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Article; Agriculture and Environmental Biotechnology

Genome-wide analysis of WRKY transcription factors and their response to abiotic stress in celery (Apium graveolens L.)

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Pages 293-302 | Received 20 Jun 2017, Accepted 04 Dec 2017, Published online: 15 Dec 2017

References

  • Pandey SP, Somssich IE. The role of WRKY transcription factors in plant immunity. Plant Physiol. 2009;150(4):1648–1655.
  • Pan Y, Tsai CJ, Ma B, et al. Mechanisms of transcription factor selectivity. Trends Genet. 2010;26(2):75–83.
  • Liu L, White MJ, MacRae TH. Transcription factors and their genes in higher plants functional domains, evolution and regulation. Eur J Biochem. 1999;262(2):247–257.
  • Jin J, Zhang H, Kong L, et al. PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucleic Acids Res. 2014;42:D1182–1187.
  • Zhuang J, Zhang J, Hou XL, et al. Transcriptomic, proteomic, metabolomic and functional genomic approaches for the study of abiotic stress in vegetable crops. Crit Rev Plant Sci. 2014;33(2–3):225–237.
  • Riechmann JL, Heard J, Martin G, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science. 2000;290(5499):2105–2110.
  • Schmutz J, Cannon SB, Schlueter J, et al. Genome sequence of the palaeopolyploid soybean. Nature. 2010;463(7278):178–183.
  • Luscombe NM, Austin SE, Berman HM, et al. An overview of the structures of protein-DNA complexes. Genome Biol. 2000 [cited 2017 Aug 26];1(1):REVIEWS001. DOI: 10.1186/gb-2000-1-1-reviews001
  • Eulgem T, Rushton PJ, Robatzek S, et al. The WRKY superfamily of plant transcription factors. Trends Plant Sci. 2000;5(5):199–206.
  • van Verk MC, Pappaioannou D, Neeleman L, et al. A novel WRKY transcription factor is required for induction of PR-1a gene expression by salicylic acid and bacterial elicitors. Plant Physiol. 2008;146(4):1983–1995.
  • Guo C, Guo R, Xu X, et al. Evolution and expression analysis of the grape (Vitis vinifera L.) WRKY gene family. J Exp Bot. 2014;65(6):1513–1528.
  • Sun C, Palmqvist S, Olsson H, et al. A novel WRKY transcription factor, SUSIBA2, participates in sugar signaling in barley by binding to the sugar-responsive elements of the iso1 promoter. Plant Cell. 2003;15(9):2076–2092.
  • Ciolkowski I, Wanke D, Birkenbihl RP, et al. Studies on DNA-binding selectivity of WRKY transcription factors lend structural clues into WRKY-domain function. Plant Mol Biol. 2008;68(1-2):81–92.
  • Brand LH, Kirchler T, Hummel S, et al. DPI-ELISA: a fast and versatile method to specify the binding of plant transcription factors to DNA in vitro. Plant Methods. 2010 [cited 2017 Aug 26];6:25. DOI: 10.1186/1746-4811-6-25
  • Ishiguro S, Nakamura K. Characterization of a cDNA encoding a novel DNA-binding protein, SPF1, that recognizes SP8 sequences in the 5' upstream regions of genes coding for sporamin and beta-amylase from sweet potato. Mol Gen Genet. 1994;244(6):563–571.
  • Dong J, Chen C, Chen Z. Expression profiles of the Arabidopsis WRKY gene superfamily during plant defense response. Plant Mol Biol. 2003;51(1):21–37.
  • Ling J, Jiang W, Zhang Y, et al. Genome-wide analysis of WRKY gene family in Cucumis sativus. BMC Genomics. 2011 [cited 2017 Aug 26];12:471. DOI: 10.1186/1471-2164-12-471
  • Qiu YP, Jing SJ, Fu J, et al. Cloning and analysis of expression profile of 13 WRKY genes in rice. Chinese Sci Bull. 2004;49(20):2159–2168.
  • Huang S, Gao Y, Liu J, et al. Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum. Mol Genet Genomics. 2012;287(6):495–513.
  • Zhu XL, Liu SW, Meng C, et al. WRKY transcription factors in wheat and their induction by biotic and abiotic stress. Plant Mol Biol Rep. 2013;31(5):1053–1067.
