PA4843 (GcbA, also called AdcA) is a soluble PleD-like response regulator diguanylate cyclase of Pseudomonas aeruginosa, with two receiver domains and a C-terminal GGEEF domain that synthesises cyclic di-GMP. Its transcription is directly repressed by AmrZ. GcbA-made c-di-GMP suppresses flagellar reversals and swimming and swarming motility, and so promotes initial surface attachment. Early in biofilm growth GcbA is needed for processing of the chemosensory protein BdlA, which later allows biofilms to disperse in response to environmental cues. Derepression of GcbA in amrZ mutants raises c-di-GMP and causes a hyperbiofilm phenotype.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000160 phosphorelay signal transduction system | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO from the receiver domains. One receiver lacks conserved residues (UniProt caution); no cognate kinase or phosphorylation of GcbA is known. Reason: Plausible from domain architecture but not shown; peripheral to the cyclase function. Supporting Evidence: file:PSEAE/PA4843/PA4843-notes.md two receiver domains (125-242, 251-367) |
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: IBA from PTN002895351, seeded by E. coli transmembrane DGCs. GcbA is a soluble receiver-receiver-GGEEF protein with no TM segment. Reason: The seeds' TM-based location does not transfer. The node-level GO_CENTRAL defect is recorded once, on wspR. Propagation Review Root cause: PROPAGATION BAD Failure modes: COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN002895351 Β· PTN002895351 SUPPORTS SOURCE BUT NOT TARGET Six E. coli inner-membrane DGC seeds (IDA, PMID:15919996); GcbA is predicted soluble. Supporting Evidence: file:PSEAE/PA4843/PA4843-notes.md finds no hydrophobic window, so it is predicted soluble |
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | MARK AS OVER ANNOTATED | Summary: Mapped from the UniProt location "Cell inner membrane", which rests only on an ARBA rule. Reason: Same claim as the IBA row; soluble response regulator. Supporting Evidence: file:PSEAE/PA4843/PA4843-notes.md finds no hydrophobic window, so it is predicted soluble |
| GO:0043709 cell adhesion involved in single-species biofilm formation | IBA GO_REF:0000033 | MODIFY | Summary: IBA from PTN002895351 with E. coli DgcZ as sole seed (itself IMP, acts_upstream_of_or_within). GcbA promotes initial attachment by repressing motility, a regulatory role. Reason: Regulation of attachment, not adhesion itself. The node-level GO_CENTRAL defect is recorded once, on wspR. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: ROLE CONFLATION Sources checked: UniProtKB:P31129 Β· E. coli DgcZ (sole seed) SOURCE WEAK OR INFERRED Seed annotation is IMP with qualifier acts_upstream_of_or_within (PMID:19460094). Proposed replacements: positive regulation of cell adhesion involved in single-species biofilm formation Supporting Evidence: PMID:24891445 promotes initial attachment to surfaces, but not biofilm formation |
| GO:0052621 diguanylate cyclase activity | EXP PMID:24603766 ChIP-Seq and RNA-Seq reveal an AmrZ-mediated mechanism for c... | ACCEPT | Summary: PseudoCAP seed row. Expression of PA4843 raises c-di-GMP about 30-fold (full text read). Seed verdict SOUND. Reason: Direct measurement of c-di-GMP produced on PA4843 expression. Supporting Evidence: PMID:24603766 expression of PA4843 in these strains generated nearly thirty fold more c-di-GMP |
| GO:0052621 diguanylate cyclase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the PTN002895344 IBD (19 seeds, including GcbA itself, which is expected). The IBD stands on many independent seeds. Reason: Core activity. Supporting Evidence: PMID:24891445 PAO1/pJN- gcbA cultures on average contained 228 pmol of c-di-GMP per mg of total cell protein |
| GO:0052621 diguanylate cyclase activity | IDA PMID:24891445 The Pseudomonas aeruginosa diguanylate cyclase GcbA, a homol... | ACCEPT | Summary: PseudoCAP seed row. GcbA overexpression gives 228 pmol/mg c-di-GMP versus under 35 for controls; deletion halves planktonic c-di-GMP (full text read). Seed verdict SOUND. Reason: Direct c-di-GMP measurements. Supporting Evidence: PMID:24891445 PAO1/pJN- gcbA cultures on average contained 228 pmol of c-di-GMP per mg of total cell protein |
| GO:0052621 diguanylate cyclase activity | IEA GO_REF:0000003 | ACCEPT | Summary: EC 2.7.7.65 mapping. Reason: Consistent with the experimental rows. Supporting Evidence: PMID:24891445 PAO1/pJN- gcbA cultures on average contained 228 pmol of c-di-GMP per mg of total cell protein |
| GO:0052621 diguanylate cyclase activity | IMP PMID:24603766 ChIP-Seq and RNA-Seq reveal an AmrZ-mediated mechanism for c... | ACCEPT | Summary: PseudoCAP seed row. Deleting adcA in an amrZ mutant returns c-di-GMP to wild-type levels (full text read). Seed verdict SOUND. Reason: Loss-of-function evidence for the activity in vivo. Supporting Evidence: PMID:24603766 Deletion of adcA in a ΞamrZ mutant eliminated the accumulation of c-di-GMP and the hyper biofilm phenotype |
| GO:1900233 positive regulation of single-species biofilm formation on inanimate substrate | IMP PMID:24603766 ChIP-Seq and RNA-Seq reveal an AmrZ-mediated mechanism for c... | KEEP AS NON CORE | Summary: PseudoCAP IMP. In an amrZ mutant, deleting adcA reduces flow-cell biofilm biomass. In a wild-type background GcbA promotes initial attachment but not later biofilm formation (PMID:24891445). Reason: Shown when GcbA is derepressed; its role in wild-type cells is in initial attachment and dispersal priming rather than biofilm development. Supporting Evidence: PMID:24603766 the ΞamrZ ΞadcA double mutant produces biofilms with significantly less biomass than the ΞamrZ mutant |
| GO:1902065 response to L-glutamate | IMP PMID:25331436 The diguanylate cyclase GcbA facilitates Pseudomonas aerugin... | MARK AS OVER ANNOTATED | Summary: PseudoCAP IMP. gcbA mutant biofilms fail to disperse in response to many cues because GcbA is needed earlier for BdlA processing. The role is in biofilm dispersal generally, not in sensing L-glutamate, which the abstract does not name (abstract only). Reason: Dispersal-deficient mutants lack the response to every cue, so the glutamate response is a consequence of a general dispersal defect. GO has no biofilm dispersal term; this is raised as a question. Supporting Evidence: PMID:25331436 plays an essential role in allowing biofilm cells to disperse in response to increasing concentrations of a variety of substances, including carbohydrates, heavy metals, and nitric oxide |
| GO:1902201 negative regulation of bacterial-type flagellum-dependent cell motility | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN002895351; gene-level support from deletion and overexpression motility phenotypes. Reason: GcbA represses swimming and swarming by suppressing flagellar reversals. Supporting Evidence: PMID:24891445 Inactivation of gcbA resulted in small, but significant increases in both swimming and swarming motilities, while overexpression of gcbA suppressed both forms of flagellum-driven motility |
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