VP40

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0003723 RNA binding	IEA GO_REF:0000043	ACCEPT	Summary: The octameric ring form of VP40 binds a specific single-stranded RNA sequence in a pocket formed at the dimer-dimer interface, so the keyword-derived RNA-binding term is correct and is a genuine second activity alongside the matrix function. Reason: The 1.6 A crystal structure of the VP40 N-terminal domain octamer was solved in complex with RNA, and the octamer is detectable in infected cells, so this is not an in vitro artefact. UniProt assigns the octamer to genome replication and RNA binding, distinguishing it from the hexameric form that performs budding. The term is at the right granularity: the ligand is a short single-stranded sequence rather than a defined functional RNA class. Supporting Evidence: PMID:12679020 This strongly indicates, together with the RNA binding properties of full-length oligomeric VP40 in vitro, that octameric VP40 bound to a specific RNA sequence plays a role in the virus life cycle. file:genes/EBOZM/VP40/VP40-uniprot.txt Octamers function in genome replication and RNA binding (PubMed:12919741).
GO:0005515 protein binding	IPI PMID:33673144 Ubiquitin Ligase SMURF2 Interacts with Filovirus VP40 and Pr...	MODIFY	Summary: The interaction recorded here is with the HECT E3 ubiquitin ligase SMURF2, engaged through the VP40 PPxY late-budding motif; a specific ubiquitin-ligase-binding term carries that information, whereas bare protein binding does not. Reason: Bare GO:0005515 is uninformative, and under the protein-binding policy it should be replaced where the cited paper supports a more specific molecular function. It does here: GST pulldowns map the interaction to the multiple WW domains of SMURF2 and show it is PPxY-dependent, and SMURF2 knockdown inhibits VP40 VLP egress, so VP40 is acting as a PPxY ligand for a host E3 ubiquitin ligase. GO:0031625 ubiquitin protein ligase binding also covers the same VP40 activity towards NEDD4, WWP1 and ITCH recorded in UniProt, so the replacement generalises correctly rather than being paper-specific. Proposed replacements: ubiquitin protein ligase binding Supporting Evidence: PMID:33673144 We go on to show by GST pulldown assays that the multiple WW domains of SMURF2 interact with eVP40 and mVP40 in a PPxY-dependent manner. file:genes/EBOZM/VP40/VP40-uniprot.txt a PPXY motif which interacts with the WW domain 3 of NEDD4 E3 ubiquitin ligase and the three WW domains of SMURF2 E3 ubiquitin ligase
GO:0005576 extracellular region	IEA GO_REF:0000044	MODIFY	Summary: The extracellular pool of VP40 is specifically the exosomal pool, so the curated location supports the more precise extracellular exosome term. Reason: The SubCell term behind this mapping is "Secreted, extracellular exosome", curated from an experimental study (ECO:0000269) showing VP40 packaged into exosomes that reduce recipient immune-cell viability. GO:0070062 extracellular exosome is a descendant of GO:0005576 and is exactly what the curated statement asserts; leaving the row at extracellular region loses the vesicle identity, which is the biologically interesting part (it is also what links this location to the dysregulated extracellular-vesicle biogenesis seen in PMID:30169850). This is a peripheral, not a core, location for VP40. Proposed replacements: extracellular exosome Supporting Evidence: file:genes/EBOZM/VP40/VP40-uniprot.txt Secreted, extracellular exosome file:genes/EBOZM/VP40/VP40-uniprot.txt May play a role in immune cell dysfunction by being packaged into exosomes that can decrease the viability of recipient cells
GO:0020002 host cell plasma membrane	EXP PMID:21987757 Characterization of filovirus protein-protein interactions i...	ACCEPT	Summary: Bimolecular complementation imaging showed VP40-VP40 complexes concentrated at the plasma membrane of mammalian cells, which is where the matrix assembles. Reason: This is a direct, sub-compartment-resolved observation in living mammalian cells, and it distinguishes the VP40-VP40 signal (plasma membrane) from the VP40-NP and NP-NP signal (dispersed cytoplasmic), so the plasma-membrane assignment is not a bulk-membrane default. It agrees with every other localisation study of VP40 and is the location of the core activity. Supporting Evidence: PMID:21987757 We demonstrate that VP40-VP40 complexes localized predominantly at the plasma membrane, whereas VP40-NP and NP-NP complexes displayed a more dispersed pattern throughout the cytoplasm.