  • Li MY, Xu ZS, Tian C, et al. Genomic identification of WRKY transcription factors in carrot (Daucus carota) and analysis of evolution and homologous groups for plants. Sci Rep. 2016 [cited 2017 Aug 26];6:23101. DOI: 10.1038/srep23101
  • Wu ZJ, Li XH, Liu ZW, et al. Transcriptome-wide identification of Camellia sinensis WRKY transcription factors in response to temperature stress. Mol Genet Genomics. 2016;291(1):255–269.
  • Luo M, Dennis ES, Berger F, et al. 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 U S A. 2005;102(48):17531–17536.
  • Jiang WB, Yu DQ. Arabidopsis WRKY2 transcription factor mediates seed germination and postgermination arrest of development by abscisic acid. BMC Plant Biol. 2009 [cited 2017 Aug 26];9:96. DOI: 10.1186/1471-2229-9-96
  • Rushton PJ, Somssich IE, Ringler P, et al. WRKY transcription factors. Trends Plant Sci. 2010;15(5):247–258.
  • Besseau S, Li J, Palva ET. WRKY54 and WRKY70 co-operate as negative regulators of leaf senescence in Arabidopsis thaliana. J Exp Bot. 2012;63(7):2667–2679.
  • Schluttenhofer C, Yuan L. Regulation of specialized metabolism by WRKY transcription factors. Plant Physiol. 2015;167(2):295–306.
  • Chen LG, Song Y, Li SJ, et al. The role of WRKY transcription factors in plant abiotic stresses. Biochim Biophys Acta. 2012;1819(2):120–128.
  • Mukhtar MS, Deslandes L, Auriac MC, et al. The Arabidopsis transcription factor WRKY27 influences wilt disease symptom development caused by Ralstonia solanacearum. Plant J. 2008;56(6):935–947.
  • Jiang YQ, Deyholos MK. Functional characterization of Arabidopsis NaCl-inducible WRKY25 and WRKY33 transcription factors in abiotic stresses. Plant Mol Biol. 2009;69(1-2):91–105.
  • Li SJ, Fu QT, Chen LG, et al. Arabidopsis thaliana WRKY25, WRKY26, and WRKY33 coordinate induction of plant thermotolerance. Planta. 2011;233(6):1237–1252.
  • Zhou QY, Tian AG, Zou HF, et al. Soybean WRKY-type transcription factor genes, GmWRKY13, GmWRKY21, and GmWRKY54, confer differential tolerance to abiotic stresses in transgenic Arabidopsis plants. Plant Biotechnol J. 2008;6(5):486–503.
  • Li MY, Hou XL, Wang F, et al. Advances in the research of celery, an important Apiaceae vegetable crop. Crit Rev Biotechnol. Forthcoming 2017 [cited 2017 Aug 26]:1–12. DOI: 10.1080/07388551.2017.1312275
  • Sowbhagya HB. Chemistry, technology, and nutraceutical functions of celery (Apium graveolens L.): an overview. Crit Rev Food Sci Nutr. 2014;54(3):389–398.
  • Jia XL, Wang GL, Xiong F, et al. De novo assembly, transcriptome characterization, lignin accumulation, and anatomic characteristics: novel insights into lignin biosynthesis during celery leaf development. Sci Rep. 2015 [cited 2017 Aug 26];5:8259. DOI: 10.1038/srep08259
  • Li MY, Wang F, Jiang Q, et al. Identification of SSRs and differentially expressed genes in two cultivars of celery (Apium graveolens L.) by deep transcriptome sequencing. Hortic Res. 2014 [cited 2017 Aug 26];1:10. DOI: 10.1038/hortres.2014.10
  • Rhee SY, Beavis W, Berardini TZ, et al. The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res. 2003;31(1):224–228.
  • Perez-Rodriguez P, Riano-Pachon DM, Correa LGG, et al. PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Res. 2010;38(Database issue):D822–D827.
  • Thompson JD, Higgins DG, Gibson TJ. Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22(22):4673–4680.
  • Tamura K, Peterson D, Peterson N, et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011;28(10):2731–2739.
  • Wilkins MR, Gasteiger E, Bairoch A, et al. Protein identification and analysis tools in the ExPASy server. Methods Mol Biol. 1999;112:531–552.
  • Bailey TL, Boden M, Buske FA, et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009;37(Web Server issue):W202–W208.
