Plant Molecular Biology

, Volume 44, Issue 2, pp 199–207 | Cite as

Two dioxygenase genes, Ids3 and Ids2, from Hordeum vulgare are involved in the biosynthesis of mugineic acid family phytosiderophores

  • Hiromi Nakanishi
  • Hirotaka Yamaguchi
  • Tetsuo Sasakuma
  • Naoko K. Nishizawa
  • Satoshi Mori


A cDNA clone, Ids3 (iron deficiency-specific clone 3), was isolated from an Fe-deficient-root cDNA library of Hordeum vulgare. Ids3 encodes a protein of 339 amino acids with a calculated molecular mass of 37.7 kDa, and its amino acid sequence shows a high degree of similarity with those of plant and fungal 2-oxoglutarate-dependent dioxygenases. One aspartate and two histidine residues for ferrous Fe binding (Asp-211, His-209, His-265) and arginine and serine residues for 2-oxoglutarate binding (Arg-275, Ser-277) are conserved in the predicted amino acid sequence of Ids3. Ids3 expression was rapidly induced by Fe deficiency, and was suppressed by re-supply of Fe. Among eight graminaceous species tested, Ids3 expression was observed only in Fe-deficient roots of H. vulgare and Secale cereale, which not only secrete 2′-deoxymugineic acid (DMA), but also mugineic acid (MA) and 3-epihydroxymugineic acid (epiHMA, H. vulgare), and 3-hydroxymugineic acid (HMA, S. cereale). The Ids3 gene is encoded on the long arm of chromosome 4H of H. vulgare, which also carries the hydroxylase gene that converts DMA to MA. Moreover, the Ids2 gene, which is the plant dioxygenase with the highest homology to Ids3, is encoded on the long arm of chromosome 7H of H. vulgare, which carries the hydroxylase gene that converts MA to epiHMA. The observed expression patterns of the Ids3 and Ids2 genes strongly suggest that IDS3 is an enzyme that hydroxylates the C-2′ positions of DMA and epiHDMA, while IDS2 hydroxylates the C-3 positions of MA and DMA.

