Prokaryotic homologs of the major vault protein form engineerable vault nanocapsules

Abstract

Vaults are the largest ribonucleoprotein particles in eukaryotic cells, built from 78 copies of the major vault protein (MVP), yet their function remains unknown four decades after their discovery. MVP homologs occur in prokaryotes and bacteriophages, but whether they form vaults is unknown. Here, we show that prokaryotic and bacteriophage MVP homologs assemble into vault particles. We surveyed approximately 15 billion proteins, found MVP homologs in 29 bacterial and 4 archaeal phyla, and used size-exclusion chromatography to rapidly screen and isolate vault particles of eight homologs expressed in Escherichia coli. Cryo-electron microscopy structures of the phage homolog L05 at high resolution reveal a shell of 96 MVP chains enclosing a volume ~25% larger than human vaults, among the largest protein shells of defined size outside virus capsids. Prokaryotic MVPs typically carry seven wall repeats and eukaryotic MVPs nine, and adding wall repeats to L05 yields larger vaults. Prokaryotic vaults expand the known diversity of vault architecture and offer a tractable system for studying vault assembly and a size-tunable scaffold for cargo encapsulation.