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Real-time imaging of axonal membrane protein life cycles

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Abstract

The construction of neuronal membranes is a dynamic process involving the biogenesis, vesicular packaging, transport, insertion and recycling of membrane proteins. Optical imaging is well suited for the study of protein spatial organization and transport. However, various shortcomings of existing imaging techniques have prevented the study of specific types of proteins and cellular processes. Here we describe strategies for protein tagging and labeling, cell culture and microscopy that enable the real-time imaging of axonal membrane protein trafficking and subcellular distribution as they progress through some stages of their life cycle. First, we describe a process for engineering membrane proteins with extracellular self-labeling tags (either HaloTag or SNAPTag), which can be labeled with fluorescent ligands of various colors and cell permeability, providing flexibility for investigating the trafficking and spatiotemporal regulation of multiple membrane proteins in neuronal compartments. Next, we detail the dissection, transfection and culture of dorsal root ganglion sensory neurons in microfluidic chambers, which physically compartmentalizes cell bodies and distal axons. Finally, we describe four labeling and imaging procedures that utilize these enzymatically tagged proteins, flexible fluorescent labels and compartmentalized neuronal cultures to study axonal membrane protein anterograde and retrograde transport, the cotransport of multiple proteins, protein subcellular localization, exocytosis and endocytosis. Additionally, we generated open-source software for analyzing the imaging data in a high throughput manner. The experimental and analysis workflows provide an approach for studying the dynamics of neuronal membrane protein homeostasis, addressing longstanding challenges in this area. The protocol requires 5–7 days and expertise in cell culture and microscopy.

Key points

  • The workflow includes the use of multiple fluorescent ligands and optical pulse–chase axonal long-distance imaging to study vesicular transport of axonal proteins, and the sequential labeling of surface proteins to measure their rates of insertion and removal within axonal membranes. The protocol includes open-source software for data analysis.

  • HaloTag and SNAPTag labeling strategies together with optical pulse–chase axonal long-distance imaging enhance the signal-to-noise ratio, enabling specific and multiplexed imaging of membrane proteins.

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Fig. 1: Flowchart of axonal membrane protein imaging assays.
Fig. 2: An example of an extracellular tagging strategy for a protein with two intracellular termini.
Fig. 3: MFCs separate neuronal axons from somas.
Fig. 4: Live-cell imaging assays to interrogate the trafficking of membrane proteins and their behavior at different stages of their life cycle.
Fig. 5: Evaluation of axonal protein surface expression using protein labeling.
Fig. 6: Visualizing vesicular trafficking of axonal membrane proteins.
Fig. 7: Super-resolution imaging of tagged membrane proteins.
Fig. 8: Evaluating cotrafficking of axonal membrane proteins in vesicles.
Fig. 9: Visualizing protein insertion and removal at the axonal membrane.

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Data availability

The main data discussed in this protocol are available in the supporting primary research papers25,26,44,45,46,47,48. The raw datasets are too large to be publicly shared but are available for research purposes from the corresponding authors upon reasonable request. All data in this protocol are available within the paper and its Supplementary Information.

Code availability

Source code for software can be accessed at https://github.com/ycnrr/NatureProtocols_2023. All software is Open Source under the Apache License, version 2.0.

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Acknowledgements

This work was supported by Merit Review Awards B9253-C and BX004899 from the US Department of Veterans Affairs Rehabilitation Research and Development Service and Biomedical Laboratory Research and Development Service, respectively (S.G.W. and S.D.D.-H.). The Center for Neuroscience and Regeneration Research is a collaboration of the Paralyzed Veterans of America with Yale University. S.T. and G.P.H.-R. are supported by NIH/NIGMS Medical Scientist Training Program T32GM007205. S.T. is supported by NIH/NINDS T32NS041228. G.P.H.-R. is supported by NIH/NINDS 1F31NS122417-01. E.J.A. is supported by NIH/NIGMS P20GM130459. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. We thank D. Sosniak and M. Alsaloum for technical assistance. We thank L. Lavis and J. Grimm for their generous gifts of the JaneliaFluors. We thank J. Huttler for helpful discussions. Schematics were created with BioRender.com.

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Author notes

  1. Elizabeth J. Akin

    Present address: Department of Pharmacology, University of Nevada, Reno School of Medicine, Reno, NV, USA

  2. These authors contributed equally: Sidharth Tyagi, Grant P. Higerd-Rusli.

Authors and Affiliations

  1. Medical Scientist Training Program, Yale School of Medicine, New Haven, CT, USA

    Sidharth Tyagi & Grant P. Higerd-Rusli

  2. Center for Neuroscience and Regeneration Research, West Haven, CT, USA

    Sidharth Tyagi, Grant P. Higerd-Rusli, Elizabeth J. Akin, Christopher A. Baker, Shujun Liu, Fadia B. Dib-Hajj, Stephen G. Waxman & Sulayman D. Dib-Hajj

  3. Department of Neurology, Yale School of Medicine, New Haven, CT, USA

    Sidharth Tyagi, Grant P. Higerd-Rusli, Elizabeth J. Akin, Christopher A. Baker, Shujun Liu, Fadia B. Dib-Hajj, Stephen G. Waxman & Sulayman D. Dib-Hajj

