Genome and transcriptome analysis of the grapevine (Vitis vinifera L.) WRKY gene family

Abstract

The plant WRKY gene family represents an ancient and complex class of zinc-finger transcription factors (TFs) that are involved in the regulation of various physiological processes, such as development and senescence, and in plant response to many biotic and abiotic stresses. Despite the growing number of studies on the genomic organisation of WRKY gene family in different species, little information is available about this family in grapevine (Vitis vinifera L.). In the present study, a total number of 59 putative grapevine WRKY transcription factors (VvWRKYs) were identified based on the analysis of various genomic and proteomic grapevine databases. According to their structural and phylogentic features, the identified grapevine WRKY transcription factors were classified into three main groups. In order to shed light into their regulatory roles in growth and development as well as in response to biotic and abiotic stress in grapevine, the VvWRKYs expression profiles were examined in publicly available microarray data. Bioinformatics analysis of these data revealed distinct temporal and spatial expression patterns of VvWRKYs in various tissues, organs and developmental stages, as well as in response to biotic and abiotic stresses. To also extend our analysis to situations not covered by the arrays and to validate our results, the expression profiles of selected VvWRKYs in response to drought stress, Erysiphe necator (powdery mildew) infection, and hormone treatments (salicilic acid and ethylene), were investigated by quantitative real-time reverse transcription PCR (qRT-PCR). The present study provides a foundation for further comparative genomics and functional studies of this important class of transcriptional regulators in grapevine.

References

[1] Kunkel BN, Brooks DM . Cross talk between signaling pathways in pathogen defense. Curr Opin Plant Biol 2002; 5: 325-331.

[2] Singh K, Foley RC, Onate-Sanchez L . Transcription factors in plant defense and stress responses. Curr Opin Plant Biol 2002; 5: 430-436.

[3] Mahalingam R, Gomez-Buitrago A, Eckardt N et al. Characterizing the stress/defense transcriptome of Arabidopsis. Genome Biol 2003; 4: R20.

[4] Katagiri F . A global view of defense gene expression regulation-a highly interconnected signaling network. Curr Opin Plant Biol 2004; 7: 506-511.

[5] Eulgem T, Rushton PJ, Schmelzer E, Hahlbrock K, Somssich IE . Early nuclear events in plant defence signalling: rapid gene activation by WRKY transcription factors. EMBO J 1999; 18: 4689-4699.

[6] Ulker B, Somssich IE . WRKY transcription factors: from DNA binding towards biological function. Curr Opin Plant Biol 2004; 7: 491-498.

[7] van Verk MC, Pappaioannou D, Neeleman L, Bol JF, Linthorst HJ . A novel WRKY transcription factor is required for induction of PR-1a gene expression by salicylic acid and bacterial elicitors. Plant Physiol 2008; 146: 1983-1995.

[8] Rushton PJ, Somssich IE, Ringler P, Shen QJ . WRKY transcription factors. Trends Plant Sci 2010; 15: 247-258.

[9] Durrant WE, Dong X . Systemic acquired resistance. Annu Rev Phytopathol 2004; 42: 185-209.

[10] Bostock RM . Signal crosstalk and induced resistance: straddling the line between cost and benefit. Annu Rev Phytopathol 2005; 43: 545-580.

[11] Mur LA, Kenton P, Atzorn R, Miersch O, Wasternack C . The outcomes of concentration-specific interactions between salicylate and jasmonate signaling include synergy, antagonism, and oxidative stress leading to cell death. Plant Physiol 2006; 140: 249-262.

[12] Wang D, Amornsiripanitch N, Dong X . A genomic approach to identify regulatory nodes in the transcriptional network of systemic acquired resistance in plants. PLoS Pathog 2006; 2: e123.

[13] Knoth C, Ringler J, Dangl JL, Eulgem T . Arabidopsis WRKY70 is required for full RPP4-mediated disease resistance and basal defense against Hyaloperonospora parasitica. Mol Plant Microbe Interact 2007; 20: 120-128.

[14] Lai Z, Vinod K, Zheng Z, Fan B, Chen Z . Roles of Arabidopsis WRKY3 and WRKY4 transcription factors in plant responses to pathogens. BMC Plant Biol 2008; 8: 68.

[15] Kim KC, Fan BF, Chen ZX . Pathogen-induced Arabidopsis WRKY7 is a transcriptional repressor and enhances plant susceptibility to Pseudomonas syringae. Plant Physiol 2006; 142: 1180-1192.

[16] Kim KC, Lai ZB, Fan BF, Chen ZX . Arabidopsis WRKY38 and WRKY62 transcription factors interact with histone deacetylase 19 in basal defense. Plant Cell 2008; 20: 2357-2371.

