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

  • Arun K. Shanker
  • Adithie Maddaala
  • M. Anil Kumar
  • S. K. Yadav
  • M. Maheswari
  • B. Venkateswarlu


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.

Key words

AP2/ERF homology model stress tolerance intrinsic disorder DNA binding in silico mining 


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Copyright information

© International Association of Scientists in the Interdisciplinary Areas and Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Arun K. Shanker
    • 1
  • Adithie Maddaala
    • 2
  • M. Anil Kumar
    • 1
  • S. K. Yadav
    • 1
  • M. Maheswari
    • 1
  • B. Venkateswarlu
    • 1
  1. 1.Division of Crop SciencesCentral Research Institute for Dryland Agriculture (CRIDA)Saidabad P.O.India
  2. 2.Department of BioinformaticsSRM UniversitySRM NagarIndia

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