Architecture and self-assembly of the jumbo bacteriophage nuclear shell

Abstract

Bacteria encode myriad defences that target the genomes of infecting bacteriophage, including restriction–modification and CRISPR–Cas systems1. In response, one family of large bacteriophages uses a nucleus-like compartment to protect its replicating genomes by excluding host defence factors2–4. However, the principal composition and structure of this compartment remain unknown. Here we find that the bacteriophage nuclear shell assembles primarily from one protein, which we name chimallin (ChmA). Combining cryo-electron tomography of nuclear shells in bacteriophage-infected cells and cryo-electron microscopy of a minimal chimallin compartment in vitro, we show that chimallin self-assembles as a flexible sheet into closed micrometre-scale compartments. The architecture and assembly dynamics of the chimallin shell suggest mechanisms for its nucleation and growth, and its role as a scaffold for phage-encoded factors mediating macromolecular transport, cytoskeletal interactions, and viral maturation.

The ϕPA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice

“…The subunits forming the lattice appear to be a single, ~60 by 40 Å protein species. Recent low-resolution in situ tomography of phage nuclear shells from phages 201ϕ2-1 and Goslar reported p4 symmetry but is otherwise consistent with this observation, demonstrating a lattice with similarly sized subunits 17 . The isolated shell fragments often appear folded over and the lattice can vary in directionality, suggestive of both structural plasticity and imperfections as well as locally altered symmetry within the lattice of endogenous mature phage nuclear shells (Fig.…”

“…5a, b ). Moreover, the tetrameric ϕPA3 model from our in vitro assembled lattices has an excellent fit into the 24 Å cryo-electron tomography density 17 obtained from 201ϕ2-1 infected cells (Fig. 5c–e ) (masked correlation coefficients: 0.69 ϕPA3 tetramer; 0.49 calculated and 0.56 reported 17 for the 201ϕ2-1 cuboid tetramer).…”

“…During the review of this manuscript, a publication reported in vitro assembled four-fold symmetric cuboids of the homologous PhuN protein from bacteriophage 201ϕ2-1 17 . Despite the clear difference in observed symmetries, the core domains of the 201ϕ2-1 monomers closely match the ϕPA3 monomers we describe in this work (Fig.…”

Disordered-to-ordered transitions in assembly factors allow the Complex II catalytic subunit to switch binding partners

“…A second example of changes in disorder regulating self-assembly is found in the bacteriophage nuclear shell 48,49 . Dynamics and disorder observed at the N-and C-termini of the chimallin protein of this nuclear shell (Figure S12a, S12b) (PDB entry 7SQU) 50 .…”

“…A common theme of changes in disorder during assembly is that newly ordered regions tend to lack substantial secondary structure. The paucity of secondary structure is observed in the newly ordered regions of SDHAF2, SDHAF4, arrestin 46,47 and chimallin 50 but is perhaps best exemplified in mammalian mitochondrial complex I (PDB entry 5XTD) 51,52 (Figure S13a). NDUFS4 and NDUFS6 are assembly factors that double as accessory subunits for Complex I.…”