[17] Mao P, Duan MR, Wei CH, Li Y . WRKY62 transcription factor acts downstream of cytosolic NPR1 and negatively regulates jasmonate-responsive gene expression. Plant Cell Physiol 2007; 48: 833-842.

[18] Xing DH, Lai ZB, Zheng ZY, Vinod KM, Fan BF, Chen ZX . Stress- and pathogen-induced Arabidopsis WRKY48 is a transcriptional activator that represses plant basal defense. Mol Plant 2008; 1: 459-470.

[19] Tao Z, Liu H, Qiu D et al. A pair of allelic WRKY genes play opposite roles in rice-bacteria interactions. Plant Physiol 2009; 151: 936-948.

[20] Shimono M, Sugano S, Nakayama A et al. Rice WRKY45 plays a crucial role in benzothiadiazole-inducible blast resistance. Plant Cell 2007; 19: 2064-2076.

[21] Shen QH, Saijo Y, Mauch S et al. Nuclear activity of MLA immune receptors links isolate-specific and basal disease-resistance responses. Science 2007; 315: 1098-1103.

[22] Skibbe M, Qu N, Galis I, Baldwin IT . Induced plant defenses in the natural environment: Nicotiana attenuata WRKY3 and WRKY6 coordinate responses to herbivory. Plant Cell 2008; 20: 1984-2000.

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

[24] Jiang Y, Deyholos MK . Functional characterization of Arabidopsis NaCl-inducible WRKY25 and WRKY33 transcription factors in abiotic stresses. Plant Mol Biol 2009; 69: 91-105.

[25] Li S, Fu Q, Huang W, Yu D . Functional analysis of an Arabidopsis transcription factor WRKY25 in heat stress. Plant Cell Rep 2009; 28: 683-693.

[26] Xie Z, Zhang ZL, Hanzlik S, Cook E, Shen QJ . Salicylic acid inhibits gibberellin-induced alpha-amylase expression and seed germination via a pathway involving an abscisic-acid-inducible WRKY gene. Plant Mol Biol 2007; 64: 293-303.

[27] Zou X, Neuman D, Shen QJ . Interactions of two transcriptional repressors and two transcriptional activators in modulating gibberellin signaling in aleurone cells. Plant Physiol 2008; 148: 176-186.

[28] Johnson CS, Kolevski B, Smyth DR . TRANSPARENT TESTA GLABRA2, a trichome and seed coat development gene of Arabidopsis, encodes a WRKY transcription factor. Plant Cell 2002; 14: 1359-1375.

[29] Ishida T, Hattori S, Sano R et al. Arabidopsis TRANSPARENT TESTA GLABRA2 is directly regulated by R2R3 MYB transcription factors and is involved in regulation of GLABRA2 transcription in epidermal differentiation. Plant Cell 2007; 19: 2531-2543.

[30] Robatzek S, Somssich IE . A new member of the Arabidopsis WRKY transcription factor family, AtWRKY6, is associated with both senescence- and defence-related processes. Plant J 2001; 28: 123-133.

[31] Miao Y, Laun T, Zimmermann P, Zentgraf U . Targets of the WRKY53 transcription factor and its role during leaf senescence in Arabidopsis. Plant Mol Biol 2004; 55: 853-867.

[32] Robatzek S, Somssich IE . Targets of AtWRKY6 regulation during plant senescence and pathogen defense. Genes Dev 2002; 16: 1139-1149.

[33] Jing SJ, Zhou X, Song Y, Yu DQ . Heterologous expression of OsWRKY23 gene enhances pathogen defense and dark-induced leaf senescence in Arabidopsis. Plant Growth Regul 2009; 58: 181-190.

[34] Rushton PJ, Torres JT, Parniske M, Wernert P, Hahlbrock K, Somssich IE . Interaction of elicitor-induced DNA-binding proteins with elicitor response elements in the promoters of parsley PR1 genes. EMBO J 1996; 15: 5690-5700.

[35] Eulgem T, Rushton PJ, Robatzek S, Somssich IE . The WRKY superfamily of plant transcription factors. Trends Plant Sci 2000; 5: 199-206.

[36] Xie Z, Zhang ZL, Zou X et al. Annotations and functional analyses of the rice WRKY gene superfamily reveal positive and negative regulators of abscisic acid signaling in aleurone cells. Plant Physiol 2005; 137: 176-189.

[37] Maleck K, Levine A, Eulgem T et al. The transcriptome of Arabidopsis thaliana during systemic acquired resistance. Nat Genet 2000; 26: 403-410.

[38] Mare C, Mazzucotelli E, Crosatti C, Francia E, Stanca AM, Cattivelli L . Hv-WRKY38: a new transcription factor involved in cold- and drought-response in barley. Plant Mol Biol 2004; 55: 399-416.

