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Genome-wide identification of major transcription factor superfamilies in rice identifies key candidates involved in abiotic stress dynamism

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Abstract

Transcription factors (TFs) are pivotal players in plant stress signaling and signal transduction pathways. Among the key TFs, NAC, ZF-HD, AP2-EREBP, WRKY and bHLH proteins play crucial roles in the regulation of reprogramming the transcriptome and associated responses in stress. Considering this, genome-wide identification of NAC, ZF-HD, AP2-EREBP, WRKY and bHLH TF families were performed in the C3 model plant, Oryza sativa. The computational study identified 144 NAC, 15 ZF-HD, 164 AP2-EREBP, 103 WRKY, and 135 bHLH proteins and their physicochemical properties and, expression profiling by computational analysis. Genome-wide in silico expression analysis of NAC, ZF-HD, AP2-EREBP, WRKY, bHLH genes showed their differential expression profiling in different tissues. Expression patterns, gene structure, subcellular localization, gene ontology of 17 NAC, 3 ZF-HD, 13 AP2-EREBP, 11 WRKY, 8 bHLH key genes suggested the putative novel variants in stress and signal transduction. These key players are needed to be studied in order to categorize and outline their functional roles in AbS signaling network.

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Abbreviations

AbS:

Abiotic stress

AbSR:

Abiotic stress responsive

GO:

Gene ontology

TFs:

Transcription factors

References

  • Albrecht C, Russinova E, Hecht V, Baaijens E, de Vries S (2005) The Arabidopsis thaliana somatic embryogenesis receptor like kinases1 and 2 control male sporogenesis. Plant Cell 17:3337–3349

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bakshi M, Oelmüller R (2014) WRKY transcription factors: Jack of many trades in plants. Plant Signal. Behav 9:e27700

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • CaiY Chen X, Xie K, Xing Q, WuY Li J, Du C, Sun Z, Guo Z (2014) Dlf1, a WRKY transcription factor, is involved in the control of flowering time and plant height in rice. PLoS One 9(7):e102529

    Article  CAS  Google Scholar 

  • Cao Y, Song F, Goodmand RM, Zheng Z (2006) Molecular characterization of four rice genes encoding ethylene-responsive transcriptional factors and their expressions in response to biotic and abiotic stress. J Plant Physiol 163:1167–1178

    Article  PubMed  CAS  Google Scholar 

  • Cao P, Jung KH, Choi D, Hwang D, Zhu J, Ronald PC (2012) The rice oligonucleotide array database: an atlas of rice gene expression. Rice. 5:17

    Article  PubMed  PubMed Central  Google Scholar 

  • Chen YF, Li L, Xu Q, Kong YH, Wang H, Wu WH (2009) The WRKY6 transcription factor modulates PHOSPHATE1 expression in response to low Pi stress in Arabidopsis. Plant Cell 21:3554–3566

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chen L, Han J, Deng X, Tan S, Li L, Li L, Zhou J, Peng H, Yang G, He G, Zhang W (2016) Expansion and stress responses of AP2/EREBP superfamily in Brachypodium Distachyon. Scientific reports 6:21623

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M, Claverie JM, Gascuel O (2008) Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 36:W465–W469

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Deslandes L, Olivier J, Theulieres F, Hirsch J, Feng DX, Bittner- Eddy P, Beynon J, Marco Y (2002) Resistance to Ralstonia solanacearum in Arabidopsis thaliana is conferred by the recessive RRS1-R gene, a member of a novel family of resistance genes. Proc Natl Acad Sci USA 99:2404–2409

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ding ZJ, Yan JY, Li GX, Wu ZC, Zhang SQ, Zheng SJ (2014) WRKY41 controls Arabidopsis seed dormancy via direct regulation Of ABI3 transcript levels not downstream of ABA. Plant J 79:810–823

    Article  PubMed  CAS  Google Scholar 

  • Du L, Chen Z (2000) Identification of genes encoding receptor-like protein kinases as possible targets of pathogen-and salicylic acid- induced WRKY DNA-binding proteins in Arabidopsis. Plant J 24:837–847

