Architecture and self-assembly of the jumbo bacteriophage nuclear shell

Abstract

Bacteria encode myriad defenses that target the genomes of infecting bacteriophage, including restriction-modification and CRISPR/Cas systems. In response, one family of large bacteriophage employs a nucleus-like compartment to protect their replicating genomes by excluding host defense factors. However, the principle composition and structure of this compartment remain unknown. Here, we find that the bacteriophage nuclear shell assembles primarily from one protein, termed chimallin. 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 cooperatively self-assembles as a flexible sheet into closed micron-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.

A cytoskeletal vortex drives phage nucleus rotation during jumbo phage replication in E. coli

“…Here we characterize Goslar infecting E. coli and demonstrate that this phage also has a complex replication cycle with both a nucleus-like compartment and a tubulin-based cytoskeleton that rotates it (Figure 7). Our findings regarding the Goslar phage nucleus are supported by our recent work showing that Goslar chimallin shares high structural homology with chimallin from other jumbo phages like 20142-1, and assembles into a flexible lattice that is the primary component of the Goslar nuclear shell (Laughlin et al, 2022). Surprisingly, Goslar PhuZ filaments assemble a vortex-like cytoskeletal structure in which filaments wrap around the entire phage nucleus and project radially toward the membrane (Figure 7).…”

A family of novel immune systems targets early infection of nucleus-forming jumbo phages

“…Indeed, we previously reported that experimentally arrested infections left a stable DNA puncta at the pole, with no degradation of phage DNA by restriction enzymes 5 . This protective structure could be the “round compartments” 25 or “unidentified spherical bodies” 26 revealed by recent electron microscopy studies. The experiments reported here identified some of the likely IB protein components of this structure and uncovered a novel immune strategy that apparently destabilizes it, rendering the phage DNA susceptible to cytoplasmic nucleases.…”

The logic of virus evolution

“…A remarkable case of enzyme exaptation for a structural role in viruses are the major proteins of the nucleus-like shell formed by certain jumbo phages for protection of the virus DNA from cellular defense systems, such as restriction endonucleases and CRISPR-Cas (Guan and Bondy-Denomy, 2020). Structural comparisons showed that the major shell protein, chimallin, comprises two domains, the N-terminal domain with an α+β fold similar to that of an uncharacterized bacterial protein, and the C-terminal domain that is derived from a GCN5-related Nacetyltransferase most similar to E. coli AtaT and homologous to tRNA-acetylating toxins (Laughlin et al, 2022). Notably, as in many other cellular enzymes exapted by viruses, the acetyltransferase active site residues of chimallin are mutated, apparently abrogating the enzymatic activity.…”