Structural plasticity of mumps virus nucleocapsids with cryo-EM structures

Abstract

Mumps virus (MuV) is a highly contagious human pathogen and frequently causes worldwide outbreaks despite available vaccines. Similar to other mononegaviruses such as Ebola and rabies, MuV uses a single-stranded negative-sense RNA as its genome, which is enwrapped by viral nucleoproteins into the helical nucleocapsid. The nucleocapsid acts as a scaffold for genome condensation and as a template for RNA replication and transcription. Conformational changes in the MuV nucleocapsid are required to switch between different activities, but the underlying mechanism remains elusive due to the absence of high-resolution structures. Here, we report two MuV nucleoprotein-RNA rings with 13 and 14 protomers, one stacked-ring filament and two nucleocapsids with distinct helical pitches, in dense and hyperdense states, at near-atomic resolutions using cryo-electron microscopy. Structural analysis of these in vitro assemblies indicates that the C-terminal tail of MuV nucleoprotein likely regulates the assembly of helical nucleocapsids, and the C-terminal arm may be relevant for the transition between the dense and hyperdense states of helical nucleocapsids. Our results provide the molecular mechanism for structural plasticity among different MuV nucleocapsids and create a possible link between structural plasticity and genome condensation.

Molecular mechanisms of stress-induced reactivation in mumps virus condensates

“…Interestingly, both structural classes existed within the same nucleocapsid (Extended Data Fig. 6f), confirming previous studies on MeV and MuV nucleocapsids 36,37 that lead to a hypothesis of a regulatory role of the C-terminus of N in transcription and replication of paramyxoviridae 38,39 . Indeed, tighter packing of subunits in the minority class resulted in an 8.4 Å shift of a loop in the upper subunits towards the lower subunits, resulting in less surface-exposed RNA binding pocket (Fig.…”

“…The two maps reflect the structural plasticity of N 12,35,37,40 (Supplementary Discussion), which has been previously suggested to contribute to different functional outcomes: protection of the viral genome from the host defense versus genome accessibility to promote viral replication. The tighter nucleocapsid structure of the minority class would protect the RNA from the host antiviral response, or may constitute a compacted state ready for virion assembly and release.…”

Insights into Paramyxovirus Nucleocapsids from Diverse Assemblies

“…Among the 78 paramyxovirus nucleoproteins, 7 of them have been resolved in the context of their respective nucleocapsids at near-atomic resolutions via either X-ray crystallography or cryo-electron microscopy (cryo-EM) (Figure 2) [9][10][11][12][13][14][15]. Conforming well with the idea of high sequence similarity, these paramyxovirus nucleoproteins exhibit a high structural similarity with a root-mean-square-deviation (R.M.S.D) of less than 1.3 Å.…”

“…The N-arm connects the core of the NTD via an extended loop (Loop 20-46 ). The Loop 20-46 is surprisingly inflexible in structure and has been found at high resolution in almost every well-resolved paramyxovirus nucleocapsid (Figure 2) [9][10][11][12][13][14][15]. The CTD of a paramyxovirus nucleoprotein has about 200 residues and also exists in a globular shape.…”

“…In the MeV nucleoprotein, the cleft is composed of several residues, such as T 183 , K 180 , R 194 , R 195 , Q 202 , Y 260 , A 267 , and R 354 [12,19]. These charged residues are quite conserved among all paramyxovirus nucleoproteins and are essential to bind the negatively charged RNA nucleotides via electrostatic interactions [9][10][11][13][14][15]. Each nucleoprotein binds six nucleotides in a "three-bases-in, three-bases-out" pattern [20,21].…”