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Research Articles

Isolation of a transcription factor DREB1A gene from Phaseolus vulgaris and computational insights into its characterization: protein modeling, docking and mutagenesis

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Pages 3107-3118 | Received 17 Aug 2016, Accepted 23 Sep 2016, Published online: 14 Oct 2016

References

  • Agarwal, P. K., Agarwal, P., Reddy, M. K., & Sopory, S. K. (2006). Role of DREB transcription factors in abiotic and biotic stress tolerance in plants. Plant Cell Reports, 25, 1263–1274.10.1007/s00299-006-0204-8
  • Agarwal, P. K., Shukla, P. S., Gupta, K., & Jha, B. (2013). Bioengineering for salinity tolerance in plants: State of the art. Molecular Biotechnology, 54, 102–123.10.1007/s12033-012-9538-3
  • Alexandrov, N. N., Brover, V. V., Freidin, S., Troukhan, M. E., Tatarinova, T. V., Zhang, H., ... Feldmann, K. A. (2009). Insights into corn genes derived from large-scale cDNA sequencing. Plant Molecular Biology, 69, 179–194.10.1007/s11103-008-9415-4
  • Allen, M. D., Yamasaki, K., Ohme-Takagi, M., Tateno, M., & Suzuki, M. (1998). A novel mode of DNA recognition by a β-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA. The EMBO Journal, 17, 5484–5496.10.1093/emboj/17.18.5484
  • Bendl, J., Stourac, J., Sebestova, E., Vavra, O., Musil, M., Brezovsky, J., & Damborsky, J. (2016). HotSpot Wizard 2.0: Automated design of site-specific mutations and smart libraries in protein engineering. Nucleic Acids Research, gkw416.
  • Cao, Z. F., Li, J., Chen, F., Li, Y. Q., Zhou, H. M., & Liu, Q. (2001). Effect of two conserved amino acid residues on DREB1A function. Biochemistry (Moscow), 66, 623–627.10.1023/A:1010251129429
  • Chen, H., Liu, L., Wang, L., Wang, S., & Cheng, X. (2016). VrDREB2A, a DREB-binding transcription factor from Vigna radiata, increased drought and high-salt tolerance in transgenic Arabidopsis thaliana. Journal of Plant Research, 129, 263–273.10.1007/s10265-015-0773-0
  • Chen, M., Wang, Q. Y., Cheng, X. G., Xu, Z. S., Li, L. C., Ye, X. G., ... Ma, Y. Z. (2007). GmDREB2, a soybean DRE-binding transcription factor, conferred drought and high-salt tolerance in transgenic plants. Biochemical and Biophysical Research Communications, 353, 299–305.10.1016/j.bbrc.2006.12.027
  • Chen, J., Xia, X., & Yin, W. (2009). Expression profiling and functional characterization of a DREB2-type gene from Populus euphratica. Biochemical and Biophysical Research Communications, 378, 483–487.10.1016/j.bbrc.2008.11.071
  • Contreras-Moreira, B., Fitzjohn, P. W., & Bates, P. A. (2001). Comparative modelling: An essential methodology for protein structure prediction in the post-genomic era. Applied Bioinformatics, 1, 177–190.
  • Doudna, J. A. (2000). Structural genomics of RNA. Nature Structural & Molecular Biology, 7, 954–956.10.1038/80729
  • Doyle, J. J., & Doyle, J. L. (1990). Isolation of plant DNA from fresh tissue. Focus, 12, 13–15.
  • Dubouzet, J. G., Sakuma, Y., Ito, Y., Kasuga, M., Dubouzet, E. G., Miura, S., ... Yamaguchi-Shinozaki, K. (2003). OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought-, high-salt-and cold-responsive gene expression. The Plant Journal, 33, 751–763.10.1046/j.1365-313X.2003.01661.x
  • Gao, S. Q., Chen, M., Xia, L. Q., Xiu, H. J., Xu, Z. S., Li, L. C., ... Ma, Y. Z. (2009). A cotton (Gossypium hirsutum) DRE-binding transcription factor gene, GhDREB, confers enhanced tolerance to drought, high salt, and freezing stresses in transgenic wheat. Plant Cell Reports, 28, 301–311.10.1007/s00299-008-0623-9
  • Gupta, K., Jha, B., & Agarwal, P. K. (2014). A dehydration-responsive element binding (DREB) transcription factor from the succulent halophyte salicornia brachiata enhances abiotic stress tolerance in transgenic tobacco. Marine Biotechnology, 16, 657–673.10.1007/s10126-014-9582-z
  • Hall, T. A. (1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95–98.