Fe deficiency graminaceous plants Hordeum vulgare mugineic acid phytosiderophores roots 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Britsch, L., Ruhnau, B. and Forkmann, G. 1992. Molecular cloning, sequence analysis and heterologous expression of flavanone 3?-hydroxylase from Petunia hybrida. J. Biol. Chem. 267: 5380–5387.PubMedGoogle Scholar
  2. Butt, T.R., Sternberg, E.J., Gorman, J.A., Clark, P., Hamer, D., Rosenberg, M. and Crooke, S.T. 1984. Copper metallothionein of yeast, structure of the gene, and regulation of expression. Proc. Natl. Acad. Sci. USA 81: 3332–3336.PubMedGoogle Scholar
  3. Church, G. and Gilbert, W. 1984. Genomic sequencing. Proc. Natl. Acad. Sci. USA 81: 1991–1995.PubMedGoogle Scholar
  4. De Carolis, E. and De Luca, V. 1994. 2-oxoglutarate-dependent dioxygenase and related enzymes: biochemical characterization. Phytochemistry 36: 1093–1107.CrossRefPubMedGoogle Scholar
  5. Frohman, M.A., Dush, M.K. and Martin, G.R. 1988. Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer. Proc. Natl. Acad. Sci. USA 85: 8998–9002.PubMedGoogle Scholar
  6. Hashimoto, T. and Yamada, Y. 1987. Purification and characterization of hyoscyamine 6?-hydroxylase from root cultures of Hyoscyamus niger L. Eur. J. Biochem. 164: 277–285.PubMedGoogle Scholar
  7. Hashimoto, T., Hayashi, A., Amano, Y., Kohno, J., Iwanari, H., Usuda, S. and Yamada, Y. 1991. Hyoscyamine 6?-hydroxylase, an enzyme involved in tropane alkaloid biosynthesis, is localized at the pericycle of the root. J. Biol. Chem. 266: 4648–4653.PubMedGoogle Scholar
  8. Higuchi, K., Kanazawa, K., Nishizawa, N.K., Chino, M. and Mori, S. 1994. Purification and characterization of nicotianamine synthase from Fe-deficient barley roots. Plant Soil 165: 173–179.Google Scholar
  9. Higuchi, K., Kanazawa, K., Nishizawa, N.-K. and Mori, S. 1996. The role of nicotianamine synthase in response to Fe nutrition status in Gramineae. Plant Soil 178: 171–177.Google Scholar
  10. Higuchi, K., Nakanishi, H., Suzuki, K., Nishizawa, N. K. and Mori, S. 1999a. Presence of nicotianamine synthase isozymes and their homologues in the root of graminaceous plants. Soil Sci. Plant Nutr. 45: 681–691.Google Scholar
  11. Higuchi, K., Suzuki, K., Nakanishi, H., Yamaguchi, H., Nishizawa, N.K. and Mori, S. 1999b. Cloning of nicotianamine synthase genes involved in the biosynthesis of phytosiderophores. Plant Physiol. 119: 471–480.PubMedGoogle Scholar
  12. Imbert, J., Culotta, V., Furst, P., Gedamu, L. and Hamer, D. 1990. Regulation of metallothionein gene transcription by metals. In: G.L. Eichhorn and L.G. Marzilli (Eds.) Metal-Ion Induced Regulation of Gene Expression, Elsevier, Amsterdam, pp. 159–164.Google Scholar
  13. Islam, A., Shepherd, K. and Sparrow, D. 1981. Isolation and characterization of euplasmic wheat-barley chromosome addition lines. Heredity 46: 161–174.Google Scholar
  14. Itai, R., Suzuki, K., Yamaguchi, H., Nakanishi, H., Nishizawa, N. K. and Mori, S. 2000. Induced activity of adnenine phosphoribosyltransferase (APRT) in iron-deficient barley roots. A possible role of adenine salvage in the methionine cycle in phytosiderophore production. J. Exp. Bot. 51: 1179–1188.PubMedGoogle Scholar
  15. Kanazawa, K., Higuchi, K., Nishizawa, N.K., Fushiya, S., Chino, M. and Mori, S. 1994. Nicotianamine aminotransferase activities are correlated to the phytosiderophore secretion under Fe-deficient conditions in Gramineae. J. Exp. Bot. 45: 1903–1906.Google Scholar
  16. Kanazawa, K., Higuchi, K., Nakanishi, H., Nishizawa, N.K. and 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: 717–721.Google Scholar
