NSs is the 265-residue nonstructural protein encoded by the genomic-sense open reading frame of the ambisense S segment of Rift Valley fever virus, and the virus's principal virulence factor. It is not part of the replication machinery: genome replication is carried out by the L polymerase and the N nucleoprotein, and viruses lacking the NSs open reading frame replicate normally in interferon-incompetent cells. Instead, NSs works as a substrate-recognition adaptor that redirects host SCF ubiquitin ligases onto host antiviral proteins. In the host nucleus, a C-terminal OmegaXaV motif docks NSs onto the p62/GTF2H1 subunit of the general transcription factor TFIIH and recruits the F-box protein FBXO3 together with SKP1, destroying p62 by the ubiquitin-proteasome pathway; NSs additionally competes with XPD for the p44 subunit and self-assembles into amyloid-like nuclear filaments that sequester p44 and XPB, so that TFIIH cannot be assembled. The resulting loss of TFIIH shuts down host RNA polymerase II transcription initiation globally, which is the mechanism by which NSs prevents induction of the interferon-beta gene while leaving the IRF-3, NF-kappaB and AP-1 transcription factors themselves fully activated. In the host cytoplasm, NSs binds the double-stranded RNA-activated protein kinase EIF2AK2/PKR and recruits FBXW11, degrading PKR and so preventing eIF2-alpha phosphorylation and preserving translation. Secondary consequences of the transcriptional block include failure of the antiviral upregulation of Abl2, with loss of lamellipodia, altered cell shape and motility, and dissolution of adherens junctions. NSs is the only RVFV protein that accumulates in the nucleus, which is unusual for a virus whose replication cycle is entirely cytoplasmic.
Definition: A process in which a symbiont stops, prevents or reduces the production of type I interferons by its host, for example by preventing transcriptional induction of interferon genes. This is distinct from suppression of the host type I interferon-mediated signaling pathway (GO:0039502), which concerns interference with signalling downstream of the type I interferon receptor. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Justification: GO has symbiont-mediated terms for suppression of type I, II and III interferon-mediated signalling (GO:0039502, GO:0140884, GO:0140885, under GO:0140886) but no symbiont-mediated counterpart of GO:0032480 negative regulation of type I interferon production. Viral proteins that block interferon induction rather than interferon signalling are therefore annotated to the signalling terms, which misstate the step affected. Three existing branches might be thought to cover these cases, and none covers the output they share. The signalling branch concerns events downstream of the interferon receptor, which nothing in any of these three genes' literature addresses. The induction-side branch names the sensor or transducer antagonised (GO:0039540 RIG-I, GO:0039548 IRF3, and siblings under GO:0039536). Neither NSs protein antagonises any of them: IRF-3, NF-kappaB and AP-1 are all activated normally [PMID:15331713], the lesion lying downstream of every sensor and IRF, in the host transcription machinery itself, through sequestration of TFIIH p44 and XPB and degradation of p62 [PMID:14980221]. Sendai virus V is the opposite case and is the reason this branch must be discussed rather than dismissed: it does antagonise sensors and carries those terms, yet they name what it attacks and not what results, which is the coexistence question set out below. The transcription branch holds the NSs lesion, and the two NSs cases carry terms from it that these reviews accept as core (GO:0039602 and GO:0039653 here, GO:0039523 twice on Bunyamwera NSs), so an editor may reasonably ask whether the interferon outcome is simply its consequence. It is not, for two reasons. Mechanism and outcome are complementary rather than redundant, which is the ground on which this review already keeps GO:0039602 and GO:0039653 together: one names the polymerase II step, the other the general outcome, and neither entails the specific outcome at issue. And the interferon block is measured in its own right rather than inferred from the transcription phenotype, since deletion mutants accumulate interferon-beta mRNA while the parental virus does not [PMID:16501102] and NSs is characterised as not inhibiting the interferon-specific transcription factors but blocking interferon gene expression at a later step [PMID:15331713]. What is missing is a mechanism-agnostic production term, naming the outcome rather than the sensor attacked. Three cases need it, and they span two different mechanisms. RVFV NSs (P21698) and Bunyamwera virus NSs (P16494) are the transcription-shutdown cases, both carrying GO:0039502 rows that this review and its companion correct. Sendai virus V (P69282) is the third and is mechanistically unlike them: it does not shut down host transcription, and it is sensor-directed, carrying GO:0039540 suppression of host RIG-I activity and GO:0039548 suppression of host IRF3 activity, both annotated IDA and both accepted in that review. The IRF3 row has SeV-specific functional support, the V protein inhibiting IRF3 activation driven by a constitutively active RIG-I; the RIG-I row rests on SeV-specific interaction data, its mechanistic experiments having been performed with the Nipah, measles and PIV5 V proteins, so the sensor-directed character of this case is carried mainly by the IRF3 arm. Yet the measured output for it is interferon production: IFN-beta secretion is much greater in infection by the V-deficient virus than by wild type, with replication controlled, and