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Author: search.filters.author.Bahadur, Ranjit PrasadSubject: search.filters.subject.Setaria italica

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    The DNA-binding activity of an AP2 protein is involved in transcriptional regulation of a stress-responsive gene, SiWD40, in foxtail millet
    (Elsevier, 2012) Mishra, Awdhesh Kumar; Puranik, Swati; Bahadur, Ranjit Prasad; Prasad, Manoj
    A differentially expressed transcript, encoding a putative WD protein (Setaria italica WD40; SiWD40), was identified in foxtail millet. Tertiary structure modeling revealed that its C-terminus possesses eight blade β-propeller architecture. Its N-terminal has three α-helices and two 310-helices and was highly induced by different abiotic stresses. The SiWD40:GFP fusion protein was nuclear localized. Promoter analysis showed the presence of many cis-acting elements, including two dehydration responsive elements (DRE). A stress-responsive SiAP2 domain containing protein could specifically bind to these elements in the SiWD40 promoter. Thus, for the first time, we report that DREs probably regulate expression of SiWD40 during envi- ronmental stress. Molecular docking analysis revealed that the circumference of the β‐propeller structure was involved in an interaction with a SiCullin4 protein, supporting the adaptability of SiWD40 to act as a scaf- fold. Our study thus provides a vital clue for near future research on the stress-regulation of WD proteins.
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    Association of SNP in a novel DREB2-like gene SiDREB2 with stress tolerance in foxtail millet [Setaria italica (L.)]
    (Oxford University Press, 2011) Lata, Charu; Bhutty, Sarita; Bahadur, Ranjit Prasad; Majee, Manoj; Prasad, Manoj
    The DREB genes code for important plant transcription factors involved in the abiotic stress response and signal transduction. Characterization of DREB genes and development of functional markers for effective alleles is important for marker-assisted selection in foxtail millet. Here the characterization of a cDNA (SiDREB2) encoding a putative dehydration-responsive element-binding protein 2 from foxtail millet and the development of an allele-specific marker (ASM) for dehydration tolerance is reported. A cDNA clone (GenBank accession no. GT090998) coding for a putative DREB2 protein was isolated as a differentially expressed gene from a 6 h dehydration stress SSH library. A 5' RACE (rapid amplification of cDNA ends) was carried out to obtain the full-length cDNA, and sequence analysis showed that SiDREB2 encoded a polypeptide of 234 amino acids with a predicted mol. wt of 25.72 kDa and a theoretical pI of 5.14. A theoretical model of the tertiary structure shows that it has a highly conserved GCC-box-binding N-terminal domain, and an acidic C-terminus that acts as an activation domain for transcription. Based on its similarity to AP2 domains, SiDREB2 was classified into the A-2 subgroup of the DREB subfamily. Quantitative real-time PCR analysis showed significant up-regulation of SiDREB2 by dehydration (polyethylene glycol) and salinity (NaCl), while its expression was less affected by other stresses. A synonymous single nucleotide polymorphism (SNP) associated with dehydration tolerance was detected at the 558th base pair (an A/G transition) in the SiDREB2 gene in a core set of 45 foxtail millet accessions used. Based on the identified SNP, three primers were designed to develop an ASM for dehydration tolerance. The ASM produced a 261 bp fragment in all the tolerant accessions and produced no amplification in the sensitive accessions. The use of this ASM might be faster, cheaper, and more reproducible than other SNP genotyping methods, and thus will enable marker-aided breeding of foxtail millet for dehydration tolerance.