Skip to main content

Thank you for visiting 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.

A novel sensor to map auxin response and distribution at high spatio-temporal resolution


Auxin is a key plant morphogenetic signal1 but tools to analyse dynamically its distribution and signalling during development are still limited. Auxin perception directly triggers the degradation of Aux/IAA repressor proteins2,3,4,5,6. Here we describe a novel Aux/IAA-based auxin signalling sensor termed DII-VENUS that was engineered in the model plant Arabidopsis thaliana. The VENUS fast maturing form of yellow fluorescent protein7 was fused in-frame to the Aux/IAA auxin-interaction domain (termed domain II; DII)5 and expressed under a constitutive promoter. We initially show that DII-VENUS abundance is dependent on auxin, its TIR1/AFBs co-receptors4,5,6,8 and proteasome activities. Next, we demonstrate that DII-VENUS provides a map of relative auxin distribution at cellular resolution in different tissues. DII-VENUS is also rapidly degraded in response to auxin and we used it to visualize dynamic changes in cellular auxin distribution successfully during two developmental responses, the root gravitropic response and lateral organ production at the shoot apex. Our results illustrate the value of developing response input sensors such as DII-VENUS to provide high-resolution spatio-temporal information about hormone distribution and response during plant growth and development.

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

Access options

Rent or buy this article

Prices vary by article type



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

Figure 1: DII-VENUS degradation is dependent on auxin, TIR1/AFBs and proteasome activity.
Figure 2: DII-VENUS provides a sensor to map auxin distribution in plant tissues.
Figure 3: DII-VENUS monitors changes in auxin response and distribution at high temporal resolution.
Figure 4: DII-VENUS allows visualization of changes in auxin distribution during development.

Similar content being viewed by others


  1. Friml, J. Auxin transport — shaping the plant. Curr. Opin. Plant Biol. 6, 7–12 (2003)

    Article  CAS  Google Scholar 

  2. Chapman, E. J. & Estelle, M. Mechanism of auxin-regulated gene expression in plants. Annu. Rev. Genet. 43, 265–285 (2009)

    Article  CAS  Google Scholar 

  3. 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 

  4. 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 

  5. Tan, X. et al. Mechanism of auxin perception by the TIR1 ubiquitin ligase. Nature 446, 640–645 (2007)

    Article  ADS  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  7. Shaner, N. C., Steinbach, P. A. & Tsien, R. Y. A guide to choosing fluorescent proteins. Nature Methods 2, 905–909 (2005)

    Article  CAS  Google Scholar 

  8. Greenham, K. et al. The AFB4 auxin receptor is a negative regulator of auxin signaling in seedlings. Curr. Biol. 21, 520–525 (2011)

    Article  CAS  Google Scholar 

  9. Ulmasov, T., Hagen, G. & Guilfoyle, T. J. ARF1, a transcription factor that binds to auxin response elements. Science 276, 1865–1868 (1997)

    Article  CAS  Google Scholar 

  10. Guilfoyle, T. J. & Hagen, G. Auxin response factors. Curr. Opin. Plant Biol. 10, 453–460 (2007)

    Article  CAS  Google Scholar 

  11. Sabatini, S. et al. An auxin-dependent distal organizer of pattern and polarity in the Arabidopsis root. Cell 99, 463–472 (1999)

    Article  CAS  Google Scholar 

  12. Ulmasov, T., Murfett, J., Hagen, G. & Guilfoyle, T. J. Aux/IAA proteins repress expression of reporter genes containing natural and highly active synthetic auxin response elements. Plant Cell 9, 1963–1971 (1997)

    Article  CAS  Google Scholar 

  13. Gray, W. M., Kepinski, S., Rouse, D., Leyser, O. & Estelle, M. Auxin regulates SCFTIR1-dependent degradation of AUX/IAA proteins. Nature 414, 271–276 (2001)

    Article  ADS  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  15. 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 

  16. Dreher, K. A., Brown, J., Saw, R. E. & Callis, J. The Arabidopsis Aux/IAA protein family has diversified in degradation and auxin responsiveness. Plant Cell 18, 699–714 (2006)