    Article  PubMed  CAS  Google Scholar 

  • Feller A, Machemer K, Braun EL, Grotewold E (2011) Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. Plant J 66:94–116

    Article  PubMed  CAS  Google Scholar 

  • Figueiredo DD, Barros PM, Cordeiro AM, Serra TS, Lourenc T, Chander S, Oliveira MM, Saibo NJ (2012) Seven zinc-finger transcription factors are novel regulators of the stress responsive gene OsDREB1B. J Exp Bot 63(10):3643–3656

    Article  PubMed  CAS  Google Scholar 

  • Garg A, Raghava GP (2008) ESLpred2: improved method for predicting subcellular localization of eukaryotic proteins. BMC Bioinform 9:503

    Article  CAS  Google Scholar 

  • Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A (2005) Protein identification and analysis tools on the ExPASy server. In: Walker JM (ed) The proteomics protocols handbook. Springer, NewYork, pp 571–607

    Chapter  Google Scholar 

  • Giri J, Dansana PK, Kothari KS, Sharma G, Vij S, Tyagi AK (2013) SAPs as novel regulators of abiotic stress response in plants. BioEssays 35:639–648

    Article  PubMed  CAS  Google Scholar 

  • Golldack D, Lu’king I, Yang O (2011) Plant tolerance to drought and salinity: stress regulating transcription factors and their functional significance in the cellular transcriptional network. Plant Cell Rep 30:1383–1391

    Article  PubMed  CAS  Google Scholar 

  • Gong W, Shen YP, Ma LG, Pan Y, Du YL, Wang DH, Yang JY, Hu LD, Liu XF, Dong CX, Ma L, Chen YH, Yang XY, Gao Y, Zhu D, Tan X, Mu JY, Zhang DB, Liu YL, DineshKumar SP, Li Y, Wang XP, Gu HY, Qu LJ, Bai SN, Lu YT, Li JY, Zhao JD, Zuo J, Huang H, Deng XW, Zhu YX (2004) Genome-wide ORFeome cloning and analysis of Arabidopsis transcription factor genes. Plant Physiol 135:773–782

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • GuanY Meng X, Khanna R, LaMontagne E, Liu Y, Zhang S (2014) Phosphorylation of a WRKY transcription factor by MAPKs is required for pollen development and function in Arabidopsis. PLoS Genet 10:e1004384

    Article  CAS  Google Scholar 

  • Guo Y, Gan S (2006) AtNAP, a NAC family transcription factor, has an important role in leaf senescence. Plant J 46:601–612

    Article  PubMed  CAS  Google Scholar 

  • Gutha LR, Reddy AR (2008) Rice DREB1B promoter shows distinct stress-specific responses, and the overexpression of cDNA in tobacco confers improved abiotic and biotic stress tolerance. Plant Mol Biol 68:533–555

    Article  PubMed  CAS  Google Scholar 

  • Gutterson N, Reuber TL (2004) Regulation of disease resistance pathways by AP2/ERF transcription factors. Curr Opin Plant Biol 7:465–471

    Article  PubMed  CAS  Google Scholar 

  • Hadiarto T, Tran LS (2011) Progress studies of drought-responsive genes in rice. Plant Cell Rep 30:297–310

    Article  PubMed  CAS  Google Scholar 

  • Hattori Y, Nagai K, Furukawa S, Song XJ, Kawano R, Sakakibara H, Wu J, Matsumoto T, Yoshimura A, Kitano H (2009) The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water. Nature 460:1026–1030

    Article  PubMed  CAS  Google Scholar 

  • Hirayama T, Shinozaki K (2010) Research on plant abiotic stress responses in the post-genome era: past, present and future. Plant J. 61:1041–1052

    Article  PubMed  CAS  Google Scholar 

  • Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K (2007) WoLF PSORT: protein localization predictor. Nucl Acids Res 35:W585–W587

    Article  PubMed  PubMed Central  Google Scholar 

  • Hsieh EJ, Cheng MC, Lin TP (2013) Functional characterization of an abiotic stress-inducible transcription factor AtERF53 in Arabidopsis thaliana. Plant Mol Biol 82:223–237