  • Huang, B., & Liu, J. Y. (2006). Cloning and functional analysis of the novel gene GhDBP3 encoding a DRE-binding transcription factor from Gossypium hirsutum. Biochimica et Biophysica Acta (BBA)-Gene Structure and Expression, 1759, 263–269.10.1016/j.bbaexp.2006.04.006
  • Kaplan, W., & Littlejohn, T. G. (2001). Swiss-PDB viewer (deep view). Briefings in Bioinformatics, 2, 195–197.10.1093/bib/2.2.195
  • Kelley, L. A., & Sternberg, M. J. (2009). Protein structure prediction on the web: A case study using the phyre server. Nature Protocols, 4, 363–371.10.1038/nprot.2009.2
  • Kizis, D., & Lumbreras, V. (2001). Role of AP2/EREBP transcription factors in gene regulation during abiotic stress. FEBS Letters, 498, 187–189.10.1016/S0014-5793(01)02460-7
  • Koussevitzky, S., Nott, A., Mockler, T. C., Hong, F., Sachetto-Martins, G., Surpin, M., Chory, J. (2007). Signals from chloroplasts converge to regulate nuclear gene expression. Science, 316, 715–719.10.1126/science.1140516
  • Kumar, A., Kumar, S., Kumar, U., Suravajhala, P., & Gajula, M. P. (2016). Functional and structural insights into novel DREB1A transcription factors in common wheat (Triticum aestivum L.): A molecular modeling approach. Computational Biology and Chemistry, 64, 217–226.10.1016/j.compbiolchem.2016.07.008
  • Li, H., Zhang, D., Li, X., Guan, K., & Yang, H. (2016). Novel DREB A-5 subgroup transcription factors from desert moss (Syntrichia caninervis) confers multiple abiotic stress tolerance to yeast. Journal of Plant Physiology, 194, 45–53.10.1016/j.jplph.2016.02.015
  • Liu, Q., Kasuga, M., Sakuma, Y., Abe, H., Miura, S., Yamaguchi-Shinozaki, K., & Shinozaki, K. (1998). Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought- and low-temperature-responsive gene expression, respectively, in Arabidopsis. The Plant Cell, 10, 1391–1406.10.1105/tpc.10.8.1391
  • Liu, J. G., Zhang, Z., Qin, Q. L., Peng, R. H., Xiong, A. S., Chen, J. M., ... Yao, Q. H. (2007). Isolated and characterization of a cDNA encoding ethylene-responsive element binding protein (EREBP)/AP2-type protein, RCBF2, in Oryza sativa L. Biotechnology Letters, 29, 165–173.
  • Liu, X. Q., Zhu, J. J., Wei, C. J., Guo, Q., Bian, C. K., Xiang, Z. H., & Zhao, A. C. (2015). Genome-wide identification and characterization of the DREB transcription factor gene family in mulberry. Biologia Plantarum, 59, 253–265.10.1007/s10535-015-0498-x
  • Madden, T. (2013). The BLAST sequence analysis tool.
  • Magnani, E., Sjölander, K., & Hake, S. (2004). From endonucleases to transcription factors: Evolution of the AP2 DNA binding domain in plants. The Plant Cell, 16, 2265–2277.10.1105/tpc.104.023135
  • Maruyama, K., Sakuma, Y., Kasuga, M., Ito, Y., Seki, M., Goda, H., ... Yamaguchi-Shinozaki, K. (2004). Identification of cold-inducible downstream genes of the Arabidopsis DREB1A/CBF3 transcriptional factor using two microarray systems. The Plant Journal, 38, 982–993.10.1111/tpj.2004.38.issue-6
  • Matsukura, S., Mizoi, J., Yoshida, T., Todaka, D., Ito, Y., Maruyama, K., ... Yamaguchi-Shinozaki, K. (2010). Comprehensive analysis of rice DREB2-type genes that encode transcription factors involved in the expression of abiotic stress-responsive genes. Molecular Genetics and Genomics, 283, 185–196.10.1007/s00438-009-0506-y
  • Mizoi, J., Shinozaki, K., & Yamaguchi-Shinozaki, K. (2012). AP2/ERF family transcription factors in plant abiotic stress responses. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms, 1819, 86–96.10.1016/j.bbagrm.2011.08.004
  • Nakano, T., Suzuki, K., Fujimura, T., & Shinshi, H. (2006). Genome-wide analysis of the ERF gene family in Arabidopsis and rice. Plant Physiology, 140, 411–432.10.1104/pp.105.073783
  • Nakashima, K., Shinwari, Z. K., Sakuma, Y., Seki, M., Miura, S., Shinozaki, K., & Yamaguchi-Shinozaki, K. (2000). Organization and expression of two Arabidopsis DREB2 genes encoding DRE-binding proteins involved in dehydration-and high-salinity-responsive gene expression. Plant Molecular Biology, 42, 657–665.10.1023/A:1006321900483