    Article  CAS  Google Scholar 

  17. Abel, S., Oeller, P. W. & Theologis, A. Early auxin-induced genes encode short-lived nuclear proteins. Proc. Natl Acad. Sci. USA 91, 326–330 (1994)

    Article  ADS  CAS  Google Scholar 

  18. Vernoux, T. et al. The auxin signalling network translates dynamic input into robust patterning at the shoot apex. Mol. Syst. Biol. 7, 508 (2011)

    Article  Google Scholar 

  19. Parry, G. et al. Complex regulation of the TIR1/AFB family of auxin receptors. Proc. Natl Acad. Sci. USA 106, 22540–22545 (2009)

    Article  ADS  CAS  Google Scholar 

  20. Benková, E. et al. Local, efflux-dependent auxin gradients as a common module for plant organ formation. Cell 115, 591–602 (2003)

    Article  Google Scholar 

  21. Ottenschläger, I. et al. Gravity-regulated differential auxin transport from columella to lateral root cap cells. Proc. Natl Acad. Sci. USA 100, 2987–2991 (2003)

    Article  ADS  Google Scholar 

  22. Santuari, L. et al. Positional information by differential endocytosis splits auxin response to drive Arabidopsis root meristem growth. Curr. Biol. 21, 1918–1923 (2011)

    Article  CAS  Google Scholar 

  23. Petersson, S. V. et al. An auxin gradient and maximum in the Arabidopsis root apex shown by high-resolution cell-specific analysis of IAA distribution and synthesis. Plant Cell 21, 1659–1668 (2009)

    Article  CAS  Google Scholar 

  24. Boonsirichai, K., Guan, C., Chen, R. & Masson, P. H. Root gravitropism: an experimental tool to investigate basic cellular and molecular processes underlying mechanosensing and signal transmission in plants. Annu. Rev. Plant Biol. 53, 421–447 (2002)

    Article  CAS  Google Scholar 

  25. Boonsirichai, K., Sedbrook, J. C., Chen, R., Gilroy, S. & Masson, P. H. ALTERED RESPONSE TO GRAVITY is a peripheral membrane protein that modulates gravity-induced cytoplasmic alkalinization and lateral auxin transport in plant statocytes. Plant Cell 15, 2612–2625 (2003)

    Article  CAS  Google Scholar 

  26. Reinhardt, D. et al. Regulation of phyllotaxis by polar auxin transport. Nature 426, 255–260 (2003)

    Article  ADS  CAS  Google Scholar 

  27. Heisler, M. G. et al. Patterns of auxin transport and gene expression during primordium development revealed by live imaging of the Arabidopsis inflorescence meristem. Curr. Biol. 15, 1899–1911 (2005)

    Article  CAS  Google Scholar 

  28. Silverstone, A. L. et al. Repressing a repressor: gibberellin-induced rapid reduction of the RGA protein in Arabidopsis . Plant Cell 13, 1555–1566 (2001)

    Article  CAS  Google Scholar 

  29. Fu, X. & Harberd, N. P. Auxin promotes Arabidopsis root growth by modulating gibberellin response. Nature 421, 740–743 (2003)

    Article  ADS  CAS  Google Scholar 

  30. Santner, A. & Estelle, M. Recent advances and emerging trends in plant hormone signalling. Nature 459, 1071–1078 (2009)

    Article  ADS  CAS  Google Scholar 

  31. Friml, J. et al. Efflux-dependent auxin gradients establish the apical-basal axis of Arabidopsis . Nature 426, 147–153 (2003)

    Article  ADS  CAS  Google Scholar 

  32. 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 

  33. Rogg, L. E., Lasswell, J. & Bartel, B. A gain-of-function mutation in IAA28 suppresses lateral root development. Plant Cell 13, 465–480 (2001)

    Article  CAS  Google Scholar 

  34. Cutler, S. R., Ehrhardt, D. W., Griffitts, J. S. & Somerville, C. R. Random GFP:cDNA fusions enable visualization of subcellular structures in cells of Arabidopsis at a high frequency. Proc. Natl Acad. Sci. USA 97, 3718–3723 (2000)