    Article  PubMed  CAS  Google Scholar 

  • Hu H, Dai M, Yao J, Xiao B, Xianghua L, Zhang Q, Xiong L (2006) Overexpressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice. Proc Natl Acad Sci USA 103:12987–12992

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hu H, You J, Fang Y, Zhu X, Qi Z, Xiong L (2008) Characterization of transcription factor gene SNAC2 conferring cold and salt tolerance in rice. Plant Mol Biol 67:169–181

    Article  PubMed  CAS  Google Scholar 

  • Hu Y, Jiang L, Wang F, Yu D (2013) Jasmonate regulates the inducer of cbf expression-C-repeat binding factor/DRE binding factor1 cascade and freezing tolerance in Arabidopsis. Plant Cell 25:2907–2924

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hu B, Jin J, Guo A-Y, Zhang H, Luo J, Gao G (2015) GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics 31(8):1296–1297

    Article  PubMed  Google Scholar 

  • Hua S, Sun Z (2001) Support vector machine approach for protein subcellular localization prediction. Bioinformatics 17:721–728

    Article  PubMed  CAS  Google Scholar 

  • Huh SU, Choi LM, Lee GJ, Kim YJ, Paek KH (2012) Capsicum annuum WRKY transcription factor (CaWRKYd) regulates hypersensitive response and defense response upon Tobacco mosaic virus infection. Plant Sci 197:50–58

    Article  PubMed  CAS  Google Scholar 

  • Jiang Y, Deyholos MK (2009) Functional characterization of Arabidopsis NaCl-inducible WRKY25 and WRKY33 transcription factors in abiotic stresses. Plant Mol Biol 69:91–105

    Article  PubMed  CAS  Google Scholar 

  • Jin J, Zhang H, Kong L, Gao G, Luo J (2014) PlantTFDB3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucl Acids Res 42:D1182–D1187

    Article  PubMed  CAS  Google Scholar 

  • Johnson CS, Kolevski B, Smyth DR (2002) Transparent testa glabra2, a trichome and seed coat development gene of Arabidopsis, encodes a WRKY transcription factor. Plant Cell 14:1359–1375

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, Batistic O, D’Angelo C, Bornberg-Bauer E, Kudla J, Harter K (2007) The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J 50:347–363

    Article  PubMed  CAS  Google Scholar 

  • Kim KC, Lai Z, Fan B, Chen Z (2008) Arabidopsis WRKY38 and WRKY62 transcription factors interact with histone deacetylase 19 in basal defense. Plant Cell 20:2357–2371

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kiribuchi K, Sugimori M, Takeda M, Otani T, Okada K, Onodera H, Ugaki M, Tanaka Y, Tomiyama-Akimoto C, Yamaguchi T, Minami E, Shibuya N, Omori T, Nishiyama M, Nojiri H, Yamane H (2004) RERJ1, a jasmonic acid-responsive gene from rice, encodes a basic helixloop—helix protein. Biochem Biophys Res Commun 325:857–863

    Article  PubMed  CAS  Google Scholar 

  • Kiribuchi K, Jikumaru Y, Kaku H, Minami E, Hasegawa M, Kodama O, Seto H, Okada K, Nojiri H, Yamane H (2005) Involvement of the basic helix-loop-helix transcription factor RERJ1 in wounding and drought stress responses in rice plants. Biosci Biotechnol Biochem 69:1042–1044

    Article  PubMed  CAS  Google Scholar 

  • Kreps JA, Wu Y, Chang HS, Zhu T, Wang X, Harper JF (2002) Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiol 130:2129–2141

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kume S, Kobayashi F, Ishibashi M, Ohno R, Nakamura C, Takumi S (2005) Differential and coordinated expression of Cbf and Cor/Lea genes during long-term cold acclimation in two wheat cultivars showing distinct levels of freezing tolerance. Genes Genet Syst 80:185–197

    Article  PubMed  CAS  Google Scholar 

  • Lata C, Muthamilarasan M, Prasad M (2015) Drought stress responses and signal transduction in plants. In: Pandey GK (ed) Elucidation of abiotic stress signaling in plants. Springer, New York, pp 195–225

