Negri bodies and other virus membrane-less replication compartments

Abstract

Viruses reshape the organization of the cell interior to achieve different steps of their cellular cycle. Particularly, viral replication and assembly often take place in viral factories where specific viral and cellular proteins as well as nucleic acids concentrate. Viral factories can be either membrane-delimited or devoid of any cellular membranes. In the latter case, they are referred as membrane-less replication compartments. The most emblematic ones are the Negri bodies, which are inclusion bodies that constitute the hallmark of rabies virus infection. Interestingly, Negri bodies and several other viral replication compartments have been shown to arise from a liquid-liquid phase separation process and, thus, constitute a new class of liquid organelles. This is a paradigm shift in the field of virus replication. Here, we review the different aspects of membrane-less virus replication compartments with a focus on the Mononegavirales order and discuss their interactions with the host cell machineries and the cytoskeleton. We particularly examine the interplay between viral factories and the cellular innate immune response, of which several components also form membrane-less condensates in infected cells.

Keywords: Innate immunity; Interferon; Liquid organelle; Membrane-less compartment; Viral factory; Viral replication.

Fig. 1

Diversity of viro-induced compartments. Those compartments are viral factories that host essential steps of the viral cycle and shield viral components from host defenses. These viral replication compartments can be membrane-delimited or membrane-less compartments.

Fig. 2

Structures of rhabdovirus (VSV) and paramyxovirus (MeV) nucleoproteins. A) Bar diagram showing the domain organization of VSV nucleoprotein. NTD stands for N-terminal domain CTD and CTD for C-terminal domain. B) Structure of VSV nucleoprotein. Left part: Space-filling model of VSV N-RNA complex (X-Ray structure of a 10 N subunit ring (in shades of purple) associated with 90 RNA bases (in red) (2GIC.pdb) [158]. Each VSV N subunit interacts with 9 RNA bases. In this conformation, the RNA molecule is clamped at the interface of the NTD and the CTD. Each N subunit is shown in a different color indicating that the NTD arm from the nth subunit reaches over to the (n − 1)th sub-unit and its CTD arm reaches over to the (n + 1)th sub-unit. This arrangement leads to the interaction of both (n + 1)th NTD and (n − 1)th CTD with each other and the surface of sub-unit nth. Middle part: Ribbon diagram of a N protomer associated with 9 RNA bases (in orange). Two small subdomains (NTD arm and CTD arm) emerge from NTD (in purple) and CTD (in green) resp. Right part: Ribbon diagram of VSV N°P RNA free structure (3PMK.pdb) [44]. VSV NΔ21 (lacking the NTD arm) was crystallized in complex with the 60 first residues of VSV P (P₆₀) in orange. P₆₀ folds upon binding to N and avoid RNA binding by filling the RNA-binding groove of N. C) Bar diagram showing the domain organization of MeV nucleoprotein. Same abbreviations than in A; MoRE stands for molecular recognition element. D) Structure of MeV Nucleoprotein. Left part: Space-filling model of the structure of the MeV N_core-RNA helical nucleocapsid (side view and top view) obtained by cryoEM (4UFT.pdb) [159]. The top view allows the visualization of the protomers. The RNA molecule is in red. Middle part: Ribbon diagram of a MeV N_core promoter associated with 6 RNA bases (in red). Right part: Ribbon diagram of MeV N°P RNA free complex (5E4V.pdb [45]). N_core (lacking the 21 first amino acids) was crystallized in complex with the 48 first residues of P (P₄₈). P₄₈ chaperone N°, preventing both binding to RNA and self-assembly.

Fig. 3

Structures of rhabdoviruses (RABV and VSV) and paramyxovirus (MeV) phosphoproteins. A) Bar diagram showing the conserved domain organization of RABV and VSV P. NTD stands for N-terminal domain and CTD for C-terminal domain. IDD is for intrinsically disordered domain and DD for dimerization domain. B) RABV P dimer. Only the X-ray structures of its dimerization domain (3L32.pdb and CTD (1VYI.pdb [50]) are known so far. RABV L interacts with the IDD1 of P. L is composed of an RNA-dependent RNA polymerase (RdRp) domain, capping (CAP) domain, connector domain (CD), methyltransferase (MT) domain, and C-terminal domain (CTD) (6UEB.pdb [47]). C) VSV P dimer. The X-ray structure of the dimerization domain is indicated (2FQM.pdb [53]). The CTD (2K47.pdb [160]) binds to N-RNA complex. VSV L interacts with the N-terminal part of P (6U1X.pdb [46]). VSV RNA free N sub-units interacts with the P NTD (3PMK.pdb [44]) preventing RNA binding in the N RNA cavity. D) Bar diagram showing the modular organization of MeV P. Same abbreviations than in A. TD strands for tetramerization domain. E) MeV P tetramer associates via its oligomerization domain (3ZDO.pdb [161]).The P NTD binds to the N° RNA free sub-units (5E4V.pdb [45]). The XD C-terminal domain of P folds into a small helix bundle that interacts with a MoRE located in the extremity of the N_tail domain of N-RNA nucleocapsid (1T6O.pdb [162])_.