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Transcriptome-wide analysis of WRKY transcription factors in wheat and their leaf rust responsive expression profiling

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Abstract

WRKY, a plant-specific transcription factor family, has important roles in pathogen defense, abiotic cues and phytohormone signaling, yet little is known about their roles and molecular mechanism of function in response to rust diseases in wheat. We identified 100 TaWRKY sequences using wheat Expressed Sequence Tag database of which 22 WRKY sequences were novel. Identified proteins were characterized based on their zinc finger motifs and phylogenetic analysis clustered them into six clades consisting of class IIc and class III WRKY proteins. Functional annotation revealed major functions in metabolic and cellular processes in control plants; whereas response to stimuli, signaling and defense in pathogen inoculated plants, their major molecular function being binding to DNA. Tag-based expression analysis of the identified genes revealed differential expression between mock and Puccinia triticina inoculated wheat near isogenic lines. Gene expression was also performed with six rust-related microarray experiments at Gene Expression Omnibus database. TaWRKY10, 15, 17 and 56 were common in both tag-based and microarray-based differential expression analysis and could be representing rust specific WRKY genes. The obtained results will bestow insight into the functional characterization of WRKY transcription factors responsive to leaf rust pathogenesis that can be used as candidate genes in molecular breeding programs to improve biotic stress tolerance in wheat.

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Abbreviations

ESTs:

Expressed sequence tags

GEO:

Gene expression omnibus

GRAVY:

Grand average of hydropathicity

IWGSC:

International wheat genome sequencing consortium

MEGA:

Molecular evolutionary genetic analysis

NCBI:

National Centre for Biotechnology Information

NLS:

Nuclear localization signals

SAGE:

Serial analysis of gene expression

SOLiD:

Sequencing by oligonucleotide ligation and detection

SRA:

Sequence read archive

R-genes:

Resistant genes

TF:

Transcription factor

References

  • Alnemer LM, Seetan RI, Bassi FM, Chitraranjan C, Helsene A, Loree P, Goshn SB, Gu YQ, Luo MC, Iqbal MJ, Lazo GR, Denton AM, Kianian SF (2013) Wheat Zapper: a flexible online tool for colinearity studies in grass genomes. Funct Integr Genomics 13:11–17

    Article  CAS  PubMed  Google Scholar 

  • Atkinson NJ, Urwin PE (2012) The interaction of plant biotic and abiotic stresses: from genes to the field. J Exp Bot 63:3523–3543

    Article  CAS  PubMed  Google Scholar 

  • Babu MM, Iyer LM, Balaji S, Aravind L (2006) The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons. Nucleic Acids Res 34:6505–6520

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Bahrini I, Sugisawa M, Kikuchi R, Ogawa T, Kawahigashi H, Ban T, Handa H (2011) Characterization of wheat transcription factor, TaWRKY45, and its effect on Fusarium head blight resistance in transgenic wheat plants. Breeding Sci 61:121–129

    Article  CAS  Google Scholar 

  • Bailey TL, Bodén M, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS (2009) Noble MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37:W202–W208

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Bevan MW, Uauy C (2013) Genomics reveals new landscapes for crop improvement. Genome Biol 14:206

    Article  PubMed Central  PubMed  Google Scholar 

  • Bipinraj A, Honrao B, Prashar M, Bhardwaj S, Rao S, Tamhankar S (2011) Validation and identification of molecular markers linked to the leaf rust resistance gene Lr28 in wheat. J Appl Genet 52:171–175

    Article  CAS  PubMed  Google Scholar 

  • Bjellqvist B, Basse B, Olsen E, Celis JE (1994) Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions. Electrophoresis 15:529–539

    Article  CAS  PubMed  Google Scholar 

  • Blom N, Gammeltoft S, Brunak S (1999) Sequence and structure based prediction of eukaryotic protein phosphorylation sites. J Mol Biol 294:1351–1362

    Article  CAS  PubMed  Google Scholar 

  • Botha AM, Swanevelder ZH, Lapitan NLV (2010) Transcript profiling of wheat genes expressed during feeding by two different biotypes of Diuraphis noxia. Environ Entomol 39:1206–1231