no existing term states that output. Its case is also the cleanest demonstration of the gap, because nothing was mis-annotated: no curator put it on GO:0039502, so the gap appears as an absence rather than as an error to correct. Influenza A NS1 (P03496) carries GO:0039502 too but is not offered, since NS1's documented mechanism is RIG-I and TRIM25 antagonism and the production side of its phenotype was not assessed for this review. Two scope questions for the editors. First, granularity: the evidence in all three cases is interferon-beta specifically, and none of the papers assays interferon-alpha, so a symbiont-mediated counterpart of GO:0032688 negative regulation of interferon-beta production would match the data more exactly than the type I term proposed here. The type I scope is proposed because the existing symbiont-side signalling terms are organised by interferon class rather than by individual cytokine, and consistency with that organisation seems more useful than a minimal fit; if the editors prefer the narrower scope, GO:0032688 is the host-side term to mirror. Second, completeness: GO created the signalling set GO:0140884, GO:0140885 and GO:0140886 together, so the editors may prefer to create the type I, type II and type III production terms as a set under a class-neutral parent, rather than the type I term alone. This review has candidate genes only for type I. The question the editors should weigh is the converse of the one this request first anticipated. Sendai virus V shows that a gene can need the production term while already carrying the sensor-specific terms for the mechanism by which it achieves the outcome, which is the same outcome-versus-mechanism relation set out above for the transcription branch. If that is accepted, the term layers over the induction branch generally: any symbiont whose interferon output is separately measured could carry it alongside whichever sensor term describes its mechanism. That may be the right structure, mirroring how the transcription and production claims coexist here, but it is a deliberate decision about redundancy rather than a side effect, and it should be made explicitly. The criterion this review would apply is that the production term is warranted where the interferon output is measured in its own right, and not where it is merely inferred from a mechanism term the gene already carries. Two viral proteins that block interferon-beta induction downstream of IRF3 activation, KSHV vIRF1 and HSV-1 ICP0, were considered as further cases and are not offered here - not because acting on IRF3 disqualifies them, which the Sendai case shows it does not, but because neither of those papers was read in full for this review.
Parent term: symbiont-mediated suppression of host innate immune response
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0030291 protein serine/threonine kinase inhibitor activity | IEA GO_REF:0000043 | MODIFY | Summary: Keyword-derived molecular function from KW-1102 (Inhibition of host PKR by virus). NSs does antagonise PKR, but not by the mechanism this term describes: GO:0030291 is defined as binding to and reducing the activity of a protein serine/threonine kinase, whereas NSs binds PKR and recruits the F-box protein FBXW11 so that PKR is destroyed by the proteasome. The activity NSs has is substrate-recognition adaptor activity for a ubiquitin ligase. Reason: The underlying biology (loss of host PKR activity, with consequent loss of eIF2-alpha phosphorylation) is right, but the molecular function is mis-assigned. UniProt's own curated FUNCTION statement describes degradation, not occupancy-based inhibition, and the same adaptor activity accounts for the parallel destruction of TFIIH p62 through FBXO3. GO:1990756 ubiquitin-like ligase-substrate adaptor activity is the activity actually enabled, and is a descendant of the GO:0030674 term that UniProt already annotates to this protein by IDA, so the two molecular-function rows converge on one claim. This is a lateral correction of the keyword mapping rather than a refinement, so the replacement is not a descendant of GO:0030291. Proposed replacements: ubiquitin-like ligase-substrate adaptor activity Supporting Evidence: file:RVFVZ/NSS/NSS-uniprot.txt Cytoplasmic NSs interacts with host FBXW11 to degrade PKR PMID:24403578 F-box proteins form the variable substrate recognition subunit of the so-called SCF ubiquitin ligases |
| GO:0030430 host cell cytoplasm | EXP PMID:25918396 A Ξ©XaV motif in the Rift Valley fever virus NSs protein is e... | ACCEPT | Summary: NSs is present in the host cytoplasm as well as the nucleus. The cytoplasmic pool is the functionally relevant one for PKR degradation, which is carried out through FBXW11, while the nuclear pool handles TFIIH p62. Reason: UniProt records host cytoplasm for this protein with experimental evidence attributed to this very publication, and the division of labour between the two pools is a curated, mechanistically supported feature of the protein rather than an incidental localisation. The cached record for PMID:25918396 is abstract-only, so the sub-cellular detail is taken from the curated UniProt statement that cites it. Supporting Evidence: file:RVFVZ/NSS/NSS-uniprot.txt cytoplasm {ECO:0000269|PubMed:25918396} file:RVFVZ/NSS/NSS-uniprot.txt Cytoplasmic NSs interacts with host FBXW11 to degrade PKR |
| GO:0030430 host cell cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: Subcellular-location mapping of SL-0381 (Host cytoplasm). It asserts the same claim as the EXP row above and is supported by the same curated evidence. Reason: The mapping is faithful to the curated UniProt subcellular location, and the cytoplasmic pool of NSs has a defined activity there (FBXW11 recruitment and PKR degradation), so the term is informative rather than a bare default. Supporting Evidence: file:RVFVZ/NSS/NSS-uniprot.txt cytoplasm {ECO:0000269|PubMed:25918396} |
