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


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.


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



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)


  1. Cakmak I (2008) Enrichment of cereal grain with zinc: agronomic or genetic Biofortification? Plant Soil 302:1–17CrossRefGoogle Scholar
  2. Ceballos-Laita L, Gutierrez-Carbonell E, Takahashi D, Abadía A, Uemura M, Abadía J, López-Millán AF (2018) Effects of Fe and Mn deficiencies on the protein profiles of tomato (Solanum lycopersicum) xylemsap as revealed by shotgun analyses. J Proteom 170:117–129CrossRefGoogle Scholar
  3. Domingues FS, Lackner P, Andreeva A, Sippl MJ (2000) Structure based evaluation of sequence comparison and fold recognition alignment accuracy. J Mol Biol 297:1003–1013CrossRefGoogle Scholar
  4. Endo TR, Gill BS (1996) The deletion stock of common wheat. J Hered 87:295–307CrossRefGoogle Scholar
  5. Farre G, Serrano JC, Portero-Otin M, Christou P (2017) Biofortification of crops with nutrients: factors affecting utilization and storage. Curr Opin Biotechnol 44:1–9Google Scholar
  6. Gajula MNVP, Steinhoff HJ, Kumar A, Kumar AP, Siddiq EA (2015) Displacement of the tyrosyl radical in RNR enzyme: a sophisticated computational approach to analyze experimental data. In: Saeed F, Haspel N (eds) Proceedings of international conference on bioinformatics and computational biology (BICOB-2015), vol 7, pp 211–219, March 9–11, Honolulu, Hawaii, USAGoogle Scholar
  7. Gajula MNVP, Kumar A, Ijaq J (2016) Protocol for molecular dynamics simulations of proteins. Bio-protocol 6:1–11CrossRefGoogle Scholar
  8. Guo Z, Mohanty U, Noehre J, Sawyer TK, Sherman W, Krilov G (2010) Probing the α-helical structural stability of stapled p53 peptides: molecular dynamics simulations and analysis. Chem Biol Drug Des 75:348–359CrossRefGoogle Scholar
  9. Higuchi K, Kanazawa K, Nishizawa NK, Mori S (1996) The role of nicotianamine synthase in response to Fe nutrition status in Gramineae. Plant Soil 178:171–177CrossRefGoogle Scholar
  10. Hoover WG (1985) Canonical dynamics: equilibrium phase-space distributions. Phys Rev A 31:1695–1697. CrossRefGoogle Scholar
  11. Jee B, Kumar S, Yadav R, Singh Y, Kumar A, Sharma N (2017) Ursolic acid and carvacrol may be potential inhibitors of dormancy protein small heat shock protein 16.3 of Mycobacterium tuberculosis. J Biomol Struct Dyn.
  12. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935CrossRefGoogle Scholar
  13. Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118:11225CrossRefGoogle Scholar
  14. Kaminski G, Friesner RA, Tirado-Rives J, Jorgensen WL (2001) Evaluation and reparameterization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B 105:6474–6487CrossRefGoogle Scholar
  15. Kanazawa K, Higuchi K, Nakanishi H, Nishizawa NK, Mori S (1998) Characterizing nicotianamine aminotransferase: improving its assay system and details of the regulation of its activity by Fe nutrition status. Soil Sci Plant Nutr 44:717–721CrossRefGoogle Scholar
  16. Kobayashi T, Nishizawa NK (2012) Iron uptake, translocation and regulation in higher plants. Annu Rev Plant Biol 63:131–152CrossRefGoogle Scholar
  17. Kobayashi T, Yoshihara T, Itai RN, Nakanishi H, Takahashi M, Mori S, Nishizawa NK (2007) Promoter analysis of iron-deficiency-inducible barley IDS3 gene in Arabidopsis and tobacco plants. Plant Physiol Biochem 45:262–269CrossRefGoogle Scholar
  18. Kumar A, Mishra DC, Sharma M, Rai A, Gajula MNVP (2013) In-silico analysis of protein–protein interaction between resistance and virulence protein during leaf rust disease in wheat (Triticum aestivum L.). World Res J Pept Protein 2:52–58Google Scholar