GO:0020002 host cell plasma membrane	EXP PMID:26753796 The Ebola Virus matrix protein, VP40, requires phosphatidyli...	ACCEPT	Summary: VP40 requires the plasma-membrane-restricted lipid PI(4,5)P2 for extensive oligomerisation at the cell surface and for VLP egress, confirming the plasma membrane as its functional site. Reason: Depletion of PI(4,5)P2 with a plasma-membrane-targeted 5-phosphatase increased the EGFP-VP40 diffusion coefficient and shifted the oligomer distribution from 12-mer-and-above towards monomer-hexamer at the cell surface, with the catalytically inactive phosphatase having no effect. Since PI(4,5)P2 is essentially confined to the plasma membrane inner leaflet, this is lipid-specific confirmation of the plasma-membrane location rather than a generic membrane association. Supporting Evidence: PMID:26753796 VP40 is the most abundant protein in EBOV virions and can form authentic looking virus like particles (VLPs) that bud from the plasma membrane of live cells in the absence of other EBOV proteins PMID:26753796 The subcellular location of PI(4,5)P2 is restricted to the plasma membrane inner leaflet (major)
GO:0020002 host cell plasma membrane	EXP PMID:28768865 Ubiquitin Ligase WWP1 Interacts with Ebola Virus VP40 To Reg...	ACCEPT	Summary: Confocal colocalisation of VP40 with the host E3 ligase WWP1 placed VP40 at budding sites on the plasma membrane. Reason: The colocalisation was observed at the plasma membrane of cotransfected cells and depended on the WWP1 WW domains, so the signal reports the functional VP40 pool engaging its host ligase at the budding site rather than bulk membrane staining. Consistent with all other VP40 localisation data and with the UniProt curated host cell membrane location. Supporting Evidence: PMID:28768865 results from confocal microscopy experiments demonstrated that WWP1 colocalizes with eVP40 at the site of budding at the plasma membrane in a WW-domain-dependent manner
GO:0020002 host cell plasma membrane	IEA GO_REF:0000044	ACCEPT	Summary: Keyword/SubCell mapping of the curated UniProt "Host cell membrane" location, which for Q05128 is itself backed by three experimental papers. Reason: The SubCell term SL-0375 is annotated on Q05128 with ECO:0000269 evidence from PubMed:21987757, PubMed:26753796 and PubMed:28768865, all of which are separately present in this review as EXP rows for the same term. The electronic mapping therefore reproduces an experimentally grounded location at the correct granularity, and it reinforces rather than duplicates the EXP rows. Supporting Evidence: file:genes/EBOZM/VP40/VP40-uniprot.txt Host cell membrane {ECO:0000269\|PubMed:21987757,
GO:0020002 host cell plasma membrane	ISS GO_REF:0000024	ACCEPT	Summary: Transfer from Marburg virus VP40 (P35260), which carries the additional detail that the protein is a peripheral protein on the cytoplasmic side of the membrane. Reason: The donor is the orthologous filovirus matrix protein in the same Filoviridae VP40 family, and the inherited claim is independently established for the Zaire protein by the three EXP rows on this same term. The topological detail carried with the transfer (peripheral, cytoplasmic side) matches the measured 8.1 A penetration of VP40 into the plasma membrane hydrocarbon core from the cytoplasmic face, so the transfer is sound rather than an over-propagation. Supporting Evidence: file:genes/EBOZM/VP40/VP40-uniprot.txt SIMILARITY: Belongs to the filoviridae matrix protein VP40 family. PMID:23663837 Experimental results indicate that VP40 penetrates 8.1 Å into the hydrocarbon core of the plasma membrane bilayer.
GO:0030430 host cell cytoplasm	EXP PMID:21987757 Characterization of filovirus protein-protein interactions i...	KEEP AS NON CORE	Summary: A dispersed cytoplasmic pool of VP40 exists, seen as VP40-NP complexes and as the monomer/dimer reservoir, but the matrix activity happens after recruitment to the plasma membrane. Reason: The cytoplasmic signal is real and directly observed: VP40-NP and NP-NP complexes were dispersed throughout the cytoplasm in the same experiment that put VP40-VP40 complexes at the plasma membrane, and number-and-brightness analysis independently shows the cytosolic pool is predominantly monomeric and dimeric. The term is as precise as that evidence allows. It is non-core because this pool is the pre-assembly reservoir: the oligomerisation, membrane deformation and budding that define VP40 occur at the plasma membrane, not in the cytoplasm. Supporting Evidence: PMID:21987757 VP40-NP and NP-NP complexes displayed a more dispersed pattern throughout the cytoplasm PMID:23297401 the majority of VP40 in the cytoplasm or premembrane zone in the current and previous study ( 24 ) is monomeric or dimeric
GO:0030430 host cell cytoplasm	IEA GO_REF:0000044	KEEP AS NON CORE	Summary: Electronic mapping of the curated UniProt "Host cytoplasm" location, itself backed by the same experimental paper as the EXP row for this term. Reason: SL-0381 is annotated on Q05128 with ECO:0000269 evidence from PubMed:21987757, so the mapping reproduces an experimentally grounded location at the correct granularity. Kept as non-core for the same reason as the EXP row: the cytoplasmic pool is where VP40 waits, not where it works. Supporting Evidence: file:genes/EBOZM/VP40/VP40-uniprot.txt SUBCELLULAR LOCATION: Host cytoplasm {ECO:0000269\|PubMed:21987757}.
