The Nucleocapsid of Paramyxoviruses: Structure and Function of an Encapsidated Template

Abstract

Viruses of the Paramyxoviridae family share a common and complex molecular machinery for transcribing and replicating their genomes. Their non-segmented, negative-strand RNA genome is encased in a tight homopolymer of viral nucleoproteins (N). This ribonucleoprotein complex, termed a nucleocapsid, is the template of the viral polymerase complex made of the large protein (L) and its co-factor, the phosphoprotein (P). This review summarizes the current knowledge on several aspects of paramyxovirus transcription and replication, including structural and functional data on (1) the architecture of the nucleocapsid (structure of the nucleoprotein, interprotomer contacts, interaction with RNA, and organization of the disordered C-terminal tail of N), (2) the encapsidation of the genomic RNAs (structure of the nucleoprotein in complex with its chaperon P and kinetics of RNA encapsidation in vitro), and (3) the use of the nucleocapsid as a template for the polymerase complex (release of the encased RNA and interaction network allowing the progress of the polymerase complex). Finally, this review presents models of paramyxovirus transcription and replication.

Structural landscape of the Respiratory Syncytial Virus nucleocapsids

“…Similarly to other Mononegavirales 20,21 , the N- and C-terminal extensions of RSV N, termed NTD-arm (residues 1-36) and CTD-arm (residues 360-391) (Figure 1h), interact with the laterally adjacent N protomers thereby stabilising their oligomeric assembly on the RNA strand by subdomain swapping (Figure 2a). The visible part of the CTD-arm of N i lies on top of the CTD of N i+1 implying that in a helical NC it should be situated in between consecutive turns 4 .…”

“…All Mononegavirales NCs are left-handed helices, with the CTDs and the 3'-end of the RNA oriented towards the pointed end of the filaments and the NTDs and the 5'-end towards the barbed ends 20 . The paramyxoviral clam-shaped assemblies were proposed to seed the growth of the double-headed helices from the 5' to the 3' end, protect the 5' end from nucleases 10 and support encapsidation of several NCs per virion 24 , also documented for RSV 19,25 .…”

CryoEM of Viral Ribonucleoproteins and Nucleocapsids of Single-Stranded RNA Viruses

“…Other RNP-like particle structures have been solved in recent years by cryoEM for other paramyxoviruses (e.g., a cetacean morbillivirus or Sendai virus) [ 44 , 45 ]. Additional reviews specific to the nucleocapsid structure of paramyxoviruses can be found in [ 37 , 46 , 47 ].…”

The cryoEM structure of theHendra henipavirusnucleoprotein reveals insights into paramyxoviral nucleocapsid architectures

“…For example, the HeV N protein α5-loop region contains two amino acid substitutions compared with the NiV N protein; L108V and E137D, both of which are solvent exposed [32]. Whether there is a functional relevance to these substitutions is unknown, however in the context of a helical nucleocapsid the α5-loop region is the main solvent exposed section of the N protomer and may be important for interactions with the RdRp complex during transcription and replication, or could potentially interface in-phase with the M protein lattice during virion assembly, as proposed for other paramyxoviruses [17][18][19]. Furthermore, the α5-loop region has also been identified as the main interface in intercalating interactions in the HeV N protein assembly (Figure 5), as well as in clamshell formation in NDV, NiV, and SeV nucleocapsid-like filaments (NLFs) [32,37,38].…”

“…The nucleocapsid associates with the viral RNA dependent RNA polymerase (RdRp) comprising the large (L) and phospho (P) proteins to form the holonucleocapsid. The N-RNA interaction is critical for virus multiplication as genomic RNA is only recognised by the RdRp as a template for mRNA transcription and genome replication when in the context of the assembled nucleocapsid (reviewed in [17]), and incorporation of genomic RNA into new virions depends on interactions between N protein within the nucleocapsid and the viral matrix (M) protein [17–19].…”