Structural basis for dsRNA recognition and interferon antagonism by Ebola VP35

Leung, Daisy W.; Prins, Kathleen C.; Borek, Dominika; Farahbakhsh, Mina; Tufariello, Jo Ann M.; Ramanan, Parameshwaran; Nix, Jay C.; Helgeson, Luke A.; Otwinowski, Zbyszek; Honzatko, Richard B.; Basler, Christopher F.; Amarasinghe, Gaya K.

doi:10.1038/nsmb.1765

Cited by 180 publications

(419 citation statements)

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“…Ebolavirus proteins contain a significant fraction (20%) of structurally disordered regions, and the fraction of variable positions in these regions is significantly higher (p < 0.01) than in the structurally ordered regions. The 3D structures of globular regions are mostly known (Table S2) [54][55][56][57][58][59][60][61][62][63][64][65][66][67][68][69][70][71] except for the N-terminal zinc-finger domain of VP30, the coiled-coil domain of VP35, and protein L. Identification and analysis of structurally characterized homologs allowed us to predict the structure of the zinc-finger domain in VP30, the overall topology of NP, and the structure and catalytic sites for the catalytic domains of protein L.…”

Section: Resultsmentioning

confidence: 99%

Predictive and comparative analysis of Ebolavirus proteins

2015

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Ebolavirus is the pathogen for Ebola Hemorrhagic Fever (EHF). This disease exhibits a high fatality rate and has recently reached a historically epidemic proportion in West Africa. Out of the 5 known Ebolavirus species, only Reston ebolavirus has lost human pathogenicity, while retaining the ability to cause EHF in long-tailed macaque. Significant efforts have been spent to determine the three-dimensional (3D) structures of Ebolavirus proteins, to study their interaction with host proteins, and to identify the functional motifs in these viral proteins. Here, in light of these experimental results, we apply computational analysis to predict the 3D structures and functional sites for Ebolavirus protein domains with unknown structure, including a zinc-finger domain of VP30, the RNA-dependent RNA polymerase catalytic domain and a methyltransferase domain of protein L. In addition, we compare sequences of proteins that interact with Ebolavirus proteins from RESTV-resistant primates with those from RESTV-susceptible monkeys. The host proteins that interact with GP and VP35 show an elevated level of sequence divergence between the RESTV-resistant and RESTV-susceptible species, suggesting that they may be responsible for host specificity. Meanwhile, we detect variable positions in protein sequences that are likely associated with the loss of human pathogenicity in RESTV, map them onto the 3D structures and compare their positions to known functional sites. VP35 and VP30 are significantly enriched in these potential pathogenicity determinants and the clustering of such positions on the surfaces of VP35 and GP suggests possible uncharacterized interaction sites with host proteins that contribute to the virulence of Ebolavirus.

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Section: Resultsmentioning

confidence: 99%

Predictive and comparative analysis of Ebolavirus proteins

2015

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“…Structural and biochemical studies on Zaire EBOV (ZEBOV) and Reston EBOV (REBOV) VP35 IFN inhibitory domains (IID) (termed zVP35 and zIID or rVP35 and rIID, for VP35 protein and IID, respectively) in free and dsRNA-bound forms identified a number of functionally critical basic residues (21,(26)(27)(28). These are located in the central basic patch (CBP) in the β-sheet subdomain and the first basic patch (FBP) in the α-helical subdomain (21,(26)(27)(28). Based on the dsRNA-bound structures of VP35 IIDs, it was suggested that these basic patches are important for protein-protein and protein-RNA interactions (21,27,28).…”

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confidence: 99%

“…These are located in the central basic patch (CBP) in the β-sheet subdomain and the first basic patch (FBP) in the α-helical subdomain (21,(26)(27)(28). Based on the dsRNA-bound structures of VP35 IIDs, it was suggested that these basic patches are important for protein-protein and protein-RNA interactions (21,27,28). Consistent with this, mutation of CBP residues abrogates the dsRNA-binding and IFN-inhibitory activities of zVP35 and greatly attenuated virus replication in IFN-competent cells and in vivo (15,21,27,29).…”

