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Online Journal of Bioinformatics©
Volume 9 (2): 130-145, 2008.
In silico analysis of PCR amplified DOF (DNA binding with one finger) transcription factor domain
and cloned genes from cereals and millets
Kushwaha H, Gupta N, Singh VK, Kumar A, Yadav D.
Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar (UttaraKhand), India
Kushwaha H, Gupta N, Singh VK, Kumar A, Yadav D., In silico analysis of PCR amplified DOF (DNA binding with one finger) transcription factor domain and cloned genes from cereals and millets, On J Bioinform, 9 (2): 130, 2008. The PCR amplified DOF domain of different cereals and millets were gel eluted, sequenced and subjected to homology search, multiple sequence alignment, phylogenetic tree construction and motif analysis. The presence of four cysteine residues associated with a typical zinc like finger and a conserved motif with multilevel consensus sequence QPRHFCKSCQRYWTA was uniformly observed across different cereals and millets. The putative DOF genes of Eleusine coracana along with Oryza sativa, Triticum aestivum, Hordeum vulgare and Zea mays were PCR amplified, gel eluted, cloned and assigned accession numbers EU760631, EU586268, EU586269, EU586267 and EU586266 respectively after sequencing. The homology search confirmed their identity to PBF (Prolamin-box Binding Factor) DOF genes except for O. sativa. Multiple sequence alignment of these PBF DOF genes revealed the presence of conserved DOF domain with four cysteine residues in E. coracana while partial sequences were observed in other cloned genes. The presence of conserved motifs involved with regulation of seed storage protein genes further confirmed their identity to PBF DOF genes. Phylogenetic tree constructed based on protein sequences of cloned DOF genes resulted in distinct clusters for PBF DOF genes of monocots and dicots.
Keywords: DOF, Transcription factor, Cereals, Millets, PBF, Multiple sequence alignment, Motif, Domain.