Ring-stacked capsids of white spot syndrome virus and structural transitions with genome ejection

Abstract

White spot syndrome virus (WSSV) is one of the largest DNA viruses and the major pathogen responsible for white spot syndrome in crustaceans. The WSSV capsid is critical for genome encapsulation and ejection and exhibits the rod-shaped and oval-shaped structures during the viral life cycle. However, the detailed architecture of the capsid and the structural transition mechanism remain unclear. Here, using cryo-electron microscopy (cryo-EM), we obtained a cryo-EM model of the rod-shaped WSSV capsid and were able to characterize its ring-stacked assembly mechanism. Furthermore, we identified an oval-shaped WSSV capsid from intact WSSV virions and analyzed the structural transition mechanism from the oval-shaped to rod-shaped capsids induced by high salinity. These transitions, which decrease internal capsid pressure, always accompany DNA release and mostly eliminate the infection of the host cells. Our results demonstrate an unusual assembly mechanism of the WSSV capsid and offer structural insights into the pressure-driven genome release.

Fig. 1.. Barrel-shaped structure of the body and its assembly mechanism.

(A) Typical cryo-EM micrographs of the WSSV capsids after different treatments. The rod-shaped capsid is zoomed in two times the size of other structures for better labeling with the head, the body, and the base. (B) The length and width statistics of the rod-shaped WSSV capsids. (C) Barrel-like structure of the body. The thick and thin layers are colored in blue and green, respectively. The same color scheme is used throughout the study unless specified. Arch-like and diamond-like structures in one protofilament are colored in dark gray and light gray, respectively. One diamond-like structure is divided into two parts (in purple and yellow) based on the symmetry. (D) Structural analyses on the arch-like and diamond-like structures. Twofold symmetry axis is labeled as red dashed lines. (E) Intertwined hooks lock neighboring arch-like structures together.

Fig. 2.. Disc-shaped structure of the base and its assembly mechanism.

(A) Cryo-EM model of the base and part of the body. One typical region is circled in red for further structural analysis in (E). (B) Cryo-EM model of the disc-shaped base and its cross-halving joint structure formed by Nail-1, Nail-2, and Nail-3. (C) Layers of Nail-1, Nail-2, and Nail-3. One cross-halving joint structure is displayed in each layer. (D) Structural comparison of Nail-1, Nail-2, and Nail-3 and the fitted VP51 model. (E) Nail-1 directly contacts the arch-like structure of the body, covered by a Diamond/2. Diamond/2 is the half of the diamond-like structure. (F) Structural change of the Diamond/2 in the base relative to the body. The arch-like and diamond-like structures from the body are colored in dark gray and light gray, respectively.

Fig. 3.. Rotor-shaped structure of the head and its assembly mechanism.

(A) Cryo-EM model of the head with the enforced 14-fold symmetry. Only Diamond/2 and arch-like layers are resolved with the desired structural features. The head region is colored in yellow. (B) Structural change of Diamond/2 in the head relative to the body. The arch-like and diamond-like structures from the body are colored in dark gray and light gray, respectively. (C) Two typical classes of the head. One has a plug, while the other is plug-free. (D) Cryo-EM models of the neck and the plug. The neck and the plug are colored in yellow and orange, respectively. Neighboring protomers in the neck and the plug are zoomed in and shown. (E) A composite cryo-EM model of the head with its central section.

Fig. 4.. The architecture of the rod-shaped WSSV capsid and the genome packaging.

(A) A composite cryo-EM model of the rod-shaped WSSV capsid and its central section. The number of layers was determined by the average length of the capsid. Layer numbers in the body are labeled. Diamond/2 layers are labeled with extra stars. (B) A typical rod-shaped capsid with clear genome packaging inside. The base and the head are colored in purple and yellow, respectively. (C) A typical cryo-EM micrograph of the rod-shaped WSSV capsids with the released DNA genomes. The released DNA is colored in blue.

Fig. 5.. Structural transition between the rod-shaped and oval-shaped WSSV capsids.

(A) The oval-shaped WSSV capsid revealed by cryo–electron tomography (cryo-ET). (B) The length and width statistics of the oval-shaped WSSV capsids. (C) The surface area statistics of the rod-shaped and oval-shaped WSSV capsids. (D) The central section of the head of the oval-shaped capsid. (E) Structural change of Diamond/2 and Arch/2 in the oval-shaped capsid relative to the rod-shaped capsid. The arch-like and diamond-like structures from the body are colored in dark gray and light gray, respectively. (F) The central section of the base of the oval-shaped capsid. (G) Structural change of Diamond/2 and Arch/2 in the oval-shaped capsid relative to the rod-shaped capsid. The arch-like and diamond-like structures from the rod-shaped capsid are colored in dark gray and light gray, respectively. (H) Modeling of the structural rearrangement of arch-like structures along the Z axis (long axis of rod-shaped and oval-shaped capsids).

Fig. 6.. Structural transition is highly relevant to WSSV infection.

(A) The volume statistics of the rod-shaped and oval-shaped WSSV capsids. (B) Cryo-ET of the intact WSSV virion with the oval-shaped capsids. (C) The replication comparison of the WSSV VP28 gene in the primarily cultured shrimp cells after different treatments at different time points. (D) The damage comparison of WSSV to shrimp cells after different treatments at different time points.

Fig. 7.. Model illustrating the architecture of the WSSV capsid and the pressure-driven genome ejection.

“H” and “L” stand for the high- and low- capsid pressures, respectively.