    Article  CAS  PubMed  Google Scholar 

  • Braun HJ, Atlin G, Payne T (2010) Multi location testing as a tool to identify plant response to global climate change. In: Reynolds CRP (ed) Climate change and crop production. CABI, London

    Google Scholar 

  • Brenchley R, Spannagl M, Pfeifer M, Barker GLA, Amore RD, Allen AM, McKenzie N, Kramer M, Kerhornou A, Bolser D, Kay S, Waite D, Trick M, Bancroft I, Gu Y, Huo N, Luo MC, Sehgal S, Gill B, Kianian S, Anderson O, Kersey P, Dvorak J, McCombie WR, Hall A, Mayer KFX, Edwards KJ, Bevan MW, Hall N (2012) Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 5:705–711

    Article  Google Scholar 

  • Buchan DWA, Minneci F, Nugent TCO, Bryson K, Jones DT (2013) Scalable web services for the PSIPRED protein analysis workbench. Nucleic Acids Res 41:W340–W348

    Article  Google Scholar 

  • Choulet F, Wicker T, Rustenholz C, Paux E, Salse J, Leroy P, Schlub S, Paslier MCL, Magdelenat G, Gonthier C, Couloux A, Budak H, Breen J, Pumphrey M, Liu S, Kong X, Jia J, Gut M, Brunel D, Anderson JA, Gill BS, Appels R, Keller B, Feuillet C (2010) Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces. Plant Cell 22:1686–1701

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Conesa A, Gotz S (2008) BLAST2GO: A comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics 1–13. doi: 10.1155/2008/619832

  • Coram TE, Settles ML, Chen X (2008) Transcriptome analysis of high-temperature adult-plant resistance conditioned by Yr39 during the wheat-Puccinia striiformis f. sp. tritici interaction. Mol Plant Pathol 9:479–493

    Article  CAS  PubMed  Google Scholar 

  • Dang FF, Wang YN, Yu L, Lai Y, Liu ZQ, Wang X, Qiu AL, Zhang TX, Lin J, Chen YS, Guan DY, Cai HY, Mou SL, He SL (2013) CaWRKY40, a WRKY protein of pepper, plays an important role in the regulation of tolerance to heat stress and resistance to Ralstonia solanacearum infection. Plant Cell Environ 36:757–774

    Article  CAS  PubMed  Google Scholar 

  • Dean R, Van-Kan JAL, Pretorius ZA, Hammond-Kosack KE, Pietro AD, Spanu PD, Rudd JJ, Dickman M, Kahmann R, Ellis J, Foster GD (2012) The top 10 fungal pathogens in molecular plant pathology. Mol Plant Pathol 13:414–430

    Article  PubMed  Google Scholar 

  • Dong J, Chen C, Chen Z (2003) Expression profiles of the Arabidopsis WRKY gene superfamily during plant defence response. Plant Mol Biol 51:21–37

    Article  CAS  PubMed  Google Scholar 

  • Dubcovsky J, Dvorak J (2007) Genome plasticity a key factor in the success of polyploid wheat under domestication. Science 316:1862–1866

    Article  CAS  PubMed  Google Scholar 

  • Eulgem T, Somssich IE (2007) Networks of WRKY transcription factors in defence signaling. Curr Opin Plant Biol 10:366–371

    Article  CAS  PubMed  Google Scholar 

  • Eulgem T, Rushton PJ, Robatzek S, Somssich IE (2000) The WRKY superfamily of plant transcription factors. Trends Plant Sci 5:199–206

    Article  CAS  PubMed  Google Scholar 

  • Eversmeyer MG, Kramer CL (2000) Epidemiology of wheat leaf and stem rust in the central great plains of the USA. Annu Rev Phytopathol 38:491–513

    Article  CAS  PubMed  Google Scholar 

  • F.A.O. Food and Agriculture Organization of the United Nations. http://www.fao.org. Last Accessed Feb 2014

  • Garg B, Puranik S, Misra S, Tripathy BN, Prasad M (2013) Transcript profiling identifies novel transcripts with unknown functions as primary response components to osmotic stress in wheat (Triticum aestivum L.). Plant Cell Tiss Org 113:91–101