GO:0033644 host cell membrane	IDA PMID:11333902 Ebola virus VP40-induced particle formation and association ...	MODIFY	Summary: CACAO row. Jasenosky et al. 2001 directly demonstrated VP40 membrane association by flotation gradient and Triton X-114 phase partitioning, so the claim is right; but the membrane VP40 associates with is the plasma membrane, which is the granularity the rest of the evidence (and UniProt's own curated location) supports. Reason: What the paper shows for this gene: VP40 expressed alone in mammalian cells floats with cellular membranes in a sucrose flotation gradient and is not released by 1 M NaCl, indicating hydrophobic rather than purely electrostatic membrane binding; Triton X-114 partitioning shows it has only minor integral-membrane character; and C-terminal truncation of 50 residues reduces membrane association and abolishes particle formation. The student's term is therefore supported, not a phenotype read as a location. The problem is granularity: a bulk flotation assay on total cellular membranes was annotated to the parent term GO:0033644, and the papers that resolve the compartment all place VP40 at the plasma-membrane inner leaflet (the descendant GO:0020002 this gene already carries from three EXP rows, and which is what UniProt's own SL-0375 "Host cell membrane" maps to). Replacing with GO:0020002 keeps the student's correct claim and adds the compartment the field has since established. Note GO:0033644 is not a root organelle term, so the organelle-policy exception does not apply to it. Proposed replacements: host cell plasma membrane Supporting Evidence: PMID:11333902 Flotation gradient analysis indicated that VP40 binds to membranes in a hydrophobic manner, as NaCl at 1 M did not release the protein from the lipid bilayer. PMID:23297401 WT EGFP-VP40 was predominantly localized to the PM with strong visual evidence of VLP extensions stemming from the PM
GO:0033644 host cell membrane	IMP PMID:23297401 The Ebola virus matrix protein penetrates into the plasma me...	MODIFY	Summary: CACAO row. Adu-Gyamfi et al. 2013 used hydrophobic C-terminal mutants to show that membrane insertion is required for VP40 localisation; the paper's own assays are explicitly plasma-membrane-resolved, so the parent term GO:0033644 is less specific than the evidence in hand. Reason: What the paper shows for this gene: monolayer penetration assays (Fig. 2A) distinguish a plasma-membrane mimetic (critical surface pressure ~34 mN/m) from a nuclear-membrane mimetic (~25 mN/m), so insertion is plasma-membrane-selective; confocal imaging of HEK293 cells (Fig. 3) shows WT EGFP-VP40 at the plasma membrane with VLP extensions while L213A, I293A, L295A and V298A are diffusely cytosolic with only 16-21% of cells showing detectable PM localisation; the L303A control is unaffected; and Western blots of released VLPs (Fig. 8) show loss of egress for the same mutants. The CACAO term matches the result in kind but not in granularity: every assay in the paper reads out the plasma membrane specifically, and the control monolayer was chosen to exclude other cellular membranes. Replacing with the descendant GO:0020002, which this gene already carries, records the compartment the paper actually resolved. Proposed replacements: host cell plasma membrane Supporting Evidence: PMID:23297401 Mutagenesis of this hydrophobic region consisting of Leu 213 , Ile 293 , Leu 295 , and Val 298 demonstrated that membrane penetration is critical to plasma membrane localization, VP40 oligomerization, and viral particle egress. PMID:23297401 For I293A, L295A, and V298A, only 16–21% of cells exhibited detectable PM localization
GO:0033645 host cell endomembrane system	IEA GO_REF:0000044	KEEP AS NON CORE	Summary: Mapping of a UniProt location that for Q05128 rests on similarity to Marburg VP40, reflecting association with virus-induced membrane proliferation foci and probably multivesicular bodies en route to the plasma membrane. Reason: The underlying SubCell assignment carries ECO:0000250 (similarity to P35260), not direct Zaire-virus evidence, and UniProt's own note is hedged ("probably also in multivesicular bodies"). The claim is nonetheless plausible and consistent with the exosomal pool of VP40 and with the detergent-resistant membrane results, and nothing contradicts it, so it should not be removed. It is kept as non-core and at the broad granularity the evidence actually supports: no study has resolved which endomembrane compartment the Zaire protein transits, and the functional site is the plasma membrane. Supporting Evidence: file:genes/EBOZM/VP40/VP40-uniprot.txt it is found associated with virus-induced membrane proliferation foci and probably also in multivesicular bodies
GO:0033645 host cell endomembrane system	ISS GO_REF:0000024	KEEP AS NON CORE	Summary: Curator transfer of the endomembrane location from Marburg virus VP40 (P35260) to the orthologous Zaire protein. Reason: The donor is the orthologous filovirus matrix protein, so the transfer is phylogenetically appropriate, and Marburg VP40 is the better-characterised protein for late-endosome and multivesicular-body trafficking. Kept, at the same broad granularity, for the same reasons as the IEA row on this term: the claim is sound but unresolved for the Zaire protein and peripheral to its core plasma-membrane function. Supporting Evidence: file:genes/EBOZM/VP40/VP40-uniprot.txt Host endomembrane system {ECO:0000250\|UniProtKB:P35260} file:genes/EBOZM/VP40/VP40-uniprot.txt SIMILARITY: Belongs to the filoviridae matrix protein VP40 family.
