tpbB / yfiN (PA1120, Q9I4L5) review notes

No deep-research provider was available; literature checked by hand on 2026-11-05
(cached publications, PMC web pages, Europe PMC search "PA1120", "YfiN", "TpbB").

Function

TpbB/YfiN is an inner-membrane diguanylate cyclase (2 TM helices, periplasmic PAS-like
domain, cytoplasmic HAMP and GGDEF domains; UniProt topology).
A purified truncated YfiN makes c-di-GMP from GTP PMID:20300602.
YfiR represses it and YfiB relieves that repression PMID:20300602.
The cytosolic HAMP-GGDEF construct is active in real time, and it is not product-inhibited
PMID:24278422.
Genetics: loss of tpbB suppresses the tpbA (phosphatase) mutant's high-c-di-GMP phenotypes
PMID:19543378.

Verbatim excerpts from PMID:16477007 full text (PMC1413825, PMC web page, read 2026-11-05)

Table 1 (cells overexpressing each gene in PA14, c-di-GMP measured by HPLC):

PA1120 GGDEF +(134)
PA0847 GGDEF +(16)
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 .

Text: "To detect DGC activity, cultures overexpressing genes that encode DGC-containing proteins
were extracted and analyzed for c-di-GMP content".

PseudoCAP IBA-seed assessment

Seeds from .cache/paint/IBD.gaf; other seeds' experimental rows from QuickGO, 2026-11-05.

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN005315326	GO:0052621 diguanylate cyclase activity	5	35 (16 taxa)	GO:0052621, IDA, PMID:16477007 (PseudoCAP)	SOUND	PA1120-overexpressing cells held 134 pmol c-di-GMP/mg (Table 1, full text read), well above the 12 pmol/mg limit; confirmed with purified protein (PMID:20300602, PMID:24278422).	PA0847 Q9I594 (purified PAS-GGDEF active, PMID:31114257); V. cholerae VCA0965 Q9KKY5 (IDA PMID:24490592, CACAO); E. coli DgcT P75908 (IMP PMID:18713317, PMID:20576684, EcoCyc); Dictyostelium DgcA DDB_G0283453	Yes
PTN005315326	GO:0052621 diguanylate cyclase activity	5	35 (16 taxa)	GO:0052621, IMP, PMID:19543378 (PseudoCAP)	SOUND	Full text read. Genetic epistasis: tpbB loss suppresses the high-c-di-GMP tpbA phenotypes; the activity itself is shown elsewhere. Weak as MF evidence but not wrong.	as above	Yes

The node term (the catalytic activity) suits a clade of GGDEF DGCs with intact catalytic
sites. No PSEUDOCAP or GO_CENTRAL defect. The PA0847 seed on the same node is assessed in
PA0847-notes.md (also SOUND); the two verdicts agree.

GO:0061939 c-di-GMP signaling (IBA on the same node, seeded only by DgcA): accepted; TpbB's
c-di-GMP output drives Pel/Psl production.