    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. The proteomics protocols handbook. Humana Press, Totowa, NJ

    Google Scholar 

  • Gupta R, Jung E, Brunak S (2004) Prediction of N-glycosylation sites in human proteins. Pac Symp Biocomput 7:310–322

    Google Scholar 

  • Horton P, Park K, Obayashi T, Nakai K (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res 35:W585–W587

    Article  PubMed Central  PubMed  Google Scholar 

  • Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, Widmayer P, Gruissem W, Zimmermann P (2008) Genevestigator V3: a reference expression database for the meta-analysis of transcriptomes. Adv Bioinf 2008:420747. doi:10.1155/2008/420747

  • Hu G, Rijkenberg FHJ (1998) Scanning electron microscopy of early infection structure formation by Puccinia recondita f. sp. tritici on and in susceptible and resistant wheat lines. Mycol Res 102:391–399

    Article  Google Scholar 

  • Huang S, Gao Y, Liu J, Peng X, Niu X, Fei Z, Cao S, Liu Y (2012) Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum. Mol Genet Genomics 287:495–513

    Article  CAS  PubMed  Google Scholar 

  • International Wheat Genome Sequencing Consortium. http://www.wheatgenome.org. Accessed 20 Feb 2014

  • Jia F, Wu B, Li H, Huang J, Zheng C (2013) Genome-wide identification and characterization of F-box family in maize. Mol Genet Genomics 288:559–577

    Article  CAS  PubMed  Google Scholar 

  • Kalde M, Barth M, Somssich IE, Lippok B (2003) Members of the Arabidopsis WRKY group III transcription factors are part of different plant defence signalling pathways. Mol Plant Microbe In 16:295–305

    Article  CAS  Google Scholar 

  • Kersey PJ, Allen JE, Christensen M, Davis P, Falin LJ, Grabmueller C, Hughes DS, Humphrey J, Kerhornou A, Khobova J, Langridge N, McDowall MD, Maheswari U, Maslen G, Nuhn M, Ong CK, Paulini M, Pedro H, Toneva I, Tuli MA, Walts B, Williams G, Wilson D, Youens-Clark K, Monaco MK, Stein J, Wei X, Ware D, Bolser DM, Howe KL, Kulesha E, Lawson D, Staines DM (2014) Ensembl genomes 2013: scaling up access to genome-wide data. Nucleic Acids Res 42:D546–D552

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kumar D, Kapoor A, Singh D, Satapathy L, Singh AK, Kumar M, Prabhu KV, Mukhopadhyay K (2014) Functional characterization of a WRKY transcription factor of wheat and its expression analysis during leaf rust pathogenesis. Funct Plant Biol. doi:10.1071/FP14077. Accepted 4 Jun 2014

  • Liu T, Zhu S, Tang Q, Tang S (2014) Identification of 32 full-length NAC transcription factors in ramie (Boehmeria nivea L. Gaud) and characterization of the expression pattern of these genes. Mol Genet Genomics. doi: 10.1007/s00438-014-0842-4

  • Mangelsen E, Kilian J, Berendzen KW, Kolukisaoglu UH, Harter K, Jansson C, Wanke D (2008) Phylogenetic and comparative gene expression analysis of barley (Hordeum vulgare) WRKY transcription factor family reveals putatively retained functions between monocots and dicots. BMC Genom 9:194

    Article  Google Scholar 

  • Manickavelu A, Kawaura K, Oishi K, Shin IT, Kohara Y, Yahiaoui N, Keller B, Abe R, Suzuki A, Nagayama T, Yano K, Ogihara Y (2012) Comprehensive functional analyses of expressed sequence tags in common wheat (Triticum aestivum). DNA Res 19:165–177

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH (2011) CDD: a conserved domain database for the functional annotation of proteins. Nucleic Acids Res 39:225–229

    Article  Google Scholar 

  • McIntosh RA, Pretorius ZA (2011) Borlaug global rust initiative provides momentum for wheat rust research. Euphytica 179:1–2

    Article  Google Scholar 

  • Meskauskiene R, Laule O, Ivanov NV, Martin F, Wyss M, Gruissem W, Zimmermann P (2013) Controlled vocabularies for plant anatomical parts optimized for use in data analysis tools and for cross-species studies. Plant Methods 9:33–39

