PA5017 (DipA, dispersion-induced phosphodiesterase A) is a membrane-associated c-di-GMP phosphodiesterase of Pseudomonas aeruginosa with an N-terminal GAF domain, PAS/PAC domains, a degenerate GGDEF domain (ASNEF motif, no detectable diguanylate cyclase activity) and a C-terminal EAL domain. Purified DipA hydrolyses c-di-GMP and the model substrate bis-pNPP, and both EAL motifs are needed for its activity in vivo. dipA expression rises on dispersion, and the protein lowers c-di-GMP so that biofilm cells can disperse in response to sudden nutrient (glutamate, ammonium), nitric oxide or heavy-metal cues; mutants show reduced swarming and increased attachment and Psl polysaccharide production.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0043200 response to amino acid | IMP PMID:22493016 The phosphodiesterase DipA (PA5017) is essential for Pseudom... | KEEP AS NON CORE | Summary: PseudoCAP IMP. The dipA deletion mutant fails to disperse when biofilms are exposed to a sudden increase in glutamate. Reason: The phenotype is real and fits the term in a broad sense, but it is not specific to amino acids, since the same mutant also fails to disperse in response to nitric oxide, ammonium chloride and mercury chloride. DipA is a downstream c-di-GMP phosphodiesterase acting in dispersion, not an amino-acid sensor. Not a seed row. Supporting Evidence: PMID:22493016 to be dispersion deficient in response to glutamate, nitric oxide, ammonium chloride, and mercury chloride. |
| GO:0071111 cyclic-guanylate-specific phosphodiesterase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN002403463 (PTHR44757 SF2 GGDEF-EAL clade, 14 leaves), seeded by E. coli PdeR (P77334), PA5017 itself and MucR (Q9I310). Reason: The target carries its own direct evidence (expected self-seed). The other two seeds have experimental PDE evidence (PdeR IDA PMID:17010156 and EXP PMID:23708798; MucR IDA PMID:23729646), so the IBD stands without this seed. DipA has an intact EAL domain, consistent with retained activity. Supporting Evidence: PMID:22493016 Similar low activities were observed when c-di-GMP was used as a substrate file:PSEAE/PA5017/PA5017-uniprot.txt PF00563; EAL |
| GO:0071111 cyclic-guanylate-specific phosphodiesterase activity | IDA PMID:22493016 The phosphodiesterase DipA (PA5017) is essential for Pseudom... | ACCEPT | Summary: PseudoCAP IDA and a seed of PTN002403463. Purified DipA showed PDE activity with bis-pNPP and with c-di-GMP; EAL motif mutants lost function in vivo. Reason: Seed verdict SOUND (full text read). A direct biochemical assay on purified protein supports the specific term. Supporting Evidence: PMID:22493016 Using biochemical and in vivo studies, we show that DipA associates with the membrane and exhibits phosphodiesterase activity 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 row. Reason: Consistent with the IDA and IBA rows on the same term. Supporting Evidence: PMID:22493016 Similar low activities were observed when c-di-GMP was used as a substrate |
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Download this section (compressed HTML)Q: How do cAMP and c-di-GMP binding modulate DipA phosphodiesterase activity, and is DipA activity cue-specific or common to all dispersion signals?
Experiment: Measure c-di-GMP hydrolysis kinetics (HPLC, pGpG product) of the soluble DipA EAL domain and of full-length protein, with and without cAMP, to quantify activity and GAF-domain regulation.
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