FROM ARABIDOPSIS TO CROPS: THREE DECADES OF WRKY TRANSCRIPTION FACTOR NETWORKS UNDER BIOTIC AND ABIOTIC STRESS

Authors

  • M HAMMAD Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan Author
  • SHUH SHERAZI Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan Author
  • J AHMAD Department of Agronomy, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan Author
  • H AHMED Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan Author
  • A SANAM Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan Author
  • M SHAFIQ Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan Author

DOI:

https://doi.org/10.64013/bbasrjlifess.v2026i1.67

Keywords:

WRKY transcription factors, Arabidopsis thaliana, polyploidy, hormone regulation, gene cross-regulation, genetic manipulation

Abstract

Over the past three decades, WRKY transcription factors have been identified as central regulators of plant stress-responsive translational networks. Early Studies in the mid-1990s identified WRKY proteins as pathogen-responsive transcriptional factors in Arabidopsis thaliana, and their domain structure, DNA-binding specificity, and role in salicylic acid-mediated defense signaling pathways were revealed. The further expansion of genomic resources following the year 2010 enabled the identification of expanded WRKY gene families in major crops, which exhibited significant levels of gene duplication, divergence, and stress-responsive expression. Despite the present rapid advancement, the use of WRKY-based genetic manipulation strategies to improve crop performance has been inconsistent. This review integrates the previous thirty years of WRKY research from a translational standpoint. This review is organized around three interconnected themes: the bibliometric data, which reveal changes in methodology, species bias, and stress imbalance in the literature. Next, we look at the conserved regulatory features revealed in Arabidopsis, such as autoregulation, WRKY gene cross-regulation, and hormone regulation. The proliferation of WRKY gene families in polyploid agricultural species is also discussed from the standpoint of gene duplication and redundancy. Finally, we examine the structural hurdles to translational success by contrasting successful and unsuccessful translation initiatives. Finally, we propose a network-centric approach to future WRKY research that focuses on combinatorial perturbation, quantitative modulation, and field validation. Future progress will depend on understanding how WRKY regulatory logic can be harnessed to enhance stress resilience while maintaining productivity in stress responses; the essential question now is how WRKY's regulatory logic might be used to improve stress tolerance while preserving plant productivity.

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Author Biographies

  • M HAMMAD, Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan

    NA

  • SHUH SHERAZI, Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan

    NA

  • J AHMAD, Department of Agronomy, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan

    NA

  • H AHMED, Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan

    NA

  • A SANAM, Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan

    NA

  • M SHAFIQ, Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan

    NA

References

Bailey-Serres, J., Parker, J. E., Ainsworth, E. A., Oldroyd, G. E., and Schroeder, J. I. (2019). Genetic strategies for improving crop yields. Nature 575, 109-118.

Bakshi, M., and Oelmüller, R. (2014). WRKY transcription factors: Jack of many trades in plants. Plant signaling & behavior 9, e27700.

Berens, M. L., Berry, H. M., Mine, A., Argueso, C. T., and Tsuda, K. (2017). Evolution of hormone signaling networks in plant defense. Annual review of phytopathology 55, 401-425.

Birkenbihl, R. P., Kracher, B., Roccaro, M., and Somssich, I. E. (2017a). Induced genome-wide binding of three Arabidopsis WRKY transcription factors during early MAMP-triggered immunity. The Plant Cell 29, 20-38.

Birkenbihl, R. P., Liu, S., and Somssich, I. E. (2017b). Transcriptional events defining plant immune responses. Current opinion in plant biology 38, 1-9.

Blanc, G., and Wolfe, K. H. (2004). Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. The plant cell 16, 1667-1678.

Brand, L. H., Fischer, N. M., Harter, K., Kohlbacher, O., and Wanke, D. (2013). Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays. Nucleic Acids Research 41, 9764-9778.

Brenchley, R., Spannagl, M., Pfeifer, M., Barker, G. L., D’Amore, R., Allen, A. M., McKenzie, N., Kramer, M., Kerhornou, A., and Bolser, D. (2012). Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 491, 705-710.

Chen, F., Hu, Y., Vannozzi, A., Wu, K., Cai, H., Qin, Y., Mullis, A., Lin, Z., and Zhang, L. (2017). The WRKY transcription factor family in model plants and crops. Critical Reviews in Plant Sciences 36, 311-335.

