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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.