  17. Kanegae, T., Kajiya, H., Amano, Y., Hashimoto, T. and Yamada, Y. 1994. Species-dependent expression of the hyoscyamine 6?-hydroxylase gene in the pericycle. Plant Physiol. 105: 483–490.PubMedGoogle Scholar
  18. Logmann, J., Schell, J. and Willmitzer, L. 1987. Improved method for the isolation of RNA from plant tissue. Anal. Biochem. 163: 16–20.PubMedGoogle Scholar
  19. Lukacin, R. and Britsch, L. 1987. Identification of strictly conserved histidine and arginine residues as part of the active site in Petunia hybrida flavanone 3?-hydroxylase. Eur. J. Biochem. 249: 748–757.Google Scholar
  20. Ma, J., Shinada, T., Matsuda, C. and Nomoto, K. 1995. Biosynthesis of phytosiderophores, mugineic acids associated with methionine cycling. J. Biol. Chem. 270: 16549–16554.PubMedGoogle Scholar
  21. Ma, J.F., Taketa, S., Chang, Y.-C., Iwashita, T., Matsumoto, H., Takeda, K. and Nomoto, K. 1999. Genes controlling hydroxylation of phytosiderophores are located on different chromosomes in barley (Hordeum vulgare L.). Planta 207: 590–596.Google Scholar
  22. Marschner, H., Römheld, V. and Kissel, M. 1986. Different strategies in higher plants in mobilization and uptake of iron. J. Plant Nutr. 9: 695–713.Google Scholar
  23. Matsuda, J., Okabe, S., Hashimoto, T. and Yamada, Y. 1991. Molecular cloning of hyoscyamine 6?-hydroxylase, a 2-oxoglutaratedependent dioxygenase, from cultured roots of Hyoscyamus niger. J. Biol. Chem. 266: 9460–9464.PubMedGoogle Scholar
  24. Mihashi, S. and Mori, S. 1989. Characterization of mugineic acid-Fe transporter in Fe-deficient barley roots using the multicompartment transporter box method. Biol. Metals 2: 146–154.Google Scholar
  25. Milligan, S.B. and Gasser, C.S. 1995. Nature and regulation of pistil-expressed genes in tomato. Plant Mol. Biol. 28: 691–711.PubMedGoogle Scholar
  26. Mori, S. and Nishizawa, N. 1987. Methionine as a dominant precursor of phytosiderophores in Graminaceae plants. Plant Cell Physiol. 28: 1081–1092.Google Scholar
  27. Mori, S. and Nishizawa, N. 1989. Identification of barley chromosome no. 4, possible encoder of genes for mugineic acid synthesis from 2'-deoxymugineic acid using wheat-barley addition lines. Plant Cell Physiol. 30: 1057–1061.Google Scholar
  28. Mori, S., Nishizawa, N. and Fujigaki, J. 1990. Identification of rye chromosome 5R as a carrier of the genes for mugineic acid synthetase using wheat-rye addition lines. Jpn. J. Genet. 65: 343–352.Google Scholar
  29. Nakanishi, H., Okumura, N., Umehara, Y., Nishizawa, N.K., Chino, M. and Mori, S. 1993. Expression of a gene specific for iron deficiency (Ids3) in the roots of Hordeum vulgare. Plant Cell Physiol. 34: 401–410.PubMedGoogle Scholar
  30. Nakanishi, H., Bughio, N., Matsuhashi, S., Ishioka, N., Uchida, H., Tsuji, A., Osa, A., Sekine, T., Kume, T. and Mori, S. 1999. Visualising real time [11C]methionine translocation in Fe-sufficient and Fe-deficient barley using a Positron Emitting Tracer Imaging System (PETIS). J. Exp. Bot. 50: 637–643.Google Scholar
  31. Nomoto, K., Sugiura, Y. and Takagi, S. 1987. Mugineic acids: studies on phytosiderophores. In: G. Winkelmann, D. van der Helm and J.B. Neilands (Eds.) Iron Transport in Microbes, Plants and Animals, VCH Publishers, Weinheim, Germany, pp. 401–425.Google Scholar
  32. Okumura, N., Nishizawa, N.K., Umehara, Y. and Mori, S. 1991. An iron deficiency-specific cDNA from barley roots having two homologous cystein-rich MT domains. Plant Mol. Biol. 17: 531–533.PubMedGoogle Scholar
  33. Okumura, N., Nishizawa, N.K., Umehara, Y., Ohata, T. and Mori, S. 1992. Iron deficiency specific cDNA (Ids1) with two homologous cystein rich domains from the roots of barley. J. Plant Nutr. 15: 2157–2172.Google Scholar