    Chapter  Google Scholar 

  • Ledent V, Vervoort M (2001) The basic helix-loop-helix protein family: comparative genomics and phylogenetic analysis. Genome Res 11(5):754–770

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Li S, Fu Q, Huang W, Yu D (2009) Functional analysis of an Arabidopsis transcription factor WRKY25 in heat stress. Plant Cell Rep 28:683–693

    Article  PubMed  CAS  Google Scholar 

  • Li S, Fu Q, Chen L, Huang W, Yu D (2011) Arabidopsis thaliana WRKY25, WRKY26, and WRKY33 coordinate induction of plant thermotolerance. Planta 233:1237–1252

    Article  PubMed  CAS  Google Scholar 

  • Luo M, Dennis ES, Berger F, Peacock WJ, Chaudhury A (2005) Miniseed3 (MINI3), a WRKY family gene, and HAIKU2 (IKU2), a leucine- rich repeat (LRR) Kinase gene, are regulators of seed size in Arabidopsis. Proc Natl Acad Sci USA 102:17531–17536

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ma D, Pu G, Lei C, Ma L, Wang H, GuoY Chen J, Du Z, Wang H, Li G, Ye H, Liu B (2009) Isolation and characterization of AaWRKY1, an Artemisia annua transcription factor that regulates the amorpha- 4,11-diene synthase gene, a key gene of artemisin in biosynthesis. Plant Cell Physiol 50:2146–2161

    Article  PubMed  CAS  Google Scholar 

  • Marchive C, Mzid R, Deluc L, Barrieu F, Pirrello J, Gauthier A, Corio-Costet MF, Regad F, Cailleteau B, Hamdi S, Lauvergeat V (2007) Isolation and characterization of a Vitis vinifera transcription factor, VvWRKY1, and its effect on responses to fungal pathogens in transgenic tobacco plants. J Exp Bot 58:1999–2010

    Article  PubMed  CAS  Google Scholar 

  • MiaoY Laun T, Zimmermann P, Zentgraf U (2004) Targets of the WRKY53 transcription factor and its role during leaf senescence in Arabidopsis. Plant Mol Biol 55:853–867

    Article  Google Scholar 

  • Mickelbart MV, Hasegaw PM, Bailey-Serres J (2015) Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability. Nat Rev Genet 16:237–251

    Article  PubMed  CAS  Google Scholar 

  • Mittler R, Kim Y, Song LH, Coutu J, Coutu A, Ciftci-Yilmaz S, Lee H, Stevenson B, Zhu JK (2006) Gain- and loss-of-function mutations in Zat10 enhance the tolerance of plants to ablotic stress. FEBS Lett 580:6537–6542

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Mukhopadhyay A, Vij S, Tyagi AK (2004) Overexpression of a zinc finger protein gene from rice confers tolerance to cold, dehydration, and salt stress in transgenic tobacco. Proc Natl Acad Sci USA 101:6309–6314

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Muthamilarasan M, Prasad M (2013) Plant innate immunity: an updated insight into defense mechanism. J Bio Sci 38:433–449

    CAS  Google Scholar 

  • Muthuramalingam P, Krishnan SR, Pothiraj R, Ramesh M (2017) Global transcriptome analysis of combined abiotic stress signaling genes unravels key players in Oryza sativa L.: an in silico approach. Front. Plant Sci 8:759

    Google Scholar 

  • Nakashima K, Tran LS, Van Nguyen D, Fujita M, Maruyama K, Todaka D, Ito Y, Hayashi N, Shinozaki K, Yamaguchi-Shinozaki K (2007) Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress responsive gene expression in rice. Plant J 51:617–630

    Article  PubMed  CAS  Google Scholar 

  • Nakashima K, Ito Y, Yamaguchi-Shinozaki K (2009) Transcriptional regulatory networks in response to abiotic stresses in Arabidopsis and grasses. Plant Physiol 149:88–95

