Investigating members of Arabidopsis WRKYs transcription factors with differential expression under various stresses using bioinformatics approaches

Document Type : Original research paper


Genetics and agricultural biotechnology institute of Tabarestan, Sari agricultural sciences and natural resources university, Iran


In the current study, a comprehensive analysis was performed on Arabidopsis WRKY transcription factor (TF) family members that their differential expression (DE) was reported under various stresses in GEO profile database. First, WRKY members with DE were extracted from GEO profile and information of the data set, sequence and their gene structure were obtained. Then, the concept of the intersection of sets was used to select some of WRKY TFs for downstream analysis. DE of candidate members was compared by t-test. The protein– protein interaction network were predicted by STRING web server. A total of 16 WRKY genes were identified in the 11 dataset of GEO profile. Analysis of the gene structure showed that 56% of the studied WRKY genes have 3 exons and all 16 members are distributed across all five chromosomes of Arabidopsis. Also, the results showed that WRKY40, WRKY46, WRKY18, and WRKY33 were most frequently responsive to various stresses. The protein-protein interaction network showed that WRKY40, WRKY46, WRKY18, and WRKY70 have high interactions with four genes: MPK4, ACS6, MKS1, and STZ. Therefore, WRKY40, WRKY46, WRKY18, and WRKY33 can be considered the most important WRKY TFs of Arabidopsis at response to various stresses and may find applications in genetic and metabolic engineering projects.


