title: Modulation of transcription factor and metabolic pathway genes in response to water-deficit stress in rice.
abstract: Water-deficit stress is detrimental for rice growth, development, and yield. Transcriptome analysis of 1-week-old rice (Oryza sativa L. var. IR64) seedling under water-deficit stress condition using Affymetrix 57 K GeneChip® has revealed 1,563 and 1,746 genes to be up- and downregulated, respectively. In an effort to amalgamate data across laboratories, we identified 5,611 differentially expressing genes under varying extrinsic water-deficit stress conditions in six vegetative and one reproductive stage of development in rice. Transcription factors (TFs) involved in ABA-dependent and ABA-independent pathways have been found to be upregulated during water-deficit stress. Members of zinc-finger TFs namely, C₂H₂, C₂C₂, C₃H, LIM, PHD, WRKY, ZF-HD, and ZIM, along with TF families like GeBP, jumonji, MBF1 and ULT express differentially under water-deficit conditions. NAC (NAM, ATAF and CUC) TF family emerges to be a potential key regulator of multiple abiotic stresses. Among the 12 TF genes that are co-upregulated under water-deficit, salt and cold stress conditions, five belong to the NAC TF family. We identified water-deficit stress-responsive genes encoding key enzymes involved in biosynthesis of osmoprotectants like polyols and sugars; amino acid and quaternary ammonium compounds; cell wall loosening and structural components; cholesterol and very long chain fatty acid; cytokinin and secondary metabolites. Comparison of genes responsive to water-deficit stress conditions with genes preferentially expressed during panicle and seed development revealed a significant overlap of transcriptome alteration and pathways.
authors.affiliation: Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
authors.forename: Swatismita
authors.initials: S
authors.lastname: Ray
authors.forename: Prasant K
authors.initials: PK
authors.lastname: Dansana
authors.forename: Jitender
authors.initials: J
authors.lastname: Giri
authors.forename: Priyanka
authors.initials: P
authors.lastname: Deveshwar
authors.forename: Rita
authors.initials: R
authors.lastname: Arora
authors.forename: Pinky
authors.initials: P
authors.lastname: Agarwal
authors.forename: Jitendra P
authors.initials: JP
authors.lastname: Khurana
authors.forename: Sanjay
authors.initials: S
authors.lastname: Kapoor
authors.forename: Akhilesh K
authors.initials: AK
authors.lastname: Tyagi
mesh_terms: D003681:Dehydration / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics*; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
chemical_list: D014157:Transcription Factors
references.citation: Trends Plant Sci. 2001 Nov;6(11):510-3
references.pmid: 11701378
references.citation: Plant Physiol. 2002 Nov;130(3):1143-51
references.pmid: 12427981
references.citation: Plant Physiol. 2003 Feb;131(2):568-82
references.pmid: 12586881
references.citation: Nucleic Acids Res. 2007;35(11):3612-23
references.pmid: 17485478
references.citation: Plant Cell. 2005 Dec;17(12):3470-88
references.pmid: 16284313
references.citation: Plant Biotechnol J. 2007 May;5(3):361-80
references.pmid: 17430544
references.citation: Biochem Biophys Res Commun. 2006 Jun 30;345(2):646-51
references.pmid: 16690022
references.citation: Photochem Photobiol. 1997 May;65(5):765-76
references.pmid: 9155253
references.citation: Plant Mol Biol. 2009 Jan;69(1-2):133-53
references.pmid: 18931976
references.citation: Plant Mol Biol. 2007 Mar;63(5):591-608
references.pmid: 17225073
references.citation: PLoS Genet. 2005 Aug;1(2):e26