GO:0039660 structural constituent of virion	IEA GO_REF:0000043	ACCEPT	Summary: VP40 is the matrix protein: the most abundant protein in the virion, forming the packed layer on the inner face of the viral envelope. This is its defining molecular function. Reason: The keyword mapping is exact rather than merely permissible. VP40 oligomers are present in authentic Ebola virions as well as in VLPs, the protein lines the inner side of the virion membrane, and expression of VP40 alone in mammalian cells is sufficient to generate particles with the characteristics of real virions, which is the behaviour of a structural matrix constituent rather than of an accessory factor. Supporting Evidence: file:genes/EBOZM/VP40/VP40-uniprot.txt MISCELLANEOUS: Most abundant protein in the virion. PMID:14673115 Here, we demonstrate VP40 oligomers in lipid rafts of mammalian cells, virus-like particles, and in the authentic Ebola virus. PMID:11333902 These findings demonstrate that VP40 alone possesses the information necessary to induce particle formation
GO:0039702 viral budding via host ESCRT complex	IEA GO_REF:0000043	ACCEPT	Summary: VP40 carries two overlapping late-budding motifs that recruit ESCRT and ESCRT-associated host factors, and this recruitment is required for efficient particle release. Reason: The keyword rests on a substantial curated body of work: the PTAP/PSAP motif engages the TSG101 UEV domain, the PPxY motif engages NEDD4 WW3 and the WW domains of SMURF2, and ALIX and VPS4 are also recruited, with knockdown or motif mutation reducing egress. VP40 performs part of the work of this process rather than merely being required for it: it is the component that supplies the late-domain binding sites that bring the host machinery to the budding site. The term is at the right level, naming the host machinery used rather than the generic process. Supporting Evidence: file:genes/EBOZM/VP40/VP40-uniprot.txt Acts by interacting with viral ribonucleocapsid and host members of the ESCRT (endosomal sorting file:genes/EBOZM/VP40/VP40-uniprot.txt VP40 contains two overlapping L domains: a PMID:33673144 siRNA knockdown of endogenous SMURF2 led to inhibition of eVP40 VLP egress
GO:0042802 identical protein binding	IPI PMID:10864502 Structural characterization and membrane binding properties ...	ACCEPT	Summary: VP40 self-associates; chemical cross-linking and electron microscopy of purified protein showed that the C-terminally truncated form assembles into hexamers. Reason: Self-association is not an incidental interaction for this protein, it is the mechanism by which the matrix layer is built, so GO:0042802 is informative here in a way that bare protein binding would not be. The evidence is direct (cross-linking plus EM on defined constructs), and the oligomer series was subsequently confirmed in cells and in authentic virions. The target appearing as its own interaction partner is correct for a homo-oligomer and is not circular. Supporting Evidence: PMID:10864502 As indicated by chemical cross-linking studies and electron microscopy, the larger polypeptide was present in a monomeric form, whereas the truncated one formed hexamers. file:genes/EBOZM/VP40/VP40-uniprot.txt Q05128; Q05128: VP40; NbExp=4; IntAct=EBI-25753960, EBI-25753960;
GO:0042802 identical protein binding	IPI PMID:12679020 The matrix protein VP40 from Ebola virus octamerizes into po...	ACCEPT	Summary: The same self-association claim from the octamer crystal structure: VP40 N-terminal domains assemble into a pore-like octameric ring. Reason: This row is a second, structurally resolved line of evidence for the same claim as the PMID:10864502 row, and the two reinforce each other. The X-ray structure defines the intradimeric and dimer-dimer interfaces that mediate self-association, and the SDS-resistant octamer is detectable in virus-infected cells, so the oligomer is not a crystallisation artefact. Supporting Evidence: PMID:12679020 Here we present the X-ray structure of octameric VP40 assembled through its N-terminal domain (NTD). PMID:12679020 This indicates that the SDS resistance is an intrinsic feature of octameric ring-like VP40 in complex with RNA.
