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OJBTM
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
ABSTRACT
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, Online J
Bioinformatics, 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.