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Structure and activation mechanism of the rice Salt Overly Sensitive 1 (SOS1) Na+/H+ antiporter

Nature Plants volume 9, pages 1924–1936 (2023)Cite this article

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Abstract

Salinity is one of the most severe abiotic stresses that adversely affect plant growth and agricultural productivity. The plant Na+/H+ antiporter Salt Overly Sensitive 1 (SOS1) located in the plasma membrane extrudes excess Na+ out of cells in response to salt stress and confers salt tolerance. However, the molecular mechanism underlying SOS1 activation remains largely elusive. Here we elucidate two cryo-electron microscopy structures of rice (Oryza sativa) SOS1, a full-length protein in an auto-inhibited state and a truncated version in an active state. The SOS1 forms a dimeric architecture, with an NhaA-folded transmembrane domain portion in the membrane and an elongated cytosolic portion of multiple regulatory domains in the cytoplasm. The structural comparison shows that SOS1 adopts an elevator transport mechanism accompanied by a conformational transition of the highly conserved Pro148 in the unwound transmembrane helix 5 (TM5), switching from an occluded conformation in the auto-inhibited state to a conducting conformation in the active state. These findings allow us to propose an inhibition–release mechanism for SOS1 activation and elucidate how SOS1 controls Na+ homeostasis in response to salt stress.

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Fig. 1: Architecture of the OsSOS1.
Fig. 2: Structural domains of the OsSOS1.
Fig. 3: Domain interfaces in the OsSOS1.
Fig. 4: Auto-inhibitory motifs in the OsSOS1.
Fig. 5: Structure of the constitutively active SOS1976.
Fig. 6: The activation model of OsSOS1.

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Data availability

All data generated or analysed in this paper are presented in the main text, figures, extended data figures and supplementary videos or are available from the corresponding author upon request. The cryo-EM maps of the OsSOS1 full-length (OsSOS1FL) and truncated versions (OsSOS1976) have been deposited in the Electron Microscopy Data Bank with accession codes EMD-35775 and EMD-35950, respectively, and their structural models have been deposited in the PDB with accession codes 8IWO and 8J2M, respectively (Extended Data Table 1). Source data are provided with this paper.

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Acknowledgements

This project is financially supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA24020305 to Y.C.) and the National Key Research and Development Program of China (2020YFA0509903 to Y.C. and 2021YFA1300702 to M.S.).

Author information

Author notes

  1. These authors contributed equally: Xiang-yun Zhang, Ling-hui Tang, Jia-wei Nie, Chun-rui Zhang, Xiaonan Han.

Authors and Affiliations

  1. State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China

    Xiang-yun Zhang, Ling-hui Tang, Jia-wei Nie, Chun-rui Zhang, Qi-yu Li, Li Qin, Mei-hua Wang, Xiahe Huang, Min Su, Yingchun Wang & Yu-hang Chen

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

    Xiang-yun Zhang, Ling-hui Tang, Jia-wei Nie, Chun-rui Zhang, Qi-yu Li, Li Qin, Mei-hua Wang, Yingchun Wang, Rui-ming Xu, Qi Xie & Yu-hang Chen

  3. National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China

    Xiaonan Han & Rui-ming Xu

  4. College of Grassland Science and Technology, China Agricultural University, Beijing, China

    Feifei Yu

  5. State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China

    Yan Guo

  6. State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China

    Qi Xie

  7. National Center of Technology Innovation for Maize, State Key Laboratory of Crop Germplasm Innovation and Molecular Breeding, Syngenta Group China, Beijing, China

    Qi Xie

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Contributions

X.Z. performed protein purification, cryo-EM data collection, yeast experiments and data analysis; L.T. and X. Han performed cryo-EM data collection, structural determination and structural analysis; C.Z. performed model building, structural analysis and sequence analysis; J.N., X. Han, Q.L., X. Huang, L.Q. and M.W. performed experiments; F.Y., M.S., R.X., Y.W., Y.G. and Q.X. analysed data; Y.C. initiated the project, planned and analysed experiments, supervised the research and wrote the manuscript with input from all authors.

