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3 Biotech

, 8:219 | Cite as

Identification, expression analysis, and molecular modeling of Iron-deficiency-specific clone 3 (Ids3)-like gene in hexaploid wheat

  • Priyanka Mathpal
  • Upendra Kumar
  • Anuj Kumar
  • Sanjay Kumar
  • Sachin Malik
  • Naveen Kumar
  • H. S. Dhaliwal
  • Sundip Kumar
Original Article
  • 52 Downloads

Abstract

Graminaceous plants secrete hydroxylated phytosiderophores encoded by the genes iron-deficiency-specific clone 2 (Ids2) and iron-deficiency-specific clone 3 (Ids3). An effort was made to identify a putative ortholog of Hodeum vulgare Ids3 gene in hexaploid wheat. The protein structure of TaIDS3 was modeled using homology modeling and structural behavior of modeled structure was analyzed at 20 ns. The simulation trajectory using molecular dynamics simulation suggested the model to be stable with no large fluctuations in residues and local domain level RMSF values (< 2.4 Å). In addition, the ProFunc results also predict the functional similarity between the proteins of HvIDS3 and its wheat ortholog (TaIDS3). The TaIds3 gene was assigned to the telomeric region of chromosome arm 7AS which supports the results obtained through bioinformatics analysis. The relative expression analysis of TaIds3 indicated that the detectable expression of TaIds3 is induced after 5th day of Fe starvation and increases gradually up to 15th day, and thereafter, it decreases until 35th day of Fe-starvation. This reflects that Fe deficiency directly regulates the induction of TaIds3 in the roots of hexaploid wheat. The identification of HvIds3-like gene in wheat has opened up new opportunities to enhance the nutrient quality in wheat through biofortification program.

Keywords

Phytosiderophores Ids3 Hexaploid wheat Chromosomal assignment Fe deficient Homology modeling Molecular dynamics simulations 

Notes

Acknowledgements

Authors would like to give their sincere thanks to Dr. B. S. Gill, University Distinguished Professor, Kansas State University, USA for providing the cytogenetic stocks for mapping. Authors are also thankful to Dr. H. S. Balyan, Hon. Emeritus Professor & INSA Senior Scientist, Ch. Charan Singh University, Meerut for proofreading the final manuscript.

Author contributions

SK and HSD designed and supervised the study. PM, UK, and AK designed experiment and analyzed the data as a whole and wrote the manuscript. SM, PM, and NK collected samples for the analysis. SK and AK performed the molecular dynamics analysis. All authors read and approved the final manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest whatsoever.

Supplementary material

13205_2018_1230_MOESM1_ESM.docx (771 kb)
Supplementary material 1 (DOCX 771 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Priyanka Mathpal
    • 1
  • Upendra Kumar
    • 2
  • Anuj Kumar
    • 3
  • Sanjay Kumar
    • 4
  • Sachin Malik
    • 1
  • Naveen Kumar
    • 1
  • H. S. Dhaliwal
    • 5
  • Sundip Kumar
    • 1
  1. 1.Molecular Cytogenetics Laboratory, Molecular Biology and Genetic Engineering, College of Basic Sciences and HumanitiesGB Pant University of Agriculture and TechnologyPantnagarIndia
  2. 2.Department of Molecular Biology, Biotechnology and Bioinformatics, College of Basic Sciences and HumanitiesCh. Charan Singh Haryana Agricultural UniversityHisarIndia
  3. 3.Advanced Centre for Computational and Applied BiotechnologyUttarakhand Council for BiotechnologyDehradunIndia
  4. 4.Centre for Bioinformatics, Biotech ParkLucknowIndia
  5. 5.Akal School of BiotechnologyEternal UniversityBaru SahibIndia

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