TpbB (also called YfiN; PA1120) is an inner-membrane diguanylate cyclase with two transmembrane helices flanking a periplasmic sensory domain, followed by cytoplasmic HAMP and GGDEF domains. It condenses two GTP into cyclic di-GMP. It is the output enzyme of the YfiBNR tripartite module: the periplasmic protein YfiR binds and inhibits it, and the outer-membrane lipoprotein YfiB relieves the inhibition by sequestering YfiR. The tyrosine phosphatase TpbA also restrains its activity. The c-di-GMP made by TpbB stimulates Pel and Psl exopolysaccharide production, giving the small colony variant phenotype, biofilm formation and persistence in infection models. Unlike many diguanylate cyclases, it is not feedback-inhibited by its product, and the HAMP domain is needed for dimerisation and catalysis.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Subcellular-location mapping from the curated UniProt entry (cell inner membrane, two transmembrane helices). Reason: TpbB/YfiN is a membrane-integral DGC whose periplasmic domain binds YfiR; the inner (plasma) membrane is where it acts. Supporting Evidence: PMID:20300602 YfiN is a membrane-integral diguanylate cyclase file:PSEAE/tpbB/tpbB-uniprot.txt SUBCELLULAR LOCATION: Cell inner membrane |
| GO:0007165 signal transduction | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO from the HAMP domain. True but general. Reason: TpbB relays a periplasmic signal (YfiR release) to cytoplasmic c-di-GMP synthesis. The specific process is GO:0061939 c-di-GMP signaling, which the gene already carries by IBA; that term is not an is_a descendant of signal transduction in current GO, so MODIFY rather than TOO_GENERAL. Proposed replacements: c-di-GMP signaling Supporting Evidence: PMID:20300602 Activation of YfiN results in c-di-GMP production, and the activation of several downstream targets affecting cell motility and exopolysaccharide production. |
| GO:0016020 membrane | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO membrane from the HAMP domain. Reason: Correct but general; the protein is in the inner (plasma) membrane, a term the gene already carries. Proposed replacements: plasma membrane Supporting Evidence: PMID:20300602 YfiN is a membrane-integral diguanylate cyclase |
| GO:0052621 diguanylate cyclase activity | EXP PMID:20300602 YfiBNR mediates cyclic di-GMP dependent small colony variant... | ACCEPT | Summary: UniProt EXP row. A purified truncated YfiN made c-di-GMP from GTP. Reason: Direct assay of purified protein; core function. Supporting Evidence: PMID:20300602 In accordance with these findings, truncated-YfiN-His6 generated c-di-GMP from GTP, confirming that YfiN functions as a DGC (Figure 2A). |
| GO:0052621 diguanylate cyclase activity | EXP PMID:24278422 Investigating the allosteric regulation of YfiN from Pseudom... | ACCEPT | Summary: UniProt EXP row. Real-time activity assay of the cytosolic HAMP-GGDEF construct, with crystal structure of the GGDEF domain. Reason: Direct enzymology; core function. Supporting Evidence: PMID:24278422 Here we show that, unlike other DGC enzymes, YfiN does not undergo product feedback inhibition, and that the in vitro activity depends on the presence of the HAMP domain. |
| GO:0052621 diguanylate cyclase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN005315326. TpbB is one of five seeds; its own experimental rows are among the descendant evidence, as expected. The other seeds (PA0847, VCA0965, E. coli DgcT, Dictyostelium DgcA) also carry experimental DGC evidence. Reason: Consistent with the direct assays on TpbB. Seed verdict SOUND (see notes); the IBD stands with or without this seed. Supporting Evidence: PMID:20300602 In accordance with these findings, truncated-YfiN-His6 generated c-di-GMP from GTP, confirming that YfiN functions as a DGC (Figure 2A). |
| GO:0052621 diguanylate cyclase activity | IDA PMID:16477007 Analysis of Pseudomonas aeruginosa diguanylate cyclases and ... | ACCEPT | Summary: PseudoCAP seed row for PTN005315326. PA14 cells overexpressing PA1120 accumulated 134 pmol c-di-GMP per mg wet cell weight (Table 1; full text read on PMC), far above the 12 pmol/mg detection limit. Reason: Seed verdict SOUND. An in vivo product measurement on overexpressing cells is direct enough for the activity, and purified-protein assays confirm it. Supporting Evidence: file:PSEAE/tpbB/tpbB-notes.md PA1120 GGDEF +(134) |
| 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:20300602 In accordance with these findings, truncated-YfiN-His6 generated c-di-GMP from GTP, confirming that YfiN functions as a DGC (Figure 2A). |
| GO:0052621 diguanylate cyclase activity | IMP PMID:19543378 Connecting quorum sensing, c-di-GMP, pel polysaccharide, and... | ACCEPT | Summary: PseudoCAP seed row for PTN005315326 (full text read). Loss of tpbB suppresses the high-c-di-GMP phenotypes of a tpbA mutant, and tpbB expression complements; c-di-GMP is measured in the tpbA mutant only, and TpbB's activity is inferred. Reason: Seed verdict SOUND. Genetic epistasis is weaker MF evidence than an assay, but the claim is true and is directly shown by PMID:20300602 and PMID:24278422. No defect. Supporting Evidence: PMID:19543378 Loss of an uncharacterized GGDEF protein, PA1120 (TpbB), suppressed these phenotypes, indicating that TpbA controls c-di-GMP production through TpbB. |
| GO:0061939 c-di-GMP signaling | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN005315326, seeded by Dictyostelium DgcA. TpbB is the c-di-GMP-producing output of the YfiBNR signalling module. Reason: TpbB makes the second messenger whose level controls Pel/Psl production and the SCV phenotype, so it takes part in c-di-GMP signalling. Supporting Evidence: PMID:20300602 Our research suggests that YfiB and YfiR are upstream regulatory components of the YfiN diguanylate cyclase, which represents the cellular readout of the system. |
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