Genome-wide analysis of two-component systems and prediction of stress-responsive two-component system members in soybean.
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.
Mochida
Keiichi
K
RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. mochida@psc.riken.jp
Yoshida
Takuhiro
T
Sakurai
Tetsuya
T
Yamaguchi-Shinozaki
Kazuko
K
Shinozaki
Kazuo
K
Tran
Lam-Son Phan
LS
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
D010940:Plant Proteins; D011494:Protein Kinases; D000071677:Histidine Kinase
Mol Genet Genomics. 2008 Dec;280(6):547-63
18813954
Proc Natl Acad Sci U S A. 2002 Nov 26;99(24):15800-5
12426401
J Biol Chem. 2004 Nov 19;279(47):48734-41
15358768
Funct Integr Genomics. 2009 Aug;9(3):411-7
19277738
Plant Physiol. 2004 Apr;134(4):1654-61
15064375
Plant Cell Physiol. 2008 Jan;49(1):47-57
18037673
Genes Dev. 2004 Apr 15;18(8):926-36
15078816
Plant Cell Physiol. 2005 May;46(5):686-98
15767265
FEBS Lett. 1998 May 8;427(2):175-8
9607306
DNA Res. 2009 Aug;16(4):237-47
19675111
Methods Enzymol. 2007;428:109-28
17875414
Plant Cell. 2006 Jan;18(1):55-69
16326927
Plant Cell Physiol. 2009 Mar;50(3):447-62
19131357
Plant Cell. 2005 Mar;17(3):791-803
15705949
Biosci Biotechnol Biochem. 2005 Dec;69(12):2263-76
16377883
Funct Integr Genomics. 2008 May;8(2):175-80
17990013
Nature. 2010 Jan 14;463(7278):178-83
20075913
Plant Cell. 2007 Dec;19(12):3901-14
18065689
Plant Cell. 2009 Jul;21(7):2008-21
19622803
Curr Biol. 2006 Jun 6;16(11):1116-22
16753566
Science. 2001 Nov 2;294(5544):1108-11
11691995
Plant Cell Physiol. 2008 Feb;49(2):201-13
18178585
Annu Rev Plant Biol. 2006;57:781-803
16669782
J Exp Bot. 2006;57(15):4225-33
17099079
Plant Cell Physiol. 2007 Feb;48(2):375-80
17202180
Plant Cell Physiol. 2005 Feb;46(2):339-55
15695462
Plant Cell. 2006 Nov;18(11):3073-87
17122069
Science. 2006 Jan 6;311(5757):94-8
16400151
Plant Physiol. 2009 Jun;150(2):535-46
19357200
Plant Signal Behav. 2010 Feb;5(2):148-50
20023424
Plant Cell Environ. 2009 Sep;32(9):1147-60
19183294
Plant Cell Physiol. 2005 Apr;46(4):609-19
15695441
PLoS One. 2008 Jun 18;3(6):e2491
18560512
J Med Invest. 2008 Aug;55(3-4):167-73
18797128
Plant Physiol. 2004 Oct;136(2):2971-81
15466243
Nat Rev Genet. 2009 Apr;10(4):252-63
19274049
J Proteome Res. 2008 Sep;7(9):3649-60
18642946
BMC Plant Biol. 2006 Feb 13;6:1
16472405
Trends Plant Sci. 2009 May;14(5):270-9
19375376
Plant Cell. 2008 Apr;20(4):1101-17
18441212
Curr Opin Plant Biol. 2009 Oct;12(5):527-38
19740698
Trends Plant Sci. 2006 Apr;11(4):176-83
16531097
DNA Res. 2009 Dec;16(6):353-69
19884168
Sci STKE. 2001 Nov 20;2001(109):re18
11717470
J Exp Bot. 2003 May;54(386):1489-90
12709495
Plant Physiol. 2007 Feb;143(2):707-19
17189334
Plant Physiol. 2009 Jul;150(3):1459-73
19448035
Plant Cell Physiol. 2007 Jan;48(1):84-96
17132632
J Exp Bot. 2007;58(10):2595-607
17545225
Trends Plant Sci. 2000 Feb;5(2):67-74
10664616
Nucleic Acids Res. 2000 Jan 1;28(1):231-4
10592234
Gene. 2006 Nov 1;382:57-65
16919402
Plant Cell. 2005 Nov;17(11):3007-18
16227453
Mol Genet Genomics. 2009 Jun;281(6):647-64
19277718
Trends Plant Sci. 2005 Feb;10(2):88-94
15708346
Proc Natl Acad Sci U S A. 1998 Nov 10;95(23):13976-81
9811911
Plant Physiol. 2006 Oct;142(2):380-97
16891544
Arabidopsis Book. 2008;6:e0112
22303237
EMBO J. 2004 Aug 18;23(16):3290-302
15282545
Plant Cell. 1999 Sep;11(9):1743-54
10488240
J Mol Biol. 2001 Jan 19;305(3):567-80
11152613
Plant Physiol. 2007 Feb;143(2):612-6
17284582
Mol Biol Evol. 2007 Aug;24(8):1596-9
17488738
BMC Genomics. 2007 Nov 23;8:431
18036212
Biosci Biotechnol Biochem. 2004 Feb;68(2):462-5
14981318
Plant Cell. 2004 Mar;16(3):658-71
14973166
Adv Bioinformatics. 2008;2008:420747
19956698
Plant Physiol. 2004 Oct;136(2):2913-20
15466220
Proc Natl Acad Sci U S A. 1998 Mar 3;95(5):2691-6
9482949
BMC Genomics. 2007 Sep 19;8:330
17880721
Plant Cell Physiol. 2004 Jan;45(1):28-39
14749483
Plant Physiol. 2008 Dec;148(4):1964-84
18923020
Plant Physiol. 2004 Oct;136(2):2961-70
15466228
FEBS Lett. 1998 Oct 16;437(1-2):11-4
9804162
Bioinformatics. 2005 Jul 15;21(14):3074-81
15890746
DNA Res. 2008 Aug;15(4):227-39
18511435
Plant Physiol. 2002 Jun;129(2):500-15
12068096
Plant Physiol. 2004 Jun;135(2):927-37
15173562
DNA Res. 2007 Dec 31;14(6):235
18180258
Microbiology (Reading). 2005 Jul;151(Pt 7):2159-2173
16000707
FEBS Lett. 2000 Aug 4;478(3):227-32
10930573
Nature. 2005 Dec 22;438(7071):1172-5
16372013
Phytother Res. 2003 Sep;17(8):845-69
13680814
Proc Natl Acad Sci U S A. 2004 Jun 8;101(23):8821-6
15166290
Nucleic Acids Res. 2010 Jan;38(Database issue):D843-6
20008513
Science. 2000 Dec 15;290(5499):2105-10
11118137
Plant Cell Physiol. 2004 Aug;45(8):1063-77
15356332
Plant Physiol. 2007 Feb;143(2):555-7
17284581
Annu Rev Biochem. 2000;69:183-215
10966457
Proc Natl Acad Sci U S A. 2007 Dec 18;104(51):20623-8
18077346
Mol Genet Genomics. 2007 Feb;277(2):115-37
17061125
Plant Cell Physiol. 2007 Feb;48(2):263-77
17202182
Genetics. 2008 May;179(1):31-9
18493038
Genomics. 2007 Jun;89(6):697-707
17408920
Proc Natl Acad Sci U S A. 2006 Jul 18;103(29):11081-5
16832061
Plant Physiol. 2009 Oct;151(2):782-91
19675156
Nucleic Acids Res. 1997 Dec 15;25(24):4876-82
9396791