Structure and assembly of double-headed Sendai virus nucleocapsids

Na Zhang,Liuyan Yang,Wenzhi Sun,Tianhao Li,Lei Qi,Mingdong Liu,Yunhui Liu,Xiaofeng Chu,Xin Su,Rui Luo,Hong Shan,Qing-Tao Shen,Rui Wang

doi:10.1038/s42003-021-02027-y

Abstract

Paramyxoviruses, including the mumps virus, measles virus, Nipah virus and Sendai virus (SeV), have non-segmented single-stranded negative-sense RNA genomes which are encapsidated by nucleoproteins into helical nucleocapsids. Here, we reported a double-headed SeV nucleocapsid assembled in a tail-to-tail manner, and resolved its helical stems and clam-shaped joint at the respective resolutions of 2.9 and 3.9 Å, via cryo-electron microscopy. Our structures offer important insights into the mechanism of the helical polymerization, in particular via an unnoticed exchange of a N-terminal hole formed by three loops of nucleoproteins, and unveil the clam-shaped joint in a hyper-closed state for nucleocapsid dimerization. Direct visualization of the loop from the disordered C-terminal tail provides structural evidence that C-terminal tail is correlated to the curvature of nucleocapsid and links nucleocapsid condensation and genome replication and transcription with different assembly forms.

Highlights

Paramyxoviruses, including the mumps virus, measles virus, Nipah virus and Sendai virus (SeV), have non-segmented single-stranded negative-sense RNA genomes which are encapsidated by nucleoproteins into helical nucleocapsids
Both the N-terminal domain (NTD) and C-terminal domain (CTD) have subdomains known as arms (N-arm and C-arm, respectively), which enable paramyxovirus nucleoproteins to undertake a “domain swapping” process that enables their assembly into either ring-like structures in parainfluenza virus 5 (PIV5) or helical filaments in measles virus (MeV)[6,7,8]
Expanding beyond the known helical nucleocapsids, we recently described a clam-shaped assembly of the nucleoprotein from Newcastle disease virus (NDV), wherein two single-turn spirals are packed in a tail-to-tail way[9]

Summary

Introduction

Paramyxoviruses, including the mumps virus, measles virus, Nipah virus and Sendai virus (SeV), have non-segmented single-stranded negative-sense RNA genomes which are encapsidated by nucleoproteins into helical nucleocapsids. The interdomain cleft comprises conserved positively charged residues which function to promote clamping to nucleotides of the RNA genome, with no apparent specificity[5] Both the NTD and CTD have subdomains known as arms (N-arm and C-arm, respectively), which enable paramyxovirus nucleoproteins to undertake a “domain swapping” process that enables their assembly into either ring-like structures in parainfluenza virus 5 (PIV5) or helical filaments in measles virus (MeV)[6,7,8]. Each single-turn spiral in NDV clam-shaped assembly is similar to MeV helical nucleocapsid and enwraps one RNA molecule between NTD and CTD in a “3-bases-in, 3-bases-out” conformation. Given the understanding that biomedical technologies based on SeV have great potential for treating various cancers, obtaining detailed information for the SeV nucleoprotein structure and assembly process will both deepen a basic understanding of the underlying mechanism of SeV pathogenesis and guide efforts to develop novel anti-cancer therapies

Methods

Results

Conclusion