[39] Zhu Z, Shi J, Cao J, He M, Wang Y . VpWRKY3, a biotic and abiotic stress-related transcription factor from the Chinese wild Vitis pseudoreticulata. Plant Cell Rep 2012; 31: 2109-2120.

[40] Marchive C, Mzid R, Deluc L et al. 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 2007; 58: 1999-2010.

[41] Guillaumie S, Mzid R, Mechin V et al. The grapevine transcription factor WRKY2 influences the lignin pathway and xylem development in tobacco. Plant Mol Biol 2010; 72: 215-234.

[42] Liu H, Yang W, Liu D, Han Y, Zhang A, Li S . Ectopic expression of a grapevine transcription factor VvWRKY11 contributes to osmotic stress tolerance in Arabidopsis. Mol Biol Rep 2011; 38: 417-427.

[43] Li H, Xu Y, Xiao Y et al. Expression and functional analysis of two genes encoding transcription factors, VpWRKY1 and VpWRKY2, isolated from Chinese wild Vitis pseudoreticulata. Planta 2010; 232: 1325-1337.

[44] Jaillon O, Aury JM, Noel B et al. The grapevine genome sequence suggests ancestral hexaploidization in major Angiosperm phyla. Nature 2007; 449: 463-467.

[45] Velasco R, Zharkikh A, Troggio M et al. A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS ONE 2007; 2: e1326.

[46] Wu KL, Guo ZJ, Wang HH, Li J . The WRKY family of transcription factors in rice and Arabidopsis and their origins. DNA Res 2005; 12: 9-26.

[47] Larkin MA, Blackshields G, Brown NP et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23: 2947-2948.

[48] Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S . MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28: 2731-2739.

[49] Zhang Y, Mao L, Wang H et al. Genome-wide identification and analysis of grape aldehyde dehydrogenase (ALDH) gene superfamily. PLoS ONE 2012; 7: e32153.

[50] Rambaldi D, Ciccarelli FD . FancyGene: dynamic visualization of gene structures and protein domain architectures on genomic loci. Bioinformatics 2009; 25: 2281-2282.

[51] Bailey TL, Boden M, Buske FA et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 2009; 37: W202-208.

[52] Fasoli M, Dal Santo S, Zenoni S et al. The grapevine expression atlas reveals a deep transcriptome shift driving the entire plant into a maturation program. Plant Cell 2012; 24: 3489-3505.

[53] Saeed AI, Bhagabati NK, Braisted JC et al. TM4 microarray software suite. Methods Enzymol 2006; 411: 134-193.

[54] Yuan JS, Reed A, Chen F, Stewart CN Jr . Statistical analysis of real-time PCR data. BMC Bioinformatics 2006; 7: 85.

[55] Vannozzi A, Dry IB, Fasoli M, Zenoni S, Lucchin M . Genome-wide analysis of the grapevine stilbene synthase multigenic family: genomic organization and expression profiles upon biotic and abiotic stresses. BMC Plant Biol 2012; 12: 130.

[56] Holub EB . The arms race is ancient history in Arabidopsis, the wildflower. Nat Rev Genet 2001; 2: 516-527.

[57] Cannon SB, Mitra A, Baumgarten A, Young ND, May G . The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol 2004; 4: 10.

[58] Tiwari SB, Hagen G, Guilfoyle TJ . Aux/IAA proteins contain a potent transcriptional repression domain. Plant Cell 2004; 16: 533-543.

[59] Landschulz WH, Johnson PF, Mcknight SL . The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins. Science 1988; 240: 1759-1764.

[60] Fung RW, Gonzalo M, Fekete C et al. Powdery mildew induces defense-oriented reprogramming of the transcriptome in a susceptible but not in a resistant grapevine. Plant Physiol 2008; 146: 236-249.

[61] Albertazzi G, Milc J, Caffagni A et al. Gene expression in grapevine cultivars in response to Bois Noir phytoplasma infection. Plant Science 2009; 176: 792-804.

[62] Vega A, Gutierrez RA, Pena-Neira A, Cramer GR, Arce-Johnson P . Compatible GLRaV-3 viral infections affect berry ripening decreasing sugar accumulation and anthocyanin biosynthesis in Vitis vinifera. Plant Mol Biol 2011; 77: 261-274.

[63] Birkenbihl RP, Diezel C, Somssich IE . Arabidopsis WRKY33 is a key transcriptional regulator of hormonal and metabolic responses toward Botrytis cinerea infection. Plant Physiol 2012; 159: 266-285.

[64] Ling J, Jiang W, Zhang Y et al. Genome-wide analysis of WRKY gene family in Cucumis sativus. BMC Genomics 2011; 12: 471.

[65] He H, Dong Q, Shao Y et al. Genome-wide survey and characterization of the WRKY gene family in Populus trichocarpa. Plant Cell Rep 2012; 31: 1199-1217.

