The intracellular virus-host interface of henipaviruses

Abstract

The Henipavirus genus comprises five viral species, of which the prototype members, Hendra virus (HeV) and Nipah virus (NiV), are reported to infect humans. In humans and other spill-over hosts, HeV/NiV can cause severe respiratory and/or encephalitic disease, with mortality rates exceeding 50%; currently, there are no approved human vaccines and only limited therapeutic options. As members of the family Paramyxoviridae, henipaviruses have six "core" structural proteins and typically three additional accessory proteins that are expressed from the P gene. Several of these proteins are multifunctional, with roles in forming intracellular interfaces with the host (in particular, M, P, V, W, and C proteins), to modulate processes including antiviral responses, supporting viral replication. Understanding the molecular basis of these interfaces and their functions is critical to delineate the mechanisms of pathogenesis and may inform new strategies to combat infection and disease. Recent research has significantly advanced the understanding of the functions and interactions of multifunctional intracellular henipavirus proteins, including revealing novel roles in subverting the nucleolar DNA damage response (DDR) and modulating the functions of 14-3-3 proteins. This review will discuss the intracellular virus-host interface, focusing on the M, P, V, W, and C proteins of HeV/NiV, with a focus on recently identified functions and interactions.

Keywords: Hendra virus; Nipah virus; henipavirus; immune evasion; viral proteins; virus-host interface.

Fig 1

Transmission patterns of HeV and NiV. HeV has spilled over from fruit bats to horses, with some cases leading to human infections by HeV genotype 1 (3). NiV-Malaysia infected humans following spillover to pigs during an outbreak in Malaysia and Singapore. NiV-Bangladesh has infected humans via the consumption of date palm sap/fruit, likely contaminated by infected bats before further spreading via human-to-human transmission (2). A suspected NiV outbreak in the Philippines involved horse-to-human transmission, followed by human-to-human transmission (8).

Fig 2

HeV/NiV genome and virion structure. (A) The HeV/NiV genome contains six genes (from 3’ to 5’: N, P, M, F, G, L; P encodes P protein and V, W, and C accessory proteins) (22). (B) N protein associates with the single-stranded RNA genome (ssRNA) to form the nucleocapsid; P protein is a cofactor of L protein, the catalytic component of the RdRp; together, P and L constitute the functional RdRp complex. M protein associates with the inner leaflet of the envelope and is critical for virion budding (22). G and F proteins are transmembrane proteins embedded in the envelope that mediate receptor binding and promote fusion with cellular membranes, respectively. HeV/NiV proteins also have various host cell interactions/modulatory roles, and several can traffic to different cellular compartments including the nucleus (M, V, W, and C proteins) and nucleolus (M protein) (see text).