  4. Center for Restoration of Nervous System Function, VA Connecticut Healthcare System, West Haven, CT, USA

    Sidharth Tyagi, Grant P. Higerd-Rusli, Elizabeth J. Akin, Christopher A. Baker, Shujun Liu, Fadia B. Dib-Hajj, Stephen G. Waxman & Sulayman D. Dib-Hajj

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Contributions

These authors contributed equally and share first-authorship: S.T. and G.P.H.-R. E.J.A. conceived and developed the OPAL imaging assay. G.P.H.-R. and S.T. further developed imaging assays. G.P.H.-R., S.T., E.J.A. and C.A.B. designed the research and performed experiments. S.T. developed automated imaging analysis tools. S.L. optimized the culture protocols and provided critical research reagents. F.B.D.-H. created protein constructs and optimized the molecular biology of these protocols. S.G.W. and S.D.D.-H. supervised the project and designed research. S.T., G.P.H.-R. and E.J.A wrote the paper. C.A.B., S.G.W. and S.D.D.-H. revised and critically reviewed the manuscript.

Corresponding authors

Correspondence to Stephen G. Waxman or Sulayman D. Dib-Hajj.

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Key reference using this protocol

Tyagi, S. et al. Cell Rep. 43, 113685 (2024): https://doi.org/10.1016/j.celrep.2024.113685

Higerd-Rusli, G. P. et al. Proc. Natl Acad. Sci. USA 120, e2215417120 (2023): https://doi.org/10.1073/pnas.2215417120

Akin, E. J. et al. Sci. Adv. 5, eaax4755 (2019): https://doi.org/10.1126/sciadv.aax4755

Higerd-Rusli, G. P. et al. J. Neurosci. 42, 4794–4811 (2022): https://doi.org/10.1523/JNEUROSCI.0058-22.2022

Akin, E. J. et al. Brain 144, 1727–1737 (2021): https://doi.org/10.1093/brain/awab113

Extended data

Extended Data Fig. 1 HaloTag and SNAPTag ligands do not label DRG neurons non-specifically.

(a) Confocal Z-stacks of a DRG neuron transfected with eGFP only, imaged in different spectral channels. The neuron was incubated with JF549-cpSNAPTag ligand and JF646-HaloTag ligand, washed, then imaged. Panels from left to right: 1) DIC image of neuron showing normal DRG morphology. 2) 488 nm channel (pseudo colored yellow) showing robust eGFP fluorescence. 3) 561 nm channel (pseudo colored green) showing lack of JF549-cpSNAPTag fluorescence. 4) 637 nm channel (pseudo colored magenta) showing lack of JF646-HaloTag fluorescence. DRG neurons were transfected with either Halo-NaV1.8 only (b), or SNAP-NaV1.7 only (c), incubated with JF549-cpSNAPTag ligand and JF646-HaloTag ligand, washed, then imaged. (b) Kymographs of vesicles detected in axons of DRG neurons transfected with Halo-NaV1.8 show that the SNAPTag ligand is not trafficked in the absence of SNAPTag. (c) Kymographs of vesicles detected in axons of DRG neurons transfected with SNAP-NaV1.7 show that the HaloTag ligand is not trafficked in the absence of HaloTag. Figure adapted from ref. 26 under a Creative Commons license CC BY 4.0.

Supplementary information

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Reporting Summary

Supplementary Video 1

OPAL imaging enables direct visualization of vesicles carrying Halo-tagged membrane proteins with high signal to noise ratio. The use of bright, photostable synthetic fluorophores combined with low background provided an excellent signal-to-noise ratio for clear visualization of vesicles. Anterograde Halo-NaV1.7 vesicles are visualized using OPAL imaging. This high-resolution imaging technique allows visualization of individual Halo-NaV1.7 vesicles with single-molecule resolution. Reprinted with permission from ref. 25, AAAS.

Supplementary Video 2

OPAL imaging can be extended to investigate co-trafficking of 2 proteins in the same vesicles. Two-color time-lapse OPAL imaging was performed using cell-permeable Halo-tag ligand-JF646 (magenta) and SNAP-tag ligand-JF549 (green). White arrowheads indicate vesicles doubly positive for Halo-NaV1.8 and SNAP-NaV1.7 as they move anterogradely along the axon outlined in white. Magenta and green arrowheads indicate vesicles that are singly positive for Halo-NaV1.8 or SNAP-NaV1.7, respectively. As described previously, the ∼1 μm separation of the SNAP and Halo signals is because of the continued motion of the vesicle during the time between acquisition of images in separate channels. When the vesicle is moving, the SNAP signal is always “behind” the Halo signal because the SNAP (561 nm) channel is acquired first. When the vesicle stops, however, the two signals overlap completely. From ref. 26 under a Creative Commons license CC BY 4.0.

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Tyagi, S., Higerd-Rusli, G.P., Akin, E.J. et al. Real-time imaging of axonal membrane protein life cycles. Nat Protoc 19, 2771–2802 (2024). https://doi.org/10.1038/s41596-024-00997-x

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  • DOI: https://doi.org/10.1038/s41596-024-00997-x

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