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Oh SJ, Song SI, Kim YS, Jang HJ, Kim SY, Kim M, Kim YK, Nahm BH, Kim JK (2005) Arabidopsis CBF3/DREB1A and ABF3 in transgenic rice increased tolerance to abiotic stress without stunting growth. Plant Physiol 138:341–351

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Pierleoni A, Martelli PL, Fariselli P, Casadio R (2006) BaCelLo: a balanced subcellular localization predictor. Bioinformatics 22:e408–e416

    Article  PubMed  CAS  Google Scholar 

  • Pnueli L, Hallak-Her E, Rozenberg M, Cohen M, Goloubinoff P, Kaplan A, Mittler R (2002) Molecular and biochemical mechanisms associated with dormancy and drought tolerance in the desert legume Retama raetam. Plant J. 31:319–330

    Article  PubMed  CAS  Google Scholar 

  • Priya P, Jain M (2013) RiceSRTFDB: a database of rice transcription factors containing comprehensive expression, cis-regulatory element and mutant information to facilitate gene function analysis. Database bat027

  • Puranik S, Sahu PP, Srivastava PS, Prasad M (2012) NAC proteins: regulation and role in stress tolerance. Trends Plant Sci 17:369–381

    Article  PubMed  CAS  Google Scholar 

  • Qiu Y, Yu D (2009) Over-expression of the stress-induced OsWRKY45 enhances disease resistance and drought tolerance in Arabidopsis. Env. Exp Bot 65:35–47

    Article  CAS  Google Scholar 

  • Rashotte AM, Goertzen LR (2010) The CRF domain defines cytokinin response factor proteins in plants. BMC Plant Biol 10:74

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ren X, Chen Z, Liu Y, Zhang H, Zhang M, Liu Q, Hong X, Zhu JK, Gong Z (2010) ABO3, a WRKY transcription factor, mediates plant responses to abscisic acid and drought tolerance in Arabidopsis. Plant J. 63:417–429

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Rizhsky L, Liang H, Mittler R (2002) The combined effect of drought stress and heat shock on gene expression in tobacco. Plant Physiol 130:1143–1151

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Rushton PJ, Somssich IE, Ringler P, Shen QJ (2010) WRKY transcription factors. Trends Plant Sci 15:247–258

    Article  PubMed  CAS  Google Scholar 

  • Sakuma Y, Maruyama K, Qin F, Osakabe Y, Shinozaki K, Yamaguchi-Shinozaki K (2006) Dual function of an Arabidopsis transcription factor DREB2A in water-stress-responsive and heat-stress-responsive gene expression. Proc Natl Acad Sci USA 103:18822–18827

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sharoni AM, Nuruzzaman M, Satoh K, Shimizu T, Kondoh H, Sasaya T, Choi IR, Omura T, Kikuchi S (2010) Gene structures, classification and expression models of the AP2/EREBP transcription factor family in rice. Plant and cell physiol 52:344–360

    Article  CAS  Google Scholar 

  • Sharoni AM, Nuruzzaman M, Satoh K, Shimizu T, Kondoh H, Sasaya T, Choi IR, Omura T, Kikuchi S (2011) Gene structures, classification and expression models of the AP2/EREBP transcription factor family in rice. Plant Cell Physiol 52(2):344–360

    Article  PubMed  CAS  Google Scholar 

  • Shigyo M, Ito M (2004) Analysis of gymnosperm two-AP2-domain-containing genes. Dev Genes Evol 214:105–114

    Article  PubMed  CAS  Google Scholar 

  • Shimono M, Sugano S, Nakayama A, Jiang CJ, Ono K, Toki S, Takatsuji H (2007) Rice WRKY45 plays a crucial role in benzothiadiazole inducible BLAST resistance. Plant Cell 19:2064–2076

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Shinozaki K, Yamaguchi-Shinozaki K, Seki M (2003) Regulatory network of gene expression in the drought and cold stress responses. Curr Opin Plant Biol 6(5):410–417

    Article  PubMed  CAS  Google Scholar 

  • Singh KB, Foley RC, Oñate-Sánchez L (2002) Transcription factors in plant defense and stress responses. Curr Opin Plant Biol 5(5):430–436

