PA1107 / RoeA (Q9I4M8) review notes

Summary of the literature

PA1107 (RoeA, regulator of exopolysaccharide A) is a 398-aa protein. UniProt
(Phobius) predicts five TM helices (31-197) and a C-terminal GGDEF domain (256-390).
My scan of the UniProt sequence finds the GGEEF motif at 305 and an RxxD I-site
candidate (RSSD) at 296. No EAL domain.

Literature search (Europe PMC "(PA1107 OR RoeA) AND aeruginosa", 2026-11-05; the
service returned 503 errors for most queries that day, and PubMed E-utilities
returned 500 errors). Primary data:

  1. Kulasekara et al. 2006 PMID:16477007; full text read on PMC (PMC1413825).
  2. DGC assay: "To detect DGC activity, cultures overexpressing genes that encode
    DGC-containing proteins were extracted and analyzed for c-di-GMP content".
  3. Table 1: "PA1107 GGEEF +(35)" (pmol c-di-GMP per mg wet cell weight; detection
    limit 12).
  4. Biofilm: "insertion in PA1107 , PA1181 , PA1433 , PA1727 , and PA3702 resulted
    in biofilm reduction" and overexpression of PA1107 gave pronounced pellicles.
  5. Merritt et al. 2010 PMID:20978535, full text cached. Named RoeA. Plasmid PA1107
    raised c-di-GMP 22-fold in a deletion background, the GGAAF mutant did not, and a
    PleD*-RoeA GGDEF chimera was active in vitro PMID:20978535. Full-length purified RoeA was
    inactive in vitro. The deletion reduced biofilm and Pel production in PA14, and
    swarmed about 2-fold better than WT PMID:20978535, but flagellar reversal and swimming speed were unchanged.
  6. Eilers et al. 2022 PMID:35935233 (PAO1 deletion library): ΔroeA lowered global
    c-di-GMP but, unlike in PA14, increased flow-cell biomass PMID:35935233. The direction of the
    biofilm effect therefore depends on strain and assay.

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 and PMID:20978535 (PseudoCAP) SOUND Overexpression raised cellular c-di-GMP (35 pmol/mg; full text read). Merritt adds an LC-MS 22-fold rise that a GGAAF mutant abolishes and in vitro activity of a purified chimera carrying the RoeA GGDEF domain (full text read). E. coli DosC, DgcC, DgcJ, DgcM, DgcN, DgcP, DgcQ, DgcZ (P0AA89, P0AAP1, P76237, P77302, P46139, P76245, P76330, P31129); B. subtilis DgcK, DgcP; Shewanella DgcS; P. aeruginosa PA3177, DgcP (PA5487), WspR, SadC (PA4332), GcbA (PA4843), plus PA3343 and PA2870 Yes. Many seeds have purified-enzyme evidence (E. coli and B. subtilis DGCs, WspR). No GO_CENTRAL defect for the MF.

The same verdict applies to PA3343 and PA2870, the other P. aeruginosa seeds in this
batch (see their notes).

Node-level GO_CENTRAL defect for PTN002895351 (recorded here, once)

PA1107, PA3343 and PA2870 also receive IBAs from PTN002895351 (none of them seeds it):
GO:0043709 cell adhesion involved in single-species biofilm formation, GO:1902201
negative regulation of bacterial-type flagellum-dependent cell motility, and
GO:0005886 plasma membrane. The GO:0043709 IBD has a single seed, E. coli DgcZ
(P31129). A live QuickGO query (2026-11-05,
annotation/search?geneProductId=P31129&goId=GO:0043709) returned the seed as
IMP PMID:19460094 EcoCyc acts_upstream_of_or_within. The IBD upgrades that to
involved_in, which makes every DGC in the clade a participant in cell adhesion.
A DGC makes c-di-GMP that regulates adhesins; it does not adhere. The node term
does not suit the clade. Defect recorded on the PA1107 GO:0043709 row (most direct
evidence among the batch's DGCs), confidence PROBABLE; PA3343 and PA2870 cross-refer
here. The GO:1902201 and GO:0005886 IBDs on the same node are not challenged.

Annotation decisions

Note on the PTN002895351 cell-adhesion defect (2026-11-05)

The GO_CENTRAL defect for the GO:0043709 IBD at PTN002895351 is recorded once, on genes/PSEAE/wspR, and covers PA1107, PA3343 and PA2870 too.