Abstract
Shrimp nodaviruses, including Penaeus vannamei (PvNV) and Macrobrachium rosenbergii nodaviruses (MrNV), cause white-tail disease in shrimps, with high mortality. The viral capsid structure determines viral assembly and host specificity during infections. Here, we show cryo-EM structures of T = 3 and T = 1 PvNV-like particles (PvNV-LPs), crystal structures of the protrusion-domains (P-domains) of PvNV and MrNV, and the crystal structure of the ∆N-ARM-PvNV shell-domain (S-domain) in T = 1 subviral particles. The capsid protein of PvNV reveals five domains: the P-domain with a new jelly-roll structure forming cuboid-like spikes; the jelly-roll S-domain with two calcium ions; the linker between the S- and P-domains exhibiting new cross and parallel conformations; the N-arm interacting with nucleotides organized along icosahedral two-fold axes; and a disordered region comprising the basic N-terminal arginine-rich motif (N-ARM) interacting with RNA. The N-ARM controls T = 3 and T = 1 assemblies. Increasing the N/C-termini flexibility leads to particle polymorphism. Linker flexibility may influence the dimeric-spike arrangement.
Highlights
Shrimp nodaviruses, including Penaeus vannamei (PvNV) and Macrobrachium rosenbergii nodaviruses (MrNV), cause white-tail disease in shrimps, with high mortality
We present two distinct putative dimer–dimer conformations to mimic the multiple organizations of the dimeric spikes: a parallel model and a closed contact as a X-shaped model structure, in which the two antiparallel β-strands associated with each other form a hydrogen-bond network in one PvNVPd and two MrNVPd crystal structures that are described as follows
The cryo-EM structure of T = 3 P. vannamei nodavirus (PvNV)-LP reveals the especially long ordered polypeptide of the Nterminal arm (N-arm), which makes a specific arrangement through the β-annulus structure with three conserved proline residues (Pro51) from three subunits C5, C6, and C8, resulting in an N-terminal extended arch-shaped structure and the flexible Nterminal arginine-rich motif (N-ARM) located around the quasi 3-fold (Q3) axis
Summary
Shrimp nodaviruses, including Penaeus vannamei (PvNV) and Macrobrachium rosenbergii nodaviruses (MrNV), cause white-tail disease in shrimps, with high mortality. The white-tail disease, or the white-muscle disease caused by these shrimp nodaviruses, can infect the larvae, postlarvae and early juvenile stages, reaching to 100% mortality within 6 days after appearance of the first gross signs of syndromes, including a white or milky abdominal muscle[3,5,6,7]. This white-tail disease causes serious large-scale mortalities during the hatchery and nursery phases of the prawn aquaculture[8,9]. PvNV and MrNV belong to the family Nodaviridae, the important genera comprising two other major types: alphanodavirus, infecting insects; and betanodavirus, infecting fishes[10]
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