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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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).

Author information

Author notes

    • Caiji Gao

    Present address: Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China

    • Yu Ding

    Present address: Department of Food Science & Technology, School of Science and Technology, Jinan University, Guangzhou, China

  1. These authors contributed equally: Yong Cui, Wenhan Cao, Yilin He.


  1. School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China

    • Yong Cui
    • , Wenhan Cao
    • , Yilin He
    • , Qiong Zhao
    • , Xiaohong Zhuang
    • , Jiayang Gao
    • , Yonglun Zeng
    • , Caiji Gao
    • , Yu Ding
    • , Hiu Yan Wong
    • , Wing Shing Wong
    • , Ham Karen Lam
    • , Pengfei Wang
    • , Byung-Ho Kang
    •  & Liwen Jiang
  2. RIKEN Center for Sustainable Resource Science, Yokohama, Japan

    • Mayumi Wakazaki
    •  & Kiminori Toyooka
  3. Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Japan

    • Takashi Ueda
  4. Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA

    • Marcela Rojas-Pierce
  5. The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China

    • Liwen Jiang


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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.

Competing interests

The authors declare no competing interests.

Corresponding authors

Correspondence to Yong Cui or Liwen Jiang.

Supplementary information

  1. Supplementary Information

    Supplementary Figures 1–8.

  2. Reporting Summary

  3. Supplementary Video 1

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

  4. Supplementary Video 2

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

  5. Supplementary Video 3

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

  6. Supplementary Video 4

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

  7. Supplementary Video 5

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

  8. Supplementary Video 6

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

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