Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

IRON MAN is a ubiquitous family of peptides that control iron transport in plants

Abstract

Iron (Fe) is an essential mineral nutrient that severely affects the growth, yield and nutritional quality of plants if not supplied in sufficient quantities. Here, we report that a short C-terminal amino-acid sequence consensus motif (IRON MAN; IMA) conserved across numerous, highly diverse peptides in angiosperms is essential for Fe uptake in plants. Overexpression of the IMA sequence in Arabidopsis induced Fe uptake genes in roots, causing accumulation of Fe and manganese in all plant parts including seeds. Silencing of all eight IMA genes harboured in the Arabidopsis genome abolished Fe uptake and caused severe chlorosis; increasing the Fe supply or expressing IMA1 restored the wild-type phenotype. IMA1 is predominantly expressed in the phloem, preferentially in leaves, and reciprocal grafting showed that IMA1 peptides in shoots positively regulate Fe uptake in roots. IMA homologues are highly responsive to the Fe status and functional when heterologously expressed across species. IMA constitutes a novel family of peptides that are critical for the acquisition and cellular homeostasis of Fe across land plants.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Fig. 1: Overexpression of IMA1 triggers Fe, Mn and Zn accumulation in Arabidopsis.
Fig. 2: Phenotypic characterization of transgenic plants with altered expression of IMA genes.
Fig. 3: The C-terminal amino-acid consensus motif is critical for IMA1 function.
Fig. 4: Localization of EYFP:IMA1 expressed under the control of the IMA1 promoter.
Fig. 5: Root FCR activity of reciprocally grafted plants.
Fig. 6: IMA function is conserved across species.

Data availability

RNAseq data of IMA1 Ox and Fe-deficient wild-type Col-0 transcriptomes have been deposited to the Gene Expression Omnibus database and are available under the accession numbers GSE87745 and GSE87760, respectively. Information about IMA gene accession numbers and loci position are given in Supplementary Table 2.

References

  1. De Benoist, B. et al. Worldwide prevalence of anaemia report 1993–2005. WHO Global Database on Anaemia (WHO, 2008).

  2. Römheld, V. & Marschner, H. Evidence for a specific uptake system for iron phytosiderophores in roots of grasses. Plant Physiol. 80, 175–180 (1986).

    Article  Google Scholar 

  3. Kobayashi, T. & Nishizawa, N. K. Iron uptake, translocation, and regulation in higher plants. Annu. Rev. Plant. Biol. 63, 131–152 (2012).

    Article  CAS  Google Scholar 

  4. Curie, C. et al. Maize yellow stripe1 encodes a membrane protein directly involved in Fe(III) uptake. Nature 409, 346–349 (2001).

    Article  CAS  Google Scholar 

  5. DiDonato, R. J. et al. Arabidopsis yellow stripe-like (YSL2): a metal-regulated gene encoding a plasma membrane transporter of nicotianamine–metal complexes. Plant J. 39, 403–414 (2004).

    Article  CAS  Google Scholar 

  6. Robinson, N. J. et al. A ferric-chelate reductase for iron uptake from soils. Nature 397, 694–697 (1999).

    Article  CAS  Google Scholar 

  7. Eide, D. et al. A novel iron-regulated metal transporter from plants identified by functional expression in yeast. Proc. Natl Acad. Sci. USA 93, 5624–5628 (1996).

    Article  CAS  Google Scholar 

  8. Vert et al. IRT1, an Arabidopsis transporter essential for iron uptake from the soil and for plant growth. Plant Cell 14, 1223–1233 (2002).

    Article  CAS  Google Scholar 

  9. Santi, S. & Schmidt, W. Dissecting iron deficiency-induced proton extrusion in Arabidopsis roots. New Phytol. 183, 1072–1084 (2009).

    Article  CAS  Google Scholar 

  10. Ishimaru, Y. et al. Rice plants take up iron as an Fe3+-phytosiderophore and as Fe2+. Plant J. 45, 335–346 (2006).

    Article  CAS  Google Scholar 

  11. Rodríguez-Celma, J. et al. Mutually exclusive alterations in secondary metabolism are critical for the uptake of insoluble iron compounds by Arabidopsis and Medicago truncatula. Plant Physiol. 162, 1473–1485 (2013).

    Article  Google Scholar 

  12. Fourcroy, P. et al. Involvement of the ABCG37 transporter in secretion of scopoletin and derivatives by Arabidopsis roots in response to iron deficiency. New Phytol. 201, 155–167 (2014).

    Article  CAS  Google Scholar 

  13. Schmid, N. B. et al. Feruloyl-CoA 6'-hydroxylase1-dependent coumarins mediate iron acquisition from alkaline substrates in Arabidopsis. Plant Physiol. 164, 160–172 (2014).