    Article  PubMed Central  PubMed  Google Scholar 

  • Mochida K, Yoshida T, Sakurai T, Yamaguchi-Shinozaki K, Shinozaki K, Tran LS (2011) In silico analysis of transcription factor repertoires and prediction of stress-responsive transcription factors from six major gramineae plants. DNA Res 18:321–332

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Nguyen BAN, Pogoutse A, Provart N, Moses AM (2009) NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction. BMC Bioinf 10:202

    Article  Google Scholar 

  • Niu C, Wei W, Zhou Q, Tian A, Hao Y, Zhang W, Ma B, Lin Q, Zhang Z, Zhang J, Chen S (2012) Wheat WRKY genes TaWRKY2 and TaWRKY19 regulate abiotic stress tolerance in transgenic Arabidopsis plants. Plant Cell Environ 35(6):1156–1170

    Article  CAS  PubMed  Google Scholar 

  • Okay S, Derelli E, Unver T (2014) Transcriptome-wide identification of bread wheat WRKY transcription factors in response to drought stress. Mol Genet Genomics. doi:10.1007/s00438-014-0849-x. Online ISSN 1617-4623

  • Olga A, Postnikova, Jonathan S, Lev G, Nemchinov (2014) In silico identification of transcription factors in Medicago sativa using available transcriptomic resources. Mol Genet Genomics 289(3):457–468. doi:10.1007/s00438-014-0823-7

  • Pandey P, Somssich IE (2009) The role of WRKY transcription factors in plant immunity. Plant Physiol 150:1648–1655

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Park R, Wellings C (2011) Cereal rust survey 2011: progress report new leaf rust pathotype and re-emerging stripe rust pathotype. Cereal Rust Rep 9:1–3

    Google Scholar 

  • Poland JA, Balint-Kurti PJ, Wisser RJ, Pratt RC, Nelson RJ (2009) Shades of gray: the world of quantitative disease resistance. Trends Plant Sci 14:21–29

    Article  CAS  PubMed  Google Scholar 

  • Proietti S, Bertini L, Vander ES, Leon-Reyes A, Pieterse CMJ, Tucci M, Caporale C, Caruso C (2010) Cross activity of orthologous WRKY transcription factors in wheat and Arabidopsis. J Exp Bot 62:1975–1990

    Article  PubMed Central  PubMed  Google Scholar 

  • Puranik S, Sahu PP, Mandal SN, Suresh BV, Parida SK, Prasad M (2013) Comprehensive genome-wide survey, genomic constitution and expression profiling of the NAC transcription factor family in foxtail millet (Setaria italica L.). PLoS ONE 8:e64594. doi:10.1371/journal.pone.0064594

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Ramamoorthy R, Jiang SY, Kumar N, Venkatesh PN, Ramachandran S (2008) A comprehensive transcriptional profiling of the WRKY gene family in rice under various abiotic and phytohormone treatments. Plant Cell Physiol 49:865–879

    Article  CAS  PubMed  Google Scholar 

  • Rosegrant MW, Agcaoili M (2010) Global food demand, supply, and price prospects to 2010. International Food Policy Research Institute, Washington DC

    Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Ryu HS, Han M, Lee SK, Cho JI, Ryoo N, Heu S, Lee YH, Bhoo SH, Wang GL, Hahn TR, Jeon JS (2006) A comprehensive expression analysis of the WRKY gene superfamily in rice plants during defence response. Plant Cell Rep 25:836–847

    Article  CAS  PubMed  Google Scholar 

  • Shekhawat UKS, Ganapathi TR, Srinivas L (2011) Cloning and characterization of a novel stress-responsive WRKY transcription factor gene (Musa WRKY71) from Musa spp. cv. Karibale Monthan (ABB group) using transformed banana cells. Mol Biol Rep 38:4023–4035

    Article  CAS  PubMed  Google Scholar 

  • Singh D, Bhaganagare G, Bandopadhyay R, Prabhu KV, Gupta PK, Mukhopadhyay K (2012) Targeted spatio-temporal expression based characterization of state of infection and time-point of maximum defense in wheat NILs during leaf rust infection. Mol Biol Rep 39:9373–9382