| GO:0030674 protein-macromolecule adaptor activity | IDA PMID:24403578 Virulence factor NSs of rift valley fever virus recruits the... | MODIFY | Summary: Correct in essence: NSs physically bridges two host macromolecules, the F-box protein FBXO3 and the TFIIH subunit p62, so that p62 is ubiquitinated and degraded. The paper identified FBXO3 as an NSs interactor, showed that FBXO3 or SKP1 depletion rescues p62, and framed the result as NSs recruiting an E3 ligase subunit to a substrate. Reason: The adaptor claim is right but under-specified. The bridged pair is a ubiquitin ligase and its substrate, and GO has a term for exactly that, GO:1990756 ubiquitin-like ligase-substrate adaptor activity, which is an is_a descendant of GO:0030674 (QuickGO ancestors of GO:1990756: GO:0140767, GO:0030674, GO:0060090, GO:0003674). The same replacement makes this row and the PKR-directed molecular-function row say one thing, since NSs performs the identical adaptor role with FBXW11 on PKR. Proposed replacements: ubiquitin-like ligase-substrate adaptor activity Supporting Evidence: PMID:24403578 we identified a subunit of E3 ubiquitin ligases, F-box protein FBXO3, as a host cell interactor of NSs PMID:24403578 NSs recruits FBXO3 to destroy the general host cell transcription factor TFIIH-p62 file:RVFVZ/NSS/NSS-uniprot.txt nuclear pool binds to host FBXO3 to target TFIIH subunit GTF2H1 for |
| GO:0039502 symbiont-mediated suppression of host type I interferon-mediated signaling pathway | IEA GO_REF:0000043 | MODIFY | Summary: Keyword-derived from KW-1114 (Inhibition of host interferon signaling pathway by virus). NSs is a genuine type I interferon antagonist, but it acts on interferon production, not on interferon-mediated signalling: GO:0039502 is defined as interference with type I interferon-mediated signalling in the host, i.e. the receptor to JAK/STAT to ISG axis. Reason: The branch is wrong for this protein, and the same is true of every row in this review on this axis, so they are treated consistently. There is, however, no symbiont-mediated counterpart of GO:0032480 negative regulation of type I interferon production: a QuickGO search returns only GO:0039502, GO:0140884, GO:0140885 and GO:0140886 as symbiont-mediated interferon terms, all of them signalling-pathway terms. The replacement is therefore a proposed new term rather than an existing one. This is a consortium-wide convention, not an error of this annotation: influenza A NS1 (P03496), the textbook interferon-induction antagonist, carries GO:0039502 only through this same KW-1114 mapping. Proposed replacements: symbiont-mediated suppression of host type I interferon production Supporting Evidence: PMID:15331713 NSs, unlike other viral IFN antagonists, does not inhibit IFN-specific transcription factors but blocks IFN gene expression at a subsequent step |
| GO:0039502 symbiont-mediated suppression of host type I interferon-mediated signaling pathway | IMP PMID:15331713 NSs protein of Rift Valley fever virus blocks interferon pro... | MODIFY | Summary: CACAO row. What the paper shows is that NSs expressed alone abolishes induction of the interferon-beta gene, measured as IFN-beta transcripts and as IFN-beta promoter-reporter activity, and that NSs mutants that remain cytoplasmic lose this activity. The IMP basis is sound: the comparison is wild-type NSs against the attenuated clone 13 NSs and against deletion/substitution mutants. None of the assays interrogates signalling downstream of the interferon receptor. Reason: The claim is true as interferon antagonism but sits in the wrong branch. The paper's own conclusion is explicitly that the block is not at the level of interferon-specific signalling or transcription factors: IRF-3 still dimerises and translocates, NF-kappaB and AP-1 are activated normally by electrophoretic mobility shift assay, and a constitutive promoter is inhibited too. In other words the datum is suppression of interferon production as a special case of a general host transcription block, which this review accepts separately on GO:0039653 from the same paper. The term is therefore the wrong granularity and the wrong branch rather than unsupported, and because GO has no symbiont-mediated interferon-production term the replacement is a proposed new term. The GONUTS record could not be checked: the wiki pages for this PMID return "This site is temporarily offline while we perform upgrades" and the Internet Archive holds no snapshot. The cached publication is abstract-only, so figure-level reading was done in PMC (PMC514997): IFN-beta promoter luciferase in 293 cells (Figs. 1D, 3A, 3C), IFN-beta RT-PCR and Northern blot (Figs. 1A, 1B), cytoplasmic NSs mutants losing inhibition (Fig. 5A) and a CMV-driven reporter suppressed (Figs. 3B, 5B). Proposed replacements: symbiont-mediated suppression of host type I interferon production Supporting Evidence: PMID:15331713 we demonstrate that NSs is sufficient to block IFN-beta gene expression at the transcriptional level PMID:15331713 In the presence of NSs, IRF-3 was still activated and moved to the nucleus |
