DREB2 (dehydration-responsive element-binding protein 2) type transcription factor in sorghum (Sorghum bicolor): genome-wide identification, characterization and expression profiles under cadmium and salt stresses

Abstract

Biotic and abiotic stresses negatively affect fitness, biomass production, and crop yield in plants. The dehydration-responsive element-binding proteins (DREB) are important transcription factors (TFs), and are induced by abiotic and biotic stresses. In this study, genome-wide identification, in silico sequence, and phylogenetic analyses and expression analyses of DREB2 genes under cadmium (Cd) and salt (NaCl) stresses in sorghum (Sorghum bicolor, Sb) were performed. Six putative SbDREB2 genes were identified in sorghum genome and all contained AP2 domain (PF00847). Nucleotide diversities in SbDREB2 genes were calculated as π: 0.53 and θ: 0.39, respectively. While exon numbers of them were either one or two, length of SbDREB2 proteins ranged from 238 to 388 amino acid residues. Fifty-six cis-acting regulatory elements, which are tissue specific, light, hormone, and stress responsive, were identified in the promotor regions of SbDREB2 genes. Analyses on digital expression data indicated that SbDREB2A and SbDREB2B are more expressed genes than other SbDREB genes in sorghum. Under Cd and NaCl stresses, expressions of SbDREB2 genes were induced at different levels. All SbDREB2 genes in root were up-regulated under salt stress. In case of Cd stress, SbDREB2D gene was particularly up-regulated in leaves and roots. Co-expression analyses revealed four of TFs in co-expression network, indicating that they have roles in transcriptional cascade. Furthermore, five miRNA target regions were identified for four SbDREB2 genes, indicating their roles in post-transcriptional regulation. The predicted 3D structure of SbDREB2 proteins showed some structural divergences and structure overlap between rice and sorghum varied at between 26.58 and 50%. Finally, obtained data could be used in breeding of stress-tolerant plants, particularly genetically engineered DREB2 expressing plants. Findings in this study would also contribute to the understanding of DREB2 genes in plants, especially in sorghum.

Keywords: Abiotic stress; Gene expression; Genome-wide analyses; Sorghum.

Fig. 1

Comparison of amino acid alignments of the DREB2 proteins in Arabidopsis, rice, and sorghum, respectively. The yellow and red rectangles indicate the nuclear localization site (NLS) and AP2 domain structures, respectively. Sequences were aligned by ClustalW; identical and similar residues were shaded as black and grey, respectively, with 100% threshold

Fig. 2

Amino acid distributions of DREB2 proteins from Arabidopsis (a), rice (b), and sorghum (c)

Fig. 3

Phylogenetic tree of 19 DREB2A proteins in three plant species, including Arabidopsis, rice, and sorghum. Tree was constructed by MEGA 7 using maximum-likelihood (ML) method with 1000 bootstraps. The sorghum DREB2 proteins were indicated as red diamonds

Fig. 4

Heat map of cis-regulatory elements in DREB2 genes in sorghum (green: absent and red: present). The cis-regulatory elements were investigated using 1000-bp upstream regions of DREB2 genes

Fig. 5

Expression levels of DREB2 genes in different five development stages of sorghum, such as seedling, stem elongation, booting, flowering, and dough stages by Genevestigator database

Fig. 6

Expression levels of DREB2 genes in different six anatomical parts of sorghum, such as pith, rind, shoot, roots, leaf, and internode by Genevestigator database

Fig. 7

Expression profiles of SbDREB2A, B, C1, and D genes in various development stages, anatomical parts, tissues, and stress conditions using MOROKOSHI transcriptome database. The legends on the figures show the synonym name of SbDREB2 genes

Fig. 8

Co-expression networks of SbDREB2A gene by MOROKOSHI Sorghum transcriptome database. Sb03g004980 shows the synonym of SbDREB2A (Sobic.003G058200). In addition, the red filled octagons show the transcription factors

Fig. 9

Expression of SbDREB2 genes under Cd (a) and NaCl (b) stresses in sorghum leaves and roots detected by RT-qPCR. Bars above/below x-axis demonstrate up- and down-regulation of genes, respectively. Expression values are indicated as log2 scale to better represent the symmetry of magnitude for up and down-regulated genes. Error bars depict standard deviation of the mean (sdom; n = 3). Values with identical lowercase letters are not significantly different (P < 0.01) as compared by Student’s t test

Fig. 10

Structure overlaps of DREB2 proteins at superimposition mode by CLICK server. The orange and blue 3D structures show the rice and sorghum, respectively. In addition, structure overlaps values (%) were indicated in figure legends