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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

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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.

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Authors and Affiliations

  1. Division of Crop Sciences, Central Research Institute for Dryland Agriculture (CRIDA), Santosh Nagar, Saidabad P.O., Hyderabad, 500059, India

    Arun K. Shanker, M. Anil Kumar, S. K. Yadav, M. Maheswari & B. Venkateswarlu

  2. Department of Bioinformatics, SRM University, SRM Nagar, Kattankulathur, 603203, India

    Adithie Maddaala

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  1. Arun K. Shanker
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  2. Adithie Maddaala
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Correspondence to Arun K. Shanker.

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Shanker, A.K., Maddaala, A., Kumar, M.A. et al. 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. Interdiscip Sci Comput Life Sci 4, 133–141 (2012). https://doi.org/10.1007/s12539-012-0121-1

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  • DOI: https://doi.org/10.1007/s12539-012-0121-1

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