references.pmid: 16121258
references.citation: FEBS Lett. 2007 May 25;581(12):2325-36
references.pmid: 17462636
references.citation: Plant Mol Biol. 2005 Jul;58(5):699-720
references.pmid: 16158244
references.citation: Plant Mol Biol. 2004 Mar;54(4):471-87
references.pmid: 15316284
references.citation: Mol Genet Genomics. 2008 Dec;280(6):547-63
references.pmid: 18813954
references.citation: Proc Natl Acad Sci U S A. 2006 Aug 29;103(35):12987-92
references.pmid: 16924117
references.citation: Trends Plant Sci. 1999 Oct;4(10):394-400
references.pmid: 10498963
references.citation: Plant Mol Biol. 1995 Jan;27(2):225-35
references.pmid: 7888614
references.citation: Plant Physiol. 2010 May;153(1):185-97
references.pmid: 20335401
references.citation: Plant J. 2010 Apr;62(2):250-64
references.pmid: 20113437
references.citation: Cell Mol Life Sci. 2008 Apr;65(7-8):1150-60
references.pmid: 18193167
references.citation: Plant Mol Biol. 2007 Nov;65(4):467-85
references.pmid: 17610133
references.citation: Plant J. 2002 Aug;31(3):279-92
references.pmid: 12164808
references.citation: J Exp Bot. 2007;58(2):221-7
references.pmid: 17075077
references.citation: Plant Cell Physiol. 2004 Apr;45(4):386-91
references.pmid: 15111712
references.citation: Proc Natl Acad Sci U S A. 2007 Apr 10;104(15):6484-9
references.pmid: 17389366
references.citation: Curr Opin Plant Biol. 2002 Jun;5(3):218-23
references.pmid: 11960739
references.citation: BMC Plant Biol. 2006 Oct 12;6:25
references.pmid: 17038189
references.citation: Mol Genet Genomics. 2007 Nov;278(5):493-505
references.pmid: 17636330
references.citation: Plant Cell Physiol. 2004 Feb;45(2):225-31
references.pmid: 14988493
references.citation: Plant Physiol. 2003 Dec;133(4):1702-16
references.pmid: 14681533
references.citation: J Biol Chem. 2004 Mar 19;279(12):11736-43
references.pmid: 14722088
references.citation: Plant Physiol. 2001 Jul;126(3):1241-9
references.pmid: 11457974
references.citation: Planta. 2007 Aug;226(3):601-17
references.pmid: 17370086
references.citation: Plant Physiol. 2008 Feb;146(2):623-35
references.pmid: 18162593
references.citation: Plant Physiol. 2001 Jan;125(1):131-4
references.pmid: 11154315
references.citation: J Exp Bot. 2001 Jun;52(359):1339-52
references.pmid: 11432953
references.citation: Plant J. 2005 Jul;43(1):47-56
references.pmid: 15960615
references.citation: Mol Gen Genet. 2000 Oct;264(3):257-67
references.pmid: 11085265
references.citation: Nature. 2009 Jan 29;457(7229):551-6
references.pmid: 19189423
references.citation: Proc Natl Acad Sci U S A. 2006 Feb 7;103(6):1988-93
references.pmid: 16446457
references.citation: J Plant Physiol. 2009 Jan 30;166(2):107-16
references.pmid: 18462832
references.citation: Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):15898-903
references.pmid: 12456878
references.citation: Int J Mol Sci. 2009 Sep 01;10(9):3793-810
references.pmid: 19865519
references.citation: Plant Cell Physiol. 2007 Aug;48(8):1148-58
references.pmid: 17609218
references.citation: Annu Rev Plant Biol. 2006;57:781-803
references.pmid: 16669782
references.citation: Proc Natl Acad Sci U S A. 2007 Dec 4;104(49):19631-6
references.pmid: 18048328
references.citation: Plant Mol Biol. 2008 Jan;66(1-2):47-59
references.pmid: 17978851
references.citation: Ann N Y Acad Sci. 2007 Oct;1113:135-46
references.pmid: 17978281
references.citation: BMC Genomics. 2006 Jun 13;7:149
references.pmid: 16772040
references.citation: Theor Appl Genet. 2007 Nov;115(8):1109-26
references.pmid: 17846741
references.citation: Nature. 2005 Mar 17;434(7031):404-8
