HsbD (PA3343) is a 389-aa inner-membrane diguanylate cyclase of Pseudomonas aeruginosa, with six predicted transmembrane helices (a MASE8 domain) and a C-terminal GGDEF domain carrying the GGEEF motif and an RxxD inhibitory site that binds c-di-GMP. Overexpression raises c-di-GMP in P. aeruginosa extracts and turns E. coli colonies red on Congo red, which a GGAAF active-site mutant does not. HsbD is encoded next to the hptB-hsbR-hsbA flagellar and chemotaxis cluster, binds the anti-anti-sigma factor HsbA, and links c-di-GMP signalling to the HptB pathway. In an hptB mutant HsbD is needed for the high c-di-GMP and hyperbiofilm phenotypes, and its loss causes hyper-swarming; on its own, the hsbD deletion abolishes chemotaxis and alters twitching. HsbD lies at the cell periphery with dynamic polar foci. Single hsbD mutants show unchanged or slightly increased biofilm and attachment, so the sign of its biofilm effect depends on the state of the HptB pathway.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | ACCEPT | Summary: PM IBD at PTN002895351, seeded by membrane-anchored E. coli DGCs. This protein has predicted TM helices. Reason: Consistent with the predicted topology. Supporting Evidence: file:PSEAE/PA3343/PA3343-uniprot.txt FT TRANSMEM 52..72 FT /note="Helical" FT /evidence="ECO:0000256|SAM:Phobius" PMID:27792789 Analysis of HsbD-YFP shows that HsbD localizes to the cell periphery with some local concentration at the cell pole(s) (Fig 8A). |
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | ACCEPT | Summary: SubCell mapping (Cell inner membrane). The UniProt statement is ARBA-derived, but the Phobius TM helices support it independently. Reason: Same claim as the IBA row. Supporting Evidence: file:PSEAE/PA3343/PA3343-uniprot.txt FT TRANSMEM 52..72 FT /note="Helical" FT /evidence="ECO:0000256|SAM:Phobius" |
| GO:0043709 cell adhesion involved in single-species biofilm formation | IBA GO_REF:0000033 | MODIFY | Summary: IBA from PTN002895351, whose GO:0043709 IBD rests on one seed annotated acts_upstream_of_or_within. HsbD controls biofilm formation through c-di-GMP but is not an adhesion component. Reason: A DGC regulates biofilm formation and does not take part in adhesion. The replacement is the unsigned GO:1900190, because HsbD is needed for the hyperbiofilm of an hptB mutant but single hsbD mutants show unchanged or more biofilm. The node-level GO_CENTRAL defect is recorded once in the PA1107 review. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: ROLE CONFLATION Sources checked: PANTHER:PTN002895351 · PTN002895351 SOURCE WEAK OR INFERRED Single-seed IBD of a participation term on a DGC clade. The node-level defect is recorded once in the PA1107 review. UniProtKB:P31129 · E. coli DgcZ (sole seed) SUPPORTS SOURCE BUT NOT TARGET The seed annotation is IMP acts_upstream_of_or_within (EcoCyc, PMID:19460094; live QuickGO query 2026-11-05). It supports a regulatory role of DgcZ upstream of adhesion, not participation in adhesion by every DGC. For HsbD the right claim is regulation of biofilm formation. Proposed replacements: regulation of single-species biofilm formation Supporting Evidence: PMID:27792789 Finally, complementation of the hsbD deletion restored the hyper-biofilm phenotype of the hptB mutant (S2 Fig). PMID:35935233 Three of the mutants in a putative dgc gene resulted in a slight upregulation of attachment (fold change ranging between 1.2 and 1.4): PA2771 (dcsbis; Chen et al., 2016), PA3343 (hsbD; Valentini et al., 2016) and most significantly PA4396. file:PSEAE/PA3343/PA3343-notes.md pellicle formation (hyperbiofilm) was observed for insertions in PA0861 , PA3311 , PA3343 , PA4332 , PA4367 , and PA5017 |
| GO:0052621 diguanylate cyclase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the 19-seed PTN002895344 IBD; this gene is among its own sources because of its own IDA row, which is expected. Reason: Correct; the GGEEF motif is intact and overexpression raises cellular c-di-GMP. The IBD rests on many seeds with purified-enzyme evidence. Supporting Evidence: file:PSEAE/PA3343/PA3343-notes.md PA3343 GGEEF +(22) PA3702 GGEEF +(445) PA3825 EVL +(27) PMID:27792789 HsbD causes the red colony staining, phenotype correlated with a global increase in intracellular c-di-GMP levels [30, 31]; while a catalytic inactive GGAAF mutant does not trigger such output. |
| GO:0052621 diguanylate cyclase activity | IDA PMID:16477007 Analysis of Pseudomonas aeruginosa diguanylate cyclases and ... | ACCEPT | Summary: PseudoCAP IDA and a seed of PTN002895344. Extracts of the overexpressing strain contained c-di-GMP above the detection limit (Table 1, full text read on PMC). Reason: Seed verdict SOUND. A whole-cell extract of an overexpressing strain is a crude assay, but it measures the product directly and the GGEEF motif is intact. Supporting Evidence: file:PSEAE/PA3343/PA3343-notes.md PA3343 GGEEF +(22) PA3702 GGEEF +(445) PA3825 EVL +(27) PMID:27792789 HsbD causes the red colony staining, phenotype correlated with a global increase in intracellular c-di-GMP levels [30, 31]; while a catalytic inactive GGAAF mutant does not trigger such output. |
| GO:0052621 diguanylate cyclase activity | IEA GO_REF:0000003 | ACCEPT | Summary: EC 2.7.7.65 mapping. Reason: Same claim as the IBA and IDA rows. Supporting Evidence: file:PSEAE/PA3343/PA3343-notes.md PA3343 GGEEF +(22) PA3702 GGEEF +(445) PA3825 EVL +(27) PMID:27792789 HsbD causes the red colony staining, phenotype correlated with a global increase in intracellular c-di-GMP levels [30, 31]; while a catalytic inactive GGAAF mutant does not trigger such output. |
| GO:1902201 negative regulation of bacterial-type flagellum-dependent cell motility | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN002895351. Deleting hsbD in an hptB background gives about 9-fold hyper-swarming, so HsbD restrains swarming, a flagellum-dependent motility. Reason: Gene-specific evidence supports the inherited term. HsbD also affects chemotaxis and twitching, which this term does not cover. Supporting Evidence: PMID:27792789 the resulting strain displays a striking hyper-swarming phenotype (~9 fold increase in swarming area, Fig 4B). |
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Download this section (compressed HTML)Experiment: Purify HsbD (GGDEF domain and full length) and measure c-di-GMP synthesis with phosphorylated and unphosphorylated HsbA.
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: How HsbA binding and HptB-pathway phosphorylation control HsbD cyclase activity and its polar localisation, and which c-di-GMP effector carries its output to the flagellar and chemotaxis machinery, are unknown.
BIOLOGY
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