Fig 3

Type I IFN response to infection by RNA viruses and antagonism by henipavirus proteins. (A) IFN induction: following infection, viral RNA products (e.g., double-stranded (dsRNA), uncapped RNA) are detected by pattern-recognition receptors (PRRs), including RIG-I like receptors (RLRs; cytoplasmic receptors including retinoic acid–inducible gene I [RIG-I], melanoma differentiation-associated protein 5 [MDA5], and laboratory of Genetics and Physiology 2 [LGP2]) and Toll-like receptors (TLRs; transmembrane receptors that include endosomal TLR3 and TLR7/8) (26). RLRs are regulated by proteins including Tripartite motif 25 (TRIM25) for RIG-I; Phosphatase 1 α/γ (PP1α/γ) for MDA5; and LGP2, for both RIG-I and MDA5 (32–35). Activated PRRs interact with adapter proteins (e.g., RIG-I/MDA5 with MAVS; TLR7/8 with MyD88; TLR3 with TRIF [not shown, dashed lines]) (26), regulators of which include UBX domain-containing protein 1 (UBXN1) for MAVS (36). These adaptors recruit and activate signaling factors including kinases (e.g., Inhibitor of κB kinases [IKKs] and TANK binding kinase 1 [TBK1]), leading to phosphorylation of transcription factors including IFN-regulatory factors (IRFs) 3 and 7, and nuclear factor κB (not shown). IRFs enter the nucleus and bind to promoter regions to induce antiviral genes, including Type I IFNs (26). Viral antagonism: NiV V protein directly binds and inhibits RIG-I/MDA5 and regulates TRIM25/PP1α/γ/LGP2 to inhibit RIG-I/MDA5 activation (33, 34, 37, 38). V protein also stabilizes UBXN1 (which inhibits MAVS [36]), directly targets MAVS for degradation (39), and binds and inhibits IRF7 (40). C protein interacts with and inhibits IKKα (preventing IKKα-mediated phosphorylation/activation of IRF7) (41). W protein inhibits TBK1- and IKKε-dependent IRF3 phosphorylation (42). M protein inhibits TRIM6 (ubiquitin ligase regulator of IKKε), thereby suppressing IRF3 activation (43). (B) IFN signaling: Following production and release from cells, Type I IFN signals in autocrine or paracrine fashion by binding to the Type I IFN receptor (IFNAR), which activates receptor-associated Janus kinases (JAKs) that phosphorylate STAT1 (Signal Transducers and Activators of Transcription 1) and STAT2 at conserved tyrosine residues. Activated phospho-STAT1/2 dimerize, translocate to the nucleus, and, in a complex with IRF9, bind to genomic IFN-stimulated response elements (ISREs) to regulate the transcription of IFN-stimulated genes (ISGs) (44). Viral antagonism: P, V, W, and N proteins inhibit STAT1/2 responses (45, 46).

Fig 4

Henipavirus M protein localizes to the nucleus/nucleolus to form specific host protein interfaces. (A) Nucleocytoplasmic and nucleolar localization. HeV/NiV M protein can traffic between the cytoplasm, nucleus, and nucleolar compartments, via interactions including IMPα, XPO1, and potentially intranucleolar proteins such as Treacle (which is enriched in FC/DFC) (58), resulting in a dynamic localization (see text). (B) Interactors and key residues of HeV/NiV M protein (43). Residue R57 is important for M protein oligomerization (92). M protein also contains a NES and two characterized NLSs enabling nucleocytoplasmic trafficking (52, 57). Ubiquitination of residue K258 in the M protein bpNLS is mediated by RAD18, which facilitates the transfer of ubiquitin from the E2 ubiquitin-conjugating enzyme RAD6A (61); this ubiquitination regulates nuclear shuttling, required for efficient viral egress and host modulation. M protein interacts with Treacle to inhibit rRNA synthesis (58) and TRIM6 to suppress IFN induction (43).

Fig 5

The HeV/NiV P gene encodes multiple proteins through RNA editing and alternate reading frames. The HeV/NiV P gene generates mRNA encoding P protein through faithful transcription, or V or W through the insertion of additional Gs by the viral RdRp at a defined RNA editing site, creating a + 1 (i.e., insertion of 1, 4, 7, etc. Gs) or +2 (insertion of 2, 5, 8, etc. Gs) reading frame, respectively; insertion of multiples of three Gs (3, 6, 9, etc. that maintain the reading frame) result in expression of P protein (107). The altered reading frame downstream of the editing site for V or W protein transcripts results in translation of proteins with a common N-terminal region (NTR) (405 amino acids for HeV and 407 for NiV) and different C-terminal regions (CTR) (65, 74). Known host cell/viral interactors and localization sequences (based on NiV) are shown; those shared between the proteins are shown in red and those that are unique in black (see Table 1 for references). The NES is conserved in P, V, and W but only appears to impact the localization of V and W (74). P protein binds to L and N via its unique multimerization domain and X domain as shown (106, 108), and additionally binds N via residues in the NTR (106) (it has not been reported if these residues in V and W also bind N). Translation of P mRNA from an internal alternate start codon (using a + 2 reading frame within the region encoding the P/V/W NTR) produces C protein (23).