Andreasson, E., Jenkins, T., Brodersen, P., Thorgrimsen, S., Petersen, N.H., Zhu, S., Qiu, J.L., Micheelsen, P., Rocher, A., and Petersen, M. (2005). The MAP kinase substrate MKS1 is a regulator of plant defense responses. EMBO J 24(14): 2579-2589.
Chen, J., Wang, X., Zhang, W., Zhang, S., and Zhao, F.J. (2020). Protein phosphatase 2A alleviates cadmium toxicity by modulating ethylene production in Arabidopsis thaliana. Plant Cell Environ 43(4): 1008-1022. doi: 10.1111/pce.13716.
Dai, X., Wang, Y., and Zhang, W.H. (2016). OsWRKY74, a WRKY transcription factor, modulates tolerance to phosphate starvation in rice. J Exp Bot 67(3): 947-960. doi: 10.1093/jxb/erv515.
Deng, C., Wu, Y., Lv, X., Li, J., Liu, Y., Du, G., Chen, J., and Liu, L. (2022). Refactoring transcription factors for metabolic engineering. Biotechnol Adv 57: 107935. doi: 10.1016/j.biotechadv.2022.107935.
Geilen, K., and Bohmer, M. (2015). Dynamic subnuclear relocalisation of WRKY40 in response to Abscisic acid in Arabidopsis thaliana. Sci Rep 5(1): 13369. doi: 10.1038/srep13369.
Gonzalez-Perez, S., Gutierrez, J., Garcia-Garcia, F., Osuna, D., Dopazo, J., Lorenzo, O., Revuelta, J.L., and Arellano, J.B. (2011). Early transcriptional defense responses in Arabidopsis cell suspension culture under high-light conditions. Plant Physiol 156(3): 1439-1456. doi: 10.1104/pp.111.177766.
Jäger, T., Mokos, A., Prasianakis, N.I., and Leyer, S. (2022). Pore-level multiphase simulations of realistic distillation membranes for water desalination. Membranes 12(11): 1112.
Jia, H., Wang, C., Wang, F., Liu, S., Li, G., and Guo, X. (2015). GhWRKY68 reduces resistance to salt and drought in transgenic Nicotiana benthamiana. PLoS One 10(3): e0120646. doi: 10.1371/journal.pone.0120646.
Jia, M.Z., Liu, L.Y., Geng, C., and Jiang, J. (2021). Activation of 1-aminocyclopropane-1-carboxylic acid synthases sets stomatal density and clustered ratio on leaf epidermis of Arabidopsis in response to drought. Front Plant Sci 12: 758785. doi: 10.3389/fpls.2021.758785.
Jiang, L., Chen, Y., Bi, D., Cao, Y., and Tong, J. (2021). Deciphering evolutionary dynamics of WRKY I genes in Rosaceae species. Front Ecol Evol 9: 801490.
Jin, J., Tian, F., Yang, D.C., Meng, Y.Q., Kong, L., Luo, J., and Gao, G. (2017). PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res 45(D1): D1040-D1045. doi: 10.1093/nar/gkw982.
Lambert, S.A., Jolma, A., Campitelli, L.F., Das, P.K., Yin, Y., Albu, M., Chen, X., Taipale, J., Hughes, T.R., and Weirauch, M.T. (2018). The human transcription factors. Cell 172(4): 650-665.
Li, B., Jiang, S., Yu, X., Cheng, C., Chen, S., Cheng, Y., Yuan, J.S., Jiang, D., He, P., and Shan, L. (2015). Phosphorylation of trihelix transcriptional repressor ASR3 by MAP KINASE4 negatively regulates Arabidopsis immunity. Plant Cell 27(3): 839-856. doi: 10.1105/tpc.114.134809.
Li, S., Fu, Q., Chen, L., Huang, W., and Yu, D. (2011). Arabidopsis thaliana WRKY25, WRKY26, and WRKY33 coordinate induction of plant thermotolerance. Planta 233(6): 1237-1252. doi: 10.1007/s00425-011-1375-2.
Li, W., Pang, S., Lu, Z., and Jin, B. (2020). Function and mechanism of WRKY transcription factors in abiotic stress responses of plants. Plants (Basel) 9(11): 1515. doi: 10.3390/plants9111515.
Libault, M., Wan, J., Czechowski, T., Udvardi, M., and Stacey, G. (2007). Identification of 118 Arabidopsis transcription factor and 30 ubiquitin-ligase genes responding to chitin, a plant-defense elicitor. Mol Plant Microbe Interact 20(8): 900-911. doi: 10.1094/MPMI-20-8-0900.
Liu, X., Song, Y., Xing, F., Wang, N., Wen, F., and Zhu, C. (2016). GhWRKY25, a group I WRKY gene from cotton, confers differential tolerance to abiotic and biotic stresses in transgenic Nicotiana benthamiana. Protoplasma 253(5): 1265-1281. doi: 10.1007/s00709-015-0885-3.
Liu, Y., and Zhang, S. (2004). Phosphorylation of 1-aminocyclopropane-1-carboxylic acid synthase by MPK6, a stress-responsive mitogen-activated protein kinase, induces ethylene biosynthesis in Arabidopsis. Plant Cell 16(12): 3386-3399. doi: 10.1105/tpc.104.026609.
Mittler, R., Kim, Y., Song, L., Coutu, J., Coutu, A., Ciftci-Yilmaz, S., Lee, H., Stevenson, B., and Zhu, J.K. (2006). Gain- and loss-of-function mutations in Zat10 enhance the tolerance of plants to abiotic stress. FEBS Lett 580(28-29): 6537-6542. doi: 10.1016/j.febslet.2006.11.002.
Mochizuki, N., Brusslan, J.A., Larkin, R., Nagatani, A., and Chory, J. (2001). Arabidopsis genomes uncoupled 5 (GUN5) mutant reveals the involvement of Mg-chelatase H subunit in plastid-to-nucleus signal transduction. Proc Natl Acad Sci USA 98(4): 2053-2058. doi: 10.1073/pnas.98.4.2053.
Sakamoto, H., Maruyama, K., Sakuma, Y., Meshi, T., Iwabuchi, M., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2004). Arabidopsis Cys2/His2-type zinc-finger proteins function as transcription repressors under drought, cold, and high-salinity stress conditions. Plant Physiol 136(1): 2734-2746.
Van Hoewyk, D., Takahashi, H., Inoue, E., Hess, A., Tamaoki, M., and Pilon‐Smits, E.A. (2008). Transcriptome analyses give insights into selenium‐stress responses and selenium tolerance mechanisms in Arabidopsis. Physiol Plant 132(2): 236-253.
Wang, H., Hao, J., Chen, X., Hao, Z., Wang, X., Lou, Y., Peng, Y., and Guo, Z. (2007). Overexpression of rice WRKY89 enhances ultraviolet B tolerance and disease resistance in rice plants. Plant Mol Biol 65(6): 799-815. doi: 10.1007/s11103-007-9244-x.
Wang, J., Wang, L., Yan, Y., Zhang, S., Li, H., Gao, Z., Wang, C., and Guo, X. (2021). GhWRKY21 regulates ABA-mediated drought tolerance by fine-tuning the expression of GhHAB in cotton. Plant Cell Rep 40(11): 2135-2150. doi: 10.1007/s00299-020-02590-4.
Wang, N.N., Xu, S.W., Sun, Y.L., Liu, D., Zhou, L., Li, Y., and Li, X.B. (2019). The cotton WRKY transcription factor (GhWRKY33) reduces transgenic Arabidopsis resistance to drought stress. Sci Rep 9(1): 724. doi: 10.1038/s41598-018-37035-2.
Xie, Y., Mao, Y., Lai, D., Zhang, W., and Shen, W. (2012). H(2) enhances Arabidopsis salt tolerance by manipulating ZAT10/12-mediated antioxidant defence and controlling sodium exclusion. PLoS One 7(11): e49800. doi: 10.1371/journal.pone.0049800.
Yokotani, N., Sato, Y., Tanabe, S., Chujo, T., Shimizu, T., Okada, K., Yamane, H., Shimono, M., Sugano, S., and Takatsuji, H. (2013). WRKY76 is a rice transcriptional repressor playing opposite roles in blast disease resistance and cold stress tolerance. J Exp Bot 64(16): 5085-5097.
Yu, Y., Song, T., Wang, Y., Zhang, M., Li, N., Yu, M., Zhang, S., Zhou, H., Guo, S., Bu, Y., Wang, T., Xiang, J., and Zhang, X. (2023). The wheat WRKY transcription factor TaWRKY1-2D confers drought resistance in transgenic Arabidopsis and wheat (Triticum aestivum L.). Int J Biol Macromol 226: 1203-1217. doi: 10.1016/j.ijbiomac.2022.11.234.
Zheng, Z., Qamar, S.A., Chen, Z., and Mengiste, T. (2006). Arabidopsis WRKY33 transcription factor is required for resistance to necrotrophic fungal pathogens. Plant J 48(4): 592-605.
Volume 10, Issue 1
June 2022
Pages 48-59
  • Receive Date: 03 April 2023
  • Revise Date: 23 May 2023
  • Accept Date: 01 July 2023
  • First Publish Date: 01 July 2023