    Article  PubMed  CAS  Google Scholar 

  • Singh AK, Sopory SK, Wu R, Singla-Pareek SL (2010) Transgenic approaches. In: Pareek A, Sopory SK, Bohnert HJ, Govindjee (eds.) Abiotic stress adaptation in plants: physiological, molecular and genomic foundation, Springer, Berlin, Germany, pp 417–450

  • Song Y, Jing SJ, Yu DQ (2009) Overexpression of the stress induced OsWRKY08 improves the osmotic stress tolerance in Arabidopsis. Chin Sci Bull 54:4671–4678

    CAS  Google Scholar 

  • Song Y, Chen LG, Zhang LP, Yu DQ (2010) Overexpression of OsWRKY72 gene interferes in the ABA signal and auxin transport pathway of Arabidopsis. J Biosci 35:459–471

    Article  CAS  Google Scholar 

  • Sonnenfeld MJ, Delvecchio C, Sun X (2005) Analysis of the transcriptional activation domain of the Drosophila tango bHLH-PAS transcription factor. Dev Genes Evol 215:221–229

    Article  PubMed  CAS  Google Scholar 

  • Suttipanta N, Pattanaik S, Kulshrestha M, Patra B, Singh SK, Yuan L (2011) The transcription factor CrWRKY1 positively regulates the terpenoid indole alkaloid biosynthesis in Catharanthus roseus. Plant Physiol 157:2081–2093

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Tang J, Wang F, Wang Z, Huang Z, Xiong A, Hou X (2013) Characterization and co-expression analysis of WRKY orthologs involved in responses to multiple abiotic stresses in Pak-choi (Brassicacampestris ssp. chinensis). BMC Plant Biol 13:188

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Toledo-Ortiz G, Huq E, Quail PH (2003) The Arabidopsis basic/helixloop- helix transcription factor family. Plant Cell 15:1749–1770

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Udvardi MK, Kakar K, Wandrey M, Montanari O, Murray J, Andriankaja A, Zhang JY, Benedito V, Hofer JMI, Chueng F, Town CD (2007) Legume transcription factors: global regulators of plant Development and response to the environment. Plant Physiol 144:538–549

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ulker B, Somssich IE (2004) WRKY transcription factors: from DNA binding towards biological function. Curr Opin Plant Biol 7:491–498

    Article  PubMed  CAS  Google Scholar 

  • Urano K, Kurihara Y, Seki M, Shinozaki K (2010) ‘Omics’ analyses of regulatory networks in plant abiotic stress responses. Curr Opin Plant Biol 13:1–7

    Article  CAS  Google Scholar 

  • Vij S, Tyagi AK (2006) Genome-wide analysis of the stress associated protein (SAP) gene family containing A20/AN1 zinc-finger(s) in rice and their phylogenetic relationship with Arabidopsis. Mol Genet Genomics 276:565–575

    Article  PubMed  CAS  Google Scholar 

  • Wang YJ, Zhang ZG, He XJ, Zhou HL, Wen YX, Dai JX, Zhang JS, Chen SY (2003) A rice transcription factor OsbHLH1 is involved in cold stress response. Theor Appl Genet 107:1402–1409

    Article  PubMed  CAS  Google Scholar 

  • Wu X, Shiroto Y, Kishitani S, Ito Y, Toriyama K (2009) Enhanced heat and drought tolerance in transgenic rice seedlings overexpressing OsWRKY11 under the control of HSP101 promoter. Plant Cell Rep 28:21–30

    Article  PubMed  CAS  Google Scholar 

  • Xia N, Zhang G, Liu XY, Deng L, Cai GL, Zhang Y, Wang XJ, Zhao J, Huang LL, Kang ZS (2010) Characterization of a novel wheat NAC transcription factor gene involved in defense response against stripe rust pathogen infection and abiotic stresses. Mol Biol Rep 37:3703–3712

    Article  PubMed  CAS  Google Scholar 

  • Xiong Y, Liu T, Tian C, Sun S, Li J, Chen M (2005) Transcription factors in rice: a genome wide comparative analysis between monocots and eudicots. Plant Mol Biol 59:191–203

