Abstract
Nervous necrosis virus (NNV), a non-enveloped betanodavirus, causes neuropathies and retinopathies in farmed fish, damaging aquaculture worldwide. NNV has 60 conspicuous surface protrusions comprising the protrusion domain (P-domain) of its capsid protein. Although NNV protrusions play critical roles in infectivity, the underlying dynamics remain unclear. Our cryogenic electron microscopy (cryo-EM)-derived structures of Dragon grouper (Epinephelus lanceolatus) NNV reveal that the protrusions undergo low-pH-induced compaction and movement. We show that the P-domain is monomeric in solution at a pH germane to infection (7.0). Moreover, nuclear magnetic resonance (NMR) structures reveal a peptide (amino acids 311-330) that adopts a flexible loop to form an open pocket. NMR spectral analysis at pH 5.0 aided by molecular dynamics (MD) simulations show that this loop switches to a β-strand under acidic conditions, eliciting pocket closure and P-domain trimerization, highlighting a unique pH-sensing feature. Our docking analysis revealed the N-terminal moiety of sialic acid inserted into and interacting with conserved residues in the pocket. Additionally, a low-pH-induced conformational change in the linker region via peptide bond isomerization conferred malleability on the protrusions. Our work uncovers the protrusion dynamics of a betanodavirus governing its infectivity through a pH-dependent conformational switching mechanism, providing insights into complex virus-host interactions.
Competing Interest Statement
The authors have declared no competing interest.
Data Availability
Cryo-EM maps of GNNV VLP at pH 8.0, 6.5 and 5.0 are available from the EMDB data bank with accession numbers EMDB-39212, 39213, and 39214, and the corresponding atomic models are with PDB entries of 8YF6, 8YF7, and 8YF8 respectively; Cryo-EM maps of GNNV virion at pH 6.5 and 5.0 have EMDB accession numbers 39215 and 39217, and the atomic model of GNNV virion at pH 6.5 is with PDB entry of 8YF9. The chemical shift assignments for 2D HSQC spectra at pH 5.0 have been deposited to the Biological Magnetic Resonance Bank (BMRB) with Accession No. 52218. The NMR structure of the GNNV P-domain has been deposited to the Protein Data Bank (PDB entry 8XID).