Interactions Among Plant Transcription Factors Regulating Expression of Stress-responsive Genes

Abstract

Plants are simultaneously subjected to a variety of stress conditions in the field and are known to combat the hostile conditions by up/down-regulating number of genes. There exists a significant level of cross-talk between different stress responses in plants. In this study, we predict the interacting pairs of transcription factors that regulate the multiple abiotic stress-responsive genes in the plant Arabidopsis thaliana. We identified the interacting pair(s) of transcription factors (TFs) based on the spatial proximity of their binding sites. We also examined the interactions between the predicted pairs of TFs using molecular docking. Subsequent to docking, the best interaction pose was selected using our scoring scheme DockScore, which ranks the docked solutions based on several interface parameters and aims to find optimal interactions between proteins. We analyzed the selected docked pose for the interface residues and their conservation.

Keywords: Arabidopsis thaliana; docking; protein–protein interactions; stress conditions; transcription factors.

Figure 1

Workflow describing the method and tools/techniques adopted. Notes: Multiple stress-responsive genes (master genes) were identified and their TFBS information was also obtained. Based on the spatial proximity between TFBS, we identified putative interacting pairs of transcription factors. The interactions between these pairs of TF were studied using docking.

Figure 2

Modeled structures of transcription factors using Modeller (9v7) (A). bZIP (B). HSF (C). ARF (D). bHLH dimer. Notes: Using comparative modeling, the structures for four transcription factors were modeled and were further validated by checking the percentage allowed regions in Ramachandran map. The best model was selected on the basis of highest percentage allowed regions and least DOPE score as given by Modeller.

Figure 3

Docked posed pairs of transcription factors and their interface analysis. Notes: All four-transcription factor pairs were subjected to docking and the docked pose was selected using the scoring scheme DockScore. The figure shows the selected pose with highest score. (A) bHLH and bZIP, (B) MYB and bHLH, (C) MYB and ARF, and (D) WRKY and HSF. Chain A of each docked pose is in red and second chain in blue. The interface residues from both the chains are colored in yellow. In orange are the atoms of conserved interface residues from both the chains.