Structure of the Macrobrachium rosenbergii nodavirus: A new genus within the Nodaviridae?

Abstract

Macrobrachium rosenbergii nodavirus (MrNV) is a pathogen of freshwater prawns that poses a threat to food security and causes significant economic losses in the aquaculture industries of many developing nations. A detailed understanding of the MrNV virion structure will inform the development of strategies to control outbreaks. The MrNV capsid has also been engineered to display heterologous antigens, and thus knowledge of its atomic resolution structure will benefit efforts to develop tools based on this platform. Here, we present an atomic-resolution model of the MrNV capsid protein (CP), calculated by cryogenic electron microscopy (cryoEM) of MrNV virus-like particles (VLPs) produced in insect cells, and three-dimensional (3D) image reconstruction at 3.3 Å resolution. CryoEM of MrNV virions purified from infected freshwater prawn post-larvae yielded a 6.6 Å resolution structure, confirming the biological relevance of the VLP structure. Our data revealed that unlike other known nodavirus structures, which have been shown to assemble capsids having trimeric spikes, MrNV assembles a T = 3 capsid with dimeric spikes. We also found a number of surprising similarities between the MrNV capsid structure and that of the Tombusviridae: 1) an extensive network of N-terminal arms (NTAs) lines the capsid interior, forming long-range interactions to lace together asymmetric units; 2) the capsid shell is stabilised by 3 pairs of Ca2+ ions in each asymmetric unit; 3) the protruding spike domain exhibits a very similar fold to that seen in the spikes of the tombusviruses. These structural similarities raise questions concerning the taxonomic classification of MrNV.

The Unexplored Virome of Two Atlantic Coast Fish: Contribution of Next-Generation Sequencing to Fish Virology

“…Interestingly, VNNV is endemic in the Mediterranean Sea, with several reports in fish samples [37][38][39], being in direct communication with the Atlantic Ocean through the Strait of Gibraltar, located at the south of Spain near the Algarve region, where part of this study was focused. In addition, other nodaviruses were also identified, namely the Macrobrachium rosenbergii nodavirus or Penaeus vannamei nodavirus, both pathogens of freshwater crustaceans that pose a threat to food security, and cause significant economic losses in the aquaculture industries [40].…”

Molecular biology of Macrobrachium rosenbergii nodavirus infection in giant freshwater prawn

“…In spite of the distinct genomic sequences that have been observed, the atomic resolution structure of Mr NV unequivocally disputes the correctness of the virus taxonomic classification (Ho et al., ). Unlike the known nodavirus capsids that assemble into trimeric spikes, Mr NV capsids assemble into dimeric spikes, in which the folding of the protruding spike domain displays a very high similarity to tombusviruses in the family of Tombusviridae (Ho et al., ). These findings provoke the reclassification of Mr NV to a proposed new genera.…”

Macrobrachium rosenbergii nodavirus virus‐like particles attach to fucosylated glycans in the gills of the giant freshwater prawn

“…MrNV is a single‐protein capsid non‐enveloped virus, with a single‐stranded RNA+ bipartite genome, and exhibits a T = 3 icosahedral conformation. Phylogenetic and structural analyses based on the amino acid sequences of the RNA2 region encoding the capsid protein suggests that MrNV could be classified in its own genus Gammanodavirus , distinct from the insect and fish infecting Alpha‐ and Betanodavirus genera (Ho et al, 2018; NaveenKumar, Shekar, Karunasagar, & Karunasagar, 2013). MrNV virus‐like particles (MrNV‐VLPs) can be generated from the expression in either bacterial or insect‐based systems of the capsid gene of RNA2, and they appear structurally identical to infectious MrNV virions (Bonami et al, 2005; Bonami & Widada, 2011; Ho, Kueh, Beh, Tan, & Bhella, 2017).…”