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Gibberellin-induced DELLA recognition by the gibberellin receptor GID1

Abstract

Gibberellins control a range of growth and developmental processes in higher plants and have been widely used in the agricultural industry. By binding to a nuclear receptor, GIBBERELLIN INSENSITIVE DWARF1 (GID1), gibberellins regulate gene expression by promoting degradation of the transcriptional regulator DELLA proteins, including GIBBERELLIN INSENSITIVE (GAI). The precise manner in which GID1 discriminates and becomes activated by bioactive gibberellins for specific binding to DELLA proteins remains unclear. Here we present the crystal structure of a ternary complex of Arabidopsis thaliana GID1A, a bioactive gibberellin and the amino-terminal DELLA domain of GAI. In this complex, GID1A occludes gibberellin in a deep binding pocket covered by its N-terminal helical switch region, which in turn interacts with the DELLA domain containing DELLA, VHYNP and LExLE motifs. Our results establish a structural model of a plant hormone receptor that is distinct from the mechanism of the hormone perception and effector recognition of the known auxin receptors.

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Figure 1: Structure of the GA 3 –GID1A–DELLA complex.
Figure 2: Architecture of GID1A.
Figure 3: Recognition of GA 3 by GID1A.
Figure 4: Architecture of the DELLA domain of GAI.
Figure 5: Recognition of the DELLA domain by GID1A.
Figure 6: A model of GA-regulated GID1–DELLA protein interactions.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Structure coordinates and structural factors are deposited in the Protein Data Bank under accession numbers 2ZSH (GA3–GID1A–DELLA) and 2ZSI (GA4–GID1A–DELLA).

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Acknowledgements

We thank S. Terawaki and T. Mori for technical advice and J. Tsukamoto for technical support in performing the matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy analysis, and the beamline staff of BL41XU of SPring-8 at Harima for help with the data collection. We also acknowledge A. Isogai for advice and encouragement. This work was supported by a research grant in the natural sciences from the Mitsubishi Foundation, Japan (to T.H.), and in part by a Grant-in-Aid for Scientific Research (A) and Scientific Research on Priority Areas from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan (to T.H.). This work was also supported in part by grants from the National Science Foundation of the United States (IBN-0348814 to T.-p.S.). K.M. is a recipient of a postdoctoral fellowship for Young Scientists from the Japan Society for the Promotion of Science and an international research fellowship from the Global COE Program in NAIST (Frontier Biosciences: strategies for survival and adaptation in a changing global environment) from MEXT of Japan.

Author Contributions K.M., T.-p.S. and T.H. conceived and designed the project. T.-p.S. provided all cDNA and constructs as well as expertise in the GA signalling mechanism. Y.H., K.M. and T.H. were responsible for construct design for protein preparation. K.M. was responsible for subcloning and execution of protein biochemistry, crystallization and data collection, helped by Y.H. and directed by T.H. Y.H. solved and refined the complex structures. K.M. performed binding studies with GID1A and DELLA variants, as well as circular dichroism measurements, directed by Y.H. Y.H, K.M. and T.H. interpreted data and T.H. wrote the manuscript.

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Correspondence to Toshio Hakoshima.

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Murase, K., Hirano, Y., Sun, Tp. et al. Gibberellin-induced DELLA recognition by the gibberellin receptor GID1. Nature 456, 459–463 (2008). https://doi.org/10.1038/nature07519

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