    Article  ADS  CAS  Google Scholar 

  35. Karimi, M., De Meyer, B. & Hilson, P. Modular cloning in plant cells. Trends Plant Sci. 10, 103–105 (2005)

    Article  CAS  Google Scholar 

  36. Levesque, M. P. et al. Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis . PLoS Biol. 4, e143 (2006)

    Article  Google Scholar 

  37. Barbier de Reuille, P., Bohn-Courseau, I., Godin, C. & Traas, J. A protocol to analyse cellular dynamics during plant development. Plant J. 44, 1045–1053 (2005)

    Article  CAS  Google Scholar 

  38. Fernandez, R. et al. Imaging plant growth in 4D: robust tissue reconstruction and lineaging at cell resolution. Nature Methods 7, 547–553 (2010)

    Article  CAS  Google Scholar 

  39. Grandjean, O. et al. In vivo analysis of cell division, cell growth, and differentiation at the shoot apical meristem in Arabidopsis . Plant Cell 16, 74–87 (2004)

    Article  CAS  Google Scholar 

  40. Holman, T. J. et al. Statistical evaluation of transcriptomic data generated using the Affymetrix one-cycle, two-cycle and IVT-Express RNA labelling protocols with the Arabidopsis ATH1 microarray. Plant Methods 6, 9 (2010)

    Article  Google Scholar 

  41. French, A., Ubeda-Tomas, S., Holman, T. J., Bennett, M. J. & Pridmore, T. High-throughput quantification of root growth using a novel image-analysis tool. Plant Physiol. 150, 1784–1795 (2009)

    Article  CAS  Google Scholar 

  42. Lohmann, D. et al. SLOW MOTION is required for within-plant auxin homeostasis and normal timing of lateral organ initiation at the shoot meristem in Arabidopsis . Plant Cell 22, 335–348 (2010)

    Article  CAS  Google Scholar 

Download references


We thank A. Erktan and C. Cellier for help with marker expression analysis; J. Neve, A. Miyawaki, M. Heisler and M. Estelle for providing the 35S::Flag-TIR1 line, VENUS complementary DNA, DR5::VENUS plasmids and TIR/AFB GUS lines, respectively; the PLATIM for access to confocal microscopes; F. Parcy, O. Hamant, A. Boudaoud and P. Das for discussions. T.V. was supported by the Human Frontier Science Program Organization (CDA 0047/2007 HFSPO) and the Agence National de la Recherche (ANR-07-JCJC-0115 and EraSysBio+ iSAM). D.M.W., A.L. and M.J.B. acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC) and Engineering and Physical Sciences Research Council (EPSRC) funding to the Centre for Plant Integrative Biology (CPIB); BBSRC grants BB/F013981/1 and BB/F007418/1 to S.K.; BBSRC Professorial Research Fellowship funding to D.M.W. & M.J.B.; and Belgian Scientific policy (BELSPO contract BARN) to A.L., T.B. and M.J.B.

Author information

Authors and Affiliations



T.V. designed the DII-VENUS tool. G.B., M.O. and T.V. engineered and characterized DII-VENUS transgenic lines. D.M.W., G.B., A.L. and V.M. quantified the spatial and temporal dynamics of DII-VENUS. A.H.B. did the pull-down assay. T.V. and M.J.B. designed the experiments with the help of T.B., S.K. and J.T. T.V. and M.J.B. analysed the data and wrote the paper. All authors discussed the results and commented on the manuscript.

Corresponding author

Correspondence to Teva Vernoux.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

The file contains Supplementary Text, Supplementary References, Supplementary Figures 1-10 with legends and Supplementary Table 1. (PDF 2832 kb)

Supplementary Movie 1

This file shows DII-VENUS degradation upon auxin treatment. (MOV 4466 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Brunoud, G., Wells, D., Oliva, M. et al. A novel sensor to map auxin response and distribution at high spatio-temporal resolution. Nature 482, 103–106 (2012).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


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.


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