GO:0043657 host cell	IEA GO_REF:0000108	KEEP AS NON CORE	Summary: An inter-ontology inference that VP40 is somewhere in the host cell. The claim is true but says much less than the host cell plasma membrane and host cell cytoplasm rows kept in this review; it is retained only as the host-agnostic umbrella location. Reason: GO:0043657 says only that the protein is inside a host cell. The accepted GO:0020002 host cell plasma membrane rows and the non-core GO:0030430 host cell cytoplasm rows name host cell parts, and GO's cellular-component graph does not place them under GO:0043657, so this row is not formally entailed by them and is kept rather than marked too general. It is non-core: no VP40 activity is localised by it. Worth flagging for provenance, though: this row was generated by logical inference from GO:0075733 intracellular transport of virus (GO_REF:0000108), which is the CACAO process annotation this review modifies, so a single questionable student process call propagated into a second annotation. Supporting Evidence: PMID:21987757 We demonstrate that VP40-VP40 complexes localized predominantly at the plasma membrane
GO:0044071 symbiont-mediated perturbation of host cell cycle progression	EXP PMID:30169850 Ebola Virus VP40 Modulates Cell Cycle and Biogenesis of Extr...	KEEP AS NON CORE	Summary: Nuclear VP40 binds the cyclin D1 promoter and raises cyclin D1 levels, accelerating the cell cycle of producer cells; a real but peripheral host-perturbing activity. Reason: VP40 performs part of the work of this perturbation rather than merely being required for it: it enters the nucleus and is found bound to the cyclin D1 promoter by chromatin immunoprecipitation, and cyclin D1 transcription and cell-cycle acceleration follow. The term is the right granularity for a perturbation whose direct target is a host transcriptional response. It is non-core because it is remote from the matrix and budding programme that defines VP40, and because the evidence comes from VP40-expressing clones rather than from virus infection. Supporting Evidence: PMID:30169850 VP40 clones were accelerated in growth due to cyclin D1 upregulation, and nuclear VP40 was found bound to the cyclin D1 promoter. PMID:30169850 Nuclear VP40 upregulates cyclin D1 levels, resulting in dysregulated cell cycle and EV biogenesis.
GO:0044185 host cell late endosome membrane	IEA GO_REF:0000044	KEEP AS NON CORE	Summary: Mapping of a UniProt location that for Q05128 is a similarity transfer from Marburg VP40, consistent with transit through multivesicular bodies. Reason: Like the endomembrane rows, this rests on ECO:0000250 similarity to P35260 rather than on direct Zaire-virus evidence; UniProt records it as a peripheral membrane association. Marburg VP40 is well documented at late endosomal membranes, the Zaire protein is secreted in exosomes (which derive from multivesicular bodies), and no evidence contradicts the location, so removal is not warranted. Kept as non-core: this is a trafficking waypoint, not the site of the budding activity. Supporting Evidence: file:genes/EBOZM/VP40/VP40-uniprot.txt Host late endosome membrane {ECO:0000250\|UniProtKB:P35260}
GO:0044185 host cell late endosome membrane	ISS GO_REF:0000024	KEEP AS NON CORE	Summary: Curator transfer of the late-endosome-membrane location from Marburg virus VP40 to the orthologous Zaire protein. Reason: Same judgment as the IEA row on this term, and the same reasoning: the donor P35260 is the orthologous filovirus matrix protein, the transferred claim is plausible for the Zaire protein and compatible with its exosomal secretion, but it has not been demonstrated directly here and is peripheral to the plasma-membrane budding function. Supporting Evidence: file:genes/EBOZM/VP40/VP40-uniprot.txt SIMILARITY: Belongs to the filoviridae matrix protein VP40 family. file:genes/EBOZM/VP40/VP40-uniprot.txt Host late endosome membrane {ECO:0000250\|UniProtKB:P35260}
GO:0045121 membrane raft	IDA PMID:14673115 In vivo oligomerization and raft localization of Ebola virus...	ACCEPT	Summary: CACAO row, and a well-chosen one: Panchal et al. 2003 directly demonstrated VP40 oligomers in lipid rafts of mammalian cells, in VLPs and in authentic Ebola virus, and showed VP40 actively recruits TSG101 into rafts. Reason: What the paper shows for this gene: VP40 oligomers are detected in lipid rafts in three independent systems (transfected mammalian cells, VP40-derived VLPs, and authentic Ebola virus particles), and C-terminal mutagenesis coordinately disrupts oligomerisation at the plasma membrane, association with detergent-resistant membranes, and vesicular release, which ties the raft residence to the function rather than leaving it as a bystander observation. The CACAO term matches the result exactly and is at the right granularity. This is not the single-assay-localization failure pattern: the raft association is replicated across systems within the paper and is independently corroborated by the detergent-resistant-membrane results cited in PMID:23297401. GO has no host-specific raft term, so GO:0045121 is the only available choice. The cached record is abstract-only and the GONUTS wiki page for this PMID was offline when checked, so the student's own figure citations could not be inspected; the abstract alone is explicit enough to support the row. Supporting Evidence: PMID:14673115 Here, we demonstrate VP40 oligomers in lipid rafts of mammalian cells, virus-like particles, and in the authentic Ebola virus. PMID:14673115 Furthermore, we demonstrate the active recruitment of TSG101 into lipid rafts by VP40. PMID:23297401 VP40 oligomers are essential for the formation of VLPs and have been found to be associated with detergent-resistant membranes
