The phytohormone auxin indole-3-acetic acid (IAA) regulates nearly all aspects of plant growth and development. Despite substantial progress in our understanding of auxin biology, delineating specific auxin response remains a major challenge. Auxin regulates transcriptional response via its receptors, TIR1 and AFB F-box proteins. Here we report an engineered, orthogonal auxin–TIR1 receptor pair, developed through a bump-and-hole strategy, that triggers auxin signaling without interfering with endogenous auxin or TIR1/AFBs. A synthetic, convex IAA (cvxIAA) hijacked the downstream auxin signaling in vivo both at the transcriptomic level and in specific developmental contexts, only in the presence of a complementary, concave TIR1 (ccvTIR1) receptor. Harnessing the cvxIAA–ccvTIR1 system, we provide conclusive evidence for the role of the TIR1-mediated pathway in auxin-induced seedling acid growth. The cvxIAA–ccvTIR1 system serves as a powerful tool for solving outstanding questions in auxin biology and for precise manipulation of auxin-mediated processes as a controllable switch.

  • Compound

    2-(5-(3-methoxyphenyl)-1H-indol-3-yl)acetic acid

  • Compound

    2-(5-(2-methoxyphenyl)-1H-indol-3-yl)acetic acid

  • Compound

    2-(5-(4-methoxyphenyl)-1H-indol-3-yl)acetic acid

  • Compound

    2-(5-(4-(trifluoromethyl)phenyl)-1H-indol-3-yl)acetic acid

  • Compound

    2-(5-([1,1'-biphenyl]-4-yl)-1H-indol-3-yl)acetic acid

  • Compound

    2-(5-phenyl-1H-indol-3-yl)acetic acid

  • Compound

    2-(5-(naphthalen-2-yl)-1H-indol-3-yl)acetic acid

  • Compound

    2-(naphthalen-1-yl)acetic acid

  • Compound

    2-(2,4-dichlorophenoxy)acetic acid

  • Compound

    2-(4-phenyl-1H-indol-3-yl)acetic acid

  • Compound

    methyl 2-(5-(2-methoxyphenyl)-1H-indol-3-yl)acetate

  • Compound

    methyl 2-(5-(3-methoxyphenyl)-1H-indol-3-yl)acetate

  • Compound

    methyl 2-(5-(4-methoxyphenyl)-1H-indol-3-yl)acetate

  • Compound

    methyl 2-(5-(naphthalen-2-yl)-1H-indol-3-yl)acetate

  • Compound

    methyl 2-(5-(4-(trifluoromethyl)phenyl)-1H-indol-3-yl)acetate

  • Compound

    methyl 2-(5-([1,1'-biphenyl]-4-yl)-1H-indol-3-yl)acetate

  • Compound

    2-(4-bromo-1H-indol-3-yl)-2-oxoacetic acid

  • Compound

    2-(4-bromo-1H-indol-3-yl)acetic acid

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We thank M. Estelle (University of California, San Diego) for inspiring us and providing tir1-1 afb2-3 seeds; H. Fukaki (Kobe University) for slr-1 seeds; Yeast Genetics Resource Center and Y. Tsuchiya (Nagoya University) for Y2H vectors; Peptide/protein center at WPI-ITbM for biotinyl peptides; J. Bode for his visionary comments during the conceptualization of the project; J. Nemhauser and R. Cleland for commenting on the manuscript. K.U.T. dedicates this manuscript to R. Cleland, who proposed the acid growth theory in 1970, for his continued mentorship at the Univ. Washington. This work was funded by MEXT/JSPS KAKENHI (JP26291057, JP16H01237 and JP17H06476 to K.U.T.; JP16H01462, JP17H03695 and JP17KT0017 to N.U.; JP26440140 to K.T.; JP15H05956 to T.K.; JP17H06350 to S.H.; JP16H01472 and S1511023 to S.K.), Japan Science and Technology Agency (PRESTO, JPMJPR15Q9 to S.H.; ERATO, JPMJER1302 to K.I.), Howard Hughes Medical Institute (HHMI) and Gordon and Betty Moore Foundation (GBMF3035) to K.UT. S.H. is a JST PRESTO investigator, K.I. is a JST ERATO investigator and K.U.T. is an HHMI-GBMF Investigator and University Washington Endowed Distinguished Professor of Biology.

Author information

Author notes

    • Naoyuki Uchida
    •  & Koji Takahashi

    These authors contributed equally to this work.


  1. Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, Japan.

    • Naoyuki Uchida
    • , Koji Takahashi
    • , Rie Iwasaki
    • , Hua Zhang
    • , Toshinori Kinoshita
    • , Kenichiro Itami
    • , Shinya Hagihara
    •  & Keiko U Torii
  2. Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan.

    • Naoyuki Uchida
    • , Koji Takahashi
    • , Ryotaro Yamada
    • , Masahiko Yoshimura
    • , Mika Nomoto
    • , Toshinori Kinoshita
    • , Kenichiro Itami
    • , Shinya Hagihara
    •  & Keiko U Torii
  3. Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.

    • Takaho A Endo
  4. Department of Bioresource and Environmental Sciences, Kyoto Sangyo University, Kyoto, Japan.

    • Seisuke Kimura
  5. Center for Gene Research, Nagoya University, Chikusa, Nagoya, Japan.

    • Yasuomi Tada
  6. PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.

    • Shinya Hagihara
  7. Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA.

    • Keiko U Torii
  8. Department of Biology, University of Washington, Seattle, Washington, USA.

    • Keiko U Torii


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K.U.T. conceived the project; N.U., S.H., K.T. and K.U.T. designed research; N.U. and R.I. performed molecular cloning, yeast two-hybrid assays, and transgenic plants generation; N.U., R.I., and K.T. conducted qRT-PCR and phenotypic characterization; S.H., H.Z., R.Y., and M.Y. performed synthesis and NMR analyses of auxin analogs; K.T. performed biochemical analyses; S.K. performed next generation sequencing, and S.K., N.U. and T.A.E. performed bioinformatics; T.A.E. developed the Bobbin Dendrogram Plot Generator; M.N. and Y.T. provided reagents; N.U., S.H., K.T., T.K., K.I., and K.U.T. analyzed data; K.U.T. performed R-drc analysis; K.U.T., N.U., K.T., and S.H. wrote the manuscript; all authors read and approved the manuscript.

Competing interests

The cvxIAA–ccvTIR1 system reported here has been filed for a US provisional patent (No. 62/468642) in which N.U., R.I., K.I., S.H., and K.U.T. appear as inventors.

Corresponding authors

Correspondence to Shinya Hagihara or Keiko U Torii.

Supplementary information

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  1. 1.

    Supplementary Text and Figures

    Supplementary Tables 1–3, Supplementary Figures 1–14

  2. 2.

    Reporting Summary

  3. 3.

    Supplementary Note 1

    Synthetic procedures

Excel files

  1. 1.

    Supplementary Data Set 1

    Differentially expressed genes in wild type, 35S::TIR1 and 35S::ccvTIR1 by IAA and cvxIAA treatments

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