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Structural basis of abscisic acid signalling

Nature volume 462, pages 609–614 (2009)Cite this article

Abstract

The phytohormone abscisic acid (ABA) mediates the adaptation of plants to environmental stresses such as drought and regulates developmental signals such as seed maturation. Within plants, the PYR/PYL/RCAR family of START proteins receives ABA to inhibit the phosphatase activity of the group-A protein phosphatases 2C (PP2Cs), which are major negative regulators in ABA signalling. Here we present the crystal structures of the ABA receptor PYL1 bound with (+)-ABA, and the complex formed by the further binding of (+)-ABA-bound PYL1 with the PP2C protein ABI1. PYL1 binds (+)-ABA using the START-protein-specific ligand-binding site, thereby forming a hydrophobic pocket on the surface of the closed lid. (+)-ABA-bound PYL1 tightly interacts with a PP2C domain of ABI1 by using the hydrophobic pocket to cover the active site of ABI1 like a plug. Our results reveal the structural basis of the mechanism of (+)-ABA-dependent inhibition of ABI1 by PYL1 in ABA signalling.

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Figure 1: (+)-ABA-binding specificity and (+)-ABA-dependent interaction of PYL1 with ABI1.
Figure 2: Overall structure of (+)-ABA-bound PYL1.
Figure 3: (+)-ABA recognition by PYL1.
Figure 4: Overall structure of the PYL1–(+)-ABA–ABI1 complex.
Figure 5: Recognition and inhibition of ABI1 by PYL1.
Figure 6: A model of (+)-ABA-induced ABI1 regulation by PYL1.

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Accession codes

Primary accessions

Protein Data Bank

Data deposits

Structure coordinates and structural factors are deposited in the Protein Data Bank under accession numbers 3JRS (PYL1–(+)-ABA) and 3JRQ (PYL1–(+)-ABA–ABI1).

References

  1. Boudsocq, M., Barbier-Brygoo, H. & Laurière, C. Identification of nine sucrose nonfermenting 1-related protein kinases 2 activated by hyperosmotic and saline stresses in Arabidopsis thaliana . J. Biol. Chem. 279, 41758–41766 (2004)

    Article  CAS  Google Scholar 

  2. Kobayashi, Y., Yamamoto, S., Minami, H., Kagaya, Y. & Hattori, T. Differential activation of the rice sucrose nonfermenting 1-related protein kinase 2 family by hyperosmotic stress and abscisic acid. Plant Cell 16, 1163–1177 (2004)

    Article  CAS  Google Scholar 

  3. Mustilli, A., Merlot, S., Vavasseur, A., Fenzi, F. & Giraudat, J. Arabidopsis OST1 protein kinase mediates the regulation of stomatal aperture by abscisic acid and acts upstream of reactive oxygen species production. Plant Cell 14, 3089–3099 (2002)

    Article  CAS  Google Scholar 

  4. Yoshida, R. et al. ABA-activated SnRK2 protein kinase is required for dehydration stress signaling in Arabidopsis . Plant Cell Physiol. 43, 1473–1483 (2002)

    Article  CAS  Google Scholar 

  5. Fujii, H. & Zhu, J. Arabidopsis mutant deficient in 3 abscisic acid-activated protein kinases reveals critical roles in growth, reproduction, and stress. Proc. Natl Acad. Sci. USA 106, 8380–8385 (2009)

    Article  ADS  CAS  Google Scholar 

  6. Nakashima, K. et al. Three Arabidopsis SnRK2 protein kinases, SRK2D/SnRK2.2, SRK2E/SnRK2.6/OST1 and SRK2I/SnRK2.3, involved in ABA signaling are essential for the control of seed development and dormancy. Plant Cell Physiol. 50, 1345–1363 (2009)

    Article  CAS  Google Scholar 

  7. Furihata, T. et al. Abscisic acid-dependent multisite phosphorylation regulates the activity of a transcription activator AREB1. Proc. Natl Acad. Sci. USA 103, 1988–1993 (2006)

    Article  ADS  CAS  Google Scholar 

  8. Fujii, H., Verslues, P. & Zhu, J. Identification of two protein kinases required for abscisic acid regulation of seed germination, root growth, and gene expression in Arabidopsis . Plant Cell 19, 485–494 (2007)

    Article  CAS  Google Scholar 

  9. Hirayama, T. & Shinozaki, K. Perception and transduction of abscisic acid signals: keys to the function of the versatile plant hormone ABA. Trends Plant Sci. 12, 343–351 (2007)

    Article  CAS  Google Scholar 

  10. Park, S. et al. Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins. Science 324, 1068–1071 (2009)

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  11. Pennisi, E. Plant biology. Stressed out over a stress hormone. Science 324, 1012–1013 (2009)

    Article  CAS  Google Scholar 

  12. Ma, Y. et al. Regulators of PP2C phosphatase activity function as abscisic acid sensors. Science 324, 1064–1068 (2009)

    ADS  CAS  PubMed  Google Scholar 

  13. Lee, B. & Richards, F. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55, 379–400 (1971)

    Article  CAS  Google Scholar 

  14. Tanokura, M. & Yamada, K. Heat capacity and entropy changes of calmodulin induced by calcium binding. J. Biochem. 95, 643–649 (1984)

