Identification of yellowhorn (Xanthoceras sorbifolium) WRKY transcription factor family and analysis of abiotic stress response model

Abstract

WRKY transcription factors are widely distributed in higher plants and play important roles in many biological processes, including stress resistance. The recently published genome sequence of yellowhorn, an oil tree with robust resistance to cold, drought, heat, salt and alkali, provides an excellent opportunity to identify and characterize the entire yellowhorn WRKY protein family and a basis for the study of abiotic stress resistance of WRKY gene family in forest species. In the present comprehensive analysis of WRKY transcription factors in yellowhorn, 65 WRKY genes were identified and defined based on their location on the chromosome. According to their structure and phylogenetic relationships, XsWRKY genes clustered into WRKY groups I–III. Segmental duplication events played a significant role in the expansion of WRKY gene family. Furthermore, transcriptomic data and real-time quantitative PCR analysis showed that expression of XsWRKY genes responding to salt and drought stresses and a hormone treatment. We also determined structures of the encoded proteins, cis-elements of the promoter region, and expression patterns. These results provide a foundation for the study of the biological function of WRKY transcription factors in yellowhorn.

Keywords

Yellowhorn (Xanthoceras sorbifolium) / WRKY transcription factor / Stress / ABA / Gene expression

References

[1] Agarwal P, Reddy MP, Chikara J. WRKY: its structure, evolutionary relationship, DNA-binding selectivity, role in stress tolerance and development of plants. Mol Biol Rep, 2011, 38(6): 3883-3896.

[2] Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res, 2009, 37(suppl_2): W202-W208.

[3] Bencke-Malato M, Cabreira C, Wiebke-Strohm B, Bücker-Neto L, Mancini E, Osorio MB, Homrich MS, Turchetto-Zolet AC, De Carvalho MCCG, Stolf R, Weber RLM, Westergaard G, Castagnaro AP, Abdelnoor RV, Marcelino-Guimarães FC, Margis-Pinheiro M, Bodanese-Zanettini MH. Genome-wide annotation of the soybean WRKY family and functional characterization of genes involved in response to Phakopsora pachyrhiziinfection. BMC Plant Biol, 2014 14 1 236

[4] 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.

[5] Bi QX, Zhao Y, Du W, Lu Y, Gui L, Zheng ZM, Yu HY, Cui YF, Liu Z, Cui TP, Cui DS, Liu XJ, Li YC, Fan SQ, Hu XY, Fu GH, Ding J, Ruan CJ, Wang LB. Pseudomolecule-level assembly of the Chinese oil tree yellowhorn (Xanthoceras sorbifolium) genome. Gigascience, 2019 8 6 giz070

[6] Chen CJ, Chen H, He YH, Xia R (2018) TBtools, a toolkit for biologists integrating various biological data handling tools with a user-friendly interface. BioRxiv 289660

[7] Ding ZJ, Yan JY, Li CX, Li GX, Wu YR, Zheng SJ. Transcription factor WRKY46 modulates the development of Arabidopsis lateral roots in osmotic/salt stress conditions via regulation of ABA signaling and auxin homeostasis. Plant J, 2015, 84(1): 56-69.

[8] Dong JX, Chen CH, Chen ZX. Expression profiles of the Arabidopsis WRKY gene superfamily during plant defense response. Plant Mol Biol, 2003, 51(1): 21-37.

[9] El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, Qureshi M, Richardson LJ, Salazar GA, Smart A. The Pfam protein families database in 2019. Nucleic Acids Res, 2019, 47(D1): D427-D432.

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

[11] Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A. ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res, 2003, 31(13): 3784-3788.

[12] Göhre V, Jones AM, Sklenář J, Robatzek S, Weber AP. Molecular crosstalk between PAMP-triggered immunity and photosynthesis. Mol Plant Microbe Interact, 2012, 25(8): 1083-1092.

