PilA (PP_0634) is the major type IV pilin of Pseudomonas putida KT2440, the principal structural subunit that polymerizes into type IV pili (T4P) — dynamic, retractile filaments on the bacterial cell surface. It belongs to the N-methyl-phenylalanine (type IVa) pilin family, with a hydrophobic N-terminal alpha-helix (a predicted transmembrane segment) that mediates subunit packing within the filament core, and a globular C-terminal head bearing a conserved disulfide-bonded loop. Like other T4a pilins, it is synthesized as a prepilin whose leader peptide is cleaved and whose new N-terminal phenylalanine is N-methylated by the prepilin peptidase PilD before the mature subunit is stored in the inner membrane and assembled into the filament. Cycles of pilus extension and retraction allow the assembled type IV pilus to mediate surface adhesion, twitching motility, microcolony and biofilm formation, and, in many species, DNA uptake during natural transformation. In P. putida, pilin expression is induced upon surface attachment and biofilm growth, consistent with a role in surface colonization.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0007155 cell adhesion | IEA GO_REF:0000002 | ACCEPT | Summary: Type IV pili are adhesive surface filaments, and the major pilin PilA mediates attachment to surfaces and other cells. Cell adhesion is a genuine, if general, function of this protein. Reason: Adhesion is a well-established function of type IV pili and of the major pilin subunit. The InterPro2GO inference from the Pilin domain (IPR001082) is biologically appropriate, and surface-attachment-induced pilin expression in P. putida supports an adhesion role. The term is general but not incorrect; a more specific adhesion-during-biofilm term could be considered if experimental evidence in KT2440 were available. |
| GO:0009289 pilus | IEA GO_REF:0000002 | MODIFY | Summary: PilA is the major structural subunit of a pilus, so the pilus localization is correct. However, PilA specifically forms a type IV pilus (N-methyl-phenylalanine pilin family), for which a more precise term exists. Reason: The generic "pilus" term is correct but under-specific. PilA belongs to the N-Me-Phe (type IVa) pilin family and assembles into a type IV pilus, so the more informative child term GO:0044096 (type IV pilus) better captures the localization. Proposed replacements: type IV pilus |
| GO:0015627 type II protein secretion system complex | IEA GO_REF:0000002 | REMOVE | Summary: This annotation derives from the InterPro pilin-domain mapping (IPR000983, GSPG_pilin), which is shared between type IV major pilins and the pseudopilins of the type II secretion system. PilA is a type IV pilin, not a T2SS pseudopilin, so it is not part of the type II secretion system complex. Reason: The T4P major pilin and T2SS major pseudopilin share an ancestral pilin fold and InterPro signature, which causes InterPro2GO to over-propagate T2SS terms onto type IV pilins. PilA (PP_0634) is the major pilin of the type IV pilus system; its structural component is the type IV pilus, not the T2SS complex. This is a domain-homology over-annotation and should be removed. |
| GO:0015628 protein secretion by the type II secretion system | IEA GO_REF:0000002 | REMOVE | Summary: Same InterPro2GO artifact as the T2SS complex annotation. PilA is a type IV pilin and does not function in type II protein secretion. Reason: This BP term is inferred from the shared pilin/pseudopilin domain signature and does not reflect PilA's actual role. PilA builds the type IV pilus and participates in type IV pilus assembly and twitching motility, not type II secretion. Remove as a domain-homology over-annotation; the appropriate processes (type IV pilus assembly, type IV pilus-dependent motility) are proposed as new terms. |
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Download this section (compressed HTML)Q: Does PilA (PP_0634) deletion in KT2440 abolish twitching motility and reduce surface attachment/biofilm formation, as expected for a major type IV pilin?
Q: How is the KT2440 type IV pilus assembled given the reported absence of the canonical assembly ATPase PilB, and is xcpR (or another ATPase) functionally substituting?
Experiment: Construct a markerless pilA (PP_0634) deletion in KT2440 and assay twitching motility (subsurface stab/agar interstitial assay), surface adhesion, and biofilm formation, with complementation to confirm specificity.
Experiment: Verify PilA maturation by detecting N-terminal N-methylation/leader cleavage (mass spectrometry on purified pili) and confirm surface pilus assembly by immuno-EM or pilus shearing/Western blot.
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