title: Genome-wide analysis of two-component systems and prediction of stress-responsive two-component system members in soybean.
abstract: In plants, the two-component systems (TCSs) play important roles in regulating diverse biological processes, including responses to environmental stress stimuli. Within the soybean genome, the TCSs consist of at least 21 histidine kinases, 13 authentic and pseudo-phosphotransfers and 18 type-A, 15 type-B, 3 type-C and 11 pseudo-response regulator proteins. Structural and phylogenetic analyses of soybean TCS members with their Arabidopsis and rice counterparts revealed similar architecture of their TCSs. We identified a large number of closely homologous soybean TCS genes, which likely resulted from genome duplication. Additionally, we analysed tissue-specific expression profiles of those TCS genes, whose data are available from public resources. To predict the putative regulatory functions of soybean TCS members, with special emphasis on stress-responsive functions, we performed comparative analyses from all the TCS members of soybean, Arabidopsis and rice and coupled these data with annotations of known abiotic stress-responsive cis-elements in the promoter region of each soybean TCS gene. Our study provides insights into the architecture and a solid foundation for further functional characterization of soybean TCS elements. In addition, we provide a new resource for studying the conservation and divergence among the TCSs within plant species and/or between plants and other organisms.
authors.affiliation: RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. mochida@psc.riken.jp
authors.forename: Keiichi
authors.initials: K
authors.lastname: Mochida
authors.forename: Takuhiro
authors.initials: T
authors.lastname: Yoshida
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Sakurai
authors.forename: Kazuko
authors.initials: K
authors.lastname: Yamaguchi-Shinozaki
authors.forename: Kazuo
authors.initials: K
authors.lastname: Shinozaki
authors.forename: Lam-Son Phan
authors.initials: LS
authors.lastname: Tran
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D004781:Environmental Exposure; D020440:Gene Duplication; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D000071677:Histidine Kinase; D005810:Multigene Family; D012275:Oryza / Q000235:genetics; D010766:Phosphorylation; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D011494:Protein Kinases / Q000235:genetics* / Q000378:metabolism; D015398:Signal Transduction; D013025:Glycine max / Q000235:genetics* / Q000502:physiology*; D013312:Stress, Physiological
chemical_list: D010940:Plant Proteins; D011494:Protein Kinases; D000071677:Histidine Kinase
references.citation: Mol Genet Genomics. 2008 Dec;280(6):547-63
references.pmid: 18813954
references.citation: Proc Natl Acad Sci U S A. 2002 Nov 26;99(24):15800-5
references.pmid: 12426401
references.citation: J Biol Chem. 2004 Nov 19;279(47):48734-41
references.pmid: 15358768
references.citation: Funct Integr Genomics. 2009 Aug;9(3):411-7
references.pmid: 19277738
references.citation: Plant Physiol. 2004 Apr;134(4):1654-61
references.pmid: 15064375
references.citation: Plant Cell Physiol. 2008 Jan;49(1):47-57
references.pmid: 18037673
references.citation: Genes Dev. 2004 Apr 15;18(8):926-36
references.pmid: 15078816
references.citation: Plant Cell Physiol. 2005 May;46(5):686-98
references.pmid: 15767265
references.citation: FEBS Lett. 1998 May 8;427(2):175-8
references.pmid: 9607306
references.citation: DNA Res. 2009 Aug;16(4):237-47
references.pmid: 19675111
references.citation: Methods Enzymol. 2007;428:109-28
references.pmid: 17875414