[13] Gu LJ, Li LB, Wei HL, Wang HT, Su JJ, Guo YN, Yu SX. Identification of the group IIa WRKY subfamily and the functional analysis of GhWRKY17 in upland cotton (Gossypium hirsutum L.). PLOS One, 2018 13 1 e0191681

[14] Gu LJ, Wang HT, Wei HL, Sun HR, Li LB, Chen PG, Elasad M, Su ZZ, Zhang C, Ma L, Wang CC, Yu SX. Identification, expression, and functional analysis of the group IId WRKY subfamily in upland cotton (Gossypium hirsutum L.). Front Plant Sci, 2018, 9: 1684.

[15] Jiang WB, Yu DQ. Arabidopsis WRKY2 transcription factor mediates seed germination and postgermination arrest of development by abscisic acid. BMC Plant Biol, 2009 9 1 96

[16] Jiang YJ, Liang G, Yang SZ, Yu DQ. Arabidopsis WRKY57 functions as a node of convergence for jasmonic acid-and auxin-mediated signaling in jasmonic acid-induced leaf senescence. Plant Cell, 2014, 26(1): 230-245.

[17] Jin JP, Tian F, Yang DC, Meng YQ, Kong L, Luo JC, Gao G. PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res, 2017, 45(D1): D1040-D1045.

[18] 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(9): 2357-2371.

[19] Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. Circos: an information aesthetic for comparative genomics. Genome Res, 2009, 19(9): 1639-1645.

[20] Kumar K, Srivastava V, Purayannur S, Kaladhar VC, Cheruvu PJ, Verma PK. WRKY domain-encoding genes of a crop legume chickpea (Cicer arietinum): comparative analysis with Medicago truncatula WRKY family and characterization of group-III gene (s). DNA Res, 2016, 23(3): 225-239.

[21] Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouzé P, Rombauts S. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res, 2002, 30(1): 325-327.

[22] Letunic I, Bork P. 20 years of the SMART protein domain annotation resource. Nucleic Acids Res, 2018, 46(D1): D493-D496.

[23] Letunic I, Bork P. Interactive tree of life (iTOL) v4: recent updates and new developments. Nucleic Acids Res, 2019, 47(W1): W256-W259.

[24] Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol, 2014 15 12 550

[25] Ma JC, Lu J, Xu JM, Duan BB, He XD, Liu JQ. Genome-wide identification of WRKY genes in the desert poplar Populus euphratica and adaptive evolution of the genes in response to salt stress. Evol Bioinform, 2015, 11: EBO-S22067.

[26] Marchler-Bauer A, Bo Y, Han L, He J, Lanczycki CJ, Lu S, Chitsaz F, Derbyshire MK, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Lu F, Marchler GH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C, Geer LY, Bryant SH. CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res, 2017, 45(D1): D200-D203.

[27] Meng D, Li YY, Bai Y, Li MJ, Cheng LL. Genome-wide identification and characterization of WRKY transcriptional factor family in apple and analysis of their responses to waterlogging and drought stress. Plant Physiol Biochem, 2016, 103: 71-83.

[28] Miao Y, Jiang JJ, Ren YJ, Zhao ZW. The single-stranded DNA-binding protein WHIRLY1 represses WRKY53 expression and delays leaf senescence in a developmental stage-dependent manner in Arabidopsis. Plant Physiol, 2013, 163(2): 746-756.

[29] Mistry J, Finn RD, Eddy SR, Bateman A, Punta M. Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions. Nucleic Acids Res, 2013, 41(12): e121-e121.

[30] Mount DW. Using the basic local alignment search tool (BLAST). Cold Spring Harbor Protoc, 2007 2007 7 pdb-top17

[31] Murat F, Armero A, Pont C, Klopp C, Salse J. Reconstructing the genome of the most recent common ancestor of flowering plants. Nat Genet, 2017, 49(4): 490-496.

[32] Qiu YP, Yu DQ. Over-expression of the stress-induced OsWRKY45 enhances disease resistance and drought tolerance in Arabidopsis. Environ Exp Bot, 2009, 65(1): 35-47.

[33] Robatzek S, Somssich IE. Targets of AtWRKY6 regulation during plant senescence and pathogen defense. Genes Dev, 2002, 16(9): 1139-1149.

