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.

  • Article
  • Published:

Mechanism of auxin perception by the TIR1 ubiquitin ligase

Nature volume 446, pages 640–645 (2007)Cite this article

Abstract

Auxin is a pivotal plant hormone that controls many aspects of plant growth and development. Perceived by a small family of F-box proteins including transport inhibitor response 1 (TIR1), auxin regulates gene expression by promoting SCF ubiquitin-ligase-catalysed degradation of the Aux/IAA transcription repressors, but how the TIR1 F-box protein senses and becomes activated by auxin remains unclear. Here we present the crystal structures of the Arabidopsis TIR1–ASK1 complex, free and in complexes with three different auxin compounds and an Aux/IAA substrate peptide. These structures show that the leucine-rich repeat domain of TIR1 contains an unexpected inositol hexakisphosphate co-factor and recognizes auxin and the Aux/IAA polypeptide substrate through a single surface pocket. Anchored to the base of the TIR1 pocket, auxin binds to a partially promiscuous site, which can also accommodate various auxin analogues. Docked on top of auxin, the Aux/IAA substrate peptide occupies the rest of the TIR1 pocket and completely encloses the hormone-binding site. By filling in a hydrophobic cavity at the protein interface, auxin enhances the TIR1–substrate interactions by acting as a ‘molecular glue’. Our results establish the first structural model of a plant hormone receptor.

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

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Crystal structure of the TIR1–ASK1 complex with auxin and the IAA7 degron peptide.
Figure 2: Architecture of the TIR1-LRR domain.
Figure 3: InsP 6 as a TIR1 co-factor.
Figure 4: Recognition of auxin by TIR1.
Figure 5: Binding of an Aux/IAA degron peptide on auxin-bound TIR1.
Figure 6: A model of auxin-regulated TIR1–substrate interactions.

Similar content being viewed by others

References

  1. Woodward, A. W. & Bartel, B. Auxin: regulation, action, and interaction. Ann. Bot. (Lond.) 95, 707–735 (2005)

    Article  CAS  Google Scholar 

  2. Teale, W. D., Paponov, I. A. & Palme, K. Auxin in action: signalling, transport and the control of plant growth and development. Nature Rev. Mol. Cell Biol. 7, 847–859 (2006)

    Article  CAS  Google Scholar 

  3. Dharmasiri, N. & Estelle, M. Auxin signaling and regulated protein degradation. Trends Plant Sci. 9, 302–308 (2004)

    Article  CAS  Google Scholar 

  4. Gray, W. M., Kepinski, S., Rouse, D., Leyser, O. & Estelle, M. Auxin regulates SCF(TIR1)-dependent degradation of AUX/IAA proteins. Nature 414, 271–276 (2001)

    Article  ADS  CAS  Google Scholar 

  5. Hagen, G. & Guilfoyle, T. Auxin-responsive gene expression: genes, promoters and regulatory factors. Plant Mol. Biol. 49, 373–385 (2002)

    Article  CAS  Google Scholar 

  6. Reed, J. W. Roles and activities of Aux/IAA proteins in Arabidopsis. Trends Plant Sci. 6, 420–425 (2001)

    Article  CAS  Google Scholar 

  7. Liscum, E. & Reed, J. W. Genetics of Aux/IAA and ARF action in plant growth and development. Plant Mol. Biol. 49, 387–400 (2002)

    Article  CAS  Google Scholar 

  8. Zenser, N., Ellsmore, A., Leasure, C. & Callis, J. Auxin modulates the degradation rate of Aux/IAA proteins. Proc. Natl Acad. Sci. USA 98, 11795–11800 (2001)

    Article  ADS  CAS  Google Scholar 

  9. Tiwari, S. B., Wang, X. J., Hagen, G. & Guilfoyle, T. J. AUX/IAA proteins are active repressors, and their stability and activity are modulated by auxin. Plant Cell 13, 2809–2822 (2001)

    Article  CAS  Google Scholar 

  10. Remington, D. L., Vision, T. J., Guilfoyle, T. J. & Reed, J. W. Contrasting modes of diversification in the Aux/IAA and ARF gene families. Plant Physiol. 135, 1738–1752 (2004)