  • Nawaz, M., Iqbal, N., Idrees, S., & Ullah, I. (2014). DREB1A from Oryza sativa var. IR6: Homology modelling and molecular docking. Turkish Journal of Botany, 38, 1095–1102.10.3906/bot-1403-45
  • Niu, X., Helentjaris, T., & Bate, N. J. (2002). Maize ABI4 binds coupling element1 in abscisic acid and sugar response genes. The Plant Cell, 14, 2565–2575.10.1105/tpc.003400
  • Okamuro, J. K., Caster, B., Villarroel, R., Van Montagu, M., & Jofuku, K. D. (1997). The AP2 domain of APETALA2 defines a large new family of DNA binding proteins in Arabidopsis. Proceedings of the National Academy of Sciences, 94, 7076–7081.10.1073/pnas.94.13.7076
  • Qin, F., Kakimoto, M., Sakuma, Y., Maruyama, K., Osakabe, Y., Tran, L. S. P., … Yamaguchi- Shinozaki, K. (2007). Regulation and functional analysis of ZmDREB2A in response to drought and heat stresses in Zea mays L. The Plant Journal, 50, 54–69.10.1111/j.1365-313X.2007.03034.x
  • Roy, A., Kucukural, A., & Zhang, Y. (2010). I-TASSER: A unified platform for automated protein structure and function prediction. Nature Protocols, 5, 725–738.10.1038/nprot.2010.5
  • Sakuma, Y., Liu, Q., Dubouzet, J. G., Abe, H., Shinozaki, K., & Yamaguchi-Shinozaki, K. (2002). DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration- and cold-inducible gene expression. Biochemical and Biophysical Research Communications, 290, 998–1009.10.1006/bbrc.2001.6299
  • Sakuma, Y., Maruyama, K., Osakabe, Y., Qin, F., Seki, M., Shinozaki, K., & Yamaguchi-Shinozaki, K. (2006). Functional analysis of an Arabidopsis transcription factor, DREB2A, involved in drought-responsive gene expression. The Plant Cell, 18, 1292–1309.10.1105/tpc.105.035881
  • Schmutz, J., McClean, P. E., Mamidi, S., Wu, G. A., Cannon, S. B., Grimwood, J., … Torres-Torres, M. (2014). A reference genome for common bean and genome-wide analysis of dual domestications. Nature Genetics, 46, 707–713.10.1038/ng.3008
  • Schrödinger, L. L. C. (2015). The PyMOL molecular graphics system, version 1.8.
  • Smith, L. J., Fiebig, K. M., Schwalbe, H., & Dobson, C. M. (1996). The concept of a random coil: Residual structure in peptides and denatured proteins. Folding and Design, 1, R95–R106.10.1016/S1359-0278(96)00046-6
  • Stockinger, E. J., Gilmour, S. J., & Thomashow, M. F. (1997). Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit. Proceedings of the National Academy of Sciences, 94, 1035–1040.10.1073/pnas.94.3.1035
  • Sun, S., Yu, J. P., Chen, F., Zhao, T. J., Fang, X. H., Li, Y. Q., & Sui, S. F. (2008). TINY, a ehydration-responsive Element (DRE)-binding protein-like transcription factor connecting the DRE- and ethylene-responsive element-mediated signaling pathways in Arabidopsis. Journal of Biological Chemistry, 283, 6261–6271.10.1074/jbc.M706800200
  • Tamura, K., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30, 2725–2729.10.1093/molbev/mst197
  • Tuszynska, I., Magnus, M., Jonak, K., Dawson, W., & Bujnicki, J. M. (2015). NPDock: A web server for protein–nucleic acid docking. Nucleic Acids Research, gkv493.
  • Wu, H., Lv, H., Li, L., Liu, J., Mu, S., Li, X., & Gao, J. (2015). Genome-wide analysis of the AP2/ERF transcription factors family and the expression patterns of DREB Genes in moso bamboo (Phyllostachys edulis). PLoS ONE, 10, e0126657.10.1371/journal.pone.0126657
  • Xiong, Y., & Fei, S. Z. (2006). Functional and phylogenetic analysis of a DREB/CBF-like gene in perennial ryegrass (Lolium perenne L.). Planta, 224, 878–888.10.1007/s00425-006-0273-5
  • Xue, G. P., & Loveridge, C. W. (2004). HvDRF1 is involved in abscisic acid-mediated gene regulation in barley and produces two forms of AP2 transcriptional activators, interacting preferably with a CT-rich element. The Plant Journal, 37, 326–339.10.1046/j.1365-313X.2003.01963.x
  • Yu, J., Wang, J., Lin, W., Li, S., Li, H., Zhou, J., … Zhang, J. (2005). The genomes of Oryza sativa: A history of duplications. PLoS Biology, 3, e38.10.1371/journal.pbio.0030038

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