Computational characterization of structural and functional roles of DREB1A, DREB1B and DREB1C in enhancing cold tolerance in rice plant
Authors: Gayatri Gouda
Jitendra Kumar
Sushanta Kumar Dash
Ravindra Donde
Ramakrishna Vadde
Lambodar Behera
Khirod Kumar Sahoo
Manoj Kumar Gupta
Journal: Amino acids (2019)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: Cold stress; DREB1; Molecular dynamics; Protein‚ÄìDNA interaction; Simulation.
Affiliations: ICAR-National Rice Research Institute, Cuttack, Odisha, 753 006, India., Department of Biotechnology and Bioinformatics, Yogi Vemana University, Kadapa, Andhra Pradesh, 516003, India., Department of Biotechnology, Ravenshaw University, Cuttack, Odisha, 753003, India., ICAR-National Rice Research Institute, Cuttack, Odisha, 753 006, India. .

Abstract:  Rice serves as the major food for almost half of the world population. Because of its origin in the tropical and subtropical area, rice is more sensitive towards cold stress. Three homologs of DREB1, namely DREB1A, DREB1B and DREB1C are induced Queryduring cold stress and after binding with GCC-box in the promoter region of the target gene, they enhance cold tolerance in rice plants. Though the majority of DREBs bind GCC-box, the degree of activation varies among DREBs. The protein encoded via these three transcription factors contains a common domain, namely AP2/ERF. In silico method was utilised to predict 3D structure of each AP2/ERF domain. The molecular dynamic analysis suggests, under the normal environmental condition, in each AP2/ERF domain, a positive correlation exists between Œ≤-strands and the movement of C-Œ± is constrained. However, during cold stress, when AP2/ERF domain binds with GCC-box present in the promoter region of the target gene, mean pressure of each three AP2/ERF domain gets lowered and final potential energy increases. A positive correlation between Œ≤-strands gets disrupted and C-Œ± experiences random movement suggesting enhanced activity of DREB1A, DREB1B and DREB1C during cold stress and enhancement of cold tolerance in plants. Further, MM/PBSA calculations for protein-DNA affinities reveal that, due to lack of Œ±2 in DREB1C, the binding affinity of GCC-box with AP2/ERF domain of DREB1A &gt; DREB1B &gt; DREB1C. Thus, due to a better binding affinity with GCC-box, DREB1A and DREB1B can be utilised in near future for increasing cold tolerance of rice plant and increasing yield. 

Retracted: No

PubPeer comments:
 I found several flaws in the article are as follows: 1.tIn the domain analysis section, the authors mentioned the AP2 domain of DREB1A, 1B and 1C proteins are of 58-65 aa length. But, when I saw the Figure 2B, it seems, they have 6000 residues. The question is, where did they get this much of residues? Further, how did they get so stable graph for residual fluctuation? 2.tIn figure 2C, the 2D projection graph, the units are presented in u00c5, which should be displayed in nm2. Again, how did the authors get so many projection points, where the length of the proteins are only of 58-65 AA? 3.tFigure 3D: the Rg values shown in the graphs shows so much difference between DREB1A and DREB1B 1C, despite their similar length and fold. The values presented in the Y-axis are in the nanometer or in u00c5? The same questions are also applied to Figure 5. In addition, AP2 GCC-box interaction is well studied in several plants. The crystal structures are also available. Then why did the authors consider I-TASSER web server for model building, rather they could have used MODELLER. The mode of AP2 GCC-box interactions presented in Figure 7, is merely unacceptable.  ,