| GO:0039502 symbiont-mediated suppression of host type I interferon-mediated signaling pathway | IMP PMID:16501102 Rescue of infectious rift valley fever virus entirely from c... | MODIFY | Summary: CACAO row. The reverse-genetics paper compares MP-12 with mutants lacking part or all of the NSs open reading frame and finds that interferon-beta mRNA accumulates in MRC-5 cells after infection with the deletion mutants but not with MP-12. This is a clean IMP for interferon antagonism by NSs, measured as interferon-beta transcript accumulation. Reason: Same wrong-branch issue as the other rows on this term. The measured quantity is interferon-beta mRNA, i.e. interferon production, and nothing in the paper addresses signalling through the interferon receptor. The annotation is otherwise well founded and the mutant comparison is exactly what IMP is for, so this is a granularity and branch correction, not a rejection. The GONUTS page for this PMID is unreachable (site offline, no Internet Archive snapshot) and the cached record is abstract-only, but the abstract itself states the result. Proposed replacements: symbiont-mediated suppression of host type I interferon production Supporting Evidence: PMID:16501102 accumulation of beta interferon mRNA occurred after infection by these NSs deletion mutants, but not after infection by MP-12 |
| GO:0039580 symbiont-mediated suppression of host PKR/eIFalpha signaling | IEA GO_REF:0000043 | ACCEPT | Summary: Keyword-derived from KW-1102, and an accurate statement of one of the two core activities of NSs. NSs binds PKR, recruits FBXW11 so that PKR is degraded by the proteasome, and thereby prevents eIF2-alpha phosphorylation, which is precisely what this term describes. Reason: Unlike the molecular-function keyword mapping from the same keyword, this biological-process term makes no claim about mechanism, only about the pathway suppressed, and that claim is supported by multiple curated UniProt FUNCTION statements with experimental evidence (PubMed:19197350, PubMed:19211744, PubMed:26837067). PKR degradation is independent of the transcription block, so the term is not redundant with the host-transcription terms. Supporting Evidence: file:RVFVZ/NSS/NSS-uniprot.txt Cytoplasmic NSs interacts with host FBXW11 to degrade PKR file:RVFVZ/NSS/NSS-uniprot.txt Plays a role in the escape of host innate immune response by |
| GO:0039602 symbiont-mediated suppression of host transcription initiation from RNA polymerase II promoter | IDA PMID:14980221 TFIIH transcription factor, a target for the Rift Valley hem... | ACCEPT | Summary: CACAO row, and the best of the six. The paper demonstrates that RVFV infection collapses host RNA synthesis in step with falling TFIIH levels, and that NSs interacts with the p44 subunit of TFIIH, forms nuclear filaments that also contain XPB, competes with XPD for p44, and thereby prevents TFIIH assembly. TFIIH is a general RNA polymerase II transcription factor required for promoter opening and preinitiation-complex function, so disabling it suppresses transcription initiation from polymerase II promoters. Reason: The CACAO term matches the assay and the mechanism, and is at the right granularity: the paper identifies the specific target (TFIIH) rather than merely reporting a transcriptional phenotype, which is what licenses the polymerase II initiation term over a vaguer one. Yeast two-hybrid, recombinant reconstitution and confocal microscopy are cited in the abstract, so the IDA code is defensible; the only caveat is that the host RNA synthesis measurement is made on infected cells rather than on NSs alone, with the attribution to NSs coming from the interaction and sequestration experiments. This is a core function of the protein. Supporting Evidence: PMID:14980221 infection by RVFV leads to a rapid and drastic suppression of host cellular RNA synthesis that parallels a decrease of the TFIIH transcription factor cellular concentration PMID:14980221 By competing with XPD, the natural partner of p44 within TFIIH, and sequestering p44 and XPB subunits, NSs prevents the assembly of TFIIH subunits |
| GO:0039653 symbiont-mediated suppression of host transcription | IMP PMID:15331713 NSs protein of Rift Valley fever virus blocks interferon pro... | ACCEPT | Summary: CACAO row. The paper's title claim is that NSs blocks interferon production by inhibiting host gene transcription, and its supporting observation for the general term is that NSs also inhibits the transcriptional activity of a constitutive promoter, consistent with the TFIIH target identified in the companion Cell paper. The IMP basis is the comparison of wild-type NSs with mutant forms that have lost interferon-inhibiting activity. Reason: This is the CACAO term that fits what the paper actually establishes. Unlike the interferon-signalling row from the same paper, the general host-transcription claim is exactly what the constitutive-promoter result supports, and it is the claim the authors themselves draw. GO:0039602 is not an ancestor or descendant of this term in GO, so the two accepted transcription rows are complementary rather than redundant: one names the polymerase II initiation step, the other the general outcome. The GONUTS page is unreachable (site offline, no archive snapshot) and the cached record is abstract-only, so the curator-deference rule applies; nothing in the abstract or in the PMC figures argues against the term. Supporting Evidence: PMID:15331713 NSs was found to inhibit transcriptional activity of a constitutive promoter, in agreement with recent findings showing that NSs targets the basal cellular transcription factor TFIIH |
| GO:0039657 symbiont-mediated suppression of host gene expression | IEA GO_REF:0000043 | ACCEPT | Summary: Keyword-derived from KW-1190 (Host gene expression shutoff by virus). Host shutoff is one of the defining activities of NSs and is documented both as a transcriptional block and as a failure of host protein synthesis in NSs-deficient infections. Reason: The keyword mapping is faithful and the claim is well supported. The term is broader than the transcription-initiation term also annotated here, but it is not merely a roll-up of it: the measured host shutoff spans transcription and the resulting collapse of host protein synthesis, which is what a gene-expression term covers. Supporting Evidence: PMID:16501102 failed to shut off host protein synthesis in Vero cells |
