. 2003 Mar 13;422(6928):208-15
12634794
BMC Bioinformatics. 2008;9 Suppl 1:S20
18315852
Trends Plant Sci. 2008 Apr;13(4):183-91
18329319
Annu Rev Biophys. 2008;37:465-87
18573091
Nature. 2002 May 23;417(6887):399-403
12000970
Science. 2004 Jan 23;303(5657):540-3
14704431
Plant J. 2005 Mar;41(5):767-78
15703063
J Am Chem Soc. 2005 Jan 12;127(1):146-57
15631464
Trends Plant Sci. 2008 Apr;13(4):165-71
18329321
J Exp Bot. 2008;59(4):965-72
18349053
Curr Opin Chem Biol. 2003 Oct;7(5):557-62
14580558
Mol Biol Rep. 2008 Sep;35(3):337-43
17564813
Curr Protoc Cell Biol. 2006 Jan;Chapter 21:Unit 21.3
18228482
Methods. 2008 Jul;45(3):196-206
18586107
Mol Cell Proteomics. 2007 Jul;6(7):1226-38
17426018
Plant J. 2009 Mar;57(5):932-44
19000159
Proteomics. 2007 Aug;7(16):2947-62
17654459
Nat Genet. 2006 Aug;38(8):896-903
16845399
Plant Physiol. 2007 Oct;145(2):317-29
17675552
Nat Methods. 2006 Dec;3(12):1013-9
17060908
Genome Res. 2001 Dec;11(12):2120-6
11731503
Trends Plant Sci. 2009 Feb;14(2):59-63
19150604
J Physiol. 2005 Feb 15;563(Pt 1):11-21
15611014
Mass Spectrom Rev. 2004 Sep-Oct;23(5):350-67
15264234
Cell. 2005 Sep 23;122(6):957-68
16169070
Plant Physiol. 2007 Feb;143(2):670-83
17172288
PLoS Biol. 2008 Mar 4;6(3):e68
18318603
Adv Biochem Eng Biotechnol. 2005;95:1-15
16080263
Trends Plant Sci. 2008 Oct;13(10):517-20
18771946
Nucleic Acids Res. 2008 Jan;36(Database issue):D999-1008
17962307
Plant Mol Biol. 2002 Dec;50(6):855-70
12516858
Nature. 2000 Feb 10;403(6770):623-7
10688190
Plant J. 2006 Apr;46(1):1-13
16553892
Nat Methods. 2006 Aug;3(8):597-600
16862132
Plant J. 2008 Nov;56(3):505-16
18643980
Biotechniques. 2006 Jan;40(1):61-6
16454041
EMBO J. 1999 Oct 1;18(19):5370-9
10508169
Nat Genet. 2006 Mar;38(3):285-93
16501559
Plant J. 2004 Nov;40(3):419-27
15469499
Science. 2001 Dec 14;294(5550):2364-8
11743205
Nature. 2002 Jan 10;415(6868):180-3
11805837
Mol Syst Biol. 2007;3:88
17353930
J Exp Bot. 2006;57(7):1563-71
16551681
J Proteome Res. 2008 Sep;7(9):3649-60
18642946
Trends Plant Sci. 2008 Aug;13(8):421-9
18632303
Nature. 2006 Mar 30;440(7084):637-43
16554755
Genome Biol. 2004;5(12):R96
15575970
Planta. 2006 Sep;224(4):771-81
16575597
Cell. 2002 Jul 26;110(2):163-75
12150925
Methods. 2007 Jul;42(3):298-305
17532517
Plant Physiol. 2005 Jun;138(2):558-9
15955914
Nat Rev Mol Cell Biol. 2007 Aug;8(8):645-54
17593931
J Proteomics. 2009 Apr 13;72(3):285-314
19367730
Nature. 2002 Jan 10;415(6868):141-7
11805826
Nature. 2006 Mar 30;440(7084):631-6
16429126
Plant Physiol. 2009 Mar;149(3):1478-92
19109415
Nature. 1989 Jul 20;340(6230):245-6
2547163
Nat Biotechnol. 2006 Apr;24(4):427-33
16601728
Plant J. 2004 Apr;38(1):172-81
15053770
Plant Mol Biol. 2007 Mar;63(5):703-18
17211514
Methods Enzymol. 2001;332:277-300
11305104
Annu Rev Genet. 1997;31:663-704
9442911
Science. 2004 Feb 6;303(5659):808-13
14764870
Nat Biotechnol. 2003 Jan;21(1):89-92
12483225
Microbiol Rev. 1995 Mar;59(1):94-123
7708014
Proteomics. 2006 Oct;6(20):5529-48
16991197
Curr Biol. 1998 Oct 8;8(20):1121-4
9778531
Proteomics. 2008 Feb;8(4):893-908
18210371
Plant J. 2004 Oct;40(1):22-34
15361138
Mol Cell Proteomics. 2007 Apr;6(4):601-10
17272265
Nat Genet. 2005 Oct;37(10):1147-52
16155567
Proteomics. 2004 Dec;4(12):3845-54
15540166
Science. 2003 Dec 5;302(5651):1727-36
14605208
Plant Cell. 2005 May;17(5):1424-33
15805477
BMC Genomics. 2008 May 14;9:220
18479511
J Proteome Res. 2008 Oct;7(10):4209-10
18785769
Nature. 2005 Oct 20;437(7062):1173-8
16189514
Nat Rev Genet. 2007 Jun;8(6):437-49
17510664
Mol Cell. 2002 Apr;9(4):789-98
11983170
Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4569-74
11283351
Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4945-50
12684538
Plant J. 2008 Aug;55(3):491-503
18433439