  19. Kumar A, Kumar S, Kumar U, Suravajhala P, Gajula MNVP (2016a) Functional and structural insights into novel DREB1A transcription factors in common wheat (Triticum aestivum L.): a molecular modeling approach. Comp Biol Chem 64:216–217CrossRefGoogle Scholar
  20. Kumar A, Rathore M, Singh KP, Tyagi PK, Sharma N (2016b) In silico chromosomal mapping and functional annotation of TaPHT1;1 a high affinity phosphate transporter gene in wheat (Triticumaestivum L.). Online J Bioinform 17:180–191Google Scholar
  21. Kumar A, Kumar S, Kumar A, Sharma N, Sharma M, Singh KP, Rathore M, Prasad Gajula MNV (2017) Homology modeling, molecular docking and molecular dynamics based functional insights into rice urease bound to urea. Proc Nat Acad Sci Biol India. Google Scholar
  22. Li H, Robertson AD, Jensen JH (2005) Very fast empirical prediction and interpretation of protein pKa values. Proteins 61:704–721CrossRefGoogle Scholar
  23. Ling HQ, Zhao S, Liu D, Wang J, Sun H et al (2013) Draft genome of the wheat A-genome progenitor Triticumurartu. Nature 496:87–90CrossRefGoogle Scholar
  24. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 25:402–408CrossRefGoogle Scholar
  25. Ma JF, Nomoto K (1993) Two related biosynthetic pathway of mugineic acids in gramineous plants. Plant Physiol 102:373–378CrossRefGoogle Scholar
  26. Ma JF, Nomoto K (1994) Incorporation of label form 13C-, 2H- and 15N-labeled methionine molecules during the biosynthesis of 2′-deoxymugineic acid in roots of wheat. Plant Physiol 105:607–610CrossRefGoogle Scholar
  27. Ma JF, Taketa S, Chang YC, Takeda K, Matsumoto H (1999) Biosynthesis of phytosiderophores in several Triticeae species with different genomes. J Exp Bot 50:723–726Google Scholar
  28. Maroof MA, Biyashev RM, Yang GP, Zhang Q, Allard RW (1994) Extraordinarily polymorphic microsatellite DNA in barley: species diversity, chromosomal locations and population dynamics. Proc Natl Acad Sci 91:5466–5470CrossRefGoogle Scholar
  29. Martyna GJ, Tobias DJ, Klein ML (1994) Constant pressure molecular dynamics algorithms. J Chem Phys 101:4177–4189CrossRefGoogle Scholar
  30. Mori S, Nishizawa N (1989) Identification of barley chromosome no. 4 possible encoder of genes of mugineic acid synthesis from 2-deoxymugineic acid using wheat-barley addition lines. Plant Cell Physiol 30:1057Google Scholar
  31. Mori S, Nishizawa N, Fujigaki J (1990) Identification of rye chromosome 5R as a carrier of the genes for mugineic acid synthetase and 3-hydroxymugineic acid synthetase using wheat-rye addition lines. Jpn J Genet 65:343–352CrossRefGoogle Scholar
  32. Nagaraju M, Palakolanu SD, Kumar SA, Kumar A, Suravajhala P, Ali A, Srivastava RK, Rao MD, Kavi Kishor PB (2018) Genome-wide analysis of dehydrins in Sorghum bicolor, Setaria italica and Zea mays and their expression under abiotic stress in Sorghum bicolor. Plant Gene 13:64–75CrossRefGoogle Scholar
  33. Nakanishi H, Okumura N, Umehara Y, Nishizawa NK, Chino M, Mori S (1993) Expression of a gene specific for iron deficiency (Ids3) in the roots of Hordeum vulgare. Plant Cell Physiol 34:401–410Google Scholar
  34. Nakanishi H, Yamaguchi H, Sasakuma T, Nishizawa NK, Mori S (2000) Two dioxygnase genes, Ids3 and Ids2, from Hordeum vulgare are involved in the biosynthesis of mugineic acid family phytosiderophores. Plant Mol Biol 44:199–207CrossRefGoogle Scholar
  35. Neelam K, Rawat N, Tiwari VK, Tripathi SK, Randhawa GS, Dhaliwal HS (2011) Evaluation and identification of wheat-Aegilops addition lines controlling high grain iron and zinc content and mugineic acids production. Cereal Res Commun 40:53–61CrossRefGoogle Scholar
  36. Nosé S (1984) A unified formulation of the constant temperature molecular-dynamics methods. J Chem Phys 81:511–519CrossRefGoogle Scholar