references.pmid: 15772667
references.citation: Plant Physiol. 2008 Sep;148(1):269-79
references.pmid: 18667727
references.citation: Plant Mol Biol. 2004 May;55(3):327-42
references.pmid: 15604685
references.citation: Plant Physiol. 2004 Dec;136(4):4159-68
references.pmid: 15557093
references.citation: Plant Physiol. 2005 Jun;138(2):1083-96
references.pmid: 15923334
references.citation: Ann Bot. 2002 Jun;89 Spec No:871-85
references.pmid: 12102513
references.citation: Biochem J. 1999 Dec 1;344 Pt 2:503-9
references.pmid: 10567234
references.citation: Plant Mol Biol. 1996 Mar;30(5):863-72
references.pmid: 8639746
references.citation: Plant Physiol. 2001 Apr;125(4):1655-66
references.pmid: 11299347
references.citation: Plant Physiol. 2005 Oct;139(2):847-56
references.pmid: 16183833
references.citation: J Exp Bot. 2009;60(1):9-18
references.pmid: 19036839
references.citation: Funct Integr Genomics. 2005 Apr;5(2):104-16
references.pmid: 15480887
references.citation: J Plant Physiol. 2009 Aug 15;166(12):1296-1306
references.pmid: 19324458
references.citation: Trends Plant Sci. 2006 Aug;11(8):405-12
references.pmid: 16843036
references.citation: Plant Physiol. 2008 Feb;146(2):333-50
references.pmid: 18065552
references.citation: Trends Plant Sci. 2006 Nov;11(11):550-8
references.pmid: 17035069
references.citation: BMC Genomics. 2010 Jan 29;11:73
references.pmid: 20109239
references.citation: Funct Integr Genomics. 2002 Nov;2(6):282-91
references.pmid: 12444421
references.citation: J Exp Bot. 2004 Jan;55(395):225-36
references.pmid: 14673035
references.citation: Plant J. 2004 Jun;38(5):823-39
references.pmid: 15144383
references.citation: Trends Plant Sci. 2007 May;12(5):185-8
references.pmid: 17412635
references.citation: Curr Biol. 2003 Aug 19;13(16):1378-87
references.pmid: 12932321
references.citation: J Exp Bot. 2004 Feb;55(396):397-409
references.pmid: 14739263
references.citation: Plant J. 2006 May;46(4):601-12
references.pmid: 16640597
references.citation: Biophys J. 2003 Nov;85(5):3058-65
references.pmid: 14581206
references.citation: Plant J. 2007 Jun;50(6):967-81
references.pmid: 17461790
references.citation: Cell Res. 2005 Oct;15(10):796-810
references.pmid: 16246269
references.citation: BMC Evol Biol. 2005 Jan 03;5:1
references.pmid: 15629062
references.citation: Trends Plant Sci. 2005 Feb;10(2):79-87
references.pmid: 15708345
references.citation: Plant Cell Physiol. 2005 Jan;46(1):23-47
references.pmid: 15659435
references.citation: Plant J. 2007 Apr;50(2):347-63
references.pmid: 17376166
references.citation: Plant Physiol. 2005 Oct;139(2):822-35
references.pmid: 16183841
references.citation: J Plant Physiol. 2008 Apr 18;165(6):580-7
references.pmid: 17765358
references.citation: Plant J. 1996 Dec;10(6):955-66
references.pmid: 9011080
references.citation: Plant Mol Biol. 2002 Mar-Apr;48(5-6):551-73
references.pmid: 11999834
references.citation: Phytochemistry. 2002 Jan;59(1):23-32
references.pmid: 11754940
references.citation: Plant Physiol. 2002 Dec;130(4):2129-41
references.pmid: 12481097
references.citation: Plant Physiol. 2004 Sep;136(1):2734-46
references.pmid: 15333755
references.citation: Trends Plant Sci. 2005 Feb;10(2):95-102
references.pmid: 15708347
references.citation: Mol Biol Rep. 2009 Jul;36(6):1579-85
references.pmid: 18791854
references.citation: Planta. 1999 Jul;209(1):13-24
references.pmid: 10467027
references.citation: Plant Cell Rep. 2006 Feb;25(1):71-9
references.pmid: 16362303
references.citation: Plant Cell Physiol. 2006 Jan;47(1):141-53
references.pmid: 16284406
references.citation: Curr Opin Plant Biol. 2004 Dec;7(6):701-7
