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Chemical hijacking of auxin signaling with an engineered auxin–TIR1 pair

Nature Chemical Biology volume 14, pages 299–305 (2018)Cite this article

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Abstract

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.

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Figure 1: Engineering cvxIAA-ccvTIR1 pair by a bump-and-hole approach.
Figure 2: cvxIAA, but not active auxins, promotes the association of ccvTIR1 and IAA7DII peptide.
Figure 3: cvxIAA triggers global auxin-induced gene expression only in the seedlings expressing the engineered ccvTIR1.
Figure 4: cvxIAA inhibits root elongation and induces auxin-induced lateral root development only in the seedlings expressing the engineered ccvTIR1.
Figure 5: Hypocotyl acid growth mediated by the synthetic cvxIAA and an engineered ccvTIR1 pair.

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Acknowledgements

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.

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Author notes

  1. Naoyuki Uchida and Koji Takahashi: These authors contributed equally to this work.

Authors and Affiliations

  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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  1. Naoyuki Uchida
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Contributions

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.

Corresponding authors

Correspondence to Shinya Hagihara or Keiko U Torii.

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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.

Supplementary information

Supplementary Text and Figures

Supplementary Tables 1–3, Supplementary Figures 1–14 (PDF 2824 kb)

Reporting Summary (PDF 130 kb)

Supplementary Note 1

Synthetic procedures (PDF 5619 kb)

Supplementary Data Set 1

Differentially expressed genes in wild type, 35S::TIR1 and 35S::ccvTIR1 by IAA and cvxIAA treatments (XLSX 230 kb)

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Uchida, N., Takahashi, K., Iwasaki, R. et al. Chemical hijacking of auxin signaling with an engineered auxin–TIR1 pair. Nat Chem Biol 14, 299–305 (2018). https://doi.org/10.1038/nchembio.2555

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