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Correspondence to Yu-hang Chen.

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Nature Plants thanks Jose M. Pardo, Huazhong Shi and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Structure-based sequence alignments for the representative SOS1s from both dicots and monocots.

The cryo-EM structure of OsSOS1 is used to restrict sequence gaps to inter-helical segments, with the superior coils and arrows defining extents of the secondary elements. The sequences include representative members from dicots and monocots: Oryza sativa Japonica Group (XP_015619351.1), Zea mays (XP_008645741.2), Sorghum bicolor (XP_002443674.1), Aegilops tauschii (XP_020190641.1), Brachypodium distachyon (XP_003576505.1), Dendrobium officinale (XP_020699162.1), Asparagus officinalis (XP_020256864.1), Musa acuminata subsp. malaccensis (XP_018686090.1), Phoenix dactylifera (XP_008798100.1), Amborella trichopoda (XP_006849492.1), Arabidopsis thaliana (NP_178307.2), Brassica rapa (XP_009114217.1), Eutrema salsugineum (XP_006395824.1), Beta vulgaris subsp. vulgaris (XP_010680103.2), Glycine max (NP_001244939.1), Daucus carota (XP_017226136.1), Cucumis melo (XP_008466844.1), Vitis vinifera (NP_001268140.1), Juglans regia (XP_018828660.1), Eucalyptus grandis (XP_010066529.2). The highly conserved inhibitory motifs (motif-1 and motif-2) are shown in boxes. Some critical residues are highlighted as following: 1. The putative phosphorylation residues are highlighted in cyan (S1113 and S1135 in OsSOS1). 2. The mutated residues are highlighted in yellow.

Extended Data Fig. 2 Structural determination of the OsSOS1FL.

(a) The workflow for image processing of the OsSOS1FL. 2D classification of the OsSOS1FL particles from the cryo-EM sample are shown. (b) Fourier shell correlation (FSC) curve suggests an overall resolution at 3.1 Å, as estimated using the 0.143 cut-off criterion (Left). The FSC curves for cross-validation between the model and the unmasked (Black) or masked (Pink) cryo-EM maps of OsSOS1 (Right). (c) Representative cryo-EM density map for the TM segments of TMD, helical elements of HD, CNBD, CTD and auto-inhibitory motif segments.

Extended Data Fig. 3 Structural determination of the OsSOS1976.

(a) The workflow for image processing of the OsSOS1976. 2D classification ns of the OsSOS1976 particles from the cryo-EM sample are shown. (b) Fourier shell correlation (FSC) curve suggests an overall resolution at 3.4 Å, as estimated using the 0.143 cut-off criterion (Left). The FSC curves for cross-validation between the model and the unmasked (Black) or masked (Pink) cryo-EM maps of OsSOS1976 (Right). (c) Representative cryo-EM density map for the TM segments of the TMD.

Extended Data Fig. 4 Domain organization of OsSOS1 and Salt tolerance assay.

(a) Ribbons drawing of the OsSOS1 protomer is shown, orientated as in Fig. 1a. (b) Salt tolerance assay of the OsSOS1 and its C-terminal truncated mutants in the Na+-extrusion defective yeast cells (S. cerevisiae AXT3K).

Extended Data Fig. 5 Structural analysis of the TMD of the OsSOS1.

(a) Superimposition of the TMD (OsSOS1, as colored in Fig. 2a) with archaeal Na+/H+ exchanger NhaP from Pyrococcus abyssii (pink), with an r.m.s.d. of 2.6 Å/386 superimposed Ca and 20% sequence identity. (b) Superimposition of the TMD (OsSOS1, as colored in Fig. 2a) with human Na+/H+ exchanger HsNHE1 from (light purple), with an r. m. s. d. of 2.9 Å/389 superimposed Ca and 26% sequence identity. (c) Cavities within the TMD. Zoom view are shown, as indicated. Two endogenously bound lipid molecules at the dimeric interface are shown as sticks. (d) A conserved inter-helices salt bridge (R341 vs E171) and a kink (~18°) at the middle of TM4 in the TMD.