references.pmid: 15491919
references.citation: Plant Physiol. 2000 Dec;124(4):1595-604
references.pmid: 11115877
references.citation: Plant Physiol. 2008 Mar;146(3):1142-54
references.pmid: 18162594
references.citation: Plant J. 2006 Nov;48(3):321-41
references.pmid: 17005011
references.citation: Plant Mol Biol. 2005 Sep;59(1):151-64
references.pmid: 16217609
references.citation: Plant Cell. 2004 Sep;16(9):2481-98
references.pmid: 15319476
references.citation: Anal Biochem. 2003 Mar 15;314(2):319-21
references.pmid: 12654320
references.citation: Proc Natl Acad Sci U S A. 2004 Apr 20;101(16):6309-14
references.pmid: 15079051
references.citation: Development. 2004 Oct;131(20):4965-75
references.pmid: 15371304
references.citation: BMC Genomics. 2007 Sep 02;8:303
references.pmid: 17764573
references.citation: Planta. 2000 Feb;210(3):468-77
references.pmid: 10750905
references.citation: Plant Cell. 2004 Mar;16(3):596-615
references.pmid: 14973164
references.citation: Plant Physiol. 2009 Jan;149(1):88-95
references.pmid: 19126699
references.citation: J Cell Biochem Suppl. 2001;Suppl 37:120-5
references.pmid: 11842437
references.citation: Plant Cell Environ. 2002 Feb;25(2):131-139
references.pmid: 11841658
references.citation: Plant Mol Biol. 2000 Oct;44(3):345-58
references.pmid: 11199393
references.citation: New Phytol. 2006;172(4):617-35
references.pmid: 17096789
references.citation: J Exp Bot. 2007;58(2):253-65
references.pmid: 17132712
references.citation: Science. 1998 Apr 3;280(5360):104-6
references.pmid: 9525853
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D717-23
references.pmid: 16381966
references.citation: Plant Physiol. 2000 Dec;124(4):1854-65
references.pmid: 11115899
references.citation: Genome. 2002 Feb;45(1):204-11
references.pmid: 11908663
references.citation: Plant Mol Biol. 1994 Mar;24(5):701-13
references.pmid: 8193295
references.citation: Plant Physiol. 2004 Apr;134(4):1718-32
references.pmid: 15084732
references.citation: BMC Genomics. 2007 Jul 18;8:242
references.pmid: 17640358
references.citation: Genome Biol. 2005;6(12):R101
references.pmid: 16356264
references.citation: Plant Cell. 2006 May;18(5):1292-309
references.pmid: 16617101
references.citation: Plant Cell Environ. 2002 Feb;25(2):141-151
references.pmid: 11841659
references.citation: Mol Plant. 2008 Sep;1(5):732-50
references.pmid: 19825577
references.citation: Trends Plant Sci. 2005 Dec;10(12):603-9
references.pmid: 16275051
references.citation: New Phytol. 2007;176(2):275-287
references.pmid: 17696978
references.citation: Plant Cell. 1998 Aug;10(8):1391-406
references.pmid: 9707537
references.citation: J Exp Bot. 2001 May;52(358):961-9
references.pmid: 11432913
references.citation: Ann Bot. 2006 Jun;97(6):985-91
references.pmid: 16621860
references.citation: Plant J. 2004 Sep;39(6):863-76
references.pmid: 15341629
references.citation: Glycobiology. 2002 Feb;12(2):103-10
references.pmid: 11886843
references.citation: Biochem Biophys Res Commun. 2007 Feb 9;353(2):299-305
references.pmid: 17178106
references.citation: Plant Physiol. 2006 Apr;140(4):1437-50
references.pmid: 16500996
references.citation: J Genet. 2002 Apr;81(1):25-44
references.pmid: 12357076
references.citation: Plant Cell. 2002 Feb;14(2):343-57
references.pmid: 11884679
references.citation: BMC Genomics. 2009 Nov 15;10:523
references.pmid: 19912666
references.citation: Proc Natl Acad Sci U S A. 2008 May 27;105(21):7618-23
references.pmid: 18467490
references.citation: Plant Physiol. 2004 May;135(1):309-24
references.pmid: 15122027