[34] Romero I, Alegria-Carrasco E, González de Prádena A, Vazquez-Hernandez M, Escribano MI, Merodio C, Sanchez-Ballesta MT. WRKY transcription factors in the response of table grapes (cv. Autumn Royal) to high CO₂ levels and low temperature. Postharvest Biol Technol, 2019, 150: 42-51.

[35] Rushton PJ, Somssich IE, Ringler P, Shen QJ. WRKY transcription factors. Trends Plant Sci, 2010, 15(5): 247-258.

[36] Rushton DL, Tripathi P, Rabara RC, Lin J, Ringler P, Boken AK, Langum TJ, Smidt L, Boomsma DD, Emme NJ, Chen X, Finer JJ, Shen QJ, Rushton PJ. WRKY transcription factors: key components in abscisic acid signalling. Plant Biotechnol J, 2012, 10(1): 2-11.

[37] Sahraeian SME, Mohiyuddin M, Sebra R, Tilgner H, Afshar PT, Au KF, Bani AN, Gerstein MB, Wong WH, Snyder MP, Schadt E, Lam HYK. Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis. Nat Commun, 2017, 8(1): 1-15.

[38] Shang Y, Yan L, Liu ZQ, Cao Z, Mei C, Xin Q, Wu FQ, Wang XF, Du SY, Jiang T, Zhang XF, Zhao R, Sun HL, Liu R, Yu YT, Zhang DP. 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.

[39] Shen HS, Liu CT, Zhang Y, Meng XP, Zhou X, Chu CC, Wang XP. OsWRKY30 is activated by MAP kinases to confer drought tolerance in rice. Plant Mol Biol, 2012, 80(3): 241-253.

[40] Sun C, Palmqvist S, Olsson H, Borén M, Ahlandsberg S, Jansson C. 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.

[41] Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol, 2013, 30(12): 2725-2729.

[42] Tian Y, Lu XY, Peng LS, Fang J. The structure and function of plant WRKY transcription factors. Yi Chuan, 2006, 28(12): 1607-1612.

[43] Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Déjardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjärvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leplé JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouzé P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science, 2006, 313(5793): 1596-1604.

[44] Uji Y, Kashihara K, Kiyama H, Mochizuki S, Akimitsu K, Gomi K. Jasmonic acid-induced VQ-motif-containing protein OsVQ13 influences the OsWRKY45 signaling pathway and grain size by associating with OsMPK6 in rice. Int J Mol Sci, 2019 20 12 2917

[45] Wan YQ, Mao MZ, Wan DL, Yang Q, Yang FY, Mandlaa LGJ, Wang RG. Identification of the WRKY gene family and functional analysis of two genes in Caragana intermedia. BMC Plant Biol, 2018 18 1 31

[46] Wang DP, Zhang YB, Zhang Z, Zhu J, Yu J. KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genom Proteom Bioinform, 2010, 8(1): 77-80.

[47] Wang HZ, Avci U, Nakashima J, Hahn MG, Chen F, Dixon RA. Mutation of WRKY transcription factors initiates pith secondary wall formation and increases stem biomass in dicotyledonous plants. Proc Natl Acad Sci, 2010, 107(51): 22338-22343.

[48] Wang YP, Tang HB, Debarry JD, Tan X, Li JP, Wang XY, Lee TH, Jin HZ, Marler B, Guo H, Kissinger JC, Paterson AH. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res, 2012, 40(7): e49-e49.

[49] Wang C, Deng PY, Chen LL, Wang XT, Ma H, Hu W, Yao NC, Feng Y, Chai RH, Yang GX, He GY. A wheat WRKY transcription factor TaWRKY10 confers tolerance to multiple abiotic stresses in transgenic tobacco. PLOS One, 2013 8 6 e65120

[50] Wang LN, Zhu W, Fang LC, Sun XM, Su LY, Liang ZC, Wang N, Londo JP, Li SH, Xin HP. Genome-wide identification of WRKY family genes and their response to cold stress in Vitis vinifera. BMC Plant Biol, 2014 14 1 103

[51] Wang LQ, Wang C, Qin LP, Hu P, Wang YC. ThERF1 from Tamarix hispida confers decreased tolerance to oxidative and drought stresses and is regulated by a WRKY protein. J For Res, 2016, 27(4): 767-772.