Extended Data Fig. 6 Structural analysis of the HD of the OsSOS1.

(a) Ribbons drawing and domain topology of the OsSOS1 HD, with one protomer in green and the other in grey. (b) Electrostatic potential at helical domain surface. Electronegative and electropositive potential are colored in degrees of red and blue saturation, respectively. One protomer is drawn as ribbon diagram, and colored in green. Highly conserved charged residues at the dimeric HD interface and ion-conducting pathway are shown in stick. Two conserved glycine-mediate kinks, H6 (~35°) and H7 (~34°), are indicated.

Extended Data Fig. 7 Structure-based sequence alignment of CNBDs.

The structures for both CNBDs (OsSOS1 and HCN) have been superimposed and used to restrict sequence gaps to inter-secondary structural elements. Superior coils and arrows define extents of the secondary structural elements in OsSOS1 CNBD (top) and HCN CNBD (bottom). Two loss-of-function mutations in the b-roll structure of the CNBD, including G777D (sos1-8) and G784E (sos1-9), led to impaired transport function in Arabidopsis are highlighted in magenta. The residues critical for cAMP binding in the HCN CNBD are highlighted in cyan.

Extended Data Fig. 8 Structural analysis of the domain interfaces.

(a) The TMD-HD domain interface. The dimeric TMD is shown in ribbon drawing, with one protomer in light blue and the other one in grey. The dimeric HD is shown as surface, colored with electrostatic potential. Electronegative and electropositive potential are shown in degrees of red and blue saturation, respectively. (b) Domain organization of TMD (light bule) and HD (salmon), with a dihedral angle of ~26°. (c) The HD-CNBD domain interface. The dimeric HD is shown in ribbon drawing, with one protomer in green and the other one in grey. The CNBD-CTD is shown as surface, colored with electrostatic potential. Electronegative and electropositive potential are shown in degrees of red and blue saturation, respectively.

Extended Data Fig. 9 Comparison of the truncated OsSOS1976 with the auto-inhibited OsSOS1FL.

(a, b) The elution profile of the truncated SOS1976 (magenta) and the full-length OsSOS1FL (sky-blue) on size-exclusion column Superose 6 (Increase 10/300 GL). The truncated SOS1976 elutes at 13.8 ml, whereas the full-length OsSOS1FL elutes at 14.3 ml. The high-molecular weight aggregates elute at avoid volume are indicated with *. The eluted fraction were analyzed by SDS-PAGE. (c) The superimposition of the auto-inhibited OsSOS1FL structure and the truncated SOS1976 structure, based on their dimeric TMD portions (with an r.m.s.d. of 2.38 Å/848 superimposed Ca), reveals distinctive structural differences occurred in the cytoplasmic regions. The structure of the truncated SOS1976 is represented as a density map, with the TMD portion depicted in purple and the unmodeled cytoplasmic portion in gray. The cytosolic portion of the OsSOS1FL is represented in cartoon format (light blue). This comparison highlights a substantial conformational change upon SOS1 activation. The masks of the detergent boundary are illustrated in white.

Extended Data Table 1 Statistics of data collection, image processing, and model building
Full size table

Supplementary information

Reporting Summary

Supplementary Video 1

Comparison of plant SOS1, SOS1FL (PDB ID: 8IWO, auto-inhibited state) versus SOS1976(PDB ID: 8J2M, active).

Supplementary Video 2

Comparison of human HsNHE1, occluded conformation (PDB ID: 7dsx) versus conducting conformation (PDB ID: 7dsv).

Supplementary Data 1

Validation report for the full-length SOS1FL (auto-inhibited state).

Supplementary Data 2

Validation report for the truncated SOS1976 (constitutively active state).

Source data

Source Data Fig. 1

Unprocessed size-exclusion profile and SDS–PAGE gels for ED-9a/b.

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Zhang, Xy., Tang, Lh., Nie, Jw. et al. Structure and activation mechanism of the rice Salt Overly Sensitive 1 (SOS1) Na+/H+ antiporter. Nat. Plants 9, 1924–1936 (2023). https://doi.org/10.1038/s41477-023-01551-5

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