references.citation: Plant J. 2003 Jun;34(6):868-87
references.pmid: 12795706
references.citation: Genes Dev. 2007 Oct 1;21(19):2371-84
references.pmid: 17908925
references.citation: Funct Integr Genomics. 2007 Apr;7(2):111-34
references.pmid: 17136344
references.citation: Curr Opin Plant Biol. 2000 Feb;3(1):17-22
references.pmid: 10679447
references.citation: Arch Biochem Biophys. 2005 Dec 15;444(2):139-58
references.pmid: 16309626
references.citation: Trends Plant Sci. 2001 Sep;6(9):431-8
references.pmid: 11544133
references.citation: Plant Sci. 2000 Jun 12;155(1):1-9
references.pmid: 10773334
references.citation: Z Naturforsch C J Biosci. 2001 Sep-Oct;56(9-10):745-54
references.pmid: 11724379
references.citation: Ann Bot. 2002 Jun;89 Spec No:833-9
references.pmid: 12102509
references.citation: Trends Plant Sci. 2007 Jun;12(6):239-44
references.pmid: 17499004
references.citation: Plant Mol Biol. 1995 Jul;28(4):619-34
references.pmid: 7647295
references.citation: Plant Physiol. 1993 Mar;101(3):1119-20
references.pmid: 8310052
references.citation: Plant Cell. 2004 Oct;16(10):2601-13
references.pmid: 15377760
references.citation: Development. 2005 Mar;132(5):897-911
references.pmid: 15673576
references.citation: Biochim Biophys Acta. 2007 Apr;1769(4):220-7
references.pmid: 17434609
references.citation: J Plant Physiol. 2009 Nov 15;166(17):1934-45
references.pmid: 19595478
references.citation: Plant Cell. 2003 Jan;15(1):63-78
references.pmid: 12509522
references.citation: BMC Genomics. 2008 Oct 15;9:485
references.pmid: 18922162
references.citation: Plant J. 2003 Jan;33(2):305-17
references.pmid: 12535344
references.citation: J Exp Bot. 2007;58(2):229-40
references.pmid: 17110587
references.citation: Curr Biol. 2005 Jul 12;15(13):1196-200
references.pmid: 16005291
references.citation: Annu Rev Plant Physiol Plant Mol Biol. 1996 Jun;47:405-430
references.pmid: 15012295
references.citation: J Exp Bot. 2004 Nov;55(407):2331-41
references.pmid: 15448178
references.citation: Plant Mol Biol. 1995 Nov;29(3):535-50
references.pmid: 8534851
references.citation: Funct Integr Genomics. 2007 Oct;7(4):317-33
references.pmid: 17578611
references.citation: Plant Cell. 1997 Oct;9(10):1859-68
references.pmid: 9368419
references.citation: Plant Physiol. 2008 Jul;147(3):1046-61
references.pmid: 18467451
references.citation: Cell. 1998 Jan 9;92(1):93-103
references.pmid: 9489703
references.citation: PLoS One. 2010 Jan 08;5(1):e8632
references.pmid: 20072620
references.citation: Plant Cell. 2001 Jan;13(1):61-72
references.pmid: 11158529
references.citation: Proc Natl Acad Sci U S A. 2007 Dec 18;104(51):20623-8
references.pmid: 18077346
references.citation: J Exp Bot. 2005 Jul;56(417):1975-81
references.pmid: 15928013
references.citation: Plant Mol Biol. 2004 Aug;55(6):807-23
references.pmid: 15604718
references.citation: Plant Physiol. 2007 Apr;143(4):1467-83
references.pmid: 17293439
references.citation: Ann Bot. 2007 Feb;99(2):211-7
references.pmid: 17218343
references.citation: Plant Signal Behav. 2010 May;5(5):481-3
references.pmid: 20139739
references.citation: Nat Biotechnol. 1999 Mar;17(3):287-91
references.pmid: 10096298
references.citation: Plant Physiol. 2003 Dec;133(4):1755-67
references.pmid: 14645724
references.citation: Plant Mol Biol. 2008 Aug;67(6):567-80
references.pmid: 18528765
references.citation: Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4945-50
references.pmid: 12684538
references.citation: Plant Physiol. 2007 Apr;143(4):1739-51
references.pmid: 17293435
references.citation: Plant Mol Biol. 2004 Aug;55(6):883-904
references.pmid: 15604723