Abstract
AbstractExpression of the Arabidopsis HARDY (hrd) DNA binding transcription factor (555 bp present on chromosome 2) has been shown to increase WUE in rice by Karaba et al 2007 (PNAS, 104:15270–15275). We conducted a detail analysis of the complete sorghum genome for the similarity/presence of either DNA, mRNA or protein product of the Arabidopsis HARDY (hrd) DNA binding transcription factor (555 bp present on chromosome 2). Chromosome 6 showed a sequence match of 61.5 percent positive between 61 and 255 mRNA residues of the query region. Further confirmation was obtained by TBLASTN which showed that chromosome 6 of the sorghum genome has a region between 54948120 and 54948668 which has 80 amino acid similarities out of the 185 residues. A homology model was constructed and verified using Anolea, Gromos and Verify3D. Scanning the motif for possible activation sites revealed that there was a protein kinase C phosphorylation site between 15th and 20th residue. The study indicates the possibility of the presence of a DNA binding transcription factor in chromosome 6 of Sorghum bicolor with 60 percent similarity to that of Arabidopsis hrd DNA binding transcription factor.
Highlights
The Sorghum bicolor genome project was initiated through Community Sequencing Program (CSP) by a consortium led by Paterson et al has been completed and the version 1 of the genome is released publically
In this study we took up detail analysis of the complete sorghum genome for the similarity/presence of either DNA, mRNA or protein product of the above mentioned Arabidopsis hrd DNA binding transcription factor
We conducted i) BLASTN- nucleotide query to sorghum nucleotide database, ii)TBLASTX – translated nucleotide query sequence into protein sequences in all 6 reading frames compared to sorghum nucleotide database translated on all six reading frames and iii) TBLASTN- protein query to translated 6 frame sorghum nucleotide database
Summary
In silico analysis for the presence of HARDY an Arabidopsis drought tolerance DNA binding transcription factor product in chromosome 6 of Sorghum bicolor genome Water use efficiency (WUE), if increased in terms of biomass produced at the expense of transpiration measured, will have a positive effect on crop yield, under water limiting conditions. Expression of the Arabidopsis HARDY (hrd) DNA binding transcription factor (555 bp present on chromosome 2) has been shown to increase WUE in rice by Karaba et al 2007 (PNAS, 104:15270–15275).
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