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Dynamin-dependent vesicle twist at the final stage of clathrin-mediated endocytosis

Nature Cell Biology volume 23, pages 859–869 (2021)Cite this article

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Abstract

Dynamin has an important role in clathrin-mediated endocytosis by cutting the neck of nascent vesicles from the cell membrane. Here, using gold nanorods as cargos to image dynamin action during live clathrin-mediated endocytosis, we show that, near the peak of dynamin accumulation, the cargo-containing vesicles always exhibit abrupt, right-handed rotations that finish in a short time (~0.28 s). The large and quick twist, herein named the super twist, is the result of the coordinated dynamin helix action upon GTP hydrolysis. After the super twist, the rotational freedom of the vesicle increases substantially, accompanied by simultaneous or delayed translational movement, indicating that it detaches from the cell membrane. These observations suggest that dynamin-mediated scission involves a large torque generated by the coordinated actions of multiple dynamins in the helix, which is the main driving force for vesicle scission.

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Fig. 1: Scheme of 3D-SPORT.
Fig. 2: Multidimensional imaging of a AuNR and the surrounding molecular fluorescence.
Fig. 3: A typical example of an endocytic event with vesicle rotational information.
Fig. 4: Statistics of the major events before fission and scheme of the dynamin scission model.
Fig. 5: Endocytosis of AuNRs by A549 cells expressing K44A dynamin mutants with deficient GTPase activity.
Fig. 6: Rotation step sizes at different times during endocytosis.
Fig. 7: An example of an abortive scission event.

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Data availability

Source data are provided with this paper. All other data supporting the findings of this study are available from the corresponding authors on reasonable request.

Code availability

The auto-chasing was achieved using Micro-Manager. The localization and orientation of an AuNR was analysed with MATLAB. All code is available from the corresponding authors on request.

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Acknowledgements

We thank D. Drubin for providing the gene-edited SK-MEL-2 cell line, and S. Schmid for insightful comments and help during the completion of this manuscript. This work is supported by National Institution of Health (R01GM115763). X.C. acknowledges partial support from Science and Technology Projects of Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) (RD2020050501).

Author information

Author notes

  1. These authors contributed equally: Xiaodong Cheng, Kuangcai Chen, Bin Dong.

Authors and Affiliations

  1. Department of Chemistry, Georgia State University, Atlanta, GA, USA

    Xiaodong Cheng, Kuangcai Chen, Bin Dong, Meek Yang, Seth L. Filbrun, Yong Myoung, Teng-Xiang Huang, Gufeng Wang & Ning Fang

  2. State Key Laboratory of Physical Chemistry of Solid Surfaces, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China

    Xiaodong Cheng & Ning Fang

  3. The Bristol-Myers Squibb Company, Devens, MA, USA

    Yan Gu

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Contributions

X.C., K.C. and B.D. contributed equally to this work. G.W. and N.F. conceived the idea. X.C., K.C., B.D., G.W. and N.F. designed the research. X.C., K.C. and B.D. built the imaging setup. M.Y., S.L.F., Y.M., T.-X.H. and Y.G. contributed to the experiments. All of the authors performed the experiments and wrote the manuscript.

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Correspondence to Gufeng Wang or Ning Fang.

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The authors declare no competing interests.

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Peer review information Nature Cell Biology thanks Sandra Schmid, Aurélien Roux and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.

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Extended data

Extended Data Fig. 1 Calibration curve of Δy vs. Δz and 3D localization precision of a AuNR.

a, The AuNRs were immobilized on a glass slide surface with various orientations and scanned along the z-axis from -1000 nm to 1000 nm with 10 nm steps using a high-precision objective scanner (Data were expressed as mean ± SD, n = 20 independent experiments). b, Typical upper and lower half-plane dark-field images of a AuNR with 0.02 s integration time are shown on the left. Scale bar is 5 μm. The lateral positions of the AuNR are determined by 2D elliptical Gaussian fitting (right) the intensity profile. c, Scatter plot of locations of the same AuNR in 500 frames. The x, y positions are determined using 2D elliptical Gaussian fitting of the particle image intensity profile. The z positions are obtained from feedback of the objective scanner when auto-focusing system was engaged. The localization precision is determined as the standard deviation from 1D Gaussian function fitting the histogram distribution of the AuNR locations in x, y, z, giving σx = 4.9 nm (d), σy = 6.3 nm (E) and σz = 14.0 nm (f).