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confidence: 99%

“…These include inhibition of IFN production through double-stranded (ds)RNA sequestration and inhibition of IFN regulatory factor (IRF) 3/IRF7 phosphorylation by direct association with kinases that activate IRF3/IRF7, IKKe/TBK-1 (13,15,21,25). Structural and biochemical studies on Zaire EBOV (ZEBOV) and Reston EBOV (REBOV) VP35 IFN inhibitory domains (IID) (termed zVP35 and zIID or rVP35 and rIID, for VP35 protein and IID, respectively) in free and dsRNA-bound forms identified a number of functionally critical basic residues (21,(26)(27)(28). These are located in the central basic patch (CBP) in the β-sheet subdomain and the first basic patch (FBP) in the α-helical subdomain (21,(26)(27)(28).…”

mentioning

confidence: 99%

“…EBOV VP35 interacts with several components of innate antiviral defenses, including retinoic-acid inducible gene-I (RIG-I)-like receptor (RLR) pathways that lead to IFN production (13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24). These include inhibition of IFN production through double-stranded (ds)RNA sequestration and inhibition of IFN regulatory factor (IRF) 3/IRF7 phosphorylation by direct association with kinases that activate IRF3/IRF7, IKKe/TBK-1 (13,15,21,25). Structural and biochemical studies on Zaire EBOV (ZEBOV) and Reston EBOV (REBOV) VP35 IFN inhibitory domains (IID) (termed zVP35 and zIID or rVP35 and rIID, for VP35 protein and IID, respectively) in free and dsRNA-bound forms identified a number of functionally critical basic residues (21,(26)(27)(28).…”

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confidence: 99%

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Structural basis for Marburg virus VP35–mediated immune evasion mechanisms

Ramanan

Edwards

Shabman

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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120

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Filoviruses, marburgvirus (MARV) and ebolavirus (EBOV), are causative agents of highly lethal hemorrhagic fever in humans. MARV and EBOV share a common genome organization but show important differences in replication complex formation, cell entry, host tropism, transcriptional regulation, and immune evasion. Multifunctional filoviral viral protein (VP) 35 proteins inhibit innate immune responses. Recent studies suggest double-stranded (ds)RNA sequestration is a potential mechanism that allows EBOV VP35 to antagonize retinoic-acid inducible gene-I (RIG-I) like receptors (RLRs) that are activated by viral pathogen-associated molecular patterns (PAMPs), such as double-strandedness and dsRNA blunt ends. Here, we show that MARV VP35 can inhibit IFN production at multiple steps in the signaling pathways downstream of RLRs. The crystal structure of MARV VP35 IID in complex with 18-bp dsRNA reveals that despite the similar protein fold as EBOV VP35 IID, MARV VP35 IID interacts with the dsRNA backbone and not with blunt ends. Functional studies show that MARV VP35 can inhibit dsRNA-dependent RLR activation and interferon (IFN) regulatory factor 3 (IRF3) phosphorylation by IFN kinases TRAF family member-associated NFkb activator (TANK) binding kinase-1 (TBK-1) and IFN kB kinase e (IKKe) in cell-based studies. We also show that MARV VP35 can only inhibit RIG-I and melanoma differentiation associated gene 5 (MDA5) activation by double strandedness of RNA PAMPs (coating backbone) but is unable to inhibit activation of RLRs by dsRNA blunt ends (end capping). In contrast, EBOV VP35 can inhibit activation by both PAMPs. Insights on differential PAMP recognition and inhibition of IFN induction by a similar filoviral VP35 fold, as shown here, reveal the structural and functional plasticity of a highly conserved virulence factor.T he Filoviridae family of viruses, which includes marburgvirus (MARV) and ebolavirus (EBOV), can cause intermittent outbreaks that often result in high fatality rates (1). The family consists of five species of EBOV, Zaire, Reston, Sudan, Taï Forest, and Bundibugyo; one species of MARV; and a proposed genus Cuevavirus possessing a single species Lloviu cuevavirus (2). Despite overall similarities in genome size and organization, virion structure, and disease characteristics (3), EBOV and MARV exhibit important differences, including their strategies for immune evasion (4). For example, although EBOV viral protein (VP) 24 and MARV VP40 counter IFN signaling, neither MARV VP24 nor EBOV VP40 appears to function similarly to its corresponding counterparts with regard to immune evasion (5-10).Filoviruses also counteract innate immunity through the multifunctional VP35 proteins, which perform critical roles in viral RNA synthesis, virus assembly, and virus structure (reviewed in refs. 11 and 12). EBOV VP35 interacts with several components of innate antiviral defenses, including retinoic-acid inducible gene-I (RIG-I)-like receptor (RLR) pathways that lead to IFN production (13-24). These include inhibition of ...

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