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Engineering a Novel Bacterial Encapsulin for Programmable Surface Functionalization: From Single-Target to Mosaic

India Boyton1,2, Claire Rennie2, Julia van der Hoven3

  • 1Australian Institute for Microbiology and Infection, University of Technology Sydney, Gadigal Country, Sydney, NSW 2007, Australia.

Biorxiv : the Preprint Server for Biology
|June 12, 2026
PubMed
Summary

Protein nanocages called encapsulins are engineered into a nanovaccine scaffold (Am-S) for displaying multiple disease antigens. This novel scaffold successfully generated immune responses against Alzheimer's disease targets in mice.

Keywords:
Alzheimer’s DiseaseSpyCatcher/SpyTagamyloid betaencapsulinhyperphosphorylated taunanovaccineprotein nanocage

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Area of Science:

  • Biochemistry and Structural Biology
  • Nanotechnology and Materials Science
  • Immunology and Vaccinology

Background:

  • Encapsulins are prokaryotic protein nanocages with potential as nanovaccine scaffolds.
  • Effective nanovaccine platforms require modularity, high-yield production, stability, and controlled antigen display.
  • Previous encapsulin systems faced limitations in surface engineering and antigen co-display.

Purpose of the Study:

  • To engineer a previously uncharacterized encapsulin from Alkaliphilus metalliredigens into a versatile nanoscaffold for antigen display.
  • To assess the structural integrity, production yield, and stability of the engineered nanoscaffold.
  • To demonstrate the scaffold's utility for single- and multi-antigen display and its immunogenicity in vivo.

Main Methods:

  • Engineering of an Alkaliphilus metalliredigens encapsulin with a C-terminal SpyCatcher fusion (Am-S).
  • Cryo-electron microscopy (Cryo-EM) for structural analysis of the native and engineered nanocages.
  • Production in Escherichia coli, formulation stability testing (freeze-thaw, storage), and SpyTagged peptide conjugation.
  • Immunization studies in mice using Am-S functionalized with Alzheimer's disease-associated epitopes (amyloid-β and hyperphosphorylated tau).

Main Results:

  • The engineered Am-S nanocage maintained native encapsulin structure (T=1 icosahedral symmetry) and integrity.
  • High-yield soluble production in E. coli and excellent monodisperse stability after freeze-thaw and storage were achieved.
  • Efficient conjugation of SpyTagged antigens enabled single- and multi-antigen display, including mosaic nanocages co-displaying amyloid-β and tau epitopes.
  • In mice, Am-S nanovaccines enhanced antigen-specific IgG responses and induced predominantly IgG1-biased immunity.
  • Mosaic nanocages elicited antibodies against both targets, which recognized Alzheimer's disease pathology in ex vivo mouse brain sections.

Conclusions:

  • The Am-S nanoscaffold is structurally sound, manufacturable, and stable, overcoming key limitations of previous systems.
  • It enables controlled single- and multi-antigen display for potential nanovaccine development.
  • Am-S functionalized with disease-specific epitopes elicits robust humoral immunity and demonstrates potential for targeting complex diseases like Alzheimer's.