In situ structural mechanism of epothilone-B-induced CNS axon regeneration
Summary
This Nature paper (Bodakuntla et al., published 12 November 2025) uses in situ cryo-electron tomography and single-particle analysis to show how epothilone B (EpoB), a microtubule-stabilising drug, drives central nervous system (CNS) axon regeneration at the structural level. The authors visualised regenerating axons at multiple time points after axotomy, reconstructed EpoB-bound microtubules to ~3.2 Å (PDB 9PND; EMD-71750) and linked the structural engagement of EpoB with dynamic microtubule behaviours, tubulin-oligomer transport, microtubule branching and actin/membrane rearrangements that together support regrowth.
Article Date: 12 November 2025
Article URL: https://www.nature.com/articles/s41586-025-09654-z
Article Image: https://www.nature.com/articles/s41586-025-09654-z
Key Points
- EpoB binds in situ to neuronal microtubules and the drug–tubulin interaction is resolved at high resolution (3.19 Å), enabling atomic interpretation (PDB 9PND).
- Treated axons show rapid changes after axotomy: initial retraction bulb-like swelling, then formation of microtubule “shoots” that extend beyond the cut site within 1–6 hours.
- EpoB increases plus-end microtubule dynamics and promotes EB3-marked growth at regenerating tips, while also enhancing transport of tubulin oligomers and microtubule-building material into the regeneration zone.
- Cryo-ET reveals microtubule branching, altered microtubule lumenal particle (MIP) distribution, vesicle/ER accumulation and actin stress-fibre assembly at regenerating sites—coordinated structural changes that support membrane extension and growth cone formation.
- Subtomogram averaging and SPA workflows (CryoSPARC, FREALIGN, RELION) were used to validate architectures; all analysed microtubules had 13 protofilaments and a clear seam location was determined.
- Raw tomograms, maps and coordinates are publicly deposited (EMDB: EMD-71751–EMD-71755, EMD-71750, EMD-71840; PDB: 9PND) and source data accompany the paper.
Content summary
The authors combined live-cell imaging of cultured thalamus axons with in situ cryo-electron tomography at defined time points after axotomy and EpoB treatment. Live imaging showed EpoB doses that induce sustained regrowth (effects visible up to 48 h) and EB3 dynamics indicating plus-end growth. Cryo-ET captured the ultrastructural timeline: membrane sealing and swelling at very early times, followed by the emergence of microtubule-rich shoots and branching microtubules that push beyond the cut margin.
High-resolution single-particle reconstructions of microtubules from regenerating axons revealed direct EpoB engagement with the tubulin lattice, explaining increased stability yet preserved capacity for productive plus-end growth. The team observed tubulin-oligomer clusters that are transported (co-localised with kinesin KIF5), changes in microtubule lumenal particle spacing over time, and accumulation of vesicles and ER near microtubules—features consistent with an active supply chain for polymerisation and membrane addition. Actin stress fibres and later finger-like growth cones were also documented, linking cytoskeletal coordination to morphological recovery.
Context and relevance
This work provides the missing structural link between microtubule-stabilising drugs (Taxol, EpoB) that are known to promote axon regeneration in vivo and the cellular mechanics by which they operate. Prior studies showed functional regeneration after spinal cord injury with microtubule stabilisers; here the mechanism is visualised in situ in mammalian CNS axons. The paper is relevant to researchers working on spinal cord repair, neurotrauma, cytoskeleton pharmacology and anyone designing targeted microtubule-modulating therapies—because it maps where and how a drug engages neuronal microtubules and what downstream architectural changes facilitate regrowth.
Author style
Punchy: the team lays out structural evidence and ties it to clear cellular phenotypes and deposited datasets—this is a strong, data-rich demonstration linking drug binding to regenerative architecture. If you work on neuroregeneration or cytoskeleton therapeutics, the mechanistic detail matters.
Why should I read this?
Short version: if you’re into fixing injured brains or spinal cords (or designing drugs that might actually help), this paper cuts through the guesswork. It shows, in-situ and at near-atomic detail, how epothilone B hooks up to neuronal microtubules and kick-starts the structural changes needed for axons to regrow. They’ve even shared the raw tomograms and maps — so you can dig in without spending months repeating experiments.