In silico targeted genome mining and comparative modelling reveals a putative protein similar to an Arabidopsis drought tolerance DNA binding transcription factor in Chromosome 6 of Sorghum bicolor genome

Shanker, A.K. and Maddaala, A. and Kumar, M.A. and Yadav, S.K. and Maheswari, M. and Venkateswarlu, B. (2012) In silico targeted genome mining and comparative modelling reveals a putative protein similar to an Arabidopsis drought tolerance DNA binding transcription factor in Chromosome 6 of Sorghum bicolor genome. Interdisciplinary Sciences: Computational Life Sciences , 4 (2). pp. 133-141.

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Abstract

Arabidopsis Thaliana HARDY (AtHRD) is a gene with an APETELA 2 / Ethylene Responsive Factor (AP2/ERF) domain linked to improved performance under drought in rice. We hypothesized that the sorghum genome could possess a similar gene product and were motivated to conduct a computational genome scale mining for the protein and analyse its structural and functional properties. AtHRD sequence was used as a query to BLAST against the sorghum genome dataset followed by multiple alignment analysis. A homology model of the target was built using a template detected based on the pair-wise comparison of hidden Markov models for alignments. DNA docking with a matrix of homologous interface contacts was done. Functional and structural analysis of the query and target was conducted using various online servers. A High-scoring segment pair from Chromosome 6 of the sorghum genome in the region between 54948120 and 54948668 had 68 amino acid similarities out of the 184 residues and was 1.4% above twilight zone threshold. The homology model showed 86.8% residues in most favoured regions. The target protein which had an AP2/ERF domain when docked with GCC box DNA motif had conserved residues involved in binding; it had a long unstructured region beyond the AP2 domain with several motifs for the recognition of serine/threonine protein kinase group. The protein model showed that it could bind to a GCC box which is present in several drought responsive genes. The presence of possible signalling domains and intrinsic disorder in the target protein suggest that this could play a role in drought tolerance which is an inherent character of sorghum. These results offer a jumpstart for validation experiments which could pave the way for cis/trans genic improvement of a range of crops.

Item Type: Article
Uncontrolled Keywords: AP2/ERF – homology model – stress tolerance – intrinsic disorder – DNA binding – in silico mining
Author Affiliation: CRIDA, Hyderabad, SRM University, SRM Nagar, Kattankulathur, India
Subjects: Crop Improvement
Divisions: Sorghum
Depositing User: Mr. SanatKumar Behera
Date Deposited: 05 Aug 2012 11:26
Last Modified: 05 Aug 2012 11:27
Official URL: http://dx.doi.org/10.1007/s12539-012-0121-1
URI: http://eprints.icrisat.ac.in/id/eprint/7180

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