The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism

Nai-Chi Chen^1*, Masato Yoshimura¹, Naoyuki Miyazaki^2,3, Hong-Hsiang Guan¹, Phimonphan Chuankhayan¹, Chien-Chih Lin¹, Shao-Kang Chen^1,4, Pei-Ju Lin^1,5, Yen-Chieh Huang¹, Kenji Iwasaki^2,3, Atsushi Nakagawa², Sunney I. Chan^6,7, Chun-Jung Chen^1,4,8

¹Life Science Group, National Synchrotron Radiation Research Center, Hsinchu, Taiwan
²Institute for Protein Research, Osaka University, Osaka, Japan
³Life Science Center for Survival Dynamics, University of Tsukuba, Ibaraki, Japan
⁴Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan
⁵Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
⁶Institute of Chemistry, Academia Sinica, Taipei, Taiwan
⁷Noyes Laboratory, California Institute of Technology, CA, USA
⁸Department of Physics, National Tsing Hua University, Hsinchu, Taiwan

* Presenter:Nai-Chi Chen, email:siriustan@gmail.com

Aquaculture is one of the major global economic activities, such as cultivation of marine fish and prawn, in many countries. Taiwan, an island country, is one of the major distant water fisheries and aquaculture producers in the world. The farmed fishes, such as milkfish, tilapia, grouper, giant freshwater prawn and pacific white shrimp, play important roles in export economic importance in Taiwan. However, disease is a major impact on shrimp aquaculture since shrimp farming became a significant commercial entity in this century. Major pathogens of viruses, bacteria, protozoa and fungi have emerged as serious diseases of farmed shrimp. 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. The obtained detailed crystal and cryo-EM structures of shrimp nodavirus capsids and its specific domains can also be filed to provide the new insights to develop an appropriate treatment against these two viruses in shrimp farming industry.

Keywords: Shrimp nodavirus, cryo-EM, protein X-ray crystallography, virus-like particle