    Article  CAS  Google Scholar 

  11. Overvoorde, P. J. et al. Functional genomic analysis of the AUXIN/INDOLE-3-ACETIC ACID gene family members in Arabidopsis thaliana. Plant Cell 17, 3282–3300 (2005)

    Article  CAS  Google Scholar 

  12. Okushima, Y. et al. Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19. Plant Cell 17, 444–463 (2005)

    Article  CAS  Google Scholar 

  13. Ramos, J. A., Zenser, N., Leyser, O. & Callis, J. Rapid degradation of auxin/indole acetic acid proteins requires conserved amino acids of domain II and is proteasome dependent. Plant Cell 13, 2349–2360 (2001)

    Article  CAS  Google Scholar 

  14. Dharmasiri, N., Dharmasiri, S., Jones, A. M. & Estelle, M. Auxin action in a cell-free system. Curr. Biol. 13, 1418–1422 (2003)

    Article  CAS  Google Scholar 

  15. Kepinski, S. & Leyser, O. Auxin-induced SCFTIR1-Aux/IAA interaction involves stable modification of the SCFTIR1 complex. Proc. Natl Acad. Sci. USA 101, 12381–12386 (2004)

    Article  ADS  CAS  Google Scholar 

  16. Dharmasiri, N., Dharmasiri, S. & Estelle, M. The F-box protein TIR1 is an auxin receptor. Nature 435, 441–445 (2005)

    Article  ADS  CAS  Google Scholar 

  17. Kepinski, S. & Leyser, O. The Arabidopsis F-box protein TIR1 is an auxin receptor. Nature 435, 446–451 (2005)

    Article  ADS  CAS  Google Scholar 

  18. Gagne, J. M., Downes, B. P., Shiu, S. H., Durski, A. M. & Vierstra, R. D. The F-box subunit of the SCF E3 complex is encoded by a diverse superfamily of genes in Arabidopsis. Proc. Natl Acad. Sci. USA 99, 11519–11524 (2002)

    Article  ADS  CAS  Google Scholar 

  19. Dharmasiri, N. et al. Plant development is regulated by a family of auxin receptor F box proteins. Dev. Cell 9, 109–119 (2005)

    Article  CAS  Google Scholar 

  20. Jonsson, A. Encyclopaedia of Plant Physiology 14, 959–1006 (Springer, Berlin, 1961)

    Google Scholar 

  21. Kaethner, T. Conformational change theory for auxin structure-activity relationships. Nature 267, 19–23 (1977)

    Article  ADS  CAS  Google Scholar 

  22. Farrimond, J. A., Elliott, M. C. & Clack, D. W. Charge separation as a component of the structural requirements for hormone activity. Nature 274, 401–402 (1978)

    Article  ADS  CAS  Google Scholar 

  23. Petroski, M. D. & Deshaies, R. J. Function and regulation of cullin-RING ubiquitin ligases. Nature Rev. Mol. Cell Biol. 6, 9–20 (2005)

    Article  CAS  Google Scholar 

  24. Schulman, B. A. et al. Insights into SCF ubiquitin ligases from the structure of the Skp1-Skp2 complex. Nature 408, 381–386 (2000)

    Article  ADS  CAS  Google Scholar 

  25. Zheng, N. et al. Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF ubiquitin ligase complex. Nature 416, 703–709 (2002)

    Article  ADS  CAS  Google Scholar 

  26. Kobe, B. & Kajava, A. V. The leucine-rich repeat as a protein recognition motif. Curr. Opin. Struct. Biol. 11, 725–732 (2001)

    Article  CAS  Google Scholar 

  27. Kobe, B. & Deisenhofer, J. Crystallization and preliminary X-ray analysis of porcine ribonuclease inhibitor, a protein with leucine-rich repeats. J. Mol. Biol. 231, 137–140 (1993)

    Article  CAS  Google Scholar 

  28. Choe, J., Kelker, M. S. & Wilson, I. A. Crystal structure of human toll-like receptor 3 (TLR3) ectodomain. Science 309, 581–585 (2005)

    Article  ADS  CAS  Google Scholar 

  29. Irvine, R. F. & Schell, M. J. Back in the water: the return of the inositol phosphates. Nature Rev. Mol. Cell Biol. 2, 327–338 (2001)