| GO:0039657 symbiont-mediated suppression of host gene expression | IMP PMID:16501102 Rescue of infectious rift valley fever virus entirely from c... | ACCEPT | Summary: CACAO row. Viruses lacking part or all of the NSs open reading frame failed to shut off host protein synthesis in Vero cells, whereas the parental MP-12 did; this is a direct loss-of-function demonstration that NSs is responsible for host shutoff. Reason: The term matches the assay at the right level. A protein-synthesis readout does not by itself localise the block to transcription or to translation, and GO:0039657 suppression of host gene expression is the correct non-committal term for it; downgrading to GO:0039604 suppression of host translation would overstate what this paper shows, since the block is known from other work to be transcriptional. The GONUTS page is unreachable (site offline, no archive snapshot) and the cached record is abstract-only, but the abstract states the result directly. Supporting Evidence: PMID:16501102 The NSs deletion mutants formed larger plaques than MP-12 did in Vero E6 cells and failed to shut off host protein synthesis in Vero cells |
| GO:0039689 negative stranded viral RNA replication | IMP PMID:16501102 Rescue of infectious rift valley fever virus entirely from c... | REMOVE | Summary: CACAO row, and the one row in this GOA set that the cited paper does not support. The term asserts that NSs takes part in replication of the negative-sense RNA genome. The paper's central finding is the opposite: mutants lacking part or all of the NSs open reading frame were viable and replicated efficiently in Vero and 293 cells, and expressing NSs from a protein-expression plasmid actually abolished rescue of infectious virus. The only replication defect reported is in MRC-5 cells and is interferon-dependent, i.e. a consequence of the immune evasion failing, not of a missing replication factor. Reason: Genome replication in a phlebovirus is performed by the L protein (the RNA-dependent RNA polymerase) and the N nucleoprotein, which encapsidates the template. NSs contributes none of the work of RNA synthesis: it neither catalyses a step nor supplies structure or cofactor activity that a step of replication depends on, and it is not a component of the ribonucleoprotein. What the paper establishes is a conditional requirement for NSs for virus growth in interferon-competent cells, which is necessity for an outcome rather than participation in the process, and even that necessity is absent in the cell lines where replication was measured. Removal here does not rest on second-guessing a curator's reading of a full text: the cached abstract itself states that the deletion mutants replicated efficiently, so the annotation is contradicted by its own cited source. The GONUTS page for this PMID could not be consulted (gowiki.tamu.edu returns "This site is temporarily offline while we perform upgrades" and the Internet Archive has no snapshot), so the student's recorded rationale is unavailable; the judgment rests on the paper and on the division of labour among the viral proteins. For the CACAO failure taxonomy this is a distinct shape from "phenotype read as process": a viral fitness or growth requirement read as participation in genome replication. Supporting Evidence: PMID:16501102 Mutants of MP-12 partially or completely lacking the NSs open reading frame were viable. These NSs deletion mutants replicated efficiently in Vero and 293 cells, but not in MRC-5 cells PMID:16501102 whereas NSs protein expression abolished virus rescue |
| GO:0042025 host cell nucleus | EXP PMID:10233964 The carboxy-terminal acidic domain of Rift Valley Fever viru... | ACCEPT | Summary: Nuclear localisation of NSs, from the paper that mapped its determinants. NSs expressed alone from a recombinant Semliki Forest virus forms the same nuclear filaments seen in infected cells, and deleting the acidic C-terminal domain abolishes filaments without affecting nuclear import, so the two properties are separable and nuclear residence is intrinsic to NSs. Reason: Directly demonstrated, by immunofluorescence on both infected cells and cells expressing NSs alone, and in the compartment where the protein's TFIIH-directed activity takes place. This is a core location, not an incidental one: the cached full text is available for this reference and supports the claim. Supporting Evidence: PMID:10233964 deletion of this acidic carboxy-terminal domain prevents the protein from forming filaments but does not affect its nuclear localization PMID:10233964 we expressed NSs in mammalian cells via a recombinant Semliki Forest virus and demonstrated that the protein alone was able to form structures similar to those observed in RVF virus-infected cells |
| GO:0042025 host cell nucleus | EXP PMID:25918396 A Ξ©XaV motif in the Rift Valley fever virus NSs protein is e... | ACCEPT | Summary: Nuclear localisation in the context of the OmegaXaV motif study, which showed that the motif is required for nuclear filament formation and p62 degradation and that mutating Phe261 attenuates virulence. Reason: Consistent with every other line of evidence for this protein's location, and recorded by UniProt as host nucleus with experimental evidence citing this publication. The cached record is abstract-only, but the abstract itself describes nuclear filaments formed through the NSs-TFIIH interaction. Supporting Evidence: PMID:25918396 A key component of RVFV virulence is its ability to form nuclear filaments through interactions between the viral nonstructural protein NSs and the host general transcription factor TFIIH file:RVFVZ/NSS/NSS-uniprot.txt SUBCELLULAR LOCATION: Host nucleus |
