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:

A role for the root cap in root branching revealed by the non-auxin probe naxillin

Nature Chemical Biology volume 8, pages 798–805 (2012)Cite this article

Subjects

Abstract

The acquisition of water and nutrients by plant roots is a fundamental aspect of agriculture and strongly depends on root architecture. Root branching and expansion of the root system is achieved through the development of lateral roots and is to a large extent controlled by the plant hormone auxin. However, the pleiotropic effects of auxin or auxin-like molecules on root systems complicate the study of lateral root development. Here we describe a small-molecule screen in Arabidopsis thaliana that identified naxillin as what is to our knowledge the first non-auxin-like molecule that promotes root branching. By using naxillin as a chemical tool, we identified a new function for root cap–specific conversion of the auxin precursor indole-3-butyric acid into the active auxin indole-3-acetic acid and uncovered the involvement of the root cap in root branching. Delivery of an auxin precursor in peripheral tissues such as the root cap might represent an important mechanism shaping root architecture.

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: Identification and characterization of naxillin.
Figure 2: Naxillin induces a subset of auxin responses in the basal meristem.
Figure 3: Naxillin and NAA have different primary targets.
Figure 4: Naxillin acts in the IBA-to-IAA conversion pathway.
Figure 5: IBA and naxillin act locally in the root cap.

Similar content being viewed by others

References

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

    Article  CAS  Google Scholar 

  2. Vanneste, S. & Friml, J. Auxin: a trigger for change in plant development. Cell 136, 1005–1016 (2009).

    Article  CAS  Google Scholar 

  3. De Rybel, B., Audenaert, D., Beeckman, T. & Kepinski, S. The past, present, and future of chemical biology in auxin research. ACS Chem. Biol. 4, 987–998 (2009).

    Article  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. Gray, W.M., Muskett, P.R., Chuang, H.W. & Parker, J.E. Arabidopsis SGT1b is required for SCF(TIR1)-mediated auxin response. Plant Cell 15, 1310–1319 (2003).

    Article  CAS  Google Scholar 

  6. 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  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  8. Tiwari, S.B., Hagen, G. & Guilfoyle, T. The roles of auxin response factor domains in auxin-responsive transcription. Plant Cell 15, 533–543 (2003).

    Article  CAS  Google Scholar 

  9. Ruzicka, K. et al. Arabidopsis PIS1 encodes the ABCG37 transporter of auxinic compounds including the auxin precursor indole-3-butyric acid. Proc. Natl. Acad. Sci. USA 107, 10749–10753 (2010).

    Article  CAS  Google Scholar 

  10. Strader, L.C. & Bartel, B. The Arabidopsis PLEIOTROPIC DRUG RESISTANCE8/ABCG36 ATP binding cassette transporter modulates sensitivity to the auxin precursor indole-3-butyric acid. Plant Cell 21, 1992–2007 (2009).

    Article  CAS  Google Scholar 

  11. Strader, L.C. et al. Multiple facets of Arabidopsis seedling development require indole-3-butyric acid-derived auxin. Plant Cell 23, 984–999 (2011).

    Article  CAS  Google Scholar 

  12. Zolman, B.K., Silva, I.D. & Bartel, B. The Arabidopsis pxa1 mutant is defective in an ATP-binding cassette transporter-like protein required for peroxisomal fatty acid β-oxidation. Plant Physiol. 127, 1266–1278 (2001).

    Article  CAS  Google Scholar 

  13. Zolman, B.K., Yoder, A. & Bartel, B. Genetic analysis of indole-3-butyric acid responses in Arabidopsis thaliana reveals four mutant classes. Genetics 156, 1323–1337 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Strader, L.C., Culler, A.H., Cohen, J.D. & Bartel, B. Conversion of endogenous indole-3-butyric acid to indole-3-acetic acid drives cell expansion in Arabidopsis seedlings. Plant Physiol. 153, 1577–1586 (2010).

    Article  CAS  Google Scholar 

  15. Hayashi, M., Toriyama, K., Kondo, M. & Nishimura, M. 2,4-Dichlorophenoxybutyric acid-resistant mutants of Arabidopsis have defects in glyoxysomal fatty acid β-oxidation. Plant Cell 10, 183–195 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Zolman, B.K., Martinez, N., Millius, A., Adham, A.R. & Bartel, B. Identification and characterization of Arabidopsis indole-3-butyric acid response mutants defective in novel peroxisomal enzymes. Genetics 180, 237–251 (2008).

    Article  CAS  Google Scholar 

  17. Zolman, B.K., Nyberg, M. & Bartel, B. IBR3, a novel peroxisomal acyl-CoA dehydrogenase-like protein required for indole-3-butyric acid response. Plant Mol. Biol. 64, 59–72 (2007).

    Article  CAS  Google Scholar 

  18. Péret, B. et al. Arabidopsis lateral root development: an emerging story. Trends Plant Sci. 14, 399–408 (2009).

    Article  Google Scholar 

  19. De Smet, I. et al. Auxin-dependent regulation of lateral root positioning in the basal meristem of Arabidopsis. Development 134, 681–690 (2007).