references.citation: Plant Cell. 2006 Jan;18(1):55-69
references.pmid: 16326927
references.citation: Plant Cell Physiol. 2009 Mar;50(3):447-62
references.pmid: 19131357
references.citation: Plant Cell. 2005 Mar;17(3):791-803
references.pmid: 15705949
references.citation: Biosci Biotechnol Biochem. 2005 Dec;69(12):2263-76
references.pmid: 16377883
references.citation: Funct Integr Genomics. 2008 May;8(2):175-80
references.pmid: 17990013
references.citation: Nature. 2010 Jan 14;463(7278):178-83
references.pmid: 20075913
references.citation: Plant Cell. 2007 Dec;19(12):3901-14
references.pmid: 18065689
references.citation: Plant Cell. 2009 Jul;21(7):2008-21
references.pmid: 19622803
references.citation: Curr Biol. 2006 Jun 6;16(11):1116-22
references.pmid: 16753566
references.citation: Science. 2001 Nov 2;294(5544):1108-11
references.pmid: 11691995
references.citation: Plant Cell Physiol. 2008 Feb;49(2):201-13
references.pmid: 18178585
references.citation: Annu Rev Plant Biol. 2006;57:781-803
references.pmid: 16669782
references.citation: J Exp Bot. 2006;57(15):4225-33
references.pmid: 17099079
references.citation: Plant Cell Physiol. 2007 Feb;48(2):375-80
references.pmid: 17202180
references.citation: Plant Cell Physiol. 2005 Feb;46(2):339-55
references.pmid: 15695462
references.citation: Plant Cell. 2006 Nov;18(11):3073-87
references.pmid: 17122069
references.citation: Science. 2006 Jan 6;311(5757):94-8
references.pmid: 16400151
references.citation: Plant Physiol. 2009 Jun;150(2):535-46
references.pmid: 19357200
references.citation: Plant Signal Behav. 2010 Feb;5(2):148-50
references.pmid: 20023424
references.citation: Plant Cell Environ. 2009 Sep;32(9):1147-60
references.pmid: 19183294
references.citation: Plant Cell Physiol. 2005 Apr;46(4):609-19
references.pmid: 15695441
references.citation: PLoS One. 2008 Jun 18;3(6):e2491
references.pmid: 18560512
references.citation: J Med Invest. 2008 Aug;55(3-4):167-73
references.pmid: 18797128
references.citation: Plant Physiol. 2004 Oct;136(2):2971-81
references.pmid: 15466243
references.citation: Nat Rev Genet. 2009 Apr;10(4):252-63
references.pmid: 19274049
references.citation: J Proteome Res. 2008 Sep;7(9):3649-60
references.pmid: 18642946
references.citation: BMC Plant Biol. 2006 Feb 13;6:1
references.pmid: 16472405
references.citation: Trends Plant Sci. 2009 May;14(5):270-9
references.pmid: 19375376
references.citation: Plant Cell. 2008 Apr;20(4):1101-17
references.pmid: 18441212
references.citation: Curr Opin Plant Biol. 2009 Oct;12(5):527-38
references.pmid: 19740698
references.citation: Trends Plant Sci. 2006 Apr;11(4):176-83
references.pmid: 16531097
references.citation: DNA Res. 2009 Dec;16(6):353-69
references.pmid: 19884168
references.citation: Sci STKE. 2001 Nov 20;2001(109):re18
references.pmid: 11717470
references.citation: J Exp Bot. 2003 May;54(386):1489-90
references.pmid: 12709495
references.citation: Plant Physiol. 2007 Feb;143(2):707-19
references.pmid: 17189334
references.citation: Plant Physiol. 2009 Jul;150(3):1459-73
references.pmid: 19448035
references.citation: Plant Cell Physiol. 2007 Jan;48(1):84-96
references.pmid: 17132632
references.citation: J Exp Bot. 2007;58(10):2595-607
references.pmid: 17545225
references.citation: Trends Plant Sci. 2000 Feb;5(2):67-74
references.pmid: 10664616
references.citation: Nucleic Acids Res. 2000 Jan 1;28(1):231-4
references.pmid: 10592234
references.citation: Gene. 2006 Nov 1;382:57-65
references.pmid: 16919402
references.citation: Plant Cell. 2005 Nov;17(11):3007-18
references.pmid: 16227453
references.citation: Mol Genet Genomics. 2009 Jun;281(6):647-64
references.pmid: 19277718
references.citation: Trends Plant Sci. 2005 Feb;10(2):88-94