GO:0046755 viral budding	IEA GO_REF:0000043	MODIFY	Summary: Keyword-derived parent term; VP40 budding is known to occur at the plasma membrane, so the specific descendant is the right term. Reason: The claim is correct, but the site of VP40 budding is not in doubt in this gene: every assay in the literature reads out release from the cell surface, and GO:0046761 viral budding from plasma membrane is already carried by this gene with IDA and IMP support. Refining this row to that descendant keeps the review internally consistent with the other budding rows rather than leaving a less specific duplicate of the same claim. Proposed replacements: viral budding from plasma membrane Supporting Evidence: PMID:23663837 hydrophobic residues that penetrate deeply into the plasma membrane are essential for plasma membrane localization and virus-like particle formation and release from cells. file:genes/EBOZM/VP40/VP40-uniprot.txt Plays an essential role virus particle assembly and budding
GO:0046755 viral budding	IMP PMID:16837071 A luciferase-based budding assay for Ebola virus.	MODIFY	Summary: CACAO row. McCarthy et al. 2006 built a luciferase-based budding assay and showed that a budding-deficient VP40 mutant loses luciferase from the VLP fraction, which supports a VP40 budding role; but the assay specifically measures release of particles from the cell surface, so the plasma-membrane-specific descendant is the better term. Reason: What the paper shows for this gene: VP40 expressed in mammalian cells buds as a VLP and incorporates co-expressed firefly luciferase, so luciferase in the VLP fraction is a direct quantitative readout of VP40 budding efficiency; co-expression of EBOV GP enhances release, and a budding-deficient VP40 mutant significantly reduces luciferase in the VLP fraction. The CACAO term is supported by the student's own paper and is not a phenotype read as a process. The issue is granularity: the VLP fraction is material released from the cell surface, which is GO:0046761 viral budding from plasma membrane, a term this gene already carries with IDA and IMP support. The cached record is abstract-only and the GONUTS wiki page for this PMID could not be read (the wiki was offline), so the student's figure citations were unavailable; the abstract states the mutant result explicitly, so this is a refinement, not a challenge to the row. Proposed replacements: viral budding from plasma membrane Supporting Evidence: PMID:16837071 In contrast, when luciferase is co-expressed with a budding deficient mutant of VP40, luciferase levels in the VLP fraction decrease significantly. PMID:16837071 The VP40 matrix protein of Ebola virus (EBOV) is capable of budding from mammalian cells as a virus-like particle (VLP) and is the major protein involved in virus egress.
GO:0046761 viral budding from plasma membrane	IDA PMID:23663837 The Ebola virus matrix protein deeply penetrates the plasma ...	ACCEPT	Summary: VP40 inserts 8.1 A into the plasma membrane hydrocarbon core, tubulates liposomes and vesiculates giant unilamellar vesicles, and the hydrophobic residues responsible are required for VLP formation and release. This is the core process term for the gene. Reason: VP40 does the work of this process rather than merely being needed for it: it supplies the membrane-deforming activity directly, as shown by liposome tubulation and GUV vesiculation with purified protein, and the same hydrophobic residues required for deformation are required for particle release in cells. Combined with the fact that VP40 alone is sufficient to produce and release particles, the involvement is as direct as it gets, and the term names the correct membrane. Supporting Evidence: PMID:23663837 VP40 also induces substantial changes to membrane curvature as it tubulates liposomes and induces vesiculation into giant unilamellar vesicles, effects that are abrogated by hydrophobic mutations. PMID:23663837 Experimental results indicate that VP40 penetrates 8.1 Å into the hydrocarbon core of the plasma membrane bilayer.
GO:0046761 viral budding from plasma membrane	IMP PMID:11333902 Ebola virus VP40-induced particle formation and association ...	ACCEPT	Summary: CACAO row, and the strongest of the six: Jasenosky et al. 2001 showed that VP40 expressed alone induces membrane-bound particle formation, that this depends on the N-terminal PPxY motif, and that C-terminal truncation abolishes it. Reason: What the paper shows for this gene: VP40 expressed in mammalian cells apart from all other viral proteins induces the formation of membrane-bound particles; mutation or loss of the conserved N-terminal PPxY motif markedly reduces particle formation; and truncation of the C-terminal 50 residues both disrupts hydrophobic membrane association and abolishes particle formation. The CACAO term matches this precisely and at the right granularity, and the mutant series makes it a genuine IMP rather than an inference from localisation. The authors' own conclusion, that VP40 alone possesses the information necessary to induce particle formation, is exactly the claim GO:0046761 encodes. The cached record is abstract-only and the GONUTS page was offline, but the abstract states each mutant result, so no deference problem arises. Supporting Evidence: PMID:11333902 We found that VP40 is indeed able to induce particle formation when it is expressed in mammalian cells, and this process appeared to rely on a conserved N-terminal PPXY motif, as mutation or loss of this motif resulted in markedly reduced particle formation. PMID:11333902 We confirmed previous findings that truncation of the 50 C-terminal amino acids of VP40 results in decreased association with cellular membranes and demonstrated that this deletion disrupts hydrophobic interactions of VP40 with the lipid bilayer, as well as abolishing particle formation.