    Article  CAS  Google Scholar 

  20. De Rybel, B. et al. A novel Aux/IAA28 signaling cascade activates GATA23-dependent specification of lateral root founder cell identity. Curr. Biol. 20, 1697–1706 (2010).

    Article  CAS  Google Scholar 

  21. Laskowski, M. et al. Root system architecture from coupling cell shape to auxin transport. PLoS Biol. 6, e307 (2008).

    Article  Google Scholar 

  22. Moreno-Risueno, M.A. et al. Oscillating gene expression determines competence for periodic Arabidopsis root branching. Science. 329, 1306–1311 (2010).

    Article  CAS  Google Scholar 

  23. Malamy, J.E. & Benfey, P.N. Organization and cell differentiation in lateral roots of Arabidopsis thaliana. Development 124, 33–44 (1997).

    CAS  PubMed  Google Scholar 

  24. Swarup, K. et al. The auxin influx carrier LAX3 promotes lateral root emergence. Nat. Cell Biol. 10, 946–954 (2008).

    Article  CAS  Google Scholar 

  25. 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 

  26. Himanen, K. et al. Auxin-mediated cell cycle activation during early lateral root initiation. Plant Cell 14, 2339–2351 (2002).

    Article  CAS  Google Scholar 

  27. Himanen, K. et al. Transcript profiling of early lateral root initiation. Proc. Natl. Acad. Sci. USA 101, 5146–5151 (2004).

    Article  CAS  Google Scholar 

  28. Vanneste, S. et al. Cell cycle progression in the pericycle is not sufficient for SOLITARY ROOT/IAA14-mediated lateral root initiation in Arabidopsis thaliana. Plant Cell 17, 3035–3050 (2005).

    Article  CAS  Google Scholar 

  29. Zhao, Y., Dai, X., Blackwell, H.E., Schreiber, S.L. & Chory, J. SIR1, an upstream component in auxin signaling identified by chemical genetics. Science 301, 1107–1110 (2003).

    Article  CAS  Google Scholar 

  30. Okushima, Y., Fukaki, H., Onoda, M., Theologis, A. & Tasaka, M. ARF7 and ARF19 regulate lateral root formation via direct activation of LBD/ASL genes in Arabidopsis. Plant Cell 19, 118–130 (2007).

    Article  CAS  Google Scholar 

  31. Brady, S.M. et al. A high-resolution root spatiotemporal map reveals dominant expression patterns. Science 318, 801–806 (2007).

    Article  CAS  Google Scholar 

  32. 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  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  36. Fukaki, H., Tameda, S., Masuda, H. & Tasaka, M. Lateral root formation is blocked by a gain-of-function mutation in the SOLITARY-ROOT/IAA14 gene of Arabidopsis. Plant J. 29, 153–168 (2002).

    Article  CAS  Google Scholar 

  37. 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 

  38. Lingard, M.J., Monroe-Augustus, M. & Bartel, B. Peroxisome-associated matrix protein degradation in Arabidopsis. Proc. Natl. Acad. Sci. USA 106, 4561–4566 (2009).

    Article  CAS  Google Scholar 

  39. Zolman, B.K., Monroe-Augustus, M., Silva, I.D. & Bartel, B. Identification and functional characterization of Arabidopsis PEROXIN4 and the interacting protein PEROXIN22. Plant Cell 17, 3422–3435 (2005).

    Article  CAS  Google Scholar 

  40. Arent, S., Christensen, C.E., Pye, V.E., Norgaard, A. & Henriksen, A. The multifunctional protein in peroxisomal β-oxidation: structure and substrate specificity of the Arabidopsis thaliana protein MFP2. J. Biol. Chem. 285, 24066–24077 (2010).

    Article  CAS  Google Scholar 

  41. Richmond, T.A. & Bleecker, A.B. A defect in β-oxidation causes abnormal inflorescence development in Arabidopsis. Plant Cell 11, 1911–1924 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Rylott, E.L. et al. The Arabidopsis thaliana multifunctional protein gene (MFP2) of peroxisomal β-oxidation is essential for seedling establishment. Plant J. 45, 930–941 (2006).

    Article  CAS  Google Scholar 

  43. Choi, Y. et al. Chemical genetic identification of the IGF-linked pathway that is mediated by STAT6 and MFP2. Chem. Biol. 13, 241–249 (2006).

    Article  CAS  Google Scholar 

  44. De Rybel, B. et al. Chemical inhibition of a subset of Arabidopsis thaliana GSK3-like kinases activates brassinosteroid signaling. Chem. Biol. 16, 594–604 (2009).

    Article  CAS  Google Scholar 

  45. Du, X. et al. Synthesis and structure-activity relationship study of potent trypanocidal thio semicarbazone inhibitors of the trypanosomal cysteine protease cruzain. J. Med. Chem. 45, 2695–2707 (2002).

