Over-represented promoter motifs in abiotic stress-induced DREB genes of rice and sorghum and their probable role in regulation of gene expression

Abstract

Genes coding for drought response element binding (DREB) proteins regulate transcription of a large number of downstream genes involved in the plant response to abiotic stresses. However the regulation of DREB genes themselves is not well understood. Using a bioinformatics approach, we identified the over-represented motifs in promoters of DREB genes of sorghum and rice as compared to all the other promoters in their genomes. Aligned orthologous promoter pairs of sorghum and rice DREBs were then used to identify co-localized motifs from among the over-represented ones, assuming that such motifs were likely to play a regulatory role. Finally the motifs over-represented in sorghum DREBs in comparison to their rice orthologs were identified. Results indicated over-representation of motifs pertaining to calcium, light, sugar, and hormone signaling in the DREB promoters. The co-localized motifs in DREB promoters were mainly those involved in abscisic acid-, light- and calcium-mediated regulation. These motifs along with others pertaining to ethylene signaling were over-represented in sorghum DREB promoters as compared to their orthologs from rice and could possibly contribute to its drought tolerance. Besides calcium, an integration of abscisic acid, ethylene, auxin and methyl jasmonate signaling was probably involved in regulating expression of the drought response through DREB transcription factors.

Acknowledgements

S.B. and A.S. acknowledge the financial assistance provided by Department of Biotechnology (DBT), Government of India, and also thank Dr. Sharayu Paranjpe, Statistics Department, University of Pune, for advice on statistical methods used. A.L. acknowledges the financial assistance provided by the School of Life Sciences, University of Skövde

Figures and Tables

Figure 1 Dendrogram showing the clustering of DREB 1 (black) and DREB 2 (gray) proteins of sorghum and rice. The dendrogram was constructed using the maximum parsimony algorithm with 1,000 bootstrap replicates (MEGA version 4).

Figure 2 Dendrogram showing the clustering of −1,000 nt DREB 1 (black) and DREB 2 (gray) promoter sequences of sorghum and rice. The dendrogram was constructed using the maximum parsimony algorithm with 1,000 bootstrap replicates (MEGA version 4).

Figure 3 Over-represented motifs that are co-localized on the promoter sequences of orthologous sorghum and rice DREB genes. (−) indicates presence of the motif on the negative strand.

Table 1 DREB genes of rice and sorghum

Table 2 Orthologous pairs of sorghum and rice DREB genes

Table 3 Motifs over-represented in promoters of sorghum and rice DREB1 (21 genes) and DREB2 genes (11 genes)

Table 4 Motifs showing common occurrence in the promoters of 15 orthologous DREB genes of sorghum and rice

Table 5 Motifs co-localized in aligned promoters of DREB1 and DREB2 orthologs from sorghum and rice

Table 6 Motifs over-represented in DREB promoters of sorghum (15) as compared to their occurrence in DREB promoters of rice (17)