Evolution and identification of DREB transcription factors in the wheat genome: modeling, docking and simulation of DREB proteins associated with salt stress

Abstract

Soil salinity and the resulting salt stress it imposes on crop plants is a major problem for modern agriculture. Understanding how salt tolerance mechanisms in plants are regulated is therefore important. One regulatory mechanism is the APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factor family, including dehydration responsive element binding (DREB) transcription factors. By binding to DNA, specifically upstream of genes that play roles in salt tolerance pathways, DREB proteins upregulate expression of these genes. DREB in Triticum aestivum (wheat) cluster in subgroups and in this study by scanning the recently extended predicted proteome of wheat for DREB, we increased the number of members of this sub-family. Using the wheat genome, we identified 576 genes coding for the AP2 domain of which 508 were identified to have one AP2 domain, a characteristic of the DREB/ ERF subfamily. We confirmed the existing four subgroups by sequence-based phylogenetic analyses but also identified 32 new DREB subfamily members, not belonging to any known subgroup. Transcription factor profile inference analysis identified two genes, TraesCS2B02G002700 and TraesCS2D02G015200, being homologous to DREB1A of Arabidopsis thaliana. Based on molecular simulation (25 ns) analysis, TraesCS2B02G002700 with a CCGAC motif was observed to interact very stably with DNA. In silico mutational analysis at the 19 th position in the DREB domain of TraesCS2B02G002700-DNA complex indicated this as a stable part for recognizing and forming interaction with DNA. Moreover, six target genes were predicted having an upstream CCGAC motif regulated by TraesCS2B02G002700. Our study provides an overall framework for exploring the transcription factors in plants and identifying e.g. potential salt stress target genes.

Physiological and molecular mechanism of ginger (Zingiber officinale Roscoe) seedling response to salt stress

“…This family regulates salt tolerance by binding to upstream the DNA of genes that function specifically in the salt-tolerant pathway. As a result, the DREB protein increased the expression of these salttolerant genes (Hassan et al, 2022). In addition, we discovered that the biological function of MYB under salt stress was tightly connected to the ginger root gene 122051202.…”

Improved Salinity Tolerance-Associated Variables Observed in EMS Mutagenized Wheat Lines

“…However, a low Na + and a high K + content are preferred and have previously been reported for salt tolerant genotypes [ 32 ], and high K + accumulation reportedly enhances plant growth under salt stress [ 50 ]. In addition, to understand genes directly linked to the transport and accumulation of Na + and K + during salinity stress in different compartments and tissues, the control and regulation of salinity tolerance mechanisms by transcription factor families, such as WRKY and DREB, need to be better understood [ 51 , 52 ]. That will help elucidate salinity tolerance mechanisms as they have critical roles in regulating genes linked to ion transport, antioxidant defense, and osmotic pressure [ 38 ].…”

Research Article Isolation and characterization of DREB gene in ancestral diploid wheat species from a wheat domestication center

“…Similarly, this model comprises of three-stranded antiparallel β-sheet followed by α-helix and relatively unstructured C'-terminal. By changing various amino acids within the AP2 domain, Hassan et al (2021) determined their role in the formation of the secondary structure. They also showed that some of the model structures had two beta strands and one alpha helix.…”

“…They found that TaDREB21-B/D showed alternative exon patterns, TaDREB20-D, TaDREB26-A, TaDREB52-B/D, and TaDREB58-A showed an intron-retention pattern, while only TaDREB3-A/B/D showed an exon-skipping pattern which was found on all three chromosomes. Using sequence-based phylogenetic analyses, Hassan et al (2021) identified 32 new DREB subfamily members, not belonging to any known sub-group.…”