NbdA (PA3311) is an inner-membrane c-di-GMP-specific phosphodiesterase with an N-terminal MHYT sensory domain of seven transmembrane helices, a degenerate GGDEF domain (AGDEF) and a catalytic EAL domain. A recombinant form lacking the MHYT domain hydrolyses c-di-GMP, has no diguanylate cyclase activity and is stimulated by GTP. nbdA is weakly expressed under standard conditions and is induced transcriptionally by nitric oxide. In biofilms exposed to NO, NbdA raises PDE activity and lowers c-di-GMP, and it is required for NO-induced, but not glutamate-induced, biofilm dispersion. The MHYT domain may sense NO directly through a bound metal. NbdA also inhibits flagellar motor switching and swimming reversals through the c-di-GMP adaptor MapZ.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | ACCEPT | Summary: PM IBD at PTN002105365. NbdA's MHYT domain has seven predicted TM helices, so the claim holds for this gene. Reason: Consistent with NbdA's topology. The node-level PM concern (soluble clade members) is recorded once in the rocR review. Supporting Evidence: PMID:23729646 Biochemical analyses of recombinant protein variants lacking the membrane-anchored MHYT domain support NbdA being an active PDE |
| GO:0071111 cyclic-guanylate-specific phosphodiesterase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the 18-seed PTN002105365 IBD; nbdA appears among its own sources because of its own IDA row, which is expected. Reason: Correct for NbdA. Node-level defects are recorded in the rocR review. Supporting Evidence: PMID:23729646 Biochemical analyses of recombinant protein variants lacking the membrane-anchored MHYT domain support NbdA being an active PDE |
| GO:1900190 regulation of single-species biofilm formation | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the 4-seed PTN009140332 IBD (seeds bifA, PA2133, E. coli PdeF, arr). NbdA's own data show that it mediates NO-induced biofilm dispersion by lowering c-di-GMP. Reason: Supported by gene-specific evidence. GO has no biofilm-dispersal term, so regulation of single-species biofilm formation is the most specific fitting term. Supporting Evidence: PMID:23729646 inactivation of nbdA only impaired biofilm dispersion upon exposure to NO |
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | ACCEPT | Summary: SubCell mapping (Cell inner membrane); consistent with seven predicted TM helices. Reason: Same claim as the IBA row; correct. Supporting Evidence: file:PSEAE/nbdA/nbdA-uniprot.txt FT TRANSMEM 84..104 FT /note="Helical" FT /evidence="ECO:0000255" |
| GO:0071111 cyclic-guanylate-specific phosphodiesterase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA (ARBA/EC); the activity is experimentally supported. Reason: Correct core activity. Supporting Evidence: PMID:23729646 Biochemical analyses of recombinant protein variants lacking the membrane-anchored MHYT domain support NbdA being an active PDE |
| GO:0071732 cellular response to nitric oxide | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA prediction of the same claim as the IMP row; true for NbdA by direct genetic evidence. Reason: Consistent with the experimental IMP row on the same term. Supporting Evidence: PMID:23729646 inactivation of nbdA only impaired biofilm dispersion upon exposure to NO |
| GO:0071111 cyclic-guanylate-specific phosphodiesterase activity | IDA PMID:23729646 NO-induced biofilm dispersion in Pseudomonas aeruginosa is m... | ACCEPT | Summary: PseudoCAP IDA and nbdA's seeding of PTN002105365. Recombinant NbdA lacking the MHYT domain hydrolyses c-di-GMP. Reason: Seed verdict SOUND. The abstract states the purified-protein result outright, and UniProt cites the same paper for EC 3.1.4.52. Supporting Evidence: PMID:23729646 Biochemical analyses of recombinant protein variants lacking the membrane-anchored MHYT domain support NbdA being an active PDE |
| GO:0071732 cellular response to nitric oxide | IMP PMID:23729646 NO-induced biofilm dispersion in Pseudomonas aeruginosa is m... | ACCEPT | Summary: PseudoCAP IMP. nbdA is transcriptionally induced by NO, and the deletion loses the NO-triggered rise in PDE activity, the fall in c-di-GMP and the dispersal. Reason: NbdA is a component of the NO-induced dispersal response, not only required for it: its own PDE activity is the step that lowers c-di-GMP. Not a PAINT seed. Supporting Evidence: PMID:23729646 increased PDE activity, resulting in decreased c-di-GMP levels in biofilms expressing nbdA upon exposure to NO, a response that was absent in the ΞnbdA strain |
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Download this section (compressed HTML)Q: Does the MHYT domain bind a metal and sense NO directly, so that NbdA PDE activity is stimulated by NO post-translationally as well as by transcriptional induction?
Experiment: Purify full-length NbdA in detergent, measure metal content, and assay c-di-GMP hydrolysis with and without NO donors, compared with an MHYT-deleted variant.
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