    Article  CAS  Google Scholar 

  46. Liu, X., Cohen, J.D. & Gardner, G. Low-fluence red light increases the transport and biosynthesis of auxin. Plant Physiol. 157, 891–904 (2011).

    Article  CAS  Google Scholar 

  47. Karimi, M., Depicker, A. & Hilson, P. Recombinational cloning with plant gateway vectors. Plant Physiol. 145, 1144–1154 (2007).

    Article  CAS  Google Scholar 

  48. Hilson, P. et al. Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications. Genome Res. 14, 2176–2189 (2004).

    Article  CAS  Google Scholar 

  49. De Rybel, B. et al. A versatile set of ligation-independent cloning vectors for functional studies in plants. Plant Physiol. 156, 1292–1299 (2011).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank J. Cohen and J. Normanly for helpful discussions, and E. Feraru and M. Feraru for help with mapping the nar1 mutant. This work was supported by the Interuniversity Attraction Poles Programme (IUAP VI/33) initiated by the Belgian State Science Policy Office, the Special Research Fund of Ghent University, a long-term Federation of European Biochemical Societies fellowship (pre- and post-doctoral fellowships to B.D.R.), the Robert A. Welch Foundation (C-1309 to B.B.), the US National Institutes of Health (R00-GM089987-03 to L.C.S.), the US National Science Foundation (DBI-1039655 to P.J.O., R.H. and R.B.; DBI-0923960 to P.J.O. and R.H.) and the Research Foundation Flanders (FWO, research project 3G002911). S.V. is a postdoctoral fellow of the Research Foundation-Flanders. D.A. is a postdoctoral fellow of the FWO. D.A. and L.N. are part of the VIB Compound Screening Facility.

Author information

Author notes

  1. Bert De Rybel, Lucia C Strader & Xing Liu

    Present address: Present addresses: Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands (B.D.R.); Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA (L.C.S.); and Division of Biology, California Institute of Technology, Pasadena, California, USA (X.L.).,

  2. Bert De Rybel and Dominique Audenaert: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Plant Systems Biology, VIB, Gent, Belgium

    Bert De Rybel, Dominique Audenaert, Wei Xuan, Boris Parizot, Steffen Vanneste, Leentje Jansen, Maria Fransiska Njo, Dirk Inzé & Tom Beeckman

  2. Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium

    Bert De Rybel, Dominique Audenaert, Wei Xuan, Boris Parizot, Steffen Vanneste, Leentje Jansen, Maria Fransiska Njo, Dirk Inzé & Tom Beeckman

  3. Department of Biology, Macalester College, St. Paul, Minnesota, USA

    Paul Overvoorde

  4. Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, USA

    Lucia C Strader & Bonnie Bartel

  5. Centre for Plant Sciences, University of Leeds, Leeds, UK

    Stefan Kepinski

  6. Department of Chemistry, Macalester College, St. Paul, Minnesota, USA

    Rebecca Hoye & Ronald Brisbois

  7. Department of Horticultural Science, Plant Biological Sciences Graduate Program, and Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, Minnesota, USA

    Xing Liu

  8. Department of Biology, Centre for Novel Agricultural Products, University of York, York, UK

    Alison Gilday & Ian A Graham

  9. VIB Compound Screening Facility, Gent, Belgium

    Long Nguyen

Authors
  1. Bert De Rybel
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Dominique Audenaert
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Wei Xuan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Paul Overvoorde
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Lucia C Strader
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Stefan Kepinski
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Rebecca Hoye
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Ronald Brisbois
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Boris Parizot
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Steffen Vanneste
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Xing Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Alison Gilday
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Ian A Graham
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Long Nguyen
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Leentje Jansen
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Maria Fransiska Njo
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. Dirk Inzé
    View author publications

    You can also search for this author in PubMed Google Scholar

  18. Bonnie Bartel
    View author publications

    You can also search for this author in PubMed Google Scholar

  19. Tom Beeckman
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

B.D.R., D.A., L.N. and L.J. performed chemical genetics screening; X.L. and P.O. performed the IBA-to-IAA conversion experiment; P.O., R.H. and R.B. synthesized naxillin; B.P. performed statistical analysis on data sets; M.F.N. helped with sectioning; A.G. and I.A.G. performed enzyme activity assays; S.K. performed in vitro pull-down experiment; B.D.R., D.A. and W.X. performed all other experiments; B.D.R., D.A., P.O., S.V., L.C.S., B.B., D.I. and T.B. conceived experiments and wrote the paper.

Corresponding author

Correspondence to Tom Beeckman.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Methods and Supplementary Results (PDF 21121 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

De Rybel, B., Audenaert, D., Xuan, W. et al. A role for the root cap in root branching revealed by the non-auxin probe naxillin. Nat Chem Biol 8, 798–805 (2012). https://doi.org/10.1038/nchembio.1044

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nchembio.1044

This article is cited by

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