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

Abstract

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.

Genome-wide identification of WRKY in cotton and the positive role of GhWRKY31 in response to salt and drought stress

“…This was evident through a weak physiological phenotype, increased MDA content, reduced proline accumulation, and a signi cant inhibition of stress-related gene expression levels, such as ABI3, ABF2, DREB1, DREB2, RD22, LEA5, and P5CS in WRKY-silenced seedlings. Meanwhile, the highly conserved WRKYGQK domain of SlWRKY3/4, CcWRKY1/51/70, and HvWRKY46 could also form hydrogen bonds with the W box of stress-related, and these WRKY subfamily members appeared various bonding strength (Aamir et al 2017;Pandey et al 2018;Singh et al 2019). In addition, the Y1H assay con rmed that GhABF1, GhDREB2, and GhRD29 are direct targets of GhWRKY31 protein (Fig.…”

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“…The DBD is the main feature of the WRKY transcription factors. Due to the presence of WRKY signature sequences, it termed as WRKY domain [30]. In a few cases, the signature term WRKY is displaced by WRRY, WSKY, WKRY, WVKY or WKKY [31,32].…”

A Comprehensive Study of the WRKY Transcription Factor Family in Strawberry

“…The amino acids constituting the WRKY core motif are essential for the DNA-binding activity and recognition specificity. Thus amino acid substitutions in this motif can affect the binding to the W-box [14,16,17]. Variations in this conserved sequence have been found in WRKY proteins from different plant species [3], with functional and binding activity characterization in some cases.…”