  37. Okumura N, Nishizawa NK, Umehara Y, Ohata T, Nakanishi H, Yamaguchi H, Chino M, Mori S (1994) A dioxygenase gene (Ids2) expressed under iron deficiency conditions in the roots of Hordeum vulgare. Plant Mol Biol 25:705–719CrossRefGoogle Scholar
  38. Paolacci RA, Oronzo AT, Porceddu E, Ciaffi M (2009) Identification and validation of reference genes for quantitative RT-PCR normalization in wheat. BMC Mol Biol 10:1–27CrossRefGoogle Scholar
  39. Peleg Z, Cakmak I, Ozturk L, Yazici A, Jun Y, Budak H, Korol AB, Fahima T, Saranga Y (2009) Quantitative trait loci conferring grain mineral nutrient concentrations in durum wheat X wild emmer wheat RIL population. Theor Appl Genet 119:353–369CrossRefGoogle Scholar
  40. Schrödinger Release 2017-2 (2017) Desmond molecular dynamics system. D. E Shaw Research, New YorkGoogle Scholar
  41. Sears ER (1954) The aneuploids of common wheat. University Archives of the University of Missouri-Columbia, ColumbiaGoogle Scholar
  42. Sears ER (1966) Nullisomic-tetrasomic combinations in hexaploid wheat. In: Riley R, Lewis KR (eds) Chromosome manipulations and plant genetics. Oliver and Boyd, Edinburgh, pp 29–45CrossRefGoogle Scholar
  43. Sears ER, Sears LMS (1978) The telocentric chromosomes of common wheat. In: Proceedings of the 5th international wheat genetics symposium, vol 1, pp 389–407. Indian Society of Genetics and Plant Breeding New DelhiGoogle Scholar
  44. Shivakumar D, Williams J, Wu Y, Damm W, Shelley J, Sherman W (2010) Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field. J Chem Theory Comput 6:1509–1519CrossRefGoogle Scholar
  45. Singh K, Sasakuma T, Bughio N, Takahashi M, Nakanishi H, Yoshimura E, Nishizawa NK, Mori S (2000) Ability of ancestral wheat species to secrete mugineic acid family phytosiderophores in response to iron deficiency. J Plant Nutr 23:1973–1981CrossRefGoogle Scholar
  46. Takagi S (1976) Naturally occurring iron-chelating compounds in oat- and rice- root washings I. Activity measurement and preliminary characterization. Soil Sci Plant Nutr 22:423–433CrossRefGoogle Scholar
  47. Takahashi M (2003) Overcoming Fe deficiency by a transgenic approach in rice. Plant Cell Tissue Organ Cult 72:211–220CrossRefGoogle Scholar
  48. Tegelstrom H (1992) Detection of mitochondrial DNA fragments. Molecular genetic analysis of populations: a practical approach. IRL Press, Oxford, pp 89–114Google Scholar
  49. Tiwari VK, Rawat N, Chhuneja P, Neelam K, Aggarwal R, Randhawa GS, Dhaliwal HS, Keller B, Singh K (2009) Mapping of quantitative trait loci for grain iron and zinc concentration in diploid A genome wheat. J Hered 100:771–776CrossRefGoogle Scholar
  50. Tolay I, Erenoglu B, Romheld V, Braun HJ, Cakmak I (2001) Phytosiderophore release In Aegilops tauschii and Triticum species under zinc and iron deficiency. J Exp Bot 52:1093–1099CrossRefGoogle Scholar
  51. Treeby M, Marschner H, Romheld V (1989) Mobilization of iron and other micronutrient cations from calcareous soil by plant-borne, microbial, and synthetic metal chelators. Plant Soil 114:217–226CrossRefGoogle Scholar
  52. vonWiren N, Romheld V, Shioiri T, Marschner H (1995) Competition between microorganisms and roots of barley and sorghum for iron accumulated in the root apoplasm. New Phytol 130:511–521CrossRefGoogle Scholar
  53. vonWiren N, Khodr H, Hider RC (2000) Hydroxylated phytosiderophore species possess an enhanced chelate stability and affinity for Iron(III). Plant Physiol 124:1149–1157CrossRefGoogle Scholar
  54. Waters BM, Amundsen K, Graef G (2018) Gene expression profiling of iron deficiency chlorosis sensitive and tolerant soybean indicates key roles for phenylpropanoids under alkalinity stress. Front Plant Sci 9:10. CrossRefGoogle Scholar

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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