Characterization of Soybean WRKY Gene Family and Identification of Soybean WRKY Genes that Promote Resistance to Soybean Cyst Nematode

Yang, Yan; Zhou, Yuan; Chi, Yingjun; Fan, Baofang; Chen, Zhixiang

doi:10.1038/s41598-017-18235-8

Cited by 104 publications

(76 citation statements)

References 59 publications

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“…Subgroup IIc has also been proposed to be a separate group by Zhang and Wang (2005) or subgroup Ib by Wu et al (2005). In addition to variations in zinc finger motifs, mutations in the consensus WRKYGQK sequence often appear in various plant species, and frequently observed variants include WRKYGKK and WRKYGEK (Wu et al 2005;Yao et al 2015;Jiang et al 2017b;Yang et al 2017;Song et al 2018).…”

Section: Wrky Structure and Evolutionmentioning

confidence: 99%

“…The expansion of the groups I and II WRKY genes in Gossypium occurred through WGD (whole genome duplication) and tandem duplications (Ding et al 2015a). The pineapple genome possesses relatively fewer WRKY genes than other monocots, which is possibly due to a lack of pangrass ρ WGD events during pineapple evolution (Xie et al 2018), while WGD and local gene duplication led to the existence of a large number of close GmWRKY homologs in soybean (Yang et al 2017).…”

Section: Wrky Structure and Evolutionmentioning

confidence: 99%

“…Chimeric WRKY TFs containing the WRKY domain (WD) and other novel protein domains have been discovered through genome mining (Rinerson et al 2015;Mohanta et al 2016). Genomic sequences have facilitated transcriptomic analyses of gene families, such as the WRKY genes, in a specific physiological process or stress condition and the discovery of important genes involved in particular circumstances (Ning et al 2017;Yang et al 2017;Xie et al 2018). In addition, chromatin immunoprecipitation-sequencing (ChIP-seq) and DNA affinity purification sequencing (DAP-seq) have been used to identify genome-wide binding sites for TFs, such as the WRKY TFs (Liu et al 2015;O'Malley et al 2016;Birkenbihl et al 2017).…”

Section: Introductionmentioning

confidence: 99%

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WRKY transcription factors: evolution, binding, and action

et al. 2019

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The WRKY transcription factor (TF) gene family expanded greatly in the evolutionary process from green algae to flowering plants through whole genome, segmental, and tandem duplications. Genomic sequences from diverse plant species provide valuable information about the origin and evolution of WRKY domain-containing proteins. Accumulating data indicate that WRKY TFs bind W-box and/or other cis-elements, revealing the specificity of ciselement recognition based on the structure of the WRKY protein as well as the nucleotides adjacent to the core sequences. Physical interactions among WRKY proteins or between WRKY proteins and other regulatory factors afford important insights into the regulation of this TF family. WRKY proteins are essential players in the kinase signaling network. The interaction of plant resistance (R) proteins with WRKY TFs and the existence of unusual chimeric R-WRKY proteins suggest diversity in signaling pathways for rapid immune responses. In this review, we focus mainly on progress in understanding the function of WRKY TFs in response to biotic stresses and focus on their multiple roles in Arabidopsis and rice plants.

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Section: Wrky Structure and Evolutionmentioning

confidence: 99%

Section: Wrky Structure and Evolutionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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WRKY transcription factors: evolution, binding, and action

et al. 2019

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“…Morus005757 shows significant up-regulation in response to dehydration stress, salinity stress, and SA and ABA (Abscisic acid) treatments [27]. Similar results were also found in wheat, common bean [28], grape [29], pineapple [30], soybean [31], moso bamboo [32], Caragana intermedia [33], peanut [34], and broomcorn millet [35]. These observations suggest that studying the WRKY gene families may provide valuable insights into the mechanism underlying abiotic stress tolerance in plants.…”

Section: Introductionmentioning

confidence: 64%

Identification of WRKY Gene Family from Dimocarpus longan and Its Expression Analysis during Flower Induction and Abiotic Stress Responses