    Article  CAS  PubMed  Google Scholar 

  • Smoot M, Ono K, Ruscheinski J, Wang P, Ideker T (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27:431–432

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Tamura K, Peterson D, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Tripathi P, Rabara RC, Langum TJ, Boken AK, Rushton DL, Boomsma DD, Rinerson CI, Rabara J, Reese RN, Chen X, Rohila JS, Rushton PJ (2012) The WRKY transcription factor family in Brachypodium distachyon. BMC Genom 13:270

    Article  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  Google Scholar 

  • Wei KF, Chen J, Chen YF, Wu LJ, Xie DX (2012) Molecular phylogenetic and expression analysis of the complete WRKY transcription factor family in maize. DNA Res 19:153–164

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Wu H, Ni Z, Yao Y, Guo G, Sun Q (2008) Cloning and expression profiles of 15 genes encoding WRKY transcription factor in wheat (Triticum aestivum L.). Prog Nat Sci 18:697–705

    Article  CAS  Google Scholar 

  • Xiaoming S, Gaofeng L, Weike D, Tongkun L, Zhinan H, Jun R, Ying L, Xilin H (2014) Genome-wide identification, classification and expression analysis of the heat shock transcription factor family in Chinese cabbage. Mol Genet Genomics. doi:10.1007/s00438-014-0833-5

    Google Scholar 

  • Xie Z, Ruas P, Shen QJ (2005) Regulatory networks of the phytohormone abscisic acid. Vitam Horm 72:235–269

    Article  CAS  PubMed  Google Scholar 

  • Yilmaz A, Milton Y, Nishiyama J, 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  CAS  PubMed Central  PubMed  Google Scholar 

  • Zhou QY, Tian AG, Zou HF, Xie ZM, Lei G, Huang J, Wang CM, Wang HW, Zhang JS, Chen SY (2008) Soybean WRKY-type transcription factor genes, GmWRKY13, GmWRKY21, and GmWRKY54, confer differential tolerance to abiotic stresses in transgenic Arabidopsis plants. Plant Biotechnol J 6:486–503

    Article  CAS  PubMed  Google Scholar 

  • Zhu X, Liu S, Meng C, Qin L, Kong L, Guangmin X (2013) WRKY transcription factors in wheat and their induction by biotic and abiotic stress. Plant Mol Biol Rep 31:1053–1067

    Article  CAS  Google Scholar 

  • Zou X, Seemann JR, Neuman D, Shen QJ (2004) A WRKY gene from creosote bush encodes an activator of the abscisic acid signaling pathway. J Biol Chem 279:55770–55779

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

This work was supported by Department of Biotechnology, Government of India (Grant No. BT/PR6037/AGR/02/308/05), BTISNet SubDIC (BT/BI/04/065/04), Department of Agriculture, Government of Jharkhand (5/B.K.V/Misc/12/2001) and CoE-TEQIP-II (Grant No. NPIU/TEQIP II/FIN/31/158). L. S. is grateful to Department of Science and Technology-INSPIRE (Fellowship/2011/318) and D. K. to Council of Scientific and Industrial Research [9/554 (0026) 2010-EMR-I] for Ph. D. fellowships.

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Authors and Affiliations

  1. Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, 835215, India

    Lopamudra Satapathy, Dharmendra Singh, Prashant Ranjan, Dhananjay Kumar, Manish Kumar & Kunal Mukhopadhyay

  2. Department of Genetics, Indian Agriculture Research Institute, New Delhi, 110012, India

    Kumble Vinod Prabhu

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  1. Lopamudra Satapathy
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  2. Dharmendra Singh
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  7. Kunal Mukhopadhyay
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Correspondence to Kunal Mukhopadhyay.

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Satapathy, L., Singh, D., Ranjan, P. et al. Transcriptome-wide analysis of WRKY transcription factors in wheat and their leaf rust responsive expression profiling. Mol Genet Genomics 289, 1289–1306 (2014). https://doi.org/10.1007/s00438-014-0890-9

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