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Cryo-EM structure and molecular mechanism of the jasmonic acid transporter ABCG16

Nature Plants volume 10, pages 2052–2061 (2024)Cite this article

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Abstract

Jasmonates (JAs) are a class of oxylipin phytohormones including jasmonic acid (JA) and derivatives that regulate plant growth, development and biotic and abiotic stress. A number of transporters have been identified to be responsible for the cellular and subcellular translocation of JAs. However, the mechanistic understanding of how these transporters specifically recognize and transport JAs is scarce. Here we determined the cryogenic electron microscopy structure of JA exporter AtABCG16 in inward-facing apo, JA-bound and occluded conformations, and outward-facing post translocation conformation. AtABCG16 structure forms a homodimer, and each monomer contains a nucleotide-binding domain, a transmembrane domain and an extracellular domain. Structural analyses together with biochemical and plant physiological experiments revealed the molecular mechanism by which AtABCG16 specifically recognizes and transports JA. Structural analyses also revealed that AtABCG16 features a unique bifurcated substrate translocation pathway, which is composed of two independent substrate entrances, two substrate-binding pockets and a shared apoplastic cavity. In addition, residue Phe608 from each monomer is disclosed to function as a gate along the translocation pathway controlling the accessing of substrate JA from the cytoplasm or apoplast. Based on the structural and biochemical analyses, a working model of AtABCG16-mediated JA transport is proposed, which diversifies the molecular mechanisms of ABC transporters.

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Fig. 1: Activity and overall structure of Arabidopsis ABCG16.
Fig. 2: Substrate-binding of AtABCG16.
Fig. 3: Coupled conformational change between NBD and TMD.
Fig. 4: Bifurcated substrate translocation pathway.
Fig. 5: Substrate translocation model.

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Data availability

The 3D cryo-EM density maps of AtABCG16 have been deposited in the Electron Microscopy Data Bank under the accession numbers EMD-37836, EMD-37837, EMD-37838, EMD-37839, EMD-37840 and EMD-39461, respectively. Coordinates for structure models have been deposited in the Protein Data Bank under the accession codes 8WTM, 8WTN, 8WTO and 8WTP, respectively. The protein sequence of A. thaliana ABCG16 is publicly available at Uniprot with accession code Q9M2V7. Source data are provided with this paper.

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Acknowledgements

We thank the Centre for Excellence in Molecular Plant Sciences core facility centre for mass spectrometry analysis, confocal analysis and diagnostic cryo-EM analysis. We thank H. Zhao and X. Zhang at the cryo-EM centre of Fudan University, M. Zhang at the cryo-EM centre of the Chinese Academy of Sciences interdisciplinary Research Centre on Biology and Chemistry, and L. Qi at the cryo-EM centre of Shandong University for their technical assistance on cryo-EM data collection. This work was supported by grants from the National Natural Science Foundation of China (32025020, 32230050 to P.Z. and 32100961 to X.Z.) and the Chinese Academy of Sciences (XDB0630100 to P.Z.) and grants from Shanghai Science and Technology Commission (23310710100).

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  1. These authors contributed equally: Ning An, Xiaowei Huang.

Authors and Affiliations

  1. National Key Laboratory of Plant Molecular Genetics, Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China

    Ning An, Xiaowei Huang, Zhao Yang, Minhua Zhang, Miaolian Ma, Lianyan Jing, Boya Du, Yong-Fei Wang, Xue Zhang & Peng Zhang

  2. Key Laboratory of Plant Carbon Capture, Chinese Academy of Sciences, Shanghai, China

    Ning An, Zhao Yang, Miaolian Ma, Xue Zhang & Peng Zhang

  3. University of Chinese Academy of Sciences, Beijing, China

    Ning An & Boya Du

  4. Shanghai Normal University, Shanghai, China

    Fang Yu

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Contributions

N.A., X.H., X.Z. and P.Z. designed the experiments. N.A. and X.H. carried out protein expression and purification, sample preparation, biochemical analysis and transport assay. X.Z. and X.H. carried out cryo-EM data collection and structure determination. Z.Y. and M.Z. contributed to grid sample preparation and diagnostic cryo-EM analysis. M.M. and F.Y. contributed to protein purification. L.J., B.D. and Y.-F.W. contributed to transport assay and mass spectrometry analysis. P.Z. and X.Z. wrote the manuscript with inputs from other authors.

Corresponding authors

Correspondence to Xue Zhang or Peng Zhang.

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Extended data

Extended Data Fig. 1 Transport activity assay of AtABCG16 in Xenopus oocytes.

a, GFP fluorescence indicates the expression of genes encoding N-terminal GFP tagged AtABCG16 on the membrane of Xenopus oocytes. Water was used as a control. The oocytes used for transporter assay analysis were selected based on the GFP fluence level, which indicates the protein expression amount of AtABCG16. Independent experiments have been repeated three times with similar results. Bar = 200 μm. b, Procedure of the transport activity assay.

Extended Data Fig. 2 ATPase activity of AtABCG16.

a-b, ATPase activity of AtABCG16 purified in buffer containing 0.05% digitonin (n = 4) (a) and 0.01% LMNG + 0.001% CHS + 0.0033% GDN (n = 3 for protein incubate with 0.6, 1.0 and 6.0 mM ATP; n = 4 for protein incubate with 0.1, 0.2, 0.4, 1.5, 2.0, 3.0, 4.0 and 5.0 mM ATP) (b). c-f, Effect of substrate addition on the ATPase activity of AtABCG16 purified in buffer containing 0.05% digitonin (n = 3 for protein incubate with 12.5 μM JA; n = 4 for protein incubate with 3, 6, 25, 50, 125 μM JA.) (c), 0.01% LMNG + 0.001% CHS + 0.0033% GDN (n = 3) (d), and reconstituted in nanodiscs (n = 3) (e) and liposomes (n = 3) (f). Error bars are mean ± s.e.m.

