Genome-wide promoter analysis, homology modeling and protein interaction network of Dehydration Responsive Element Binding (DREB) gene family in Solanum tuberosum

Abstract

Dehydration Responsive Element Binding (DREB) regulates the expression of numerous stress-responsive genes, and hence plays a pivotal role in abiotic stress responses and tolerance in plants. The study aimed to develop a complete overview of the cis-acting regulatory elements (CAREs) present in S. tuberosum DREB gene promoters. A total of one hundred and four (104) cis-regulatory elements (CREs) were identified from 2.5kbp upstream of the start codon (ATG). The in-silico promoter analysis revealed variable sets of cis-elements and functional diversity with the predominance of light-responsive (30%), development-related (20%), abiotic stress-responsive (14%), and hormone-responsive (12%) elements in StDREBs. Among them, two light-responsive elements (Box-4 and G-box) were predicted in 64 and 61 StDREB genes, respectively. Two development-related motifs (AAGAA-motif and as-1) were abundant in StDREB gene promoters. Most of the DREB genes contained one or more Myeloblastosis (MYB) and Myelocytometosis (MYC) elements associated with abiotic stress responses. Hormone-responsive element i.e. ABRE was found in 59 out of 66 StDREB genes, which implied their role in dehydration and salinity stress. Moreover, six proteins were chosen corresponding to A1-A6 StDREB subgroups for secondary structure analysis and three-dimensional protein modeling followed by model validation through PROCHECK server by Ramachandran Plot. The predicted models demonstrated >90% of the residues in the favorable region, which further ensured their reliability. The present study also anticipated pocket binding sites and disordered regions (DRs) to gain insights into the structural flexibility and functional annotation of StDREB proteins. The protein association network determined the interaction of six selected StDREB proteins with potato proteins encoded by other gene families such as MYB and NAC, suggesting their similar functional roles in biological and molecular pathways. Overall, our results provide fundamental information for future functional analysis to understand the precise molecular mechanisms of the DREB gene family in S. tuberosum.

Consensus genomic regions associated with multiple abiotic stress tolerance in wheat and implications for wheat breeding

“…Stress-responsive gene regulation in Arabidopsis and soybean essentially depends on the TGG TTT (ARE), activation sequence-1 (as-1) and TC-rich repeat elements [85][86][87] . In addition, WUN-motif is a dehydration-related element detected in the regulatory region of the StDREB gene in tomato 88 .…”

Genome-Wide Identification, Characterization, and Expression Analysis of Tubby-like Protein (TLP) Gene Family Members in Woodland Strawberry (Fragaria vesca)

“…Cis -elements related to the light response, development, hormonal responses, and stress responses were unevenly distributed in the promoters of FvTLP s (Figure and Table). The AAGAA-motif and as-1 element are related to development [ 33 ]; the AAGAA-motif was detected in all FvTLP promoters, with the exception of the FvTLP5 promoter, and the as-1 element was detected in all FvTLP promoters, with the exception of the FvTLP7 promoter. The RY element is involved in seed-specific regulation and was observed in the FvTLP1 , 2 , and 4 promoters.…”

Consensus genomic regions associated with multiple abiotic stress tolerance in wheat and implications for wheat breeding

“…Stress-responsive gene regulation in Arabidopsis and soybean essentially depends on the TGGTTT (ARE), activation sequence-1 (as-1) and TC-rich repeat elements 75,76,77 . In addition, WUN-motif is a dehydration-related element detected in the regulatory region of the StDREB gene in tomato 78 .…”