Gag polyprotein (Pr71Gag) of simian foamy virus, chimpanzee isolate SFVcpz. It is the sole structural protein of the viral core and, unlike orthoretroviral Gag, is not processed into matrix, capsid and nucleocapsid subunits: a single partial cleavage near the C-terminus yields p68Gag plus a 27-residue p3 peptide, and both p71 and p68 are present in mature particles. The N-terminal half is the assembly and egress module. It multimerises into the capsid shell and, because foamy Gag carries no myristoylation or other membrane-targeting signal, it reaches the budding site by binding directly to the cytoplasmic tip of the Env leader peptide; budding therefore strictly requires co-expressed cognate Env, and particles form predominantly at the endoplasmic reticulum and occasionally at the plasma membrane. A PSAP late domain in the same half recruits host TSG101 and routes a large part of egress through the ESCRT machinery, while a neighbouring PPPI motif supports release by a Vps4-independent route. The C-terminal half is intrinsically disordered and carries three glycine-arginine-rich boxes (GR boxes) that replace the Cys-His boxes of other retroviruses: they bind RNA and DNA with high affinity and little sequence specificity, package the genome, and are required for reverse transcription inside the particle and for virion morphogenesis. GR box II additionally carries a chromatin-binding sequence that tethers the incoming subviral complex to host chromosomes through H2A/H2B core histones, which is how the pre-integration complex is held on chromatin until integration, and overlaps a nuclear localization signal that drives a transient nuclear stage of newly made Gag; a CRM1-dependent nuclear export signal in the N-terminal domain returns Gag to the cytoplasm for assembly. Early after infection, Gag binds the dynein light chain DYNLL1 and carries the incoming capsid along microtubules to the centrosome, where in non-dividing cells the particle can persist uncoated for weeks until the cell re-enters the cycle.
Curated functional classes representing distinct biological activities. These may be splice variants, cleavage products, or other forms with different functions.
GAG_P68PRO_0000378592 (residues 1-626) GAG_P3PRO_0000378593 (residues 627-653) | GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003677 DNA binding | IEA GO_REF:0000043 | ACCEPT | Summary: The GR-box region of foamy virus Gag, which replaces the orthoretroviral Cys-His nucleocapsid motif, binds DNA as well as RNA with high affinity and no sequence specificity, so the keyword-derived term is correct and biologically meaningful for a virus whose particles can carry a reverse-transcribed dsDNA genome. Reason: Filter-binding assays on the expressed C-terminal NC-equivalent of foamy virus Gag show high-affinity, sequence-independent binding to both RNA and DNA, and GR box I is required for it [PMID:8970944]. This is not an artefact of in vitro excess: foamy viruses proceed to late reverse transcription, so up to 20% of extracellular particles contain dsDNA rather than RNA, and Gag is the only protein packaging it. The claim for Q87039 itself rests on sequence similarity to the PFV protein (P14349), which is the basis of UniProt's own GR-box annotation. Supporting Evidence: PMID:8970944 the NC domain of HFV Gag binds with high affinity to both RNA and DNA, in a sequence-independent manner, as determined by filter binding assays PMID:8970944 this motif is required for nucleic acid binding and for viral replication file:genes/SFVCP/gag/gag-uniprot.txt Gag protein contains 3 glycine-arginine motifs (GR-boxes) necessary for RNA packaging, the first of which has nucleic acid binding properties in vitro. |
| GO:0003723 RNA binding | IEA GO_REF:0000043 | ACCEPT | Summary: RNA binding by the GR boxes is a core activity: it is how the viral genome is selected and encapsidated, and it is required for reverse transcription within the particle. Reason: The expressed GR-box region binds RNA with high affinity in filter-binding assays [PMID:8970944], and systematic deletion and substitution of each GR box in a four-plasmid vector system shows the boxes are needed for RNA encapsidation, intraparticle reverse transcription and infectivity [PMID:21106749]. The term is at the right granularity: binding is sequence-independent, so no specific RNA-class child term applies. Supporting Evidence: PMID:21106749 the PFV Gag GR boxes are important for RNA encapsidation, genome reverse transcription, and virion infectivity as well as for particle morphogenesis PMID:21106749 particle-associated DNA content and infectivity were drastically reduced for all deletion mutants |