Chen, L., Song, Y., Li, S., Zhang, L., Zou, C., and Yu, D. (2012). The role of WRKY transcription factors in plant abiotic stresses. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1819, 120-128.

Ciolkowski, I., Wanke, D., Birkenbihl, R. P., and Somssich, I. E. (2008). Studies on DNA-binding selectivity of WRKY transcription factors lend structural clues into WRKY-domain function. Plant molecular biology 68, 81-92.

Conant, G. C., and Wolfe, K. H. (2008). Turning a hobby into a job: how duplicated genes find new functions. Nature Reviews Genetics 9, 938-950.

Consortium, I. W. G. S., Appels, R., Eversole, K., Stein, N., Feuillet, C., Keller, B., Rogers, J., Pozniak, C. J., Choulet, F., and Distelfeld, A. (2018). Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361, eaar7191.

Dong, J., Chen, C., and Chen, Z. (2003). Expression profiles of the Arabidopsis WRKY gene superfamily during plant defense response. Plant molecular biology 51, 21-37.

Doudna, J. A., and Charpentier, E. (2014). The new frontier of genome engineering with CRISPR-Cas9. Science 346, 1258096.

Eulgem, T., Rushton, P. J., Robatzek, S., and Somssich, I. E. (2000). The WRKY superfamily of plant transcription factors. Trends in plant science 5, 199-206.

Eulgem, T., and Somssich, I. E. (2007). Networks of WRKY transcription factors in defense signaling. Current opinion in plant biology 10, 366-371.

Gao, C. (2021). Genome engineering for crop improvement and future agriculture. Cell 184, 1621-1635.

Hu, W., Ren, Q., Chen, Y., Xu, G., and Qian, Y. (2021). Genome-wide identification and analysis of WRKY gene family in maize provide insights into regulatory network in response to abiotic stresses. BMC plant biology 21, 427.

Huot, B., Yao, J., Montgomery, B. L., and He, S. Y. (2014). Growth–defense tradeoffs in plants: a balancing act to optimize fitness. Molecular plant 7, 1267-1287.

Ishihama, N., and Yoshioka, H. (2012). Post-translational regulation of WRKY transcription factors in plant immunity. Current opinion in plant biology 15, 431-437.

Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., and Charpentier, E. (2012). A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. science 337, 816-821.

Jing, Y., and Lin, R. (2015). The VQ motif-containing protein family of plant-specific transcriptional regulators. Plant physiology 169, 371-378.

Karasov, T. L., Chae, E., Herman, J. J., and Bergelson, J. (2017). Mechanisms to mitigate the trade-off between growth and defense. The Plant Cell 29, 666-680.

Kitano, H. (2004). Biological robustness. Nature Reviews Genetics 5, 826-837.

Li, J., Brader, G., and Palva, E. T. (2004). The WRKY70 transcription factor: a node of convergence for jasmonate-mediated and salicylate-mediated signals in plant defense. The plant cell 16, 319-331.

Lynch, M., and Conery, J. S. (2000). The evolutionary fate and consequences of duplicate genes. science 290, 1151-1155.

Mittler, R. (2006). Abiotic stress, the field environment and stress combination. Trends in plant science 11, 15-19.

Nan, H., Li, W., Lin, Y.-l., and Gao, L.-z. (2020). Genome-wide analysis of WRKY genes and their response to salt stress in the wild progenitor of Asian cultivated rice, Oryza rufipogon. Frontiers in Genetics 11, 359.

Panchy, N., Lehti-Shiu, M., and Shiu, S.-H. (2016). Evolution of gene duplication in plants. Plant physiology 171, 2294-2316.

Pandey, S. P., and Somssich, I. E. (2009). The Role of WRKY Transcription Factors in Plant Immunity. Plant Physiology 150, 1648-1655.

Park, P. J. (2009). ChIP–seq: advantages and challenges of a maturing technology. Nature reviews genetics 10, 669-680.

Phukan, U. J., Jeena, G. S., and Shukla, R. K. (2016). WRKY Transcription Factors: Molecular Regulation and Stress Responses in Plants. Frontiers in Plant Science Volume 7 - 2016.