Jue

Sang

Liu

et al. 2018

IJMS

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Longan is an important fruit tree in the subtropical region of Southeast Asia and Australia. However, its blooming and its yield are susceptible to stresses such as droughts, high salinity, and high and low temperature. To date, the molecular mechanisms of abiotic stress tolerance and flower induction in longan have not been elucidated. WRKY transcription factors (TFs), which have been studied in various plant species, play important regulatory roles in plant growth, development, and responses to stresses. However, there is no report about WRKYs in longan. In this study, we identified 55 WRKY genes with the conserved WRKY domain and zinc finger motif in the longan genome. Based on the structural features of WRKY proteins and topology of the phylogenetic tree, the longan WRKY (DlWRKY) family was classified into three major groups (I–III) and five subgroups (IIa–IIe) in group II. Tissue expression analysis showed that 25 DlWRKYs were highly expressed in almost all organs, suggesting that these genes may be important for plant growth and organ development in longan. Comparative RNA-seq and qRT-PCR-based gene expression analysis revealed that 18 DlWRKY genes showed a specific expression during three stages of flower induction in “Sijimi” (“SJ”), which exhibited the “perpetual flowering” (PF) habit, indicating that these 18 DlWRKY genes may be involved in the flower induction and the genetic control of the perpetual flowering trait in longan. Furthermore, the RT-qPCR analysis illustrated the significant variation of 27, 18, 15, 17, 27, and 23 DlWRKY genes under SA (Salicylic acid), MeJA (Methyl Jasmonate), heat, cold, drought, or high salinity treatment, respectively, implicating that they might be stress- or hormone-responsive genes. In summary, we systematically and comprehensively analyzed the structure, evolution, and expression pattern of the DlWRKY genes. The results presented here increase our understanding of the WRKY family in fruit trees and provide a basis for the further elucidation of the biological function of DlWRKY genes in longan.

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“…The WRKY family have been involved in various physiological as well as developmental processes, for instance: seed germination [12], plant growth [13], seed and trichome development [14,15], panicle development [16], secondary metabolism [17], leaf senescence [18], bud and floral differentiation [19], and hormone signaling [20,21]. The WRKY family is also involved in responses to a range of biotic stressors like, drought, salinity [22,23], heat [24], cold [25], and abiotic stressors, such as bacteria [26], nematodes [27], fungi [28], viral pathogen resistance [29].…”

Section: Introductionmentioning

confidence: 99%

Understanding the Effect of Structural Diversity in WRKY Transcription Factors on DNA Binding Efficiency through Molecular Dynamics Simulation

Singh

Sharma²,

Singh

et al. 2019

Biology

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A precise understanding of the molecular mechanism involved in stress conditions has great importance for crop improvement. Biomolecules, such as WRKY proteins, which are the largest transcription factor family that is widely distributed in higher plants, plays a significant role in plant defense response against various biotic and abiotic stressors. In the present study, an extensive homology-based three-dimensional model construction and subsequent interaction study of WRKY DNA-binding domain (DBD) in CcWRKY1 (Type I), CcWRKY51 (Type II), and CcWRKY70 (Type III) belonging to pigeonpea, a highly tolerant crop species, was performed. Evaluation of the generated protein models was done to check their reliability and accuracy based on the quantitative and qualitative parameters. The final model was subjected to investigate the comparative binding analysis of different types of WRKY–DBD with DNA-W-box (a cis-acting element) by protein–DNA docking and molecular dynamics (MD) simulation. The DNA binding specificity with WRKY variants was scrutinized through protein–DNA interaction using the HADDOCK server. The stability, as well as conformational changes of protein–DNA complex, was investigated through molecular dynamics (MD) simulations for 100 ns using GROMACS. Additionally, the comparative stability and dynamic behavior of each residue of the WRKY–DBD type were analyzed in terms of root mean square deviation (RMSD), root mean square fluctuation (RMSF)values of the backbone atoms for each frame taking the minimized structure as a reference. The details of DNA binding activity of three different types of WRKY–DBD provided here will be helpful to better understand the regulation of WRKY gene family members in plants.

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Characterization of Soybean WRKY Gene Family and Identification of Soybean WRKY Genes that Promote Resistance to Soybean Cyst Nematode

Cited by 104 publications

References 59 publications

WRKY transcription factors: evolution, binding, and action

WRKY transcription factors: evolution, binding, and action

Identification of WRKY Gene Family from Dimocarpus longan and Its Expression Analysis during Flower Induction and Abiotic Stress Responses

Understanding the Effect of Structural Diversity in WRKY Transcription Factors on DNA Binding Efficiency through Molecular Dynamics Simulation

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