wspR (PA3702, Q9HXT9) review notes
Summary of the literature
WspR is a 347-aa response regulator with an N-terminal receiver domain (UniProt
20-137, phospho-acceptor D70) and a C-terminal GGEEF diguanylate cyclase domain
(201-339). It is the output of the Wsp chemosensory system. No hydrophobic
segment long enough for a TM helix (Kyte-Doolittle, 19-residue window, threshold
1.6; scan run in this session) and no UniProt TRANSMEM feature: it is soluble.
- Hickman et al. 2005 (PMID:16186483; full text cached). Purified WspR makes
c-di-GMP and phosphorylation stimulates it PMID:16186483. A wspF mutant (constitutively active Wsp pathway)
has more c-di-GMP and more biofilm, WspR-dependently.
- De et al. 2008 (PMID:18366254; abstract cached). Crystal structure of WspR bound
to c-di-GMP at the inhibitory site; active dimer, tetramer and product-inhibited
dimer PMID:18366254. Basis of the IntAct IPI GO:0042802 row.
- Kulasakara et al. 2006 (PMID:16477007). Full text read on the PMC web page
(PMC1413825) in this session; the cached copy is abstract-only. DGC activity was
measured as c-di-GMP extracted from cells overexpressing each protein: "To detect
DGC activity, cultures overexpressing genes that encode DGC-containing proteins
were extracted and analyzed for c-di-GMP content". Table 1 row: "PA3702 GGEEF
+(445)" (pmol c-di-GMP per mg wet cell weight), the highest value in the table.
Footnote: "Given the limits of sensitivity of the HPLC assay (12 pmol/mg cell wet
weight), we cannot conclude that any particular DGC or PDE domain does not have
the corresponding enzymatic activity in vivo".
- D'Argenio et al. 2002 (PMID:12426335; full text cached and read). Genetics only:
wspR insertions suppress the wrinkled, autoaggregative colonies of a wspF mutant
and restore motility PMID:12426335. No c-di-GMP or
enzyme assay; the GGDEF nucleotide-cyclase link is discussed only as a hypothesis
PMID:12426335.
PseudoCAP IBA-seed assessment
| PTN node |
node term |
n_seeds |
leaf IBAs |
seed annotation (term, evidence, PMID) |
verdict |
rationale |
other seeds |
IBD stands without this seed? |
| PTN002895344 |
GO:0052621 diguanylate cyclase activity |
19 |
205 (28 taxa) |
GO:0052621, IDA, PMID:16477007 (PseudoCAP) |
SOUND |
Cells overexpressing WspR accumulated 445 pmol/mg c-di-GMP (full text read); purified WspR is active (PMID:16186483). |
E. coli DosC, DgcC, DgcJ, DgcM, DgcN, DgcP, DgcQ, DgcZ; B. subtilis DgcK, DgcP; Shewanella DgcS; P. aeruginosa dgcP, PA1107, PA2870, PA3177, PA3343, PA4332, PA4843 |
Yes. Many seeds have direct activity evidence; the node term is the defining activity of GGDEF DGCs. No GO_CENTRAL defect. |
| PTN002895344 |
GO:0052621 diguanylate cyclase activity |
19 |
205 (28 taxa) |
GO:0052621, IMP, PMID:12426335 (PseudoCAP) |
INDIRECT-PHENOTYPE |
Suppressor genetics of colony morphology; no c-di-GMP measured (full text read). The term is right for WspR, but this paper does not show it. |
as above |
Yes (this row adds nothing to the node; WspR's own IDA row and the other seeds carry it). |
Batch consistency (PA3177, dgcP, wspR, PA4332, PA4843 all seed PTN002895344):
all seed rows except this IMP are SOUND, so no node-level GO_CENTRAL defect is
needed for PTN002895344.
Non-seed IBA nodes (PTN002895351)
The PM, cell-adhesion and motility IBAs come from PTN002895351, whose IBDs are
seeded by E. coli proteins only (PM: DgcN, DgcQ, DgcJ, P76236, P76147, P75801;
GO:0043709: DgcZ alone; GO:1902201: DgcJ, P76236, DgcQ, DgcN). None of my genes
seeds it, but its PM term reaches four soluble P. aeruginosa DGCs in this batch
(WspR, DgcP, PA3177, PA4843). The node-level GO_CENTRAL defects for PTN002895351
(PM; GO:0043709) are recorded once, here on wspR, and cross-referenced from the
PA3177, dgcP, PA4332 and PA4843 notes.
Annotation decisions
- GO:0052621 (IBA, IDA, IEA, IMP): ACCEPT. The IMP row carries a PSEUDOCAP defect
(paper does not show the activity).
- GO:0005886 IBA and IEA: MARK_AS_OVER_ANNOTATED (soluble response regulator).
- GO:0043709 IBA: MARK_AS_OVER_ANNOTATED (a DGC regulates attachment, it does not
perform cell adhesion).
- GO:1902201 IBA: ACCEPT (wspR loss restores motility of the wspF mutant).
- GO:0000160 IEA: KEEP_AS_NON_CORE (receiver domain of the Wsp phosphorelay).
- GO:0042802 IPI: KEEP_AS_NON_CORE (regulatory oligomerization).
Verbatim excerpts from full texts not in the cache
PMID:16477007 (PMC1413825, read on the PMC web page):
- To detect DGC activity, cultures overexpressing genes that encode DGC-containing proteins were extracted and analyzed for c-di-GMP content
- PA3702 GGEEF +(445)
- DGC activity is measured as pmol of c-diGMP produced per mg wet cell weight.
- Given the limits of sensitivity of the HPLC assay (12 pmol/mg cell wet weight), we cannot conclude that any particular DGC or PDE domain does not have the corresponding enzymatic activity in vivo
Hydrophobicity scan
Kyte-Doolittle, 19-residue window, mean above 1.6: no window found in WspR (347 aa).
The same scan finds the six TM helices of PA4332 (SadC), which UniProt also annotates.
Defects recorded (2026-11-05)
- PSEUDOCAP, GO:0052621 IMP (PMID:12426335): WRONG_REFERENCE, repoint to
PMID:16186483; CONFIRMED (full text read).
- GO_CENTRAL, PTN002895351 GO:0005886 (node-level, recorded once here for the
batch): PROBABLE. Seeds are six E. coli inner-membrane DGCs, all IDA from
PMID:15919996 (QuickGO, 2026-11-05); the node also covers soluble WspR,
PA3177, DgcP and PA4843 (no TRANSMEM in UniProt, no hydrophobic window).
- GO_CENTRAL, PTN002895351 GO:0043709 (node-level, recorded once here):
WRONG_QUALIFIER, PROBABLE. The sole seed, E. coli DgcZ (P31129), carries the
term in QuickGO only as IMP with qualifier acts_upstream_of_or_within
(EcoCyc, PMID:19460094); the IBD asserts involved_in. PA3177 deletion has no
effect on attachment (PMID:30082282).