[52] Wen F, Zhu H, Li P, Jiang M, Mao WQ, Ong C, Chu ZQ. Genome-wide evolutionary characterization and expression analyses of WRKY family genes in Brachypodium distachyon. DNA Res, 2014, 21(3): 327-339.

[53] Xiao Y, Zhou LX, Lei XT, Cao HX, Wang Y, Dou YH, Tang WQ, Xia W. Genome-wide identification of WRKY genes and their expression profiles under different abiotic stresses in Elaeis guineensis. PLOS One, 2017 12 12 e0189224

[54] Xie Z, Zhang ZL, Zou XL, Huang J, Ruas P, Thompson D, Shen QJ. 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.

[55] Xie T, Chen CJ, Li CH, Liu JR, Liu CY, He YH. Genome-wide investigation of WRKY gene family in pineapple: evolution and expression profiles during development and stress. BMC Genom, 2018 19 1 490

[56] 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(3): 459-470.

[57] Yan HR, Jia HH, Chen XB, Hao LL, An HL, Guo XQ. The cotton WRKY transcription factor GhWRKY17 functions in drought and salt stress in transgenic Nicotiana benthamiana through ABA signaling and the modulation of reactive oxygen species production. Plant Cell Physiol, 2014, 55(12): 2060-2076.

[58] Yan HF, Li MZ, Xiong YP, Wu JM, Teixeira da Silva JA, Ma GH. Genome-wide characterization, expression profile analysis of WRKY family genes in Santalum album and functional identification of their role in abiotic stress. Int J Mol Sci, 2019 20 22 5676

[59] Yokotani N, Sato Y, Tanabe S, Chujo T, Shimizu T, Okada K, Yamane H, Shimono M, Sugano S, Takatsuji H, Kaku H, Minami E, Nishizawa Y. WRKY76 is a rice transcriptional repressor playing opposite roles in blast disease resistance and cold stress tolerance. J Exp Bot, 2013, 64(16): 5085-5097.

[60] Yu CS, Chen YC, Lu CH, Hwang JK. Prediction of protein subcellular localization. Proteins Struct Funct Bioinform, 2006, 64(3): 643-651.

[61] Yu S, Chen LG, Zhang LP, Yu DQ. Overexpression of OsWRKY72 gene interferes in the abscisic acid signal and auxin transport pathway of Arabidopsis. J Biosci, 2010, 35(3): 459-471.

[62] Zhang YJ, Wang LJ. The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants. BMC Evol Biol, 2005 5 1 1

[63] Zhang Y, Yu HJ, Yang XY, Li Q, Ling J, Wang H, Gu XF, Huang SW, Jiang WJ. CsWRKY46, a WRKY transcription factor from cucumber, confers cold resistance in transgenic-plant by regulating a set of cold-stress responsive genes in an ABA-dependent manner. Plant Physiol Biochem, 2016, 108: 478-487.

[64] Zhang YQ, Liu ZJ, Wang XY, Wang JF, Fan K, Li ZW, Lin WX. DELLA proteins negatively regulate dark-induced senescence and chlorophyll degradation in Arabidopsis through interaction with the transcription factor WRKY6. Plant Cell Rep, 2018, 37(7): 981-992.

[65] Zhang LL, Zhao TT, Sun XM, Wang Y, Du C, Zhu ZF, Gichuki DK, Wang QF, Li SH, Xin HP. Overexpression of VaWRKY12, a transcription factor from Vitis amurensis with increased nuclear localization under low temperature, enhances cold tolerance of plants. Plant Mol Biol, 2019, 100(1–2): 95-110.

[66] Zhou X, Jiang Y, Yu DQ. WRKY22 transcription factor mediates dark-induced leaf senescence in Arabidopsis. Mol Cells, 2011, 31(4): 303-313.