    Article  CAS  Google Scholar 

  14. Tsai, H. H. & Schmidt, W. Mobilization of iron by plant-borne coumarins. Trends Plant Sci. 22, 538–548 (2017).

    Article  CAS  Google Scholar 

  15. Rajniak, J. et al. Biosynthesis of redox-active metabolites in response to iron deficiency in plants. Nat. Chem. Biol. 14, 442–450 (2018).

    Article  CAS  Google Scholar 

  16. Colangelo, E. P. & Guerinot, M. L. The essential basic helix-loop-helix protein FIT1 is required for the iron deficiency response. Plant Cell 16, 3400–3412 (2004).

    Article  CAS  Google Scholar 

  17. Long, T. A. et al. The bHLH transcription factor POPEYE regulates response to iron deficiency in Arabidopsis roots. Plant Cell 22, 2219–2236 (2010).

    Article  CAS  Google Scholar 

  18. Yuan, Y. X. et al. FIT interacts with AtbHLH38 and AtbHLH39 in regulating iron uptake gene expression for iron homeostasis in Arabidopsis. Cell Res. 18, 385–397 (2008).

    Article  CAS  Google Scholar 

  19. Wang, N. et al. Requirement and functional redundancy of Ib subgroup bHLH proteins for iron deficiency responses and uptake in Arabidopsis thaliana. Mol. Plant 6, 503–513 (2013).

    Article  CAS  Google Scholar 

  20. Li, X. et al. Two bHLH transcription factors, bHLH34 and bHLH104, regulate iron homeostasis in Arabidopsis thaliana. Plant Physiol. 170, 2478–2493 (2016).

    Article  CAS  Google Scholar 

  21. Zhang et al. The bHLH transcription factor bHLH104 interacts with IAA-LEUCINE RESISTANT3 and modulates iron homeostasis in Arabidopsis. Plant Cell 27, 787–805 (2015).

    Article  CAS  Google Scholar 

  22. Selote, D. et al. Iron-binding E3 ligase mediates iron response in plants by targeting basic helix-loop-helix transcription factors. Plant Physiol. 167, 273–286 (2015).

    Article  CAS  Google Scholar 

  23. Inoue, H. et al. Rice OsYSL15 is an iron-regulated iron(III)-deoxymugineic acid transporter expressed in the roots and is essential for iron uptake in early growth of the seedlings. J. Biol. Chem. 284, 3470–3479 (2009).

    Article  CAS  Google Scholar 

  24. Ogo, Y. et al. The rice bHLH protein OsIRO2 is an essential regulator of the genes involved in Fe uptake under Fe-deficient conditions. Plant J. 51, 366–377 (2007).

    Article  CAS  Google Scholar 

  25. Zheng, L. et al. Identification of a novel iron regulated basic helix-loop-helix protein involved in Fe homeostasis in Oryza sativa. BMC Plant Biol. 10, 166 (2010).

    Article  Google Scholar 

  26. Kobayashi, T. et al. Iron-binding haemerythrin RING ubiquitin ligases regulate plant iron responses and accumulation. Nat. Commun. 4, 2792 (2013).

    Article  Google Scholar 

  27. Zhang, H. et al. POSITIVE REGULATOR OF IRON HOMEOSTASIS1, OsPRI1, facilitates iron homeostasis. Plant Physiol. 175, 543–554 (2017).

    Article  CAS  Google Scholar 

  28. Grusak, M. A. & Pezeshgi, S. Shoot-to-root signal transmission regulates root Fe(III) reductase activity in the dgl mutant of pea. Plant Physiol. 110, 329–334 (1996).

    Article  CAS  Google Scholar 

  29. Rogers, E. E. & Guerinot, M. L. FRD3, a member of the multidrug and toxin efflux family, controls iron deficiency responses in Arabidopsis. Plant Cell 14, 1787–1799 (2002).

    Article  CAS  Google Scholar 

  30. Stacey, M. G. et al. The Arabidopsis AtOPT3 protein functions in metal homeostasis and movement of iron to developing seeds. Plant Physiol. 146, 589–601 (2008).

    Article  CAS  Google Scholar 

  31. Zhai, Z. et al. OPT3 is a phloem-specific iron transporter that is essential for systemic iron signalling and redistribution of iron and cadmium in Arabidopsis. Plant Cell 26, 2249–2264 (2014).

    Article  CAS  Google Scholar 

  32. Tabata, R. et al. Perception of root-derived peptides by shoot LRR-RKs mediates systemic N-demand signaling. Science 346, 343–346 (2014).

    Article  CAS  Google Scholar 

  33. Ohkubo, Y. et al. Shoot-to-root mobile polypeptides involved in systemic regulation of nitrogen acquisition. Nat. Plants 3, 17029 (2017).

