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

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.

Genome-wide analysis, identification, evolution and genomic organization of dehydration responsive element-binding (DREB) gene family in Solanum tuberosum

Background The dehydration responsive element-binding (DREB) gene family plays a crucial role as transcription regulators and enhances plant tolerance to abiotic stresses. Although the DREB gene family has been identified and characterized in many plants, knowledge about it in Solanum tuberosum (Potato) is limited. Results In the present study, StDREB gene family was comprehensively analyzed using bioinformatics approaches. We identified 66 StDREB genes through genome wide screening of the Potato genome based on the AP2 domain architecture and amino acid conservation analysis (Valine at position 14th). Phylogenetic analysis divided them into six distinct subgroups (A1–A6). The categorization of StDREB genes into six subgroups was further supported by gene structure and conserved motif analysis. Potato DREB genes were found to be distributed unevenly across 12 chromosomes. Gene duplication proved that StDREB genes experienced tandem and segmental duplication events which led to the expansion of the gene family. The Ka/Ks ratios of the orthologous pairs also demonstrated the StDREB genes were under strong purification selection in the course of evolution. Interspecies synteny analysis revealed 45 and 36 StDREB genes were orthologous to Arabidopsis and Solanum lycopersicum, respectively. Moreover, subcellular localization indicated that StDREB genes were predominantly located within the nucleus and the StDREB family’s major function was DNA binding according to gene ontology (GO) annotation. Conclusions This study provides a comprehensive and systematic understanding of precise molecular mechanism and functional characterization of StDREB genes in abiotic stress responses and will lead to improvement in Solanum tuberosum.

Characteristics and phylogeny of DREB gene subfamily in soybeans [Glycine max (L.) Meril]

Dehydration responsive element binding proteins (DREB) are transcription factors linked to cis-acting elements of the promoter region, which regulate plant gene expression in response to abiotic stress. In this study, 69 DREB gene sequences of soybean from NCBI belonging to 18 GmDREB (Glycine max DREB) genes of 1 to 8 copies distributed on 17 chromosomes were identified in which GmDREB3 has 8 copies and the rest consisted of 1 to 4 ones. The motif PTPEMAARAYDVAALALKGPSARLNFPEL containing 11 points associated with the promoter of functional genes existed in 4 main types with the most popular one RGRRWKERRWT found in 13/18 DREB proteins was regarded as the popular AP2 domain of DREB protein. The phylogenetic tree based on the nucleotide sequences of GmDREB genes and the amino acid sequences of the AP2 domain expresses the evolution and relationship of the DREB subfamily in soybean. This study provides comprehensive information about the DREB subfamily, which formed the basis for experimental analyses to clarify the function of some members of this subfamily.

ScDREB10, an A-5c type of DREB Gene of the Desert Moss Syntrichia caninervis, Confers Osmotic and Salt Tolerances to Arabidopsis

Drought and salinity are major factors limiting crop productivity worldwide. DREB (dehydration-responsive element-binding) transcription factors play important roles in plant stress response and have been identified in a wide variety of plants. Studies on DREB are focused on the A-1 (DREB1) and A-2 (DREB2) groups. Studies on A-5 group DREBs, which represent a large proportion of the DREB subfamily, is limited. In this study, we characterized and analyzed the stress tolerance function of ScDREB10, an A-5c type DREB gene from the desert moss Syntrichia caninervis. Transactivation assay in yeast showed that ScDREB10 had transactivation activity. Transient expression assay revealed that ScDREB10 was distributed both in the nucleus and cytosol of tobacco leaf epidermal cells. Overexpression of ScDREB10 significantly increased the germination percentage of Arabidopsis seeds under osmotic and salt stresses, and improved the osmotic and salt stress tolerances of Arabidopsis at the seedling stage and is associated with the expression of downstream stress-related genes and improved reactive oxygen species (ROS) scavenging ability. Our study provides insight into the molecular mechanism of stress tolerance of A-5 type DREB proteins, as well as providing a promising candidate gene for crop salt and drought stress breeding.

Expression level of DREB gene of local corn cultivars from Kisar Island-Maluku, Indonesia, using quantitative real time polymerase chain reaction

The research objective was to determine the expression level of dehydration responsive element binding (DREB) gene of local corn cultivars from Kisar Island Maluku, Indonesia. The study was designed as randomized block design with single factor consist of six local corn cultivars obtained from farmers in Kisar Island and one reference varieties which has been released as a drought-tolerant varieties and obtained from Cereal Crops Research Institute Maros South Sulawesi. Isolation of total RNA from the second leaf after the flag leaf at the 65 days after planting were carried out according to the protocols of the R and ABlueTM Total RNA Extraction Kit, and was used as a template for cDNA synthesis. Amplification of cDNA from total RNA was carried out according to the protocol of One-Step Reverse Transcriptase PCR Premix Kit. Real Time-PCR was performed usingcDNA from reverse transcription following the procedures of Real MODTM Green Real-Time PCR Master Mix Kit. The real time-PCR data were analyzed using relative quantification method based on the critical point/cycle threshold. The highest DREB gene expression was showed by Deep Yellow local corn cultivar, and the lowest one was showed by Rubby Brown Cob cultivar. The DREB gene expression level of deep yellow local corn cultivar was even higher than Srikandi variety as a reference variety.