    Article  CAS  Google Scholar 

  15. Tanokura, M. & Yamada, K. A calorimetric study of Ca2+ binding by wheat germ calmodulin. Regulatory steps driven by entropy. J. Biol. Chem. 268, 7090–7092 (1993)

    CAS  PubMed  Google Scholar 

  16. Das, A., Helps, N., Cohen, P. & Barford, D. Crystal structure of the protein serine/threonine phosphatase 2C at 2.0 Å resolution. EMBO J. 15, 6798–6809 (1996)

    Article  CAS  Google Scholar 

  17. Meyer, K., Leube, M. & Grill, E. A protein phosphatase 2C involved in ABA signal transduction in Arabidopsis thaliana . Science 264, 1452–1455 (1994)

    Article  ADS  CAS  Google Scholar 

  18. Leung, J. et al. Arabidopsis ABA response gene ABI1: features of a calcium-modulated protein phosphatase. Science 264, 1448–1452 (1994)

    Article  ADS  CAS  Google Scholar 

  19. Koornneef, M., Reuling, G. & Karssen, C. The isolation and characterization of abscisic acid-insensitive mutants of Arabidopsis thaliana . Physiol. Plant. 61, 377–383 (1984)

    Article  CAS  Google Scholar 

  20. Kabsch, W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallogr. 26, 795–800 (1993)

    Article  CAS  Google Scholar 

  21. Matthews, B. W. Solvent content of protein crystals. J. Mol. Biol. 33, 491–497 (1968)

    Article  CAS  Google Scholar 

  22. Schneider, T. & Sheldrick, G. Substructure solution with SHELXD. Acta Crystallogr. D 58, 1772–1779 (2002)

    Article  Google Scholar 

  23. Bricogne, G., Vonrhein, C., Flensburg, C., Schiltz, M. & Paciorek, W. Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0. Acta Crystallogr. D 59, 2023–2030 (2003)

    Article  CAS  Google Scholar 

  24. Terwilliger, T. Automated main-chain model building by template matching and iterative fragment extension. Acta Crystallogr. D 59, 38–44 (2003)

    Article  Google Scholar 

  25. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53, 240–255 (1997)

    Article  CAS  Google Scholar 

  26. McRee, D. E. XtalView/Xfit–A versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125, 156–165 (1999)

    Article  CAS  Google Scholar 

  27. Lovell, S. C. et al. Structure validation by Cα geometry: φ,ψ and Cβ deviation. Proteins 50, 437–450 (2003)

    Article  CAS  Google Scholar 

  28. Delaglio, F. et al. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277–293 (1995)

    Article  CAS  Google Scholar 

  29. Johnson, B. Using NMRView to visualize and analyze the NMR spectra of macromolecules. Methods Mol. Biol. 278, 313–352 (2004)

    CAS  Google Scholar 

Download references

Acknowledgements

The synchrotron-radiation experiments were performed at BL5A in the Photon Factory (2008S2-001). This work was supported by the Targeted Proteins Research Program (TPRP) of the Ministry of Education, Culture, Sports, Science, and Technology, Japan. We thank Y. Sakaguchi (DKSH Japan K.K.) and Y. Asami (TA Instruments Japan Inc.) for the ITC measurements and T. Mitani (GE Healthcare Japan Corp.) for the SPR experiments.

Author Contributions M. Tanokura conceived and designed the project. K.-i.M., T.M., Y.S. and K. Kubota performed the construct design, subcloning, protein expression, purification, crystallization, structure determination and all biochemical assays. H.-J.K., A.A., Y.M, M. Takahashi and Y.Z. also assisted in the subcloning, protein expression, purification and crystallization. Y.F., T.Y. and K. Kodaira performed the cloning. K.-i.M., T.M., Y.S, K. Kubota, K.Y.-S. and M. Tanokura wrote the manuscript and M. Tanokura edited the manuscript.

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Author notes

  1. Ken-ichi Miyazono, Takuya Miyakawa, Yoriko Sawano and Keiko Kubota: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan

    Ken-ichi Miyazono, Takuya Miyakawa, Yoriko Sawano, Keiko Kubota, Hee-Jin Kang, Atsuko Asano, Yumiko Miyauchi, Mihoko Takahashi, Yuehua Zhi & Masaru Tanokura

  2. Biological Resources Division, Japan International Research Center for Agricultural Sciences, Ibaraki 305-8686, Japan

    Yasunari Fujita, Takuya Yoshida, Ken-Suke Kodaira & Kazuko Yamaguchi-Shinozaki

  3. Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan

    Takuya Yoshida, Ken-Suke Kodaira & Kazuko Yamaguchi-Shinozaki

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Correspondence to Masaru Tanokura.

Supplementary information

Supplementary Information

This file contains Supplementary Results and Discussion, Supplementary References, Supplementary Tables 1 - 2 and Supplementary Figures 1 - 8 with Legends. This file was replaced on 24 December 2009 to correct minor errors in Supplementary Table 1. (PDF 4241 kb)

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Miyazono, Ki., Miyakawa, T., Sawano, Y. et al. Structural basis of abscisic acid signalling . Nature 462, 609–614 (2009). https://doi.org/10.1038/nature08583

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