  34. Okumura, N., Nishizawa, N.K., Umehara, Y., Ohata, T., Nakanishi, H., Yamaguchi, H., Chino, M. and Mori, S. 1994. A dioxygenase gene (Ids2) expressed under iron deficiency conditions in the roots of Hordeum vulgare. Plant Mol. Biol. 25: 705–719.PubMedGoogle Scholar
  35. Prescott, A.G. 1993. A dilemma of dioxygenases (or where biochemistry and molecular biology fail to meet). J. Exp. Bot. 44: 849–861.Google Scholar
  36. Römheld, V. 1987. Different strategies for iron acquisition in higher plants. Plant Physiol. 70: 231–234.Google Scholar
  37. Shojima, S., Nishizawa, N.K., Fushiya, S., Nozoe, S., Irifune, T. and Mori, S. 1990. Biosynthesis of phytosiderophores. In vitro biosynthesis of 2'-deoxymugineic acid from L-methionine and nicotianamine. Plant Physiol. 93: 1497–1503.Google Scholar
  38. Suzuki, K., Higuchi, K., Nakanishi, H., Nishizawa, N.K. and Mori, S. 1999. Cloning of nicotianamine synthase genes from Arabidopsis thaliana. Soil Sci. Plant Nutr. 45: 993–1002.Google Scholar
  39. Suzuki, K., Hirano, H., Yamaguchi, H., Irifune, T., Nishizawa, N.K., Chino, M. and Mori, S. 1995. Partial amino acid sequences of a peptide induced by Fe deficiency in barley roots. In: J. Abadía (Ed.) Iron Nutrition in Soils and Plants, Kluwer Acadmic Publishers, Dordrecht, Netherlands, pp. 363–369.Google Scholar
  40. Suzuki, K., Itai, R., Suzuki, K., Nakanishi, H., Nishizawa, N.K., Yoshimura, E. and Mori, S. 1998. Formate dehydrogenase, an enzyme of anaerobic metabolism, is induced by iron deficiency in barley roots. Plant Physiol. 116: 725–732.PubMedGoogle Scholar
  41. 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: 423–433.Google Scholar
  42. Takagi, S., Nomoto, K. and Takemoto, S. 1984. Physiological aspects of mugineic acid, a possible phytosiderophore of graminaceous plants. J. Plant Nutr. 7: 469–477.Google Scholar
  43. Takahashi, M., Yamaguchi, H., Nakanishi, H., Shioiri, T., Nishizawa, N.K. and Mori, S. 1999. Cloning two genes for nicotianamine aminotransferase, a critical enzyme in iron acquisition (Strategy II) in graminaceous plants. Plant Physiol. 121: 947–956.PubMedGoogle Scholar
  44. Takizawa, R., Nishizawa, N.-K., Nakanishi, H. and Mori, S. 1996. Effect of iron deficiency on S-adenosyl-methionine synthetase in barley roots. J. Plant Nutr. 19: 1189–1200.Google Scholar
  45. Tan, D.S.H. and Sim, T.-S. 1996. Functional analysis of conserved histidine residues in Cephalosporium acremonium isopenicillin N synthase by site-directed mutagenesis. J. Biol. Chem. 271: 889–894.PubMedGoogle Scholar
  46. Valegård, K., van Scheltinga, A.C.T., Lloyd, M.D., Hara, T., Ramaswamy, S., Perrakis, A., Thompson, A., Lee, H.J., Baldwin, J.E., Schofield, C.J., Hajdu, J. and Andersson, I. 1998. Structure of a cephalosporin synthase. Nature 394: 805–809.PubMedGoogle Scholar
  47. Yamaguchi, H., Nakanishi, H. and Mori, S. 2000. Induction of the IDI1 gene in Fe-deficient barley roots: a gene encoding a putative enzyme that catalyses the methionine salvage pathway for phytosiderophore production. Soil Sci. Plant Nutr. 46: 1–9.Google Scholar

Copyright information

© Kluwer Academic Publishers 2000

Authors and Affiliations

  • Hiromi Nakanishi
    • 1
  • Hirotaka Yamaguchi
    • 2
  • Tetsuo Sasakuma
    • 3
  • Naoko K. Nishizawa
    • 1
  • Satoshi Mori
    • 1
  1. 1.Department of Applied Biological Chemistry, Graduate School of Agricultural and Life SciencesUniversity of TokyoTokyoJapan
  2. 2.Core Research for Evolutional Science and Technology (CREST)Japan Science and Technology CorporationTsukubaJapan
  3. 3.Kihara Institute for Biological ResearchYokohama City UniversityYokohamaJapan

Personalised recommendations