| GO:0042025 host cell nucleus | EXP PMID:7108491 Identification of a major non-structural protein in the nucl... | ACCEPT | Summary: The original observation, from 1982: a 34-kDa nonstructural protein was demonstrated in the nuclei of RVFV-infected Vero cells by SDS-PAGE of nuclear fractions, matching the virus-induced antigen seen by immunofluorescence in intranuclear inclusions. That protein is NSs. Reason: A biochemical fractionation result corroborated by immunofluorescence, and the historical foundation for everything since; the apparent molecular weight is in reasonable agreement with the 29.9-kDa calculated mass of the 265-residue NSs, which migrates anomalously as a phosphoprotein. The claim has been confirmed repeatedly, including for NSs expressed in the absence of other viral proteins. The cached record is abstract-only but states the result explicitly. Supporting Evidence: PMID:7108491 A non-structural protein of mol. wt. 34 X 10(3) was demonstrated in the nuclei of Rift Valley fever virus-infected Vero cells |
| GO:0042025 host cell nucleus | IDA PMID:24403578 Virulence factor NSs of rift valley fever virus recruits the... | ACCEPT | Summary: This row says more than that NSs is in the nucleus: it says NSs acts there. The paper supports that directly, showing that FBXO3 is present in both compartments but that NSs removes specifically the nuclear pool of full-length FBXO3, consistent with the ubiquitination of p62 happening in the nucleus. Reason: The compartment-specific depletion of nuclear FBXO3, together with the nuclear location of the substrate p62 and of the NSs filaments that sequester p44 and XPB, makes the nucleus the site of this activity rather than merely a place the protein is found. The cached record is abstract-only, but the relevant statement is in the abstract. Supporting Evidence: PMID:24403578 NSs exclusively removes the nuclear pool of full-length FBXO3, likely due to consumption during the degradation process |
| GO:0042025 host cell nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: Subcellular-location mapping of SL-0414 (Host nucleus), asserting the same claim as the four experimental rows above. Reason: The mapping is faithful to a curated location that carries three independent experimental citations, and the nucleus is where the protein's principal activity occurs. Supporting Evidence: file:RVFVZ/NSS/NSS-uniprot.txt SUBCELLULAR LOCATION: Host nucleus |
| GO:0044067 symbiont-mediated perturbation of host cell-cell junction | EXP PMID:33087469 The NSs Protein Encoded by the Virulent Strain of Rift Valle... | KEEP AS NON CORE | Summary: NSs expression leads to dissolution of adherens junctions in hepatocytes, alongside reduced lamellipodia and altered cell spreading, in comparisons of the NSs-expressing ZH548 and MP12 strains with the ZH548-delta-NSs strain and after ectopic NSs expression. The cached full text is available for this reference. Reason: The observation is well controlled and the term describes it accurately, so the row stands. It is kept as non-core because the junctional change is a downstream consequence of the transcriptional block rather than a separate activity of NSs: the paper's own mechanism is that NSs prevents the antiviral upregulation of Abl2, a major regulator of the actin cytoskeleton, and the junction phenotype follows from that. Keeping it non-core records the cytopathic effect without implying a second, independent molecular role. Supporting Evidence: PMID:33087469 strong changes in cell morphology in nonmigrating hepatocytes, with reduction of lamellipodia, cell spreading, and dissolution of adherens junctions file:RVFVZ/NSS/NSS-uniprot.txt motility, reduction of lamellipodia, cell spreading, and dissolution of |
| GO:0052031 symbiont-mediated perturbation of host defense response | IEA GO_REF:0000043 | ACCEPT | Summary: Keyword-derived roll-up from KW-0899 (Viral immunoevasion) and KW-0922 (Interferon antiviral system evasion). NSs is the virus's main virulence factor precisely because it perturbs the host defence response. Reason: True and not redundant. NSs interferes with host defence by at least three separable routes that no single more specific term in this review subsumes: TFIIH destruction and the resulting global transcription block, PKR degradation in the cytoplasm, and suppression of the Abl2-dependent cytoskeletal arm of the antiviral response. The broad term is the only one that covers the whole of that, so it carries information rather than merely restating a descendant. Supporting Evidence: file:RVFVZ/NSS/NSS-uniprot.txt Plays a role in the escape of host innate immune response by PMID:33087469 NSs expression prevented the upregulation of Abl2 (a major regulator of the actin cytoskeleton) expression otherwise induced by avirulent infections and identified here as part of the antiviral response |