  • Szklarczyk D, Franceschini A, Wyder S, et al. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 2015;43(Database issue):D447–D452.
  • Li MY, Wang F, Jiang Q, et al. Validation and comparison of reference genes for qpcr normalization of celery (Apium graveolens) at different development stages. Front Plant Sci. 2016 [cited 2017 Aug 26];7:313. DOI: 10.3389/fpls.2016.00313
  • Pfaffl MW. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 2001 [cited 2017 Aug 26];29(9):e45. DOI: 10.1093/nar/29.9.e45
  • Zhang Y, Wang L. The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants. BMC Evol Biol. 2005 [cited 2017 Aug 26];5:1. DOI: 10.1186/1471-2148-5-1
  • Rinerson CI, Rabara RC, Tripathi P, et al. The evolution of WRKY transcription factors. BMC Plant Biol. 2015 [cited 2017 Nov 30];15:66. DOI: 10.1186/s12870-015-0456-y
  • 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(1):176–189.
  • Rensing SA, Lang D, Zimmer AD, et al. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science. 2008;319(5859):64–69.
  • Wang YT, Pan YJ, Cho CC, et al. A novel pax-like protein involved in transcriptional activation of cyst wall protein genes in Giardia lamblia. J Biol Chem. 2010;285(42):32213–32226.
  • 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(7):1199–1217.
  • Li HL, Zhang LB, Guo D, et al. Identification and expression profiles of the WRKY transcription factor family in Ricinus communis. Gene. 2012;503(2):248–253.
  • Tripathi P, Rabara RC, Langum TJ, et al. The WRKY transcription factor family in Brachypodium distachyon. BMC Genomics. 2012;13:270. DOI: 10.1186/1471-2164-13-270
  • Wei KF, Chen J, Chen YF, et al. Molecular phylogenetic and expression analysis of the complete WRKY transcription factor family in maize. DNA Res. 2012 [cited 2017 Aug 26];19(2):153–164.
  • Brand LH, Fischer NM, Harter K, et al. Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays. Nucleic Acids Res. 2013;41(21):9764–9778.
  • Soltis P S, Soltis D E. The origin and diversification of angiosperms. Am J Bot. 2004;91(10):1614–1626.
  • Jiang J, Ma S, Ye N, et al. WRKY transcription factors in plant responses to stresses. J Integr Plant Biol. 2017;59(2):86–101.
  • Phukan U J, Jeena GS, Shukla RK. WRKY transcription factors: molecular regulation and stress responses in plants. Front Plant Sci. 2016 [cited 2017 Aug 26];7:760. DOI: 10.3389/fpls.2016.00760
  • Mittler R, Kim Y, Song L, et al. Gain- and loss-of-function mutations in Zat10 enhance the tolerance of plants to abiotic stress. FEBS Lett. 2006;580(28-29):6537–6542.
  • Andreasson E, Jenkins T, Brodersen P, et al. The MAP kinase substrate MKS1 is a regulator of plant defense responses. EMBO J. 2005;24(14):2579–2589.
  • Luo X, Bai X, Sun X, et al. Expression of wild soybean WRKY20 in Arabidopsis enhances drought tolerance and regulates ABA signalling. J Exp Bot. 2013;64(8):2155–2169.
  • Song Y, Jing SJ, Yu D Q. Overexpression of the stress-induced OsWRKY08 improves osmotic stress tolerance in Arabidopsis. Chinese Sci Bull. 2009;54(24):4671–4678.
  • Shang Y, Yan L, Liu ZQ, et al. The Mg-chelatase H subunit of Arabidopsis antagonizes a group of WRKY transcription repressors to relieve ABA-responsive genes of inhibition. Plant Cell. 2010;22(6):1909–1935.
  • 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(2):457–472.
  • Schluttenhofer C, Pattanaik S, Patra B, et al. Analyses of Catharanthus roseus and Arabidopsis thaliana WRKY transcription factors reveal involvement in jasmonate signaling. BMC Genomics. 2014 [cited 2017 Aug 26];15:502. DOI: 10.1186/1471-2164-15-502
  • Guo DS, Qin GJ. EXB1/WRKY71 transcription factor regulates both shoot branching and responses to abiotic stresses. Plant Signal Behav. 2016 [cited 2017 Aug 26];11(3):e1150404. DOI: 10.1080/15592324.2016.1150404