[66] Huang S, Gao Y, Liu J et al. Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum. Mol Genet Genomics 2012; 287: 495-513.

[67] Giacomelli JI, Weigel D, Chan RL, Manavella PA . Role of recently evolved miRNA regulation of sunflower HaWRKY6 in response to temperature damage. New Phytol 2012; 195: 766-773.

[68] Ramiro D, Jalloul A, Petitot AS, de sa MFG, Maluf M, Fernandez D . Identification of coffee WRKY transcription factor genes and expression profiling in resistance responses to pathogens. Tree Genet Genomes 2010; 6: 767-781.

[69] Gao QM, Venugopal S, Navarre D, Kachroo A . Low oleic acid-derived repression of jasmonic acid-inducible defense responses requires the WRKY50 and WRKY51 proteins. Plant Physiol 2011; 155: 464-476.

[70] Zhou X, Jiang Y, Yu D . WRKY22 transcription factor mediates dark-induced leaf senescence in Arabidopsis. Mol Cells 2011; 31: 303-313.

[71] Ohno S, Wolf U, Atkin NB . Evolution from fish to mammals by gene duplication. Hereditas 1968; 59: 169-187.

[72] Chothia C, Gough J, Vogel C, Teichmann SA . Evolution of the protein repertoire. Science 2003; 300: 1701-1703.

[73] Lynch M, Conery JS . The evolutionary fate and consequences of duplicate genes. Science 2000; 290: 1151-1155.

[74] Lynch M, Conery JS . The evolutionary demography of duplicate genes. J Struct Funct Genomics 2003; 3: 35-44.

[75] Jiang W, Yu D . Arabidopsis WRKY2 transcription factor mediates seed germination and postgermination arrest of development by abscisic acid. BMC Plant Biol 2009; 9: 96.

[76] Luo M, Dennis ES, Berger F, Peacock WJ, Chaudhury A . 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 2005; 102: 17531-17536.

[77] Rushton PJ, Macdonald H, Huttly AK, Lazarus CM, Hooley R . Members of a new family of DNA-binding proteins bind to a conserved cis-element in the promoters of alpha-Amy2 genes. Plant Mol Biol 1995; 29: 691-702.

[78] Robatzek S, Somssich IE . A new member of the Arabidopsis WRKY transcription factor family, AtWRKY6, is associated with both senescence- and defence-related processes. Plant J 2001; 28: 123-133.

[79] Guo S, Zhang Z, Tong T . Cloning and characterization of cellular senescence-associated genes in human fibroblasts by suppression subtractive hybridization. Exp Cell Res 2004; 298: 465-472.

[80] Ulker B, Shahid Mukhtar M, Somssich IE . The WRKY70 transcription factor of Arabidopsis influences both the plant senescence and defense signaling pathways. Planta 2007; 226: 125-137.

[81] Ay N, Irmler K, Fischer A, Uhlemann R, Reuter G, Humbeck K . Epigenetic programming via histone methylation at WRKY53 controls leaf senescence in Arabidopsis thaliana. Plant J 2009; 58: 333-346.

[82] Honys D, Oh SA, Renak D et al. Identification of microspore-active promoters that allow targeted manipulation of gene expression at early stages of microgametogenesis in Arabidopsis. BMC Plant Biol 2006; 6: 31.

[83] Bari R, Jones JD . Role of plant hormones in plant defence responses. Plant Mol Biol 2009; 69: 473-488.

[84] Schroeder JI, Kwak JM, Allen GJ . Guard cell abscisic acid signalling and engineering drought hardiness in plants. Nature 2001; 410: 327-330.

[85] Chen H, Lai Z, Shi J, Xiao Y, Chen Z, Xu X . Roles of Arabidopsis WRKY18, WRKY40 and WRKY60 transcription factors in plant responses to abscisic acid and abiotic stress. BMC Plant Biol 2010; 10: 281.

[86] Pandey SP, Roccaro M, Schon M, Logemann E, Somssich IE . Transcriptional reprogramming regulated by WRKY18 and WRKY40 facilitates powdery mildew infection of Arabidopsis. Plant J 2010; 64: 912-923.

[87] Moreau M, Degrave A, Vedel R et al. EDS1 contributes to nonhost resistance of Arabidopsis thaliana against Erwinia amylovora. Mol Plant Microbe Interact 2012; 25: 421-430.

[88] Li J, Besseau S, Toronen P, et al. Defense-related transcription factors WRKY70 and WRKY54 modulate osmotic stress tolerance by regulating stomatal aperture in Arabidopsis. New Phytol 2013; 200: 457-472.

[89] Li HL, Zhang LB, Guo D, Li CZ, Peng SQ . Identification and expression profiles of the WRKY transcription factor family in Ricinus communis. Gene 2012; 503: 248-253.