PP_4519, annotated in UniProt as tolC and referred to in the P. putida biofilm literature as LapE, is a TolC-family outer membrane factor that forms the outer membrane exit duct of the Lap type I secretion system. In KT2440, the best-supported role is in export and surface retention of the giant adhesin LapA, thereby supporting stable attachment and biofilm formation. Automated GO annotations to generic efflux functions likely reflect family-level TolC homology and overstate the KT2440-specific biology.
Definition: Enables passage of protein substrates through the bacterial outer membrane as the TolC/LapE-family outer membrane component of a type I secretion system. The activity provides the outer membrane exit duct used during one-step protein secretion from the cytoplasm to the cell exterior.
Justification: Current GO molecular function terms force curators to choose between overly generic channel/porin terms and misleading efflux transporter terms. LapE/TolC-like secretion channels are better modeled by a dedicated outer membrane channel activity term tied to type I protein secretion.
Parent term: channel activity
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0009279 cell outer membrane | IEA GO_REF:0000044 | ACCEPT | Summary: This localization is well supported. UniProt places Q88EE6 in the cell outer membrane, and the notes summarize that PP_4519/LapE is the outer membrane component of the Lap secretion apparatus. Reason: Both the TolC-family assignment and the LapE literature point to a cell outer membrane localization. Supporting Evidence: file:PSEPK/tolC/tolC-uniprot.txt SUBCELLULAR LOCATION: Cell outer membrane file:PSEPK/tolC/tolC-notes.md PP_4519 corresponds to `lapE`, the outer membrane component of the Lap secretion apparatus |
| GO:0015288 porin activity | IEA GO_REF:0000118 | MARK AS OVER ANNOTATED | Summary: Q88EE6 does form a TolC-like outer membrane channel, but the characterized KT2440 role is as the LapE exit duct in type I secretion rather than as a classical nonspecific porin. Reason: The term captures the existence of a channel-like outer membrane conduit, but it is too generic and somewhat misleading for a secretion-specialized TolC/LapE protein whose best-supported role is in adhesin export. Supporting Evidence: file:PSEPK/tolC/tolC-uniprot.txt Belongs to the outer membrane factor (OMF) (TC 1.B.17) family. file:PSEPK/tolC/tolC-notes.md These data support treating PP_4519/tolC as a TolC-like outer membrane exit duct reused in a type I protein secretion system for LapA surface display. |
| GO:0015562 efflux transmembrane transporter activity | IEA GO_REF:0000120 | MODIFY | Summary: The automated efflux term is too specific for the best-supported biology in KT2440. PP_4519/LapE forms an outer membrane channel, but the characterized role is in LapA type I secretion rather than a standalone small-molecule efflux transporter activity. Reason: A generic channel activity term better reflects the molecular role of the outer membrane conduit, without asserting an unsupported dedicated efflux function. Proposed replacements: channel activity Supporting Evidence: file:PSEPK/tolC/tolC-notes.md PP_4519 corresponds to `lapE`, the outer membrane component of the Lap secretion apparatus file:PSEPK/tolC/tolC-notes.md These data support treating PP_4519/tolC as a TolC-like outer membrane exit duct reused in a type I protein secretion system for LapA surface display. file:PSEPK/tolC/tolC-deep-research-falcon.md **PP_4519 (tolC; Q88EE6) encodes a TolC-like outer membrane factor that likely serves as an outer-membrane exit duct for one or more tripartite efflux/secretion assemblies.** |
| GO:0019867 outer membrane | IEA GO_REF:0000002 | ACCEPT | Summary: This broader localization remains correct. The protein is an outer membrane factor/TolC-family component, although GO:0009279 is the more specific companion term already present. Reason: The InterPro/OMF assignment and the LapE literature are fully consistent with outer membrane localization. Supporting Evidence: file:PSEPK/tolC/tolC-uniprot.txt Belongs to the outer membrane factor (OMF) (TC 1.B.17) family. |
| GO:0055085 transmembrane transport | IEA GO_REF:0000002 | MODIFY | Summary: PP_4519 certainly participates in transport across the envelope, but the best-supported process is specifically protein secretion via the Lap type I secretion system. Reason: GO has a more precise biological process term for the experimentally characterized secretion pathway, which is preferable to the generic transport annotation. Proposed replacements: protein secretion by the type I secretion system Supporting Evidence: file:PSEPK/tolC/tolC-notes.md The lapE deletion prevents the LapA transport to the outside of the cell, and the biofilm should weaken. file:PSEPK/tolC/tolC-notes.md Mutations in the ABC transporter homologues, LapB, LapC, and LapE prevent LapA externalization |
| GO:1990281 efflux pump complex | IEA GO_REF:0000118 | MODIFY | Summary: The complex membership inference is directionally correct in that PP_4519/LapE is a multi-component export-system subunit, but the characterized KT2440 complex is a type I protein secretion system rather than a generic efflux pump. Reason: The type I protein secretion system complex term is more precise for LapE and better matches the literature on LapA export. Proposed replacements: type I protein secretion system complex Supporting Evidence: file:PSEPK/tolC/tolC-notes.md PP_4519 corresponds to `lapE`, the outer membrane component of the Lap secretion apparatus file:PSEPK/tolC/tolC-notes.md The third part of the LapA transporter, LapE, is described in P. fluorescens as an outer membrane subunit where LapA N-terminus will trap. |
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Download this section (compressed HTML)Q: Is PP_4519/LapE dedicated to the LapA secretion pathway in KT2440, or is the same TolC-family outer membrane channel shared with additional export or efflux systems under other growth conditions?
Q: Besides LapA, are there additional RTX-like or adhesin cargo proteins that use the PP_4519/LapE channel in P. putida KT2440?
Experiment: Construct a clean PP_4519/lapE deletion and complementation series, then measure surface-associated LapA, secreted LapA, and biofilm formation on abiotic surfaces. Pair immunoblotting or proteomics with microscopy-based attachment assays.
Hypothesis: PP_4519/LapE is required for LapA externalization and its loss will reduce stable surface retention of LapA and impair biofilm initiation.
Experiment: Test whether PP_4519/LapE is shared by other export systems by combining lapE perturbation with assays for solvent tolerance, drug susceptibility, and secretion of other extracellular proteins across multiple media conditions.
Hypothesis: If PP_4519 serves additional TolC-like roles beyond LapA secretion, lapE loss will produce conditional phenotypes outside biofilm formation; if it is largely Lap-system-specific, the strongest phenotype will remain LapA export/biofilm.
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