Molecular dynamics simulations revealed structural differences among WRKY domain-DNA interaction in barley (Hordeum vulgare)

Bharati Pandey,Abhinav Grover,Pradeep Sharma

doi:10.1186/s12864-018-4506-3

Abstract

BackgroundThe WRKY transcription factors are a class of DNA-binding proteins involved in diverse plant processes play critical roles in response to abiotic and biotic stresses. Genome-wide divergence analysis of WRKY gene family in Hordeum vulgare provided a framework for molecular evolution and functional roles. So far, the crystal structure of WRKY from barley has not been resolved; moreover, knowledge of the three-dimensional structure of WRKY domain is pre-requisites for exploring the protein-DNA recognition mechanisms. Homology modelling based approach was used to generate structures for WRKY DNA binding domain (DBD) and its variants using AtWRKY1 as a template. Finally, the stability and conformational changes of the generated model in unbound and bound form was examined through atomistic molecular dynamics (MD) simulations for 100 ns time period.ResultsIn this study, we investigated the comparative binding pattern of WRKY domain and its variants with W-box cis-regulatory element using molecular docking and dynamics (MD) simulations assays. The atomic insight into WRKY domain exhibited significant variation in the intermolecular hydrogen bonding pattern, leading to the structural anomalies in the variant type and differences in the DNA-binding specificities. Based on the MD analysis, residual contribution and interaction contour, wild-type WRKY (HvWRKY46) were found to interact with DNA through highly conserved heptapeptide in the pre- and post-MD simulated complexes, whereas heptapeptide interaction with DNA was missing in variants (I and II) in post-MD complexes. Consequently, through principal component analysis, wild-type WRKY was also found to be more stable by obscuring a reduced conformational space than the variant I (HvWRKY34). Lastly, high binding free energy for wild-type and variant II allowed us to conclude that wild-type WRKY-DNA complex was more stable relative to variants I.ConclusionsThe results of our study revealed complete dynamic and structural information about WRKY domain-DNA interactions. However, no structure base information reported to date for WRKY variants and their mechanism of interaction with DNA. Our findings highlighted the importance of selecting a sequence to generate newer transgenic plants that would be increasingly tolerance to stress conditions.

Highlights

The WRKY transcription factors are a class of DNA-binding proteins involved in diverse plant processes play critical roles in response to abiotic and biotic stresses
Threedimensional (3D) structures of WRKY domain from barley was built by homology modeling based on crystal structure of Arabidopsis WRKY gene
Structural validations for all WRKY domains in unbound and bound form was done by root mean square deviation (RMSD), root mean square fluctuation (RMSF) and radius of gyration (Rg) analysis

Summary

Introduction

The WRKY transcription factors are a class of DNA-binding proteins involved in diverse plant processes play critical roles in response to abiotic and biotic stresses. Genome-wide divergence analysis of WRKY gene family in Hordeum vulgare provided a framework for molecular evolution and functional roles. Barley (Hordeum vulgare L.) is amongst the world’s earliest domesticated and most important cereal crops. It is diploid in nature with a large genome of 5.1 Gb [1]. Several transcription factor families have been shown to be involved in the defense against these adverse stress conditions [3]. The WRKY family is among them and play key roles in modulating gene expression during defense in response to biotic and abiotic stress [4]. The first WRKY gene (SPF1) was identified in sweet potato [4], since it has been identified in various plant species [5,6,7,8,9,10,11,12,13]

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