| GO:0052039 symbiont-mediated perturbation of host cytoskeleton | EXP PMID:33087469 The NSs Protein Encoded by the Virulent Strain of Rift Valle... | KEEP AS NON CORE | Summary: NSs perturbs the host actin cytoskeleton: it prevents the antiviral upregulation of Abl2, increases the mobility of infected fibroblasts relative to delta-NSs infection, reduces lamellipodia and cell spreading, and is itself found within long actin-rich structures. Full text is cached for this reference. Reason: The term is accurate and at the right level for what was measured, but the effect is mediated through the gene-expression block (loss of Abl2 induction) rather than through any direct action of NSs on actin or on a cytoskeletal regulator. It is a real and biologically important cytopathic consequence of infection, so it is kept, but it is not one of the protein's core activities. Supporting Evidence: PMID:33087469 we have analyzed the effects of NSs expression on the actin cytoskeleton PMID:33087469 NSs expression prevented the upregulation of Abl2 (a major regulator of the actin cytoskeleton) expression otherwise induced by avirulent infections |
| GO:0052170 symbiont-mediated suppression of host innate immune response | IEA GO_REF:0000043 | ACCEPT | Summary: Keyword-derived from KW-1090 (Inhibition of host innate immune response by virus), and a correct statement of what NSs is for. Blocking interferon induction and destroying PKR are both suppression of the host innate immune response. Reason: This is the best-supported process claim for the protein and the one that the whole literature converges on, with curated UniProt FUNCTION text citing eleven experimental references. It is also, given that GO lacks a symbiont-mediated interferon-production term, the most specific existing term that correctly covers the interferon-induction block, so it does more than roll up its descendants. Supporting Evidence: file:RVFVZ/NSS/NSS-uniprot.txt Plays a role in the escape of host innate immune response by PMID:24403578 NSs recruits FBXO3 to destroy the general host cell transcription factor TFIIH-p62, resulting in suppression of the transcriptional upregulation of innate immunity |
| GO:0140886 symbiont-mediated suppression of host interferon-mediated signaling pathway | IDA PMID:24403578 Virulence factor NSs of rift valley fever virus recruits the... | MODIFY | Summary: UniProt IDA from the FBXO3 paper. What that paper measures is interferon transcription: depleting FBXO3 rescued p62 and raised interferon transcription tenfold, and the authors frame the result as suppression of the transcriptional upregulation of innate immunity. The parent term GO:0140886 is nevertheless defined as reducing interferon-mediated signalling in the host. Reason: Same branch problem as the GO:0039502 rows, and handled the same way for consistency, since GO:0039502 is a descendant of this term. The biology is interferon antagonism upstream of interferon secretion, not interference with the interferon receptor or the JAK/STAT cascade, and GO offers no symbiont-mediated interferon-production term, so the replacement is a proposed new term. Nothing here questions the underlying experiment, which is strong. Proposed replacements: symbiont-mediated suppression of host type I interferon production Supporting Evidence: PMID:24403578 Small interfering RNA (siRNA)-mediated depletion of FBXO3 rescued p62 protein levels in RVFV-infected cells and elevated IFN transcription by 1 order of magnitude PMID:24403578 RVFV NSs blocks transcriptional upregulation of antiviral type I interferons (IFN) and destroys the general transcription factor TFIIH subunit p62 via the ubiquitin/proteasome pathway |
| GO:0140313 molecular sequestering activity | IDA PMID:14980221 TFIIH transcription factor, a target for the Rift Valley hem... | NEW | Summary: Proposed molecular function not present in GOA. Besides targeting p62 for degradation, NSs withdraws two further TFIIH subunits from the functional pool: it competes with XPD for p44 and sequesters p44 together with XPB into the nuclear filaments, so that TFIIH cannot be assembled. Sequestration, not catalysis or adaptor-mediated degradation, is the activity in this step. Reason: NSs does the work of this function itself: the filaments are built from NSs self-association, demonstrated for NSs expressed alone without any other viral protein, and p44 and XPB are physically held in them. This is not a downstream phenotype or a necessity argument, and it is not covered by the two existing molecular-function rows, which describe the ligase-substrate adaptor role that destroys p62. UniProt's curated FUNCTION text states the sequestering interpretation of the filaments independently. Proposed conservatively and as a molecular function only; the process consequences are already annotated on GO:0039602 and GO:0039653. Supporting Evidence: PMID:14980221 By competing with XPD, the natural partner of p44 within TFIIH, and sequestering p44 and XPB subunits, NSs prevents the assembly of TFIIH subunits PMID:14980221 the nonstructural viral NSs protein interacts with the p44 component of TFIIH to form nuclear filamentous structures that also contain XPB subunit of TFIIH file:RVFVZ/NSS/NSS-uniprot.txt (PubMed:24403578). Forms nuclear amyloid-like filaments of about 12 nm |
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Download this section (compressed HTML)Q: Should a symbiont-mediated interferon-production term coexist with the sensor-specific induction terms on the same gene product? The proposed term now has three cases, and Sendai virus V is both sensor-directed (GO:0039540, GO:0039548, accepted by direct assay in that review) and in need of a term for its production phenotype, which settles the earlier worry that all the cases were transcription-shutdown viruses. It raises the converse question: if the production term is warranted wherever interferon output is separately measured, it will layer over much of the induction branch. That is a scoping decision for the ontology editors, not something this review can settle, and it should be put to them with the request rather than discovered afterwards.
