BifA (PA4367) is an inner-membrane c-di-GMP-specific phosphodiesterase with a single transmembrane segment, a degenerate GGDEF domain (GGDQF) and a catalytic EAL domain. Purified BifA hydrolyses c-di-GMP but has no detectable diguanylate cyclase activity. Its inactive GGDEF domain binds GTP, which regulates the adjacent EAL domain, and BifA interacts with the c-di-GMP receptor PelD. By degrading c-di-GMP, BifA keeps cellular c-di-GMP low: a bifA deletion has raised c-di-GMP, overproduces Pel polysaccharide, forms hyperbiofilms, swarms poorly and reverses its flagellar motor less often. BifA thus inversely regulates biofilm formation and swarming motility, acting genetically upstream of SadB. The regulator HecE inhibits BifA to raise c-di-GMP in a subpopulation of surface-attached cells.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | ACCEPT | Summary: PM IBD at PTN002105365. BifA has one TM segment and fractionates with the inner membrane, so the claim holds for this gene. Reason: Correct for BifA by direct fractionation. The node-level concern (soluble clade members such as RocR and PA2133) is recorded once in the rocR review. Supporting Evidence: PMID:17586641 BifA localizes to the inner membrane. |
| GO:0044010 single-species biofilm formation | IMP PMID:17586641 BifA, a cyclic-Di-GMP phosphodiesterase, inversely regulates... | MODIFY | Summary: PseudoCAP IMP; the deletion forms more biofilm, not less. BifA restrains biofilm formation by degrading c-di-GMP. Reason: The process claim is better expressed as negative regulation of single-species biofilm formation (GO:1900191), which the gene already carries from the same paper. BifA does not carry out a step of biofilm formation. Proposed replacements: negative regulation of single-species biofilm formation Supporting Evidence: PMID:17586641 Deletion of the PA4367 gene results in a severe defect in swarming motility and a hyperbiofilm phenotype |
| GO:0071111 cyclic-guanylate-specific phosphodiesterase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the 18-seed PTN002105365 IBD. BifA appears among its own sources because of its own experimental row, which is expected. Reason: Correct for BifA. The IBD stands on many independent seeds; node-level defects are recorded in the rocR review. Supporting Evidence: PMID:17586641 purified BifA protein exhibits phosphodiesterase activity in vitro but no detectable diguanylate cyclase activity |
| GO:0071111 cyclic-guanylate-specific phosphodiesterase activity | IEA GO_REF:0000003 | ACCEPT | Summary: EC 3.1.4.52 mapping; consistent with the experimental data. Reason: Correct core activity. Supporting Evidence: PMID:17586641 purified BifA protein exhibits phosphodiesterase activity in vitro but no detectable diguanylate cyclase activity |
| GO:0071111 cyclic-guanylate-specific phosphodiesterase activity | IMP PMID:17586641 BifA, a cyclic-Di-GMP phosphodiesterase, inversely regulates... | ACCEPT | Summary: PseudoCAP IMP and bifA's seeding of PTN002105365. Purified BifA hydrolyses c-di-GMP, and EAL- and GGDEF-motif mutants lose activity and fail to complement. Reason: Seed verdict SOUND (full text read). The paper also supports IDA for the same term. Supporting Evidence: PMID:17586641 purified BifA protein exhibits phosphodiesterase activity in vitro but no detectable diguanylate cyclase activity |
| GO:1900190 regulation of single-species biofilm formation | IBA GO_REF:0000033 | MODIFY | Summary: IBA from the 4-seed PTN009140332 IBD, for which bifA is the strongest seed. The node term is generic; BifA's own evidence supports the negative direction. Reason: Correct but general for BifA. The gene already carries the more specific GO:1900191 by IMP, so the IBA row is refined to it. The node-level claim is not disputed; the IBD stands without PA2133. Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN009140332 Β· PTN009140332 SUPPORTS TRANSFER Generic regulation term suits a clade of c-di-GMP PDEs; the direction is gene-specific. UniProtKB:Q9HW35 Β· bifA (self-seed; IMP PMID:17586641) SUPPORTS TRANSFER Sound deletion-plus-complementation evidence. UniProtKB:Q9I1Y2 Β· PA2133 SOURCE WEAK OR INFERRED Overexpression-only evidence (PMID:16186483); PA2133 loss of function had no phenotype. See PA2133 review. Proposed replacements: negative regulation of single-species biofilm formation Supporting Evidence: PMID:17586641 In contrast, expression of either His-BifA-AAAAA or His-BifA-AAL fails to suppress the hyperbiofilm phenotype of the Ξ bifA mutant. |
| GO:1900191 negative regulation of single-species biofilm formation | IMP PMID:17586641 BifA, a cyclic-Di-GMP phosphodiesterase, inversely regulates... | ACCEPT | Summary: PseudoCAP IMP and bifA's seeding of PTN009140332. A clean deletion hyperbiofilms, complementation restores wild type, and catalytic-motif mutants fail to complement. Reason: Seed verdict SOUND (full text read). The effect runs through BifA's own PDE activity on the c-di-GMP signal, which is how GO annotates c-di-GMP metabolising enzymes in biofilm regulation. Supporting Evidence: PMID:17586641 Deletion of the PA4367 gene results in a severe defect in swarming motility and a hyperbiofilm phenotype PMID:17586641 In contrast, expression of either His-BifA-AAAAA or His-BifA-AAL fails to suppress the hyperbiofilm phenotype of the Ξ bifA mutant. |
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Download this section (compressed HTML)Q: Should the swarming defect of bifA mutants be captured as positive regulation of swarming motility, given that it is independent of Pel and follows from raised c-di-GMP?
Experiment: Measure kcat and Km of purified full-length BifA with and without GTP, to quantify how GTP binding to the GGDQF domain regulates the EAL domain.
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