    Article  CAS  Google Scholar 

  34. Zheng, L. et al. Physiological and transcriptome analysis of iron and phosphorus interaction in rice seedlings. Plant Physiol. 151, 262–274 (2009).

    Article  CAS  Google Scholar 

  35. Rodríguez-Celma, J. et al. The transcriptional response of Arabidopsis leaves to Fe deficiency. Front. Plant Sci. 4, 276 (2013).

    Article  Google Scholar 

  36. Roschzttardtz, H. et al. New insights into Fe localization in plant tissues. Front. Plant Sci. 4, 350 (2013).

    Article  Google Scholar 

  37. Buckhout, T. J., Yang, T. J. & Schmidt, W. Early iron-deficiency-induced transcriptional changes in Arabidopsis roots as revealed by microarray analyses. BMC Genomics 10, 147 (2009).

    Article  Google Scholar 

  38. Zamboni, A. et al. Genome-wide microarray analysis of tomato roots showed defined responses to iron deficiency. BMC Genomics 13, 101 (2012).

    Article  CAS  Google Scholar 

  39. Lauter, A. N. Moran et al. Identification of candidate genes involved in early iron deficiency chlorosis signaling in soybean (Glycine max) roots and leaves. BMC Genomics 15, 702 (2014).

    Article  Google Scholar 

  40. Klatte, M. et al. The analysis of Arabidopsis nicotianamine synthase mutants reveals functions for nicotianamine in seed iron loading and iron deficiency responses. Plant Phys. 150, 257–271 (2009).

    Article  CAS  Google Scholar 

  41. Durrett, T. P. et al. The FRD3-mediated efflux of citrate into the root vasculature is necessary for efficient iron translocation. Plant Phys. 144, 197–205 (2007).

    Article  CAS  Google Scholar 

  42. Ravet, K. et al. Ferritins control interaction between iron homeostasis and oxidative stress in Arabidopsis. Plant J. 57, 400–412 (2009).

    Article  CAS  Google Scholar 

  43. Gollhofer, J. et al. Vacuolar-iron-transporter1-like proteins mediate iron homeostasis in Arabidopsis. PLoS ONE 9, e110468 (2014).

    Article  Google Scholar 

  44. Le Jean, M. et al. A loss-of-function mutation in AtYSL1 reveals its role in iron and nicotianamine seed loading. Plant J. 44, 769–782 (2005).

    Article  CAS  Google Scholar 

  45. Khan, M. A. et al. Changes in iron availability in Arabidopsis are rapidly sensed in the leaf vasculature and impaired sensing leads to opposite transcriptional programs in leaves and roots. Plant Cell Environ. 41, 2263–2276 (2018).

    Article  CAS  Google Scholar 

  46. Mustroph, A. et al. Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis. Proc. Natl Acad. Sci. USA 106, 18843–18848 (2009).

    Article  CAS  Google Scholar 

  47. Ngok-Ngam, P. et al. Roles of Agrobacterium tumefaciens RirA in iron regulation, oxidative stress response, and virulence. J. Bacteriol. 191, 2083–2090 (2009).

    Article  CAS  Google Scholar 

  48. Liu, J. et al. Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell 24, 4333–4345 (2012).

    Article  CAS  Google Scholar 

  49. Zhu, Q. H. et al. Long noncoding RNAs responsive to Fusarium oxysporum infection in Arabidopsis thaliana. New Phytol. 201, 574–584 (2014).

    Article  CAS  Google Scholar 

  50. Juntawong, P. et al. Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis. Proc. Natl Acad. Sci. USA 111, 203–212 (2013).

    Article  Google Scholar 

  51. Chadani, Y. et al. Instrinsic ribosome destabilization underlies translation and provides an organism with a strategy of environmental sensing. Mol. Cell 68, 528–539 (2017).

    Article  CAS  Google Scholar 

  52. Lindley, P. F. et al. An X-ray structural study of human ceruloplasmin in relation to ferroxidase activity. J. Biol. Inorg. Chem. 2, 454–463 (1997).

    Article  CAS  Google Scholar 

  53. Bou-Abdallah, F. The iron redox ad hydrolysis chemistry of the ferritins. Biochim. Biophys. Acta 1800, 719–731 (2010).

    Google Scholar 

  54. Bonaccorsi di Patti, M. C. et al. Specific aspartate residues in FET3 control high-affinity iron transport in Saccharomyces cerevisiae. Yeast 22, 677–687 (2005).

    Article  CAS  Google Scholar 

  55. Bernal, M. et al. Transcriptome sequencing identifies SPL7-regulated copper acquisition genes FRO4/FRO5 and the copper dependence of iron homeostasis in Arabidopsis. Plant Cell 24, 738–761 (2012).

    Article  CAS  Google Scholar 

  56. Azevedo, H. et al. Transcriptomic profiling of Arabidopsis gene expression in response to varying micronutrient zinc supply. Genom. Data 7, 256–258 (2016).