Source data

Extended Data Fig. 2 Another example of the full plane defocused image patterns of a AuNR.

The defocused images of a AuNR with a polar angle of 60° at different azimuth angles with 10° intervals were shown. Scale bar is 1 μm.

Extended Data Fig. 3 The six basic dipole emission templates used in simulation.

These basic image patterns are dependent on system-specific parameters including the numerical aperture and magnification of the objective, and the defocusing distance.

Extended Data Fig. 4 Estimated polar and azimuth angle errors for orientation recovery at S/N = 10.

a, Estimated polar errors for orientation with various combinations of the azimuth angle and polar angle at S/N = 10. b, The cross section along the black line in (a) shows the polar angle errors with various polar angles and a fixed azimuth angle of 90°. c, The cross section along the red line in (a) represents the polar angle errors with various azimuth angles and a fixed polar angle of 60°. d, Estimated azimuth errors for orientation with various combinations of the azimuth angle and polar angle at S/N = 10. e, The cross section along the black line in (d) shows the azimuth angle errors with various polar angles and a fixed azimuth angle of 90°. f, The cross section along the red line in (d) represents the azimuth angle errors with various azimuth angles and a fixed polar angle of 60°.

Source data

Extended Data Fig. 5 Dynamin and clathrin fluorescence during endocytosis of the example shown in Fig. 3.

a, Clathrin channel. b, Dynamin channel. c, Focused scattering channel for AuNRs. d, Overlapped images. e, Time evolution of clathrin and dynamin fluorescence on the entry spot, clathrin and dynamin fluorescence on the vesicle, the xy-, and the z-displacement of the particle from the entry spot during an endocytosis event. The dashed line indicates the time of fission point. The experiments have been performed 5 times and with similar results obtained.

Source data

Extended Data Fig. 6 A complete 3D trajectory, rotation information, and dynamin fluorescence of an endocytosis event.

a, The overlay of the time evolution of the cargo’s xy-, z-displacements, rotational azimuth and polar angles, and dynamin fluorescence in the background, respectively. Labels B, C, D, E and F represent various stages during the endocytosis. b, Expanded time window near the fission point (orange frame) in (a). c, Cargo’s defocused image patterns showing the “super twist” at Stage D. The scale bar is 500 nm. The experiments have been performed 45 times, with similar results obtained.

Source data

Extended Data Fig. 7 More examples of complete endocytosis events.

a, Example 1, b, Example 2, c, Example 3 and d, Example 4. The overlay of the time evolution of the cargo’s xy-, z-displacements, rotational azimuth and polar angles, and dynamin fluorescence in the background, respectively. Labels A, B, C, D, E, and F represent various stages during endocytosis.

Source data

Extended Data Fig. 8 An example of rotational tracking of a AuNR in Stage a.

The overlay of the time evolution of the cargo rotational azimuth, and polar angles in stage a. The experiments have been performed 45 times and with similar results obtained.

Source data

Supplementary information

Supplementary Information

Supplementary Discussion.

Reporting Summary

Peer Review Information

Supplementary Video 1

An example of multidimensional images of AuNR endocytosis. Clathrin fluorescence (red), dynamin fluorescence (green) and a scattering image of a AuNR (grey) are shown. The white arrow indicates the overlaid point of the clathrin channel, dynamin channel and AuNR scattering channel. Fluorescence images were acquired at 0.5 f.p.s. and played in real time. Scattering images were acquired at 50 f.p.s. and played at 50 f.p.s. Scale bar, 5 μm.

Supplementary Video 2

An example of active rotation in stage A. The video was acquired at 50 f.p.s. and played at 100 f.p.s. Scale bar, 3 μm.

Supplementary Video 3

Scattering images showing the static period and the super twists. Left, original defocused images. Right, reconstructed images using recovered azimuth and polar angles. The videos were collected at 50 f.p.s. and played at 10 f.p.s.

Supplementary Video 4

An additional example for scattering images showing the static period and the super twists. The description of the left and right parts and the video collection and play rate are the same as those in Supplementary Video 3.

Supplementary Video 5

An additional example for scattering images showing the static period and the super twists. The description of the left and right parts and the video collection and play rate are the same as those in Supplementary Video 3.

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Cheng, X., Chen, K., Dong, B. et al. Dynamin-dependent vesicle twist at the final stage of clathrin-mediated endocytosis. Nat Cell Biol 23, 859–869 (2021). https://doi.org/10.1038/s41556-021-00713-x

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