Project, I. R. G. S. (2005). The map-based sequence of the rice genome. Nature 436, 793-800.

Qiu, Y., and Yu, D. (2009). Over-expression of the stress-induced OsWRKY45 enhances disease resistance and drought tolerance in Arabidopsis. Environmental and experimental botany 65, 35-47.

Rodríguez-Leal, D., Lemmon, Z. H., Man, J., Bartlett, M. E., and Lippman, Z. B. (2017). Engineering quantitative trait variation for crop improvement by genome editing. Cell 171, 470-480. e8.

Ross, C. A., Liu, Y., and Shen, Q. J. (2007). The WRKY gene family in rice (Oryza sativa). Journal of Integrative Plant Biology 49, 827-842.

Rushton, P. J., Somssich, I. E., Ringler, P., and Shen, Q. J. (2010). WRKY transcription factors. Trends in plant science 15, 247-258.

Rushton, P. J., Torres, J. T., Parniske, M., Wernert, P., Hahlbrock, K., and Somssich, I. (1996). Interaction of elicitor‐induced DNA‐binding proteins with elicitor response elements in the promoters of parsley PR1 genes. The EMBO journal 15, 5690-5700.

Schmutz, J., Cannon, S. B., Schlueter, J., Ma, J., Mitros, T., Nelson, W., Hyten, D. L., Song, Q., Thelen, J. J., and Cheng, J. (2010). Genome sequence of the palaeopolyploid soybean. nature 463, 178-183.

Schnable, P. S., Ware, D., Fulton, R. S., Stein, J. C., Wei, F., Pasternak, S., Liang, C., Zhang, J., Fulton, L., and Graves, T. A. (2009). The B73 maize genome: complexity, diversity, and dynamics. science 326, 1112-1115.

Singh, K. B., Foley, R. C., and Oñate-Sánchez, L. (2002). Transcription factors in plant defense and stress responses. Current opinion in plant biology 5, 430-436.

Suzuki, N., Rivero, R. M., Shulaev, V., Blumwald, E., and Mittler, R. (2014). Abiotic and biotic stress combinations. New Phytologist 203, 32-43.

Verma, V., Ravindran, P., and Kumar, P. P. (2016). Plant hormone-mediated regulation of stress responses. BMC plant biology 16, 86.

Vision, T. J., Brown, D. G., and Tanksley, S. D. (2000). The origins of genomic duplications in Arabidopsis. Science 290, 2114-2117.

Wang, Z., Gerstein, M., and Snyder, M. (2009). RNA-Seq: a revolutionary tool for transcriptomics. Nature reviews genetics 10, 57-63.

Weirauch, M. T., and Hughes, T. (2011). A catalogue of eukaryotic transcription factor types, their evolutionary origin, and species distribution. In "A handbook of transcription factors", pp. 25-73. Springer.

Wendel, J. F. (2015). The wondrous cycles of polyploidy in plants. American journal of botany 102.

Wu, K.-L., Guo, Z.-J., Wang, H.-H., and Li, J. (2005). The WRKY family of transcription factors in rice and Arabidopsis and their origins. DNA research 12, 9-26.

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. Journal of experimental botany 64, 5085-5097.

Yu, D., Chen, C., and Chen, Z. (2001). Evidence for an important role of WRKY DNA binding proteins in the regulation of NPR1 gene expression. The Plant Cell 13, 1527-1540.

Zandalinas, S. I., Sengupta, S., Fritschi, F. B., Azad, R. K., Nechushtai, R., and Mittler, R. (2021). The impact of multifactorial stress combination on plant growth and survival. New Phytologist 230, 1034-1048.

Zhang, Y., Massel, K., Godwin, I. D., and Gao, C. (2018). Applications and potential of genome editing in crop improvement. Genome biology 19, 210.

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Published

09-09-2026

How to Cite

HAMMAD, M., SHERAZI, S., AHMAD, J., AHMED, H., SANAM, A., & SHAFIQ, M. (2026). FROM ARABIDOPSIS TO CROPS: THREE DECADES OF WRKY TRANSCRIPTION FACTOR NETWORKS UNDER BIOTIC AND ABIOTIC STRESS. Journal of Life and Social Sciences, 2026(1), 67. https://doi.org/10.64013/bbasrjlifess.v2026i1.67

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