| GO:0019013 viral nucleocapsid | IEA GO_REF:0000043 | ACCEPT | Summary: Gag is the protein component of the foamy virus nucleocapsid: the GR-box region is the functional equivalent of the orthoretroviral NC domain and is the only protein bound to the packaged genome. Reason: Foamy virus Gag is not cleaved into MA/CA/NC; the nucleoprotein complex in the particle is genome plus Gag, with the C-terminal GR boxes performing the NC function [PMID:8970944, PMID:21106749]. The term therefore describes a real structure this protein is part of, not a mapping artefact, even though it is keyword-derived. Supporting Evidence: PMID:8970944 The Gag protein of human foamy virus (HFV) lacks Cys-His boxes present in the nucleocapsid (NC) domains of other retroviruses; instead it contains three glycine-arginine-rich motifs (GR boxes) file:genes/SFVCP/gag/gag-uniprot.txt Mature particles do not include the usual processed retroviral structural protein (MA, CA and NC), but instead contain two large Gag proteins. |
| GO:0019028 viral capsid | IEA GO_REF:0000120 | ACCEPT | Summary: Gag multimerises into the foamy virus capsid shell; cryo-EM of native PFV particles resolves a capsid of constant dimension plus an outer shell attributed to the Gag N-terminal domain together with the Env leader peptide. Reason: This is the central structural role of the protein and is supported by direct structural work on the particle rather than only by the InterPro Gag_N signature [PMID:27399201]. Assembly-competence maps to the same N-terminal region [PMID:23618494], so the component and the mechanism agree. Supporting Evidence: PMID:27399201 Mature PFV particles have a distinct morphology with a capsid of constant dimension as well as a less ordered shell of density between the capsid and the membrane likely formed by the Gag N-terminal domain and the cytoplasmic part of the Env leader peptide gp18LP |
| GO:0019076 viral release from host cell | IEA GO_REF:0000002 | ACCEPT | Summary: Gag is required for and actively drives particle release: its N-terminal helical motif binds the Env leader peptide to license budding, and its PSAP and PPPI motifs are release determinants. Reason: Deleting the N-terminal Env-interaction domain abolishes release, while the N-terminal 129 residues alone suffice for release of a minimal Gag [PMID:23618494]; mutating the PSAP and PPPI motifs reduces egress additively [PMID:15858022]. Gag performs part of the work of release rather than merely being cargo, so the involved_in claim is sound at this level of the hierarchy. Supporting Evidence: PMID:23618494 a minimal PFV Gag protein comprising the N-terminal 129 aa was released into the supernatant, whereas proteins lacking this domain failed to do so PMID:15858022 Mutation of the PSAP and PPPI motifs individually reduced PFV egress, and their combined mutation had an additive effect |
| GO:0030430 host cell cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: The cytoplasm is where Gag does most of its work: capsid assembly in the late phase and dynein-dependent trafficking of the incoming capsid in the early phase both occur there. Reason: Direct immunofluorescence puts a third of wild-type Gag wholly in the cytoplasm and a further 39% in a nucleocytoplasmic distribution [PMID:21255441], and the published consensus is cytoplasmic, nuclear and centrosomal distribution in transfected and infected cells [PMID:22393357]. The term is as precise as the assays warrant for the bulk pool; the specific cytoplasmic sub-locations it is kept beside are the centrosome row and, for the ER budding site, a gap noted in suggested_experiments. Supporting Evidence: PMID:21255441 Wild-type Gag proteins were detected in the cytoplasm for 33% Β± 2% of transfected cells, including around the centrosome, within the nucleus (28% Β± 2%) or harbored a nucleocytoplasmic distribution (39% Β± 2%) PMID:22393357 PFV Gag displays different patterns of subcellular distribution, being localized in the cytoplasm, the nucleus and the centrosome in transfected and infected cells |
| GO:0039702 viral budding via host ESCRT complex | IEA GO_REF:0000043 | ACCEPT | Summary: The PSAP late domain of Gag behaves as a conventional class E VPS L domain: it binds TSG101 in a PSAP-dependent manner and its loss makes release insensitive to dominant negative Vps4 and largely insensitive to dominant negative TSG101. Reason: This is one of the best-evidenced parts of foamy Gag biology and is not a bare keyword transfer: yeast two-hybrid shows a PSAP-dependent Gag-TSG101 interaction, and the dominant-negative epistasis shows the motif is what routes egress through ESCRT [PMID:15858022]. Q87039 carries the PTAP/PSAP motif at residues 289-292. The second motif, PPPI, works Vps4-independently, which is why the parent viral budding term is also kept rather than being treated as redundant. Supporting Evidence: PMID:15858022 yeast two-hybrid analysis showed a PSAP motif-dependent interaction between PFV Gag and Tsg101 PMID:15858022 When PSAP was mutated, residual infectious PFV release was unaffected by dominant negative Vps4 (an ATPase involved in the final stages of budding), and sensitivity to dominant negative Tsg101 was dramatically reduced, suggesting that the PSAP motif functions as a conventional class E VPS-dependent L domain file:genes/SFVCP/gag/gag-uniprot.txt Nucleocapsid protein p14 contains one L domain: a PTAP/PSAP motif, which interacts with the UEV domain of TSG101 |
| GO:0042025 host cell nucleus | IDA PMID:21255441 A nuclear export signal within the structural Gag protein is... | ACCEPT | Summary: CACAO row. The cited paper does localize Gag to the nucleus directly: Figure 1D scores wild-type Gag by confocal immunofluorescence in transfected HeLa cells as 28% Β± 2% nuclear and 39% Β± 2% nucleocytoplasmic, and the whole paper is built on the NES that returns that nuclear pool to the cytoplasm. The CACAO term matches what the figure shows and is at the right granularity. Reason: This is the strongest of the four CACAO rows and the one that grounds the other three. The assay is a direct localization of the Gag protein itself (anti-Gag immunofluorescence, three experiments of 200 cells), not a phenotype read as a location, and the nuclear stage is a genuine, mechanistically characterised part of the replication cycle - import via the GR box II NLS [PMID:21106749], export via the CRM1-dependent NES at aa 95-112 [PMID:21255441]. The one defect is that the protein assayed is prototype foamy virus Gag (UniProtKB:P14349), a sister chimpanzee foamy virus isolate, not SFVcpz Q87039; the two Gag sequences are identical across the NES (aa 95-112 LAFQDLDLPEGPLRFGPL in both, G110 included) and 92% identical over the N-terminal 150 residues, so the claim transfers, but the correct evidence code for Q87039 is ISS rather than IDA. That is recorded as a source defect instead of a REMOVE, following the curator-deference rule. Supporting Evidence: PMID:21255441 Wild-type Gag proteins were detected in the cytoplasm for 33% Β± 2% of transfected cells, including around the centrosome, within the nucleus (28% Β± 2%) or harbored a nucleocytoplasmic distribution (39% Β± 2%) PMID:21106749 GR box II mutants lacked the typical nuclear localization pattern of PFV Gag |
| GO:0042025 host cell nucleus | IDA PMID:22393357 Investigating the intercellular spreading properties of the ... | ACCEPT | Summary: CACAO row. The term is right for this protein, but this paper is the wrong support for it: the nuclear Gag signal this study reports is the very thing it sets out to debunk. Using different fixation procedures the authors establish that the intercellular spreading and nuclear accumulation of Gag they see is artificial transport occurring during cell fixation, never observed in living cells. Reason: The claim is kept because it is true and because three other rows on this entry assert it from sound evidence - a REMOVE here would contradict them and is not the way to deal with a bad reference. But the row should not be read as independent support. The only statement in this paper that locates Gag in the nucleus in its own right is a citation to prior work ("PFV Gag displays different patterns of subcellular distribution, being localized in the cytoplasm, the nucleus and the centrosome in transfected and infected cells [5], [21], [22]"); the new data show bright nuclear fluorescence in methanol-fixed recipient cells and none in live cells, and the authors attribute it to leakage during fixation followed by retention on chromatin via the GR box II chromatin-binding sequence. Two source defects are recorded: the reference does not support an IDA, and, as for every CACAO row here, the protein assayed is PFV Gag (UniProtKB:P14349), not SFVcpz Q87039. For the CACAO failure taxonomy this is an "artefact paper read as positive evidence" - the mirror of the Ebola GP case, where the paper never localized the viral protein; here it localized it and then showed the localization was not real. Supporting Evidence: PMID:22393357 we established that spreading and nuclear localization of the PFV Gag is due to artificial transport occurring during cell fixation PMID:22393357 We conclude that uptake and nuclear accumulation of PFV Gag in naΓ―ve recipient cells represents an artificial diffusion event occurring during cell fixation with subsequent nuclear retention mediated by the CBS within the GRII box PMID:21255441 Wild-type Gag proteins were detected in the cytoplasm for 33% Β± 2% of transfected cells, including around the centrosome, within the nucleus (28% Β± 2%) or harbored a nucleocytoplasmic distribution (39% Β± 2%) |
| GO:0042025 host cell nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: The electronic route to the same component is sound: UniProt records a host-nucleus subcellular location for the Gag chain with the note that Gag is nuclear at the initial phase and cytoplasmic at assembly, which is exactly what the imaging shows. Reason: Unlike the CACAO rows, this one makes no claim that Q87039 itself was assayed, so it is the evidentially cleanest of the four host-nucleus rows. It is kept rather than treated as a duplicate: rows sharing a term reinforce the claim. The NLS lies in GR box II, which Q87039 carries at residues 540-561. Supporting Evidence: file:genes/SFVCP/gag/gag-uniprot.txt It is then actively transported into the nucleus thanks to its nuclear localization signal. PMID:21106749 GR box II mutants lacked the typical nuclear localization pattern of PFV Gag |
| GO:0042025 host cell nucleus | IMP PMID:21255441 A nuclear export signal within the structural Gag protein is... | ACCEPT | Summary: CACAO row, same paper as the IDA row but reading the mutant series rather than the wild-type images. Point mutation or deletion of the aa 95-112 nuclear export signal redistributes Gag into the nucleus (GagG110V 77% Β± 2% nuclear, GagΞNES 78% Β± 2%), and the NES-defective mutant sequesters wild-type Gag there as well. The term matches what the mutants show. Reason: Using IMP for a cellular component is unusual, but it is not a phenotype read as a location: the measured phenotype here is itself a change in the localization of the annotated protein, which is legitimate support for the component. The claim is the same as the IDA row's and the two reinforce each other, so they carry the same action. The isolate defect recorded on the IDA row applies identically - the assayed protein is PFV Gag (UniProtKB:P14349), so ISS rather than IMP is the correct code for Q87039. Supporting Evidence: PMID:21255441 Conversely, GagG110V was mainly confined in the nucleus (77% Β± 2% of transfected cells), some GagG110V-positive cells exhibiting a nucleocytoplasmic staining (23% Β± 2% of transfected cells) PMID:21255441 deleting amino acids 95 to 112 on the full length PFV Gag, and to a lesser extent, point mutations of conserved residues, led to nuclear redistribution of the corresponding mutants |
| GO:0043657 host cell | IEA GO_REF:0000120 | MODIFY | Summary: Correct but far less specific than the evidence supports. Gag's localization is known at compartment resolution - host cell cytoplasm, host cell nucleus and host cell centrosome - so the bare host cell term should be replaced by those rather than kept. Reason: The row carries no localization evidence of its own: it was generated mechanically from two biological-process terms (WITH/FROM GO:0075521 and GO:0075606), which say only that Gag moves viral material inside a host cell. The compartments are independently established and already annotated on this entry - cytoplasmic and nuclear distribution by quantified confocal immunofluorescence [PMID:21255441], and centrosomal targeting [PMID:12857789] - so the replacement terms are ones the gene already carries. Note this is a lateral refinement rather than a strict descendant substitution: GO places host cell nucleus and host cell cytoplasm under GO:0043656 host intracellular region, not under GO:0043657 host cell, so TOO_GENERAL is not available even though the intent is the same. Nothing here suggests the claim is false. Proposed replacements: host cell cytoplasm host cell nucleus Supporting Evidence: PMID:21255441 Wild-type Gag proteins were detected in the cytoplasm for 33% Β± 2% of transfected cells, including around the centrosome, within the nucleus (28% Β± 2%) or harbored a nucleocytoplasmic distribution (39% Β± 2%) |
| GO:0044163 host cytoskeleton | IEA GO_REF:0000002 | MODIFY | Summary: Correct but less specific than the evidence supports. Gag's cytoskeletal association is not diffuse: incoming and transfected Gag concentrates at the centrosome, and GO:0120148 host cell centrosome is an is_a descendant of host cytoskeleton. Reason: Gag targets the pericentrosomal region in transfected cells with no other viral protein present, in a microtubule- and dynein/dynactin-dependent way, through a direct interaction with dynein light chain 8 (DYNLL1) [PMID:12857789]; incoming capsids reach and persist at the MTOC [PMID:17530924]; and the consensus localization statement for the protein is cytoplasm, nucleus and centrosome [PMID:22393357]. The specific descendant is therefore well supported, and per the refinement rule the general term should be replaced by it rather than kept. Host cell centrosome is also the compartment where the functionally important event happens, the weeks-long pre-integration stall in non-dividing cells. Proposed replacements: host cell centrosome Supporting Evidence: PMID:12857789 the Gag protein, the scaffold component of viral capsids, targets the pericentrosomal region in transfected cells in the absence of any other viral components but in a microtubule- and dynein/dynactin-dependent manner PMID:17530924 incoming FV capsids traffic along the microtubule network to reach the microtubule-organizing centre (MTOC) |
| GO:0044383 host chromosome | IDA PMID:17530924 Centrosomal latency of incoming foamy viruses in resting cel... | ACCEPT | Summary: CACAO row. The term is right for foamy virus Gag - a chromatin-binding sequence in GR box II binds host chromosomes through H2A/H2B core histones - but the cited paper does not show it. PMID:17530924 is about centrosomal latency of incoming particles; the word "chromatin" never appears in it, and "chromosomes" appears only twice, both in one generic Introduction sentence about retroviral provirus integration. Its localization data put Gag at the centrosome, and diffusely in cytoplasm and nucleus after cell activation. Reason: The claim is kept because it is well established for this protein, just from a different paper: PMID:18627573, from the same laboratory one year later, identifies the C-terminal domain that "efficiently binds host chromosomes, by interacting with H2A/H2B core histones", and shows that mutating it abolishes chromosomal attachment of incoming subviral complexes while leaving particle production, entry and trafficking intact. That is a clean, specific demonstration of the component and of why it matters, so REMOVE would discard a true and functionally central claim. Two source defects are recorded: the reference, and the cross-isolate evidence code that affects all four CACAO rows here. For the CACAO failure taxonomy this is a pattern not yet catalogued - right term, right protein, right evidence code, wrong paper from the same group - which no mechanical check can see, because the PMID resolves, the title matches, and the paper really is about foamy virus Gag. Supporting Evidence: PMID:18627573 we identify a short domain within the C-terminus of the structural Gag protein that efficiently binds host chromosomes, by interacting with H2A/H2B core histones PMID:18627573 chromosomal attachment of incoming subviral complexes is abolished, precluding proviral integration PMID:22393357 the GRII box contains an essential chromatin-binding sequence (CBS) that, by interacting with histone proteins, allows tethering of incoming PFV pre-integration complex to host chromosomes prior to viral genome integration |
| GO:0046718 symbiont entry into host cell | IEA GO_REF:0000120 | MARK AS OVER ANNOTATED | Summary: Over-annotation from the UniProt keyword. GO:0046718 is the process by which the symbiont breaches the plasma membrane or cell envelope and enters the cell, ending when the genome is released into it. In foamy viruses that work is done by Env - receptor binding and membrane fusion by gp80SU/gp48TM - and Gag is cargo inside the entering particle. Reason: Gag's documented early-phase activities all begin after entry: dynein-dependent transport of the incoming capsid to the centrosome [PMID:12857789], the stall there until cell-cycle re-entry triggers uncoating [PMID:17530924], and chromatin tethering of the pre-integration complex [PMID:18627573]. The chromatin-tethering study makes the separation explicit, reporting that mutating the chromosome-binding domain leaves virus entry and intracellular trafficking unaffected while abolishing chromosomal attachment - entry is a separable step that this protein does not perform. The term is not simply false (Gag is physically carried in), but applying involved_in asserts participation in the breach itself, which belongs to Env. The post-entry steps are captured properly by GO:0075521 and GO:0075606 on this same entry, so nothing is lost by downgrading this row; marking it over-annotated rather than removing it reflects that KW-1160 is routinely applied to incoming structural proteins and that this is a keyword-mapping granularity problem, not a claim contradicted by data. Supporting Evidence: PMID:18627573 While viral particle production, virus entry and intracellular trafficking are not affected by mutation of this domain, chromosomal attachment of incoming subviral complexes is abolished, precluding proviral integration. PMID:27399201 The viral membrane contains trimeric Env glycoproteins partly arranged in interlocked hexagonal assemblies. |
| GO:0046755 viral budding | IEA GO_REF:0000043 | ACCEPT | Summary: Gag is the capsid component whose interaction with the Env leader peptide licenses budding, and which carries two late-domain motifs that drive release. The pathway-level term is kept alongside the ESCRT-specific child because one of those motifs, PPPI, works independently of Vps4. Reason: Foamy virus budding is Gag-driven but strictly Env-dependent, and the Gag determinant has been mapped: the N-terminal 129 residues suffice for release and their loss abolishes it [PMID:23618494]. Keeping this term is not a redundant restatement of GO:0039702, because PFV release that depends on the PPPI motif was found to be Vps4-independent and only partially TSG101-dependent [PMID:15858022], so part of Gag-driven budding lies outside the ESCRT child term. Foamy virus buds mainly into the endoplasmic reticulum rather than the plasma membrane, which is a further reason to keep the unqualified parent rather than force a membrane-specific child. Supporting Evidence: PMID:23618494 FV release requires co-expression and a highly specific interaction between capsid (Gag) and glycoprotein (Env), which cannot be complemented by heterologous Env proteins PMID:15858022 Surprisingly, PFV release which is dependent on the PPPI motif was Vps4-independent and was partially inhibited by dominant negative Tsg101, suggesting that PPPI functions by an unconventional mechanism to facilitate PFV egress file:genes/SFVCP/gag/gag-uniprot.txt They bud predominantly into the endoplasmic reticulum (ER) and occasionally at the plasma membrane. |
| GO:0075521 microtubule-dependent intracellular transport of viral material towards nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: Well supported at exactly this granularity. Gag is the adaptor that links the incoming capsid to the host minus-end motor: it binds dynein light chain 8 (DYNLL1) directly and targets the pericentrosomal region in a microtubule- and dynein/dynactin-dependent manner even when expressed alone. Reason: This is a case where Gag performs the work rather than being transported passively: the transport determinant is a 30-residue coiled-coil motif in Gag's N-terminus, and the direct Gag-DYNLL1 interaction accounts for routing of incoming capsids [PMID:12857789]. The microtubule dependence named in the term was shown, not assumed [PMID:17530924]. Despite the IEA code this is the best-evidenced process term on the entry. Supporting Evidence: PMID:12857789 we describe a direct interaction between Gag and dynein light chain 8 that probably accounts for the specific routing of the incoming capsids to the centrosome prior to nuclear import of the viral genome PMID:12857789 Trafficking of Gag towards the centrosome requires a minimal 30 amino acid coiled-coil motif in the N-terminus of the molecule. PMID:17530924 incoming FV capsids traffic along the microtubule network to reach the microtubule-organizing centre (MTOC) |
| GO:0075606 transport of viral material towards nucleus | IEA GO_REF:0000043 | TOO GENERAL | Summary: True but uninformative: it is the direct parent of GO:0075521, which this review accepts on the same entry, and the microtubule and dynein dependence that the child names is precisely what the evidence establishes. Reason: Unlike the viral budding row, where the parent carries extra information because an ESCRT-independent route exists, there is no documented microtubule-independent route by which foamy Gag moves the incoming genome towards the nucleus; the parent term therefore restates the accepted child and nothing more [PMID:12857789]. Judging the term, not the evidence - the claim is correct, and the keyword mapping behind it is sound. |
| GO:0039660 structural constituent of virion | IDA PMID:27399201 Cryo-electron Microscopy Structure of the Native Prototype F... | NEW | Summary: Proposed new annotation. The molecular-function side of this entry currently records only nucleic acid binding, which misses what the protein mainly is: the structural subunit of the foamy virus core. Cryo-EM of native particles places Gag as the capsid shell plus an outer less-ordered layer, and Gag multimerisation is what builds the capsid. Reason: Gag performs the work of this function rather than being a passenger: the capsid is composed of multimeric Gag, deletion of the N-terminal region abolishes particle formation, and mutation of the YEIL motif abolishes particle formation at an assembly step before budding [PMID:15858022, PMID:23618494]. The structural role is directly visualised in purified particles [PMID:27399201]. The term is not an ancestor or descendant of GO:0003677 or GO:0003723, the only molecular functions currently annotated, so it adds coverage rather than redundancy. The comparator check supports it: structural constituent of virion is the conventional molecular function for retroviral and other viral capsid proteins, so its absence here is a gap rather than a convention. Supporting Evidence: PMID:27399201 Mature PFV particles have a distinct morphology with a capsid of constant dimension as well as a less ordered shell of density between the capsid and the membrane likely formed by the Gag N-terminal domain and the cytoplasmic part of the Env leader peptide gp18LP PMID:15858022 Mutation of the YEIL sequence completely abolished particle formation and also reduced the rate of Gag processing by the viral protease, suggesting that the integrity of YEIL is required at an assembly step prior to budding file:genes/SFVCP/gag/gag-uniprot.txt The capsid is composed of multimeric Gag protein. |
| GO:0019074 viral RNA genome packaging | IMP PMID:21106749 Novel functions of prototype foamy virus Gag glycine- argini... | NEW | Summary: Proposed new annotation. Genome encapsidation is the function of the three GR boxes, and no process term on this entry covers it. Gag is the protein that selects and packages the genome, since foamy virus particles contain no separate nucleocapsid protein. Reason: Gag does the work of packaging: the isolated GR-box region binds RNA directly with high affinity [PMID:8970944], and deletion or substitution of the boxes in a four-plasmid vector system with uncoupled genome packaging and structural-protein translation reduces RNA encapsidation and essentially abolishes particle-associated DNA and infectivity [PMID:21106749]. This is participation, not mere requirement: the binding activity that captures the genome resides in this protein. The term is not an ancestor or descendant of any process term already annotated here; its parent GO:0019068 virion assembly is deliberately not proposed, because that is an ancestor of the already-accepted GO:0046755 viral budding. Supporting Evidence: PMID:21106749 the PFV Gag GR boxes are important for RNA encapsidation, genome reverse transcription, and virion infectivity as well as for particle morphogenesis file:genes/SFVCP/gag/gag-uniprot.txt Gag protein contains 3 glycine-arginine motifs (GR-boxes) necessary for RNA packaging |
| GO:0045503 dynein light chain binding | IPI PMID:12857789 Targeting of incoming retroviral Gag to the centrosome invol... | NEW | Summary: Proposed new annotation. The entry carries the microtubule-dependent transport process term but not the molecular function that executes it. Gag binds dynein light chain 8 (DYNLL1) directly, and that interaction is what couples the incoming capsid to the host motor. Reason: A direct Gag-DYNLL1 interaction was demonstrated, and Gag alone, with no other viral component, reaches the pericentrosomal region in a microtubule- and dynein/dynactin -dependent way through a 30-residue N-terminal coiled-coil motif [PMID:12857789]. UniProt records the same interaction as critical for microtubule-dependent genome transport. This is an informative molecular function rather than bare protein binding: it names the partner class and explains the accepted GO:0075521 process annotation, which otherwise has no molecular-function counterpart on this entry. Supporting Evidence: PMID:12857789 we describe a direct interaction between Gag and dynein light chain 8 that probably accounts for the specific routing of the incoming capsids to the centrosome prior to nuclear import of the viral genome file:genes/SFVCP/gag/gag-uniprot.txt Interacts with host light chain cytoplasmic dynein DYNLL1; this interaction is critical for intracellular microtubule-dependent viral genome transport toward the centrosome |
| GO:0042393 histone binding | IPI PMID:18627573 Chromatin tethering of incoming foamy virus by the structura... | NEW | Summary: Proposed new annotation. The host chromosome component is annotated on this entry but the activity that produces it is not. The chromatin-binding sequence in GR box II binds host chromosomes by interacting with the H2A/H2B core histones. Reason: The interaction is specific and mapped to a short C-terminal domain, and mutating that domain abolishes chromosomal attachment of incoming subviral complexes while leaving particle production, entry and trafficking intact [PMID:18627573]. This is the molecular function underlying the accepted GO:0044383 host chromosome row and the tethering of the pre-integration complex; without it the component annotation has no mechanistic counterpart. The term is informative rather than bare protein binding, naming the H2A/H2B ligand class. Only the abstract is cached, so the precise assay format is not visible, but the interaction claim is stated unambiguously and is corroborated independently [PMID:22393357]. Supporting Evidence: PMID:18627573 we identify a short domain within the C-terminus of the structural Gag protein that efficiently binds host chromosomes, by interacting with H2A/H2B core histones PMID:22393357 the GRII box contains an essential chromatin-binding sequence (CBS) that, by interacting with histone proteins, allows tethering of incoming PFV pre-integration complex to host chromosomes prior to viral genome integration |
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Download this section (compressed HTML)Q: Should experimental GO annotations derived from prototype foamy virus (UniProtKB:P14349) experiments be made on P14349 and propagated to the sister isolate SFVcpz (UniProtKB:Q87039) as ISS, rather than made directly on Q87039 with an experimental code? All four CACAO rows on Q87039 are cross-isolate transfers of PFV results, and P14349 itself carries no corresponding Gag annotation.
Suggested experts: Dirk Lindemann, Ali Saib
Q: Is the transient nuclear stage of newly synthesised Gag functionally required, or is the essential role of the aa 95-112 motif something other than nuclear export? A GR box II deletion revertant replicates in culture despite little nuclear transport, which is hard to reconcile with the lethality of NES point mutations.
Suggested experts: Maxine L Linial, Ali Saib, Dirk Lindemann
Q: Given that foamy viruses bud predominantly into the endoplasmic reticulum, should Gag carry a host endoplasmic reticulum component annotation, and is there a GO process term that distinguishes Env-licensed budding into an internal compartment from plasma membrane budding?
Suggested experts: Dirk Lindemann
Experiment: Express epitope-tagged SFVcpz Gag (Q87039) in the same HeLa transfection system used for PFV Gag and score subcellular distribution by confocal immunofluorescence, in parallel with PFV Gag as the reference, using glutaraldehyde as well as methanol fixation so that fixation-induced redistribution is controlled for. Follow with a mitotic chromosome spread and a histone H2A/H2B pull-down to test chromatin tethering, and nocodazole plus dynein inhibition to test centrosomal targeting.
Hypothesis: The SFVcpz Gag protein itself, and not only its PFV orthologue, localizes to the host nucleus, the centrosome and host chromosomes, so that the annotations currently carried on Q87039 with experimental codes can be grounded on this isolate.
Type: Comparative confocal immunofluorescence and biochemical fractionation
Experiment: Build separation-of-function GR box II mutants in the four-plasmid PFV vector system that uncouple the nuclear localization signal from the chromatin-binding sequence, and assay each for Gag localization, particle release, genomic RNA packaging, particle-associated DNA content and single-cycle infectivity. Include the aa 95-112 NES mutants as controls so that the import and export requirements are measured on the same scale.
Hypothesis: The nuclear import of Gag can be abolished without disturbing chromatin binding, and import-deficient but chromatin-binding-competent virus replicates normally.
Type: Reverse genetics with single-cycle infectivity and packaging readouts
Experiment: Co-express Gag with cognate Env, with a heterologous Env, or alone, and determine Gag distribution by immuno-electron microscopy and by membrane flotation of ER-marker-positive fractions, to establish whether a host endoplasmic reticulum component annotation is warranted and whether it is strictly Env-dependent.
Hypothesis: Gag reaches the budding site on endoplasmic reticulum membranes through the Env leader peptide, so Gag is detectable on host ER membranes only when cognate Env is co-expressed.
Type: Immuno-electron microscopy and membrane flotation
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