references.pmid: 15708346
references.citation: Proc Natl Acad Sci U S A. 1998 Nov 10;95(23):13976-81
references.pmid: 9811911
references.citation: Plant Physiol. 2006 Oct;142(2):380-97
references.pmid: 16891544
references.citation: Arabidopsis Book. 2008;6:e0112
references.pmid: 22303237
references.citation: EMBO J. 2004 Aug 18;23(16):3290-302
references.pmid: 15282545
references.citation: Plant Cell. 1999 Sep;11(9):1743-54
references.pmid: 10488240
references.citation: J Mol Biol. 2001 Jan 19;305(3):567-80
references.pmid: 11152613
references.citation: Plant Physiol. 2007 Feb;143(2):612-6
references.pmid: 17284582
references.citation: Mol Biol Evol. 2007 Aug;24(8):1596-9
references.pmid: 17488738
references.citation: BMC Genomics. 2007 Nov 23;8:431
references.pmid: 18036212
references.citation: Biosci Biotechnol Biochem. 2004 Feb;68(2):462-5
references.pmid: 14981318
references.citation: Plant Cell. 2004 Mar;16(3):658-71
references.pmid: 14973166
references.citation: Adv Bioinformatics. 2008;2008:420747
references.pmid: 19956698
references.citation: Plant Physiol. 2004 Oct;136(2):2913-20
references.pmid: 15466220
references.citation: Proc Natl Acad Sci U S A. 1998 Mar 3;95(5):2691-6
references.pmid: 9482949
references.citation: BMC Genomics. 2007 Sep 19;8:330
references.pmid: 17880721
references.citation: Plant Cell Physiol. 2004 Jan;45(1):28-39
references.pmid: 14749483
references.citation: Plant Physiol. 2008 Dec;148(4):1964-84
references.pmid: 18923020
references.citation: Plant Physiol. 2004 Oct;136(2):2961-70
references.pmid: 15466228
references.citation: FEBS Lett. 1998 Oct 16;437(1-2):11-4
references.pmid: 9804162
references.citation: Bioinformatics. 2005 Jul 15;21(14):3074-81
references.pmid: 15890746
references.citation: DNA Res. 2008 Aug;15(4):227-39
references.pmid: 18511435
references.citation: Plant Physiol. 2002 Jun;129(2):500-15
references.pmid: 12068096
references.citation: Plant Physiol. 2004 Jun;135(2):927-37
references.pmid: 15173562
references.citation: DNA Res. 2007 Dec 31;14(6):235
references.pmid: 18180258
references.citation: Microbiology (Reading). 2005 Jul;151(Pt 7):2159-2173
references.pmid: 16000707
references.citation: FEBS Lett. 2000 Aug 4;478(3):227-32
references.pmid: 10930573
references.citation: Nature. 2005 Dec 22;438(7071):1172-5
references.pmid: 16372013
references.citation: Phytother Res. 2003 Sep;17(8):845-69
references.pmid: 13680814
references.citation: Proc Natl Acad Sci U S A. 2004 Jun 8;101(23):8821-6
references.pmid: 15166290
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D843-6
references.pmid: 20008513
references.citation: Science. 2000 Dec 15;290(5499):2105-10
references.pmid: 11118137
references.citation: Plant Cell Physiol. 2004 Aug;45(8):1063-77
references.pmid: 15356332
references.citation: Plant Physiol. 2007 Feb;143(2):555-7
references.pmid: 17284581
references.citation: Annu Rev Biochem. 2000;69:183-215
references.pmid: 10966457
references.citation: Proc Natl Acad Sci U S A. 2007 Dec 18;104(51):20623-8
references.pmid: 18077346
references.citation: Mol Genet Genomics. 2007 Feb;277(2):115-37
references.pmid: 17061125
references.citation: Plant Cell Physiol. 2007 Feb;48(2):263-77
references.pmid: 17202182
references.citation: Genetics. 2008 May;179(1):31-9
references.pmid: 18493038
references.citation: Genomics. 2007 Jun;89(6):697-707
references.pmid: 17408920
references.citation: Proc Natl Acad Sci U S A. 2006 Jul 18;103(29):11081-5
references.pmid: 16832061
references.citation: Plant Physiol. 2009 Oct;151(2):782-91
references.pmid: 19675156
references.citation: Nucleic Acids Res. 1997 Dec 15;25(24):4876-82
references.pmid: 9396791