    Article  PubMed  CAS  Google Scholar 

  • Xu DQ, Huang J, Guo SQ, Yang X, Bao YM, Tang HJ, Zhang HS (2008) Overexpression of a TFIIIA-type zinc finger protein gene ZFP252 enhances drought and salt tolerance in rice (Oryza sativa L.). FEBS Lett 582:1037–1043

    Article  PubMed  CAS  Google Scholar 

  • Yang S, Vanderbeld B, Wan J, Huang Y (2010) Narrowing down the targets: towards successful genetic engineering of drought-tolerant crops. Mol Plant 3:469–490

    Article  PubMed  CAS  Google Scholar 

  • Yi K, Wu Z, Zhou J, Du L, Guo L, Wu Y, Wu P (2005) OsPTF1, a novel transcription factor involved in tolerance to phosphate starvation in rice. Plant Physiol 138:2087–2096

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Yilmaz A, Nishiyama MY, Fuentes BG, Souza GM, Janies D, Gray J, Grotewold E (2009) GRASSIUS: a platform for comparative regulatory genomics across the grasses. Plant Physiol 149:171–180

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Yu Y, Hu R, Wang H, Cao Y, He G, Fu C, Zhou G (2013) MlWRKY12, a novel Miscanthus transcription factor, participates in pith secondary cellwall formation and promotes flowering. Plant Sci 212:1–9

    Article  PubMed  CAS  Google Scholar 

  • Yu CS, Cheng CW, Su WC, Chang KC, Huang SW, Hwang JK, Lu CH (2014) CELLO2GO: a web server for protein subcellular localization prediction with functional gene ontology annotation. PLoS One 9:e99368

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhao X, de Palma J, Oane R, Gamuyao R, Luo M, Chaudhury A, Hervé P, Xue Q, Bennett J (2008) OsTDL1A binds to the LRR domain of rice receptor kinase MSP1, and is required to limit sporocyte numbers. Plant J 54:375–387

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zheng Z, Qamar SA, Chen Z, Mengiste T (2006) Arabidopsis WRKY33 transcription factor is required for resistance to necrotrophic fungal pathogens. Plant J 48:592–605

    Article  PubMed  CAS  Google Scholar 

  • Zheng X, Chen B, Lu G, Han B (2009) Overexpression of a NAC transcription factor enhances rice drought and salt tolerance. Biochem Biophys Res Commun 379:985–989

    Article  PubMed  CAS  Google Scholar 

  • Zou CS, Jiang WB, Yu DQ (2010) Male gametophyte-specific WRKY34 transcription factor negatively mediates cold stress tolerance of mature pollen in Arabidopsis. J Exp Bot 14:3901–3914

    Article  CAS  Google Scholar 

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Acknowledgements

PM acknowledges Alagappa University Research Fund (Ph.D./1215/AURF Fellowship/2015 dated 25.11.2015), Karaikudi, Tamil Nadu, India for providing Research Fellowship. The authors gratefully acknowledge the use of Bioinformatics Infrastructure Facility, Alagappa University funded by Department of Biotechnology, Ministry of Science and Technology, Government of India Grant (No.BT/BI/25/015/2012).

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  1. Subramanian Radhesh Krishnan

    Present address: Phytopharma Testing Laboratory, Herbal Division, T.Stanes & Company Ltd, 1128, Coimbatore, 641018, India

Authors and Affiliations

  1. Department of Biotechnology, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, 630 003, India

    Pandiyan Muthuramalingam, Subramanian Radhesh Krishnan, Kadarkarai Saravanan, Narayanan Mareeswaran & Manikandan Ramesh

  2. Department of Biochemistry, Panjab University, Chandigarh, 160 014, India

    Reetesh Kumar

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Muthuramalingam, P., Krishnan, S.R., Saravanan, K. et al. Genome-wide identification of major transcription factor superfamilies in rice identifies key candidates involved in abiotic stress dynamism. J. Plant Biochem. Biotechnol. 27, 300–317 (2018). https://doi.org/10.1007/s13562-018-0440-3

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