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In Silico Analysis of DREB Transcription Factor Genes and Proteins in Grasses

Abstract

Plants are exposed to various environmental stresses, including drought, salinity, low temperature, etc. Dehydration responsive element binding (DREB) genes, the members of AP2/ERF transcription factor family, regulate the biological processes against cold and dehydration stresses. In this study, we analyzed a total of 19 DREB transcription factor genes and proteins from 14 grass species by using bioinformatic approaches, including their physiochemical properties, conserved motif structures, homology models, and phylogenetic relationships. The domain analysis showed that all grass species contained an AP2 domain whereas some residual substitutions and/or insertions were observed in the AP2 domains of some grasses. The physiochemical analysis revealed that many DREB proteins (89.5 %) were of acidic character while the number of amino acids ranged from 213 (Aegilops speltoides subsp. speltoides) to 394 (Triticum aestivum). Based on the subcellular prediction, 16 of 19 DREB proteins were predicted to be localized in the nuclear region. According to the sequence analysis of grass DREBs, the average value of pairwise distance was found to be 0.588, while nucleotide diversity (π) was found to be 0.435. Thus, among all DREB proteins, two most divergent ones (Oryza sativa and Avena sativa) were selected for 3D structure and protein cavity comparison. In addition, 19 DREB proteins were analyzed according to their phylogenetic relationships, and as a consequence, two main groups were observed. In this study, our analyses could be a scientific base to understand DREB genes and proteins to further wet lab studies in plants, particularly in grass species.

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Abbreviations

DREB:

Dehydration responsive element binding

AP2:

Apetala2

LTRE:

Low-temperature-responsive element

CBF:

C-repeat binding factor

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Correspondence to Ertugrul Filiz.

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Filiz, E., Tombuloğlu, H. In Silico Analysis of DREB Transcription Factor Genes and Proteins in Grasses. Appl Biochem Biotechnol 174, 1272–1285 (2014). https://doi.org/10.1007/s12010-014-1093-x

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Keywords

  • DREB
  • AP2/ERF
  • Grass
  • Protein modeling
  • In silico analysis