Source data.

Extended Data Fig. 3 Cryo-EM analysis of AtABCG16inward-JA.

a, Gel filtration profile of a Superdex-200 column and Coomassie-blue-stained SDS-PAGE analysis of AtABCG16 in buffer containing 0.05% digitonin. Independent experiments have been repeated at least three times with similar results. b, Representative micrograph. c, 2D class averages. d, cryo-EM data analysis pipeline. e, Local resolution estimation and gold-standard Fourier shell correlation (FSC) curves. The color represents the local resolution in Å. f, cryo-EM density of representative segments superimposed with the atomic model (map contour level = 6σ) Source data.

Extended Data Fig. 4 Cryo-EM analysis of AtABCG16outward-open.

a, Gel filtration profile of a Superose 6 column and Coomassie-blue-stained SDS-PAGE analysis of AtABCG16 in buffer containing 0.01% LMNG + 0.001% CHS + 0.0033% GDN. Independent experiments have been repeated at least three times with similar results. b, Representative micrograph. c, 2D class averages. d, cryo-EM data analysis pipeline. e, Local resolution estimation and gold-standard Fourier shell correlation (FSC) curves. The color represents the local resolution in Å. f, cryo-EM density of representative segments superimposed with the atomic model (map contour level = 6σ).

Extended Data Fig. 5 Cryo-EM analysis of AtABCG16occluded.

a, Gel filtration profile of a Superose 6 column and Coomassie-blue-stained SDS-PAGE analysis of AtABCG16 in buffer containing 0.01% LMNG + 0.001% CHS + 0.0033% GDN. Independent experiments have been repeated at least three times with similar results. b, Representative micrograph. c, 2D class averages. d, cryo-EM data analysis pipeline. e, Local resolution estimation and gold-standard Fourier shell correlation (FSC) curves. The color represents the local resolution in Å. f, cryo-EM density of representative segments superimposed with the atomic model (map contour level = 6σ).

Extended Data Fig. 6 Cryo-EM analysis of AtABCG16apo.

a, Gel filtration profile of a Superose 6 column and Coomassie-blue-stained SDS-PAGE analysis of AtABCG16 in buffer containing 0.01% LMNG + 0.001% CHS + 0.0033% GDN. Independent experiments have been repeated at least three times with similar results. b, Representative micrograph. c, 2D class averages. d, cryo-EM data analysis pipeline. e, Local resolution estimation and gold-standard Fourier shell correlation (FSC) curves. The color represents the local resolution in Å. f, cryo-EM density of representative segments superimposed with the atomic model (map contour level = 6σ).

Extended Data Fig. 7 Substrate-binding sites of AtABCG16.

a-b, Cryo-EM densities of JA-binding sites superimposed with the atomic model in C2-symmetry and C1-symmetry map (contour level = 7σ). JA molecules are shown as yellow sticks. c-f, Cryo-EM densities of substrate-binding sites in AtABCG16inward-JA (c), AtABCG16apo (d), AtABCG16apo-dig (e) and AtABCG16JA-Ile (f) at different contour levels. g-i, ABA molecule modeled in the substrate-binding site of AtABCG16inward-JA structure. ABA molecule is shown as green stick, and steric clashes are shown as red dashes.

Extended Data Fig. 8 Cryo-EM map of AtABCG16JA-Ile.

a, Cryo-EM map of AtABCG16JA-Ile. Densities in the substrate-binding pocket are zoomed in and colored in yellow. b, Chemical structures of JA and JA-Ile. c, JA and JA-Ile molecules are modeled in the density separately.

Extended Data Fig. 9 NBD bound to different γ-phosphate analogues.

a, Two NBDs of AtABCG16outward-open are shown as ribbons colored in blue and orange. b, A zoom-in view showing the coordination of ADP-BeF3 in a. Mg2+ and water molecules are shown as magenta and red spheres. c, Density map of ADP-BeF3, Mg2+ and water molecules in AtABCG16outward-open (map contour level = 6σ). d, Two NBDs of AtABCG16occluded are shown as ribbons colored in purple and pink. e, A zoom-in view showing the coordination of ADP-VO4 in d. f, Density map of ADP-VO4 in AtABCG16occluded (map contour level = 3σ).

Extended Data Fig. 10

Structure and substrate-binding of the representative ABC transporters.

Supplementary information

Supplementary Information

Supplementary Fig. 1 and Table 1.

Reporting Summary

Source data

Source Data Fig. 1

Statistical source data.

Source Data Fig. 2

Statistical source data.

Source Data Extended Data Fig. 2

Statistical source data.

Source Data Extended Data Fig. 3

Full-length unprocessed sodium dodecyl sulfate–polyacrylamide gel electrophoresis.

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An, N., Huang, X., Yang, Z. et al. Cryo-EM structure and molecular mechanism of the jasmonic acid transporter ABCG16. Nat. Plants 10, 2052–2061 (2024). https://doi.org/10.1038/s41477-024-01839-0

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