Abstract
Retrograde transport is central to endomembrane homeostasis, yet the identity and origin of plant retrograde carriers remain unresolved. Prevailing models propose that plant vacuolar sorting receptors (VSRs) recycle either from multivesicular bodies (MVBs) to the trans-Golgi network (TGN) or from the TGN to the Golgi apparatus and/or endoplasmic reticulum (ER). However, the ultrastructural features of plant retrograde transport carriers remain largely unresolved. Here, we show that plant retrograde transport is likely mediated by a previously unrecognized class of MVB-derived spherical vesicles. Using correlative light and electron microscopy and three-dimensional electron tomography, we identify a distinct population of ~30–50 nm spherical vesicles adjacent to MVBs, including nascent vesicles budding from the MVB limiting membrane in Arabidopsis root cells. Immunogold labeling shows that these vesicles are enriched in retromer components and VSRs, suggesting that they possibly function as retrograde transport carriers. To investigate their biogenesis, we perform cryo-electron microscopy and liposome tubulation assays, showing that Arabidopsis SNX1 generates shorter membrane tubules than its mammalian counterpart, consistent with reduced membrane affinity linked to differences in the amphipathic helix. Notably, the SNX1-SNX2 heterodimer produces heterogeneous structures, including spherical vesicles, recapitulating in vivo observations. Lastly, knockdown of SNX1 or SNX2 results in vacuolar mislocalization and increased degradation of GFP-VSR2, and defects in SNX1 and VPS29 inhibit formation of spherical vesicles adjacent to MVBs, resulting in embryonic lethality before the globular stage. Together, these findings establish MVB-derived spherical vesicles as plant retrograde carriers and reveal a distinct SNX-mediated mechanism underlying their formation.
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Data availability
The AH helical wheel was generated using PMIpred[https://pmipred.fkt.physik.tu-dortmund.de/]. The protein structure data used in this study are available in the PDB database: Mouse SNX1 6-fold (7D6D), Mouse SNX1 7-fold (7D6E), and Fungi Vps5 (6H7W). The EM maps of helical tubules have been deposited in the EM Data Bank with the accession codes EMD-68805 for class I and EMD-68806 for class II, respectively. The corresponding fitted coordinates of the SNX1 helical array on the tubule have been deposited in the PDB with the accession codes 23AS and 23AT, respectively. Source data are provided with this paper.
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Acknowledgements
The authors thank Professor Genji Qin (Peking University, China) for providing the vps29 mutant and Professor Ruixi Li (South University of Science and Technology, China) and Professor Caiji Gao (South China Normal University, China) for providing the snx1/snx2a/snx2b mutant. This work was supported by grants from the National Natural Science Foundation of China (32270727, 32000141), the Natural Science Foundation of Fujian Province (2021J01029) and the Fundamental Research Funds for the Central Universities (20720210094) to Y.C., grants from the Research Grants Council of Hong Kong (CRS_CUHK405/23, AoE/M-402/25-N, AoE/M-05/12, CUHK14106823, C4033-19E, C4002-20W, C4002-21EF, C2003-22WF, R4005-18, C4014-23G, G-CUHK409/23 and Senior Research Fellow Scheme SRFS2122-4S01), the Chinese University of Hong Kong (CUHK) Research Committee, and Science Faculty to L.J., as well as grants from the State Key Laboratory of Chemical Biology and Drug Discovery (PolyU), the Research Grants Council (RGC) (Hong Kong) (14105517) and the Hong Kong Polytechnic University (University Grants Committee) (P0046618) to W.C.Y.L.
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Y.L., L.J., and Y.C. conceived and designed the experiments. Y.L. and Y.C. performed the electron tomography analysis. Y.L., R.T., and Y.C. generated the 3D models. Y.L., R.T., X.W., S.K.P.L., W.C.Y.L., and Y.C. perform an analysis of the cryo-EM data. Y.L., R.T., H.Z., Q.Q., X.Z., H.G., C.W., and Y.C. performed the other experiments. Z.F., X.H., W.C.Y.L., and L.J. commented on the manuscript. Y.L., R.T., W.C.Y.L., L.J., and Y.C. wrote the paper.
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Li, Y., Tao, R., Zhang, H. et al. SNX-mediated biogenesis of a plant-unique vesicle derived from the multivesicular body. Nat Commun (2026). https://doi.org/10.1038/s41467-026-71067-x
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DOI: https://doi.org/10.1038/s41467-026-71067-x
