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A whole-cell electron tomography model of vacuole biogenesis in Arabidopsis root cells


Plant vacuoles are dynamic organelles that play essential roles in regulating growth and development. Two distinct models of vacuole biogenesis have been proposed: separate vacuoles are formed by the fusion of endosomes, or the single interconnected vacuole is derived from the endoplasmic reticulum. These two models are based on studies of two-dimensional (2D) transmission electron microscopy and 3D confocal imaging, respectively. Here, we performed 3D electron tomography at nanometre resolution to illustrate vacuole biogenesis in Arabidopsis root cells. The whole-cell electron tomography analysis first identified unique small vacuoles (SVs; 400–1,000 nm in diameter) as nascent vacuoles in early developmental cortical cells. These SVs contained intraluminal vesicles and were mainly derived/matured from multivesicular body (MVB) fusion. The whole-cell vacuole models and statistical analysis on wild-type root cells of different vacuole developmental stages demonstrated that central vacuoles were derived from MVB-to-SV transition and subsequent fusions of SVs. Further electron tomography analysis on mutants defective in MVB formation/maturation or vacuole fusion demonstrated that central vacuole formation required functional MVBs and membrane fusion machineries.

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Fig. 1: Whole-cell electron tomography analysis of SVs in relationship with other organelles in a cortical cell of early developmental stage.
Fig. 2: MVBs mature and fuse to form SVs in early root cortical cells.
Fig. 3: The transition from MVB to SV accompanies gradual degradation of ILVs.
Fig. 4: Fusions among SVs generate larger-sized vacuoles.
Fig. 5: Vacuoles are gradually increasing in size along an apical-to-basal developmental gradient in the root cortex in whole-cell electron tomography analyses.
Fig. 6: Efficient fusion of SVs requires ESCRT, Rab GTPase and SNARE proteins in mutant analyses.

Data availability

The data that support the findings of this study are available from the corresponding authors upon request.


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This work was supported by grants from the Research Grants Council of Hong Kong (CUHK14130716, 14102417, 14100818, C4011-14R, C4012-16E, C4002-17G and AoE/M-05/12) and the National Natural Science Foundation of China (31270226, 31470294 and 91854201).

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Authors and Affiliations



Y.C., B.-H.K. and L.J. conceived and designed the experiments. Y.C. performed the electron tomography analysis. Y.C., W.C., Y.H., H.Y.W., W.S.W. and H.K.L. generated the 3D models. Y.C., W.C., Y.H., Q.Z., M.W., X.Z., J.G., Y.Z., C.G., Y.D. and P.W. performed the other experiments. Y.C., T.U., M.R.-P., K.T., B.-H.K. and L.J. analysed the data. Y.C. and L.J. wrote the paper.

Corresponding authors

Correspondence to Yong Cui or Liwen Jiang.

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Supplementary information

Supplementary Information

Supplementary Figures 1–8.

Reporting Summary

Supplementary Video 1

Whole-cell electron tomography analyses of SVs in relationship with other organelles in Cell 1.

Supplementary Video 2

3D tomography analyses of detailed structures and relationships of ER, Golgi, TGN, MVBs and SVs.

Supplementary Video 3

3D tomography analyses of fusion between MVBs and SVs, along with a transfer of ILVs.

Supplementary Video 4

Whole-cell electron tomography analyses of vacuoles in Cell 2.

Supplementary Video 5

Whole-cell electron tomography analyses of vacuoles in Cell 3.

Supplementary Video 6

3D tomography analyses of vacuoles in WT and various mutants.

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Cui, Y., Cao, W., He, Y. et al. A whole-cell electron tomography model of vacuole biogenesis in Arabidopsis root cells. Nature Plants 5, 95–105 (2019).

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