    Article  Google Scholar 

  57. Estelle, M. A. & Somerville, C. Auxin-resistant mutants of Arabidopsis thaliana with an altered morphology. Mol. Gen. Genet. 206, 200–206 (1987).

    Article  CAS  Google Scholar 

  58. Marsch-Martínez, N. et al. An efficient flat-surface collar-free grafting method for Arabidopsis thaliana seedlings. Plant Methods 9, 14 (2013).

    Article  Google Scholar 

  59. Karimi, M., Inze, D. & Depicker, A. GATEWAY vectors for Agrobacterium-mediated plant transformation. Trends Plant. Sci. 7, 193–195 (2002).

    Article  CAS  Google Scholar 

  60. Nakagawa, T. et al. Development of series of gateway binary vectors, pGWBs, for realizing efficient construction of fusion genes for plant transformation. J. Biosci. Bioeng. 104, 34–41 (2007).

    Article  CAS  Google Scholar 

  61. Clough, S. J. & Bent, A. F. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16, 735–743 (1998).

    Article  CAS  Google Scholar 

  62. Van Eck, J., Kirk., D. D. & Walmsley, A. M. Tomato (Lycopersicum esculentum). Methods Mol. Biol. 343, 459–473 (2006).

    Google Scholar 

  63. Bae, S., Park, J. & Kim, J.-S. Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 30, 1473–1475 (2014).

    Article  CAS  Google Scholar 

  64. Xing, H.-L. et al. A CRISPR/Cas9 toolkit for multiplex genome editing in plants. BMC Plant Biol. 14, 327 (2014).

    Article  Google Scholar 

  65. Mao, Y. et al. Application of the CRISPR-Cas system for efficient genome engineering in plants. Mol. Plant 6, 2008–2011 (2013).

    Article  CAS  Google Scholar 

  66. Grillet, L. et al. Ascorbate efflux as a new strategy for iron reduction and transport in plants. J. Biol. Chem. 289, 2515–2525 (2014).

    Article  CAS  Google Scholar 

  67. Roschzttardtz, H. et al. Identification of the endodermal vacuole as the iron storage compartment in the Arabidopsis embryo. Plant Phys. 151, 1329–1338 (2009).

    Article  CAS  Google Scholar 

  68. Bailey, T. L. et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37, 202–208 (2009).

    Article  Google Scholar 

Download references

Acknowledgements

We thank T. J. Buckhout (Humboldt University, Germany) and M. Matzke (IPMB, Academia Sinica) for valuable suggestions and critical comments on the manuscript. We further thank S. Mari and C. Curie (INRA-SUPAGRO, France) for helpful discussions and I. C. Vélez-Bermúdez for help with cross-sectioning. We are grateful to J. Bailey-Serres for kindly providing ribosome profiling data of IMA genes and J.-K. Zhu for providing the Cas9 vector that we used as a template. RNA sequencing was performed by the High Throughput Genomics Core Facility with the assistance of M.-Y. Lu, supported by Academia Sinica. We thank L.-Y. Kuang and S.-M. Chen from the Transgenic Plant Laboratory of IPMB for performing tomato and Arabidopsis transformations, M.-J. Fang from the IPMB Live Cell Imaging Core Laboratory for the help with confocal imaging, W.-D. Lin and Y.-I Lin from the Bioinformatics Core Laboratory at IPMB for bioinformatics support, Y.-R. Chen and Y.-C. Huang from the Metabolomics Core Laboratory of the Agricultural Biotechnology Research Center for the support with the electrospray ionization mass spectrometry. Elemental analysis were conducted through the use of ICP-MS by P.L. supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (grant no. XDB15030103) and the Project of Priority and Key Areas, ISSCAS (ISSASIP1605). This work was supported by an Academia Sinica Investigator Award to W.S.

Author information

Authors and Affiliations

Authors

Contributions

W.S., L.G. and P.L. designed the research; L.G., P.L., W.S., W.L. and G.M. performed and analysed experiments; W.S. and L.G. wrote the manuscript.

Corresponding author

Correspondence to Wolfgang Schmidt.

Ethics declarations

Competing interests

There is a potential competing interest as a provisional application for a patent concerning the use of IMA peptides to produce iron-enriched plants has been filed (US 20150315250 A1).

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary Figures 1–15 and Supplementary Tables 1–5

Reporting Summary

Supplementary Data Set 1

RNA-seq transcriptome analysis of IMA1 Ox and Fe-deficient WT Col-0

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Grillet, L., Lan, P., Li, W. et al. IRON MAN is a ubiquitous family of peptides that control iron transport in plants. Nature Plants 4, 953–963 (2018). https://doi.org/10.1038/s41477-018-0266-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41477-018-0266-y

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing