FliD (PA1094, HAP2) is the B-type flagellar filament cap protein of P. aeruginosa PAO1, a 474-residue protein with coiled-coil N- and C-terminal segments flanking a core (residues 78-405) whose crystal structure forms a six-pointed star hexamer, confirmed as a hexamer in solution and by negative-stain electron microscopy. The cap sits at the distal tip of the growing filament, where it keeps flagellin subunits delivered through the central channel from diffusing away and positions them for polymerisation, so filament elongation and swimming motility depend on it: a PAO1 fliD transposon mutant is non-motile and is restored by plasmid-borne fliD, whereas Salmonella fliD does not complement it. P. aeruginosa strains carry one of two sequence-divergent fliD types, of which PAO1 has the B type. Beyond its structural role in the flagellum, FliD is itself an adhesin: a fliD insertion mutant loses adhesion to mucin and purified FliD competitively blocks mucin adhesion of non-piliated cells, which is relevant to airway colonisation. The gene is transcribed from an RpoN/FleQ-dependent promoter rather than the flagellar sigma-28 promoter.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0009421 bacterial-type flagellum filament cap | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN000767631 (PTHR30288, flagellar cap/assembly protein FliD), whose only seed for this term is PAO1 FliD itself. The term is the defining structure of the family. Reason: FliD in its own With/From is the expected marker of experimental grounding, not circularity. Every one of the 20 leaves is a FliD orthologue (19 taxa, almost all named "flagellar hook-associated protein 2"), so the cap claim is exactly the family-level function, and the PAINT curator has already placed NOT annotations for both this term and GO:0071973 at two descendant nodes (PTN004740641, PTN004740642), which is the correct treatment of lineages that have lost the flagellum. The structural work on PAO1 FliD itself (hexameric cap, loss of motility in a fliD mutant) is independent confirmation. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000767631 Β· PTN000767631 (PTHR30288) SUPPORTS TRANSFER 20 leaf IBAs in 19 taxa in the PAINT leaf file, all FliD orthologues across Proteobacteria, Firmicutes, Spirochaetes, Aquificae and Thermodesulfovibrio; the node also carries explicit NOT IBDs for GO:0009421 and GO:0071973 at two sub-nodes. UniProtKB:Q9K3C5 Β· fliD (self; sole IBD seed for GO:0009421) SUPPORTS TRANSFER Grounded on the target itself; the PAO1 hexamer structure and the transposon-mutant motility phenotype (PMID:27664419) are much stronger than the cited PseudoCAP reference. Supporting Evidence: PMID:27664419 Full-length FliD1β474, by contrast, forms up to hexamers in solution (Figure 3e,f), which are likely to represent the physiologically relevant oligomerization state of this protein on the tip of the flagellum. |
| GO:0009421 bacterial-type flagellum filament cap | IDA PMID:9488388 The Pseudomonas aeruginosa flagellar cap protein, FliD, is r... | ACCEPT | Summary: PseudoCAP IDA and the sole seed of the GO:0009421 IBD at PTN000767631. The cited paper is the mucin-adhesion study, which treats FliD as the known flagellar cap protein; it purified FliD and made a chromosomal fliD insertion mutant. Reason: The claim is correct and is now established directly for this protein: the PAO1 FliD core crystallises as a hexameric cap, hexamers are seen in solution and by EM, and a PAO1 fliD transposon mutant is non-motile and complemented by fliD (PMID:27664419). The cited 1998 reference is a weaker choice, since its reported experiments are about mucin adhesion and fliD regulation; I cannot see the full text (PMC returns no body), so following the rule on not overruling curators from incomplete evidence I accept the row rather than questioning its evidence code, and record the better reference here and in the notes. The seed is therefore sound. Supporting Evidence: PMID:27664419 In the crystal, FliD78β405 monomer subunits are arranged in hexamers, resulting in a shape akin to a six-pointed star when viewed from the top of the FliD oligomer (Figure 2a), which corresponds to the distal end of the growing flagellum. PMID:9488388 We report here that the flagellar cap protein, FliD, participates in this adhesion process. |
| GO:0009421 bacterial-type flagellum filament cap | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from the FliD family signature IPR040026. Reason: The family assignment is correct and the mapped term is the structure the protein forms, so the row agrees with the experimental and IBA rows. Supporting Evidence: file:PSEAE/fliD/fliD-uniprot.txt DR InterPro; IPR040026; FliD. |
| GO:0071973 bacterial-type flagellum-dependent cell motility | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the same node, here seeded by the experimental annotations of E. coli FliD (P24216, IMP) and Bacillus subtilis FliD (P96786) rather than by the target. Reason: The inherited claim is independently true for PAO1 FliD, and by the strongest kind of evidence: a fliD transposon mutant has lost swimming motility and plasmid-borne PAO1 fliD restores it. Without the cap, flagellin is lost from the tip and no filament is built, so the cap protein does part of the work of building the motility organelle; this is the term GO uses for FliD across organisms (no FliD orthologue carries a flagellum-assembly term in QuickGO, which I checked before considering such an addition). Supporting Evidence: PMID:27664419 We found that swimming motility that was lost in the ΞfliD strain was restored in both ΞfliD/fliD1β474 and ΞfliD/fliD1β474(I167C/D253C) complementation strains, similar to our observations in the wildtype Pseudomonas PAO1 strain (Figure 4d). |
| GO:0009288 bacterial-type flagellum | IEA GO_REF:0000120 | MODIFY | Summary: Correct but general: FliD is a flagellar component, and specifically the filament cap. Reason: GO:0009421 bacterial-type flagellum filament cap is a descendant of GO:0009288 (part_of the filament, which is part_of the flagellum) and is already carried by this gene with direct and structural evidence, so the specific term should replace the generic one. This is not a root organelle term, so the keep-the-organelle exception does not apply. Proposed replacements: bacterial-type flagellum filament cap Supporting Evidence: PMID:27664419 A FliD (also called HAP2) oligomer forms the cap protein complex that is located at the tip of the flagellar filament (Yonekura et al. |
| GO:0009424 bacterial-type flagellum hook | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: InterPro2GO maps the FliD_N signature (IPR003481) to the flagellar hook. FliD's steady-state place is the cap at the distal tip of the filament, not the hook, which is the segment joining filament to basal body. Reason: The mapping is a family-wide artefact of the legacy name "hook-associated protein 2" (the genuine hook-filament junction proteins are FlgK/HAP1 and FlgL/HAP3): the same row appears on E. coli, Salmonella and B. subtilis FliD in QuickGO. I stop short of REMOVE because it is not entirely baseless: in Salmonella mutants that build no filament, FliD is reported in a layered structure at the distal end of the hook-basal body, so FliD can transiently occupy that position before filament assembly begins. That transient placement does not make FliD a hook component, and the row adds nothing beside GO:0009421; the mapping itself should be reviewed by InterPro. Supporting Evidence: PMID:27664419 A FliD (also called HAP2) oligomer forms the cap protein complex that is located at the tip of the flagellar filament (Yonekura et al. PMID:27664419 Notably, in mutants of Salmonella that lack filaments, FlgK (HAP1), FliD (HAP2) and FlgL (HAP3) form a layered structure at the distal end of the hook-basal body (Homma and Iino, 1985). |
| GO:0005576 extracellular region | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Electronic mapping of the UniProt Secreted location: FliD is exported through the flagellar export pathway and assembles outside the cell envelope. Reason: True and not refinable: GO's filament-cap and flagellum terms are not descendants of extracellular region, so the specific location cannot replace this row, but on its own "extracellular region" says little about a protein whose place in the cell is precisely defined by GO:0009421. Keep it as a peripheral location rather than part of the core function. Supporting Evidence: file:PSEAE/fliD/fliD-uniprot.txt SUBCELLULAR LOCATION: Secreted. Bacterial flagellum. |
| GO:0007155 cell adhesion | IDA PMID:9488388 The Pseudomonas aeruginosa flagellar cap protein, FliD, is r... | KEEP AS NON CORE | Summary: A chromosomal fliD insertion mutant is non-adhesive to mucin, adhesion is restored by fliD on a plasmid, and purified FliD competitively inhibits mucin adhesion of non-piliated P. aeruginosa while purified PilA and FlaG do not. Reason: Unlike a bare mutant phenotype, this includes a competition experiment with purified protein, which points at FliD itself as the mucin-binding entity rather than at the flagellum generally, so the claim is sound. It is nonetheless a secondary, host-interaction role rather than the structural function the protein is built for, and the term is as precise as the evidence allows (the assay measures binding to airway mucin, not a cell-cell junction), so it is kept as non-core rather than refined. Supporting Evidence: PMID:9488388 A polar chromosomal insertional mutation in the P. aeruginosa fliD gene made this organism nonadhesive to mucin in an in vitro mucin adhesion assay. PMID:9488388 Further supporting this observation, the in vitro competition experiments demonstrated that purified FliD protein inhibited the mucin adhesion of nonpiliated P. aeruginosa PAK-NP, while the same concentrations of PilA and FlaG proteins of P. aeruginosa were ineffective in this function. |
| GO:0007155 cell adhesion | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO mapping from the FliD_C signature, which in this case agrees with the experimental row. Reason: Same claim as the IDA row and the same disposition. The mapping generalises P. aeruginosa's mucin adhesion to the whole FliD family (it appears on E. coli, Salmonella and B. subtilis FliD too); an adhesive role has also been shown for enteropathogenic E. coli FliD binding microvillus tips, so the family-level mapping is not unreasonable, and it is in any case peripheral. Supporting Evidence: PMID:9488388 We report here that the flagellar cap protein, FliD, participates in this adhesion process. |
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Download this section (compressed HTML)Q: What mucin determinant does FliD bind, and is the binding site on the cap surface exposed at the filament tip in the assembled flagellum or only on free FliD?
Q: Why does the hexameric Pseudomonas cap not accept Salmonella FliD in complementation, and does cap stoichiometry have to match the flagellin it polymerises?
Experiment: Map the mucin-binding surface of FliD by testing structure-guided surface mutants (and the disulfide-locked hexamer FliD I167C/D253C) in the mucin adhesion and competition assays, which would show whether adhesion is a property of the assembled cap or of monomeric FliD, and could justify a specific adhesion molecular-function term.
Experiment: Determine a cryo-EM structure of the PAO1 flagellar filament tip with FliD in place, to show the cap-flagellin interface directly and test the positional-replacement elongation model in this organism.
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