GO:0052031 symbiont-mediated perturbation of host defense response	IEA GO_REF:0000043	KEEP AS NON CORE	Summary: VP40 perturbs host defences in at least two ways, suppression of RNA silencing and exosome-delivered immune-cell dysfunction, and the keyword term spans both; a peripheral activity relative to the matrix function. Reason: This is not simply a redundant parent of the RNAi-suppression row. Two distinct host-defence perturbations are documented for VP40: it acts as a suppressor of RNA silencing in an siRNA assay, and VP40 packaged into exosomes decreases the viability of recipient immune cells, with VP40-containing vesicles carrying cytokines and inducing apoptosis in recipient T cells and monocytes. The broader term is the only one covering both, so it is as precise as the combined evidence warrants rather than merely too general. Non-core because these activities are remote from the assembly and budding programme and, in the exosome case, act on bystander cells rather than the producer cell. Supporting Evidence: PMID:21228243 In addition to viral protein 35 (VP35), we found that VP30 and VP40 independently act as SRSs. PMID:30169850 VP40 EVs induced apoptosis in recipient T cells and monocytes.
GO:0052170 symbiont-mediated suppression of host innate immune response	IEA GO_REF:0000043	KEEP AS NON CORE	Summary: Keyword-derived term covering VP40's suppression of innate antiviral responses, of which RNA-silencing suppression is the documented mechanism and the exosome-mediated immune-cell killing is a second arm. Reason: Kept for the same reason as the GO:0052031 row and consistently with it. RNAi is an innate antiviral response, so the RNA-silencing suppression result supports this term directly; the exosome-delivered immune-cell apoptosis is a second, mechanistically separate suppression of innate immune cells that no narrower term captures. Non-core: neither activity is part of the matrix or budding function, and the RNAi mechanism was worked out for VP30 and VP35 rather than for VP40. Supporting Evidence: PMID:21228243 Cellular RNA interference (RNAi) provides a natural response against viral infection, but some viruses have evolved mechanisms to antagonize this form of antiviral immunity. PMID:21228243 In addition to viral protein 35 (VP35), we found that VP30 and VP40 independently act as SRSs.
GO:0055036 virion membrane	IEA GO_REF:0000044	ACCEPT	Summary: VP40 forms the matrix layer on the inner face of the virion envelope, so the virion membrane is one of its two core locations. Reason: The mapped SubCell term records a peripheral association on the inner side of the virion membrane, which is the defining arrangement of a matrix protein and is directly corroborated for the Zaire protein: VP40 oligomers were detected in authentic Ebola virus particles, and VP40 is the most abundant virion protein. The granularity is right, virion membrane rather than virion generally, and this is where the structural constituent activity is exercised in the assembled particle. Supporting Evidence: file:genes/EBOZM/VP40/VP40-uniprot.txt In virion, localizes on the inner side of the membrane. PMID:14673115 Here, we demonstrate VP40 oligomers in lipid rafts of mammalian cells, virus-like particles, and in the authentic Ebola virus.
GO:0055036 virion membrane	ISS GO_REF:0000024	ACCEPT	Summary: Curator transfer of the virion-membrane location from Marburg virus VP40 to the orthologous Zaire protein, including the peripheral-membrane topology. Reason: The donor P35260 is the orthologous filovirus matrix protein, and the transferred claim is independently supported in Zaire ebolavirus by the detection of VP40 oligomers in authentic virions and by VP40 being the most abundant virion protein. The transfer therefore adds the topological detail (peripheral, inner face) without asserting anything the Zaire data do not already bear out. Supporting Evidence: file:genes/EBOZM/VP40/VP40-uniprot.txt SIMILARITY: Belongs to the filoviridae matrix protein VP40 family. file:genes/EBOZM/VP40/VP40-uniprot.txt MISCELLANEOUS: Most abundant protein in the virion.