    Article  CAS  Google Scholar 

  30. Macbeth, M. R. et al. Inositol hexakisphosphate is bound in the ADAR2 core and required for RNA editing. Science 309, 1534–1539 (2005)

    Article  ADS  CAS  Google Scholar 

  31. Hanakahi, L. A., Bartlet-Jones, M., Chappell, C., Pappin, D. & West, S. C. Binding of inositol phosphate to DNA-PK and stimulation of double-strand break repair. Cell 102, 721–729 (2000)

    Article  CAS  Google Scholar 

  32. Steger, D. J., Haswell, E. S., Miller, A. L., Wente, S. R. & O'Shea, E. K. Regulation of chromatin remodeling by inositol polyphosphates. Science 299, 114–116 (2003)

    Article  ADS  CAS  Google Scholar 

  33. York, J. D., Odom, A. R., Murphy, R., Ives, E. B. & Wente, S. R. A phospholipase C-dependent inositol polyphosphate kinase pathway required for efficient messenger RNA export. Science 285, 96–100 (1999)

    Article  CAS  Google Scholar 

  34. Hoy, M. et al. Inositol hexakisphosphate promotes dynamin I-mediated endocytosis. Proc. Natl Acad. Sci. USA 99, 6773–6777 (2002)

    Article  ADS  CAS  Google Scholar 

  35. Moon, J., Parry, G. & Estelle, M. The ubiquitin-proteasome pathway and plant development. Plant Cell 16, 3181–3195 (2004)

    Article  CAS  Google Scholar 

  36. Xie, D. X., Feys, B. F., James, S., Nieto-Rostro, M. & Turner, J. G. COI1: an Arabidopsis gene required for jasmonate-regulated defense and fertility. Science 280, 1091–1094 (1998)

    Article  ADS  CAS  Google Scholar 

  37. Nalepa, G., Rolfe, M. & Harper, J. W. Drug discovery in the ubiquitin-proteasome system. Nature Rev. Drug Discov. 5, 596–613 (2006)

    Article  CAS  Google Scholar 

  38. Otwinowski, Z. & Minor, W. (eds) Processing of X-ray Diffraction Data Collected in Oscillation Mode (Academic Press, New York, 1997)

  39. Terwilliger, T. C. Maximum-likelihood density modification. Acta Crystallogr. D 56, 965–972 (2000)

    Article  CAS  Google Scholar 

  40. Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991)

    Article  Google Scholar 

  41. Brunger, A. T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998)

    Article  CAS  Google Scholar 

  42. CCP4. The CCP4 Suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994)

  43. Painter, J. & Merritt, E. A. Optimal description of a protein structure in terms of multiple groups undergoing TLS motion. Acta Crystallogr. D 62, 439–450 (2006)

    Article  Google Scholar 

Download references

Acknowledgements

We thank the beamline staff of the Advanced Light Source at Berkeley for help with data collection. We also thank J. Callis, W. Xu and members of the Zheng laboratory for discussions and help. This work is supported by grants from the National Institutes of Health (M.E), the Pew Scholar Program (N.Z.), the National Science Foundation (M.E.) and the Department of Energy (M.E.).

Structure coordinates and structural factors are deposited in the Protein Data Bank under accession numbers 2P1M, 2P1N, 2P1O, 2P1P and 2P1Q (see Supplementary Table 1).

Author information

Authors and Affiliations

  1. Department of Pharmacology, University of Washington, School of Medicine, Box 357280, Seattle, Washington 98195, USA,

    Xu Tan, Changxue Zheng & Ning Zheng

  2. Department of Biology, Indiana University, Bloomington, Indiana 47405, USA,

    Luz Irina A. Calderon-Villalobos & Mark Estelle

  3. Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK,

    Michal Sharon & Carol V. Robinson

Authors
  1. Xu Tan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Luz Irina A. Calderon-Villalobos
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Michal Sharon
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Changxue Zheng
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Carol V. Robinson
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Mark Estelle
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Ning Zheng
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ning Zheng.

Ethics declarations

Competing interests

Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-7 with Legends, Supplementary Table 1 and additional references. (PDF 4414 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Tan, X., Calderon-Villalobos, L., Sharon, M. et al. Mechanism of auxin perception by the TIR1 ubiquitin ligase. Nature 446, 640–645 (2007). https://doi.org/10.1038/nature05731

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature05731

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced 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