Q: NSs-directed degradation of TFIIH p62 proceeds when cullin 1, cullin 7 and Rbx1 are individually knocked down, yet requires FBXO3 and SKP1. What is the catalytic core of the ligase that NSs assembles, and is it a canonical SCF at all?
Suggested experts: Friedemann Weber, Markus Kainulainen, Andreas Pichlmair
Q: NSs uses the same OmegaXaV motif to bind p62/GTF2H1 and FBXW11. How is the choice between the TFIIH-directed and the PKR-directed complex made, and does it reduce simply to the nuclear versus cytoplasmic pool of NSs?
Suggested experts: James G. Omichinski, Tetsuro Ikegami
Q: Are the amyloid-like nuclear filaments an active sink that sequesters p44 and XPB, or a by-product of NSs overaccumulation? Mutations that abolish filaments (Phe261, Arg164) also abolish p62 degradation, which leaves the two possibilities entangled.
Suggested experts: Eliette Bonnefoy, Pierre-Yves Lozach
Q: Does NSs affect interferon-stimulated gene induction downstream of the type I interferon receptor at all, beyond the global polymerase II block? Answering this would settle whether any symbiont-mediated interferon-signalling term applies to NSs.
Suggested experts: Friedemann Weber, Michele Bouloy
Experiment: In cells expressing NSs alone (not infected, to avoid other viral products), compare two readouts side by side: induction of the interferon-beta gene after poly(I:C) stimulation, and induction of a panel of interferon-stimulated genes after addition of exogenous recombinant interferon-beta. Use nascent-transcript measurement (4sU or TT-seq) rather than steady-state mRNA so that the global transcription block can be normalised out, and include a transcription-competent NSs mutant such as clone 13 NSs and a filament-deficient but p62-degradation-competent mutant as controls. STAT1 phosphorylation and nuclear translocation should be scored in parallel. If interferon-receptor signalling is intact and only interferon-beta induction fails, the proposed production term is the correct annotation and the signalling terms should be retired for this protein.
Hypothesis: NSs blocks type I interferon production but does not interfere with signalling downstream of the type I interferon receptor.
Type: nascent transcriptomics with interferon stimulation and phospho-STAT1 immunoblotting
Experiment: Measure viral genome, antigenome and mRNA synthesis directly, by strand-specific quantitative RT-PCR and by metabolic labelling of viral RNA, for MP-12 and for delta-NSs MP-12 in interferon-competent MRC-5 cells, in the same cells after knockout of IFNAR1 or of MAVS, and in Vero cells. A minireplicon assay with L and N supplied in trans, with and without NSs, gives the cleanest version: if NSs contributed to RNA synthesis, adding it should raise minireplicon output in an interferon-null background. This directly tests the annotation that this review removes.
Hypothesis: NSs is dispensable for RVFV genome replication itself, and the growth defect of delta-NSs viruses is entirely interferon-dependent.
Type: strand-specific RT-qPCR and L/N minireplicon assay in IFNAR1- and MAVS-knockout cells
Experiment: Combine fluorescence recovery after photobleaching on GFP-tagged p44 and XPB in cells containing NSs filaments with quantitative imaging of the free versus filament-associated pools, and with a filament-disrupting but p62-binding NSs variant. Cross-linking mass spectrometry of purified filaments would establish which TFIIH subunits are physically incorporated and in what stoichiometry. The prediction is that free p44 and XPB are depleted in proportion to filament mass, and recover when filaments are dissolved.
Hypothesis: The nuclear filaments sequester TFIIH subunits and are not merely an aggregation by-product.
Type: FRAP and cross-linking mass spectrometry of nuclear filaments
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