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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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 wordsAP2/ERF homology model stress tolerance intrinsic disorder DNA binding in silico mining
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- Buchanan, C.D., Lim, S., Salzman, R.A., Kagiampakis, I., Morishige, D.T., Weers, B.D., Klein, R.R., Pratt, L.H., Cordonnier-Pratt, M.M., Klein, P.E., Mullet, J.E. 2005. Sorghum bicolor’s transcriptome response to dehydration, high salinity and ABA. Plant Mol Biol 58, 699–720.PubMedCrossRefGoogle Scholar
- Karaba, A., Dixit, S., Greco, R., Aharoni, A., Trijatmiko, K.R., Marsch-Martinez, N., Krishnan, A., Nataraja, K.N., Udayakumar, M., Pereira, A. 2007. Improvement of water use efficiency in rice by expression of HARDY, an Arabidopsis drought and salt tolerance gene. Proceedings of the National Academy of Sciences 104, 15270–15275.CrossRefGoogle Scholar
- Paterson, A.H., Bowers, J.E., Bruggmann, R., Dubchak, I., Grimwood, J., Gundlach, H., Haberer, G., Hellsten, U., Mitros, T., Poliakov, A., Schmutz, J., Spannagl, M., Tang, H., Wang, X., Wicker, T., Bharti, A.K., Chapman, J., Feltus, F.A., Gowik, U., Grigoriev, I.V., Lyons, E., Maher, C.A., Martis, M., Narechania, A., Otillar, R.P., Penning, B.W., Salamov, A.A., Wang, Y., Zhang, L., Carpita, N.C., Freeling, M., Gingle, A.R., Hash, C.T., Keller, B., Klein, P., Kresovich, S., McCann, M.C., Ming, R., Peterson, D.G., Mehboob-ur-Rahman, W.D., Westhoff, P., Mayer, K.F., Messing, J., Rokhsar, D.S. 2009. The Sorghum bicolor genome and the diversification of grasses. Nature 457, 551–556.PubMedCrossRefGoogle Scholar
- Pratt, L.H., Liang, C., Shah, M., Sun, F., Wang, H., Reid, S.P., Gingle, A.R., Paterson, A.H., Wing, R., Dean, R., Klein, R., Nguyen, H.T., Ma, H.M., Zhao, X., Morishige, D.T., Mullet, J.E., Cordonnier-Pratt, M.M. 2005. Sorghum expressed sequence tags identify signature genes for drought, pathogenesis, and skotomorphogenesis from a milestone set of 16,801 unique transcripts. Plant Physiol 139, 869–884.PubMedCrossRefGoogle Scholar
- Sanchez, A.C., Subudhi, P.K., Rosenow, D.T., Nguyen, H.T. 2002. Mapping QTLs associated with drought resistance in sorghum (Sorghum bicolor L. Moench). Plant Mol Biol 48, 713–726.Google Scholar
- Sharoni, A.M., Nuruzzaman, M., Satoh, K., Moumeni, A., Attia, K., Venuprasad, R., Serraj, R., Kumar, A., Leung, H., Islam, A.K., Kikuchi, S. 2012. Comparative transcriptome analysis of AP2/EREBP gene family under normal and hormone treatments, and under two drought stresses in NILs setup by Aday Selection and IR64. Mol Genet Genomics 284, 1–19.CrossRefGoogle Scholar