GO:0075733 intracellular transport of virus	IMP PMID:23297401 The Ebola virus matrix protein penetrates into the plasma me...	MODIFY	Summary: CACAO row, and the one genuine mis-assignment of the six. The cited paper contains no transport assay: its mutants are scored for plasma-membrane penetration, plasma-membrane localisation, oligomerisation and VLP release, which is budding, not movement of virus within the cell. Reason: GO:0075733 is defined as the directed movement of a virus, or part of a virus, within the host cell. What the paper actually shows for this gene: lipid monolayer penetration measurements in vitro (Fig. 2), confocal scoring of plasma-membrane localisation for L213A, I293A, L295A, V298A and the L303A control (Fig. 3), TIRF number-and-brightness oligomerisation analysis (Figs. 4-7), and Western blotting of released VLPs (Fig. 8). None of these follows a virus or viral component moving through the cytoplasm; the mutant phenotype is failure to reach and insert into the plasma membrane and failure to release particles. This is the egress-read-as-transport variant of the phenotype-as-process pattern. The only transport statement in the paper is a citation to earlier work that the nucleocapsid is not effectively transported to the plasma membrane without VP40, which is consistent with VP40 being required at the destination rather than performing the movement; Takamatsu et al. (PubMed:29339477, in the UniProt reference list) subsequently concluded that NP, VP35 and VP24 are essential and sufficient for nucleocapsid transport, i.e. VP40 is not part of the transport machinery. The essence of the student's reading, that these mutants break the VP40 egress pathway, is sound, so this is a lateral correction to GO:0046761 viral budding from plasma membrane, the term the paper's assays actually read out and which this gene already carries. Note also that this row seeded the GO:0043657 host cell IEA by inter-ontology inference (GO_REF:0000108). Proposed replacements: viral budding from plasma membrane Supporting Evidence: PMID:23297401 Taken together, C-terminal domain membrane penetration is important for VP40 plasma membrane localization and critical to viral egress. PMID:23297401 Release of VLPs was not detectable for L213A or L295A, whereas I293A and V298A had significantly reduced VLP release.
GO:0140533 symbiont-mediated suppression of host RNAi-mediated antiviral immune response	IMP PMID:21228243 Ebolavirus proteins suppress the effects of small interferin...	KEEP AS NON CORE	Summary: In a screen of all EBOV proteins using an siRNA-initiated RNAi assay, VP40 independently suppressed RNA silencing; the molecular mechanism was resolved for VP30 and VP35 but not for VP40. Reason: The screen result is specific to VP40, which acted as a suppressor of RNA silencing independently of VP35, so the term is correctly assigned and at the right granularity. It is kept as non-core rather than accepted as core for two reasons: the authors characterised the mechanism only for VP30 and VP35, so for VP40 we have a suppression phenotype without a defined molecular step, and this activity is unconnected to the matrix assembly and budding programme that defines the protein. Not removed: this is an experimental annotation by a GO Central curator with full-text access, and nothing contradicts it. Supporting Evidence: PMID:21228243 In addition to viral protein 35 (VP35), we found that VP30 and VP40 independently act as SRSs. PMID:21228243 Here, we present the molecular mechanisms of VP30 and VP35.
GO:1990904 ribonucleoprotein complex	IEA GO_REF:0000043	MARK AS OVER ANNOTATED	Summary: Keyword-derived part_of claim that overstates the evidence: VP40 binds RNA as an octamer, but it is the matrix protein and is not an established subunit of a ribonucleoprotein complex in the infected cell or the virion. Reason: The Ribonucleoprotein keyword follows from the RNA-binding octamer, and that activity is real (and accepted in this review as GO:0003723). But part_of a ribonucleoprotein complex is a structural membership claim, and the data do not reach it. The RNA-bound species is a crystallographic complex of the N-terminal domain with a short single-stranded sequence; VP40's role in the virion is the matrix layer beneath the envelope, not the nucleocapsid, and the authors could not detect the SDS-resistant octamer-RNA form in purified virus particles. The claim is not plainly false, since the octamer is detectable in infected cells, so this is an over-annotation to flag rather than an annotation to remove. Supporting Evidence: PMID:12679020 However, no high molecular weight band corresponding to the SDS-resistant form detected in virus-infected cells could be detected, indicating that octameric VP40 might not be abundantly present in virus particles (Figure 5C). file:genes/EBOZM/VP40/VP40-uniprot.txt MISCELLANEOUS: Most abundant protein in the virion.

Gene Description

Existing Annotations Review

Core Functions

Self-associates on the cytoplasmic face of the host plasma membrane into the oligomeric matrix layer that deforms the bilayer and forms the structural shell of the budding virion.

Recruits host HECT E3 ubiquitin ligases and ESCRT-associated factors to the budding site through its overlapping PTAP/PSAP and PPxY late-budding motifs, licensing efficient particle scission and release.

As a minor octameric ring form assembled through its N-terminal domain, binds a specific single-stranded RNA sequence in a pocket at the dimer-dimer interface, a form assigned to viral genome replication rather than to budding.

References

Suggested Questions for Experts

Suggested Experiments

📚 Additional Documentation

Notes

📄 View Raw YAML