Browsing by Author "Singh, Vinay Kumar"

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    Cloning, in silico characterization and prediction of three dimensional structure of SbDof1, SbDof19, SbDof23 and SbDof24 proteins from sorghum [Sorghum bicolor (L.) Moench]
    (Springer, 2013) Kushwaha, Hariom; Gupta, Shubhra; Singh, Vinay Kumar; Bisht, Naveen C.; Sarangi, Bijaya K.; Yadav, Dinesh
    In the present study, four full-length Dof (DNA-binding with one finger) genes from Sorghum bicolor namely SbDof1, SbDof19, SbDof23, and SbDof24 were PCR amplified, gel eluted, cloned, and sequenced (accession number HQ540084, HQ540085, HQ540086, and HQ540087, respectively). These sequences were further characterized in silico by subjecting them to homology search, multiple sequence alignment, phylogenetic tree construction, and protein functional analysis, revealing their identity to Dof like proteins. Phylogenetic analysis of cloned SbDof genes along with other reported Dof proteins revealed existence of two major groups A and B, while group A was further bifurcated into two sub-groups (viz., I and II). Motif scan analysis of SbDof proteins revealed the presence of glycine- and alanine-rich profiles in SbDof1, while proline-rich profile was observed in SbDof23. Asparagines, methionine, and serine-rich profiles were common in case of both SbDof19 and SbDof24 proteins. The three dimensional structures of SbDof proteins were predicted by I-TASSER server based on multiple threading method. The modeled structures were refined by energy minimization and their stereo chemical qualities were validated by PROCHECK and QMEAN server indicating the acceptability of the predicted models. The final models were submitted to PMDB database with assigned PMDB IDs, i.e., PM0077395, PM0077396, PM0077397, PM0077398, and PM0076448 for SbDof1, SbDof19, SbDof23, SbDof24, and Dof domain, respectively. Based on gene ontology (GO) terms in I-TASSER server putative functions of modeled SbDof proteins were also predicted.
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    Genome wide in silico characterization of Dof transcription factor gene family of sugarcane and its comparative phylogenetic analysis with Arabidopsis, rice and sorghum
    (Springer, 2014) Gupta, Shubhra; Kushwaha, Hariom; Singh, Vinay Kumar; Bisht, Naveen C.; Sarangi, Bijaya Ketan; Yadav, Dinesh
    A total of 25 Dof genes were retrieved from GRASSIUS grass regulatory information server. These sequences were in silico characterized for homology search, multiple sequence alignment for conserved Dof DNA binding domains, distribution of conserved motifs and phylogenetic relatedness with sorghum, rice and Arabidopsis. A highly conserved four cysteine residues associated with typical zinc finger of Dof family was observed on multiple sequence alignment of Dof domains. A highly conserved cysteine residue at positions 3 and 6 along with proline and sulfur at positions 4 and 8, respectively were observed. The phylogenetic tree of 119 Dof protein sequences of sugarcane, rice, sorghum and Arabidopsis revealed ten distinct clades with several orthologs and paralogs. The distributions of 25 conserved motifs were analyzed for Dof proteins of sugarcane. Dof proteins with closely related members in the phylogenetic tree shared common motif distribution revealing the possibility of functional similarities within the same subgroup. The motif 1 representing the conserved Dof domain of 50 amino acids was uniformly observed in all the Dof proteins of sugarcane except ScDof8 and ScDof14.