Arr (aminoglycoside response regulator, PA2818) is a 525-aa inner-membrane EAL-domain c-di-GMP phosphodiesterase of Pseudomonas aeruginosa PAO1, encoded on a genomic island that most strains, including PA14, lack. Two predicted transmembrane helices flank a CSS-motif domain, which is probably periplasmic, and the C-terminal cytoplasmic EAL domain has intact catalytic motifs. Membranes from arr mutants have less c-di-GMP phosphodiesterase activity, although lysates of a PA14 strain overexpressing arr showed no detectable activity. Arr is required for the biofilm formation induced by subinhibitory aminoglycosides such as tobramycin, and for biofilm-specific aminoglycoside resistance; a mutant in a predicted catalytic residue is defective in this response. Its deletion also disrupts mushroom structures in flow-cell biofilms. How aminoglycosides are sensed, and why loss of a phosphodiesterase prevents biofilm induction, are unknown.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004114 3',5'-cyclic-nucleotide phosphodiesterase activity | IDA PMID:16121184 Aminoglycoside antibiotics induce bacterial biofilm formatio... | MODIFY | Summary: PseudoCAP IDA citing Hoffman 2005, whose abstract reports reduced c-di-GMP phosphodiesterase activity in membranes of arr mutants. GO:0004114 is the PDE activity on 3',5'-cyclic nucleoside monophosphates (cAMP, cGMP) and is not an ancestor of GO:0071111, the c-di-GMP-specific activity. Reason: The activity reported is c-di-GMP hydrolysis, so the correct term is GO:0071111, which the gene already carries by IBA and IEA. This is a lateral correction, not a refinement. Arr is not a seed of the GO:0071111 node, so no IBD depends on this row. Proposed replacements: cyclic-guanylate-specific phosphodiesterase activity Supporting Evidence: PMID:16121184 membranes from arr mutants had diminished c-di-GMP phosphodiesterase activity PMID:16121184 The arr gene is predicted to encode an inner-membrane phosphodiesterase whose substrate is cyclic di-guanosine monophosphate (c-di-GMP) file:PSEAE/arr/arr-notes.md GO:0004114 is defined on 3',5'-cyclic nucleoside monophosphates and is not an ancestor of GO:0071111 |
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | ACCEPT | Summary: PM IBD at PTN002105365. Arr has two predicted TM helices, like the membrane-anchored seeds. Reason: Consistent with the predicted topology and the inner-membrane prediction in the arr paper. Node-level defects of PTN002105365 are recorded once in the rocR review. Supporting Evidence: file:PSEAE/arr/arr-uniprot.txt FT TRANSMEM 12..33 FT /note="Helical" FT /evidence="ECO:0000256|SAM:Phobius" PMID:16121184 The arr gene is predicted to encode an inner-membrane phosphodiesterase whose substrate is cyclic di-guanosine monophosphate (c-di-GMP) |
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | ACCEPT | Summary: SubCell mapping (Cell membrane; multi-pass); ARBA-derived, but supported independently by two Phobius TM helices. Reason: Same claim as the IBA row. Supporting Evidence: file:PSEAE/arr/arr-uniprot.txt FT TRANSMEM 12..33 FT /note="Helical" FT /evidence="ECO:0000256|SAM:Phobius" |
| GO:0046677 response to antibiotic | IMP PMID:16121184 Aminoglycoside antibiotics induce bacterial biofilm formatio... | ACCEPT | Summary: arr mutants fail to form biofilm in response to subinhibitory tobramycin and lose biofilm-specific aminoglycoside resistance. Reason: The aminoglycoside response is the phenotype that defines arr, shown by mutant analysis. Supporting Evidence: PMID:16121184 was essential for this induction and contributed to biofilm-specific aminoglycoside resistance PMID:16121184 P. aeruginosa cells with a mutation changing a predicted catalytic residue of Arr were defective in their biofilm response to tobramycin |
| GO:0071111 cyclic-guanylate-specific phosphodiesterase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the 18-seed PTN002105365 IBD; arr is not a seed of this node. The EAL and DDFGTG motifs are intact; mutant membranes lose c-di-GMP PDE activity, but an overexpression lysate assay detected none (PMID:16477007). Reason: The membrane assay and the catalytic-residue phenotype support the activity; the lysate negative is within the stated sensitivity limits of that assay and does not refute it. Node-level defects of PTN002105365 are recorded once in the rocR review. Supporting Evidence: PMID:16121184 membranes from arr mutants had diminished c-di-GMP phosphodiesterase activity PMID:16121184 P. aeruginosa cells with a mutation changing a predicted catalytic residue of Arr were defective in their biofilm response to tobramycin file:PSEAE/arr/arr-notes.md PA2771 GGEEF — PA2818 EAL — PA2870 GGEEF +(96) |
| GO:0071111 cyclic-guanylate-specific phosphodiesterase activity | IEA GO_REF:0000003 | ACCEPT | Summary: EC 3.1.4.52 mapping. Reason: Same claim as the IBA row; supported by the arr mutant membrane assay. Supporting Evidence: PMID:16121184 membranes from arr mutants had diminished c-di-GMP phosphodiesterase activity |
| GO:1900190 regulation of single-species biofilm formation | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the 4-seed PTN009140332 IBD, of which arr is a seed through its own row, which is expected. Reason: Correct for arr; same claim as the experimental row. Supporting Evidence: PMID:16121184 was essential for this induction and contributed to biofilm-specific aminoglycoside resistance |
| GO:1900190 regulation of single-species biofilm formation | IDA PMID:16121184 Aminoglycoside antibiotics induce bacterial biofilm formatio... | ACCEPT | Summary: PseudoCAP row and arr seeding of PTN009140332. The abstract shows that arr is essential for aminoglycoside-induced biofilm formation, through its predicted catalytic residue. Reason: Seed verdict SOUND. The term is right; the evidence described is genetic, so IMP would fit better than IDA, but the claim does not change. The full text was not read. The IBD also stands on bifA. Supporting Evidence: PMID:16121184 was essential for this induction and contributed to biofilm-specific aminoglycoside resistance PMID:16121184 P. aeruginosa cells with a mutation changing a predicted catalytic residue of Arr were defective in their biofilm response to tobramycin |
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Download this section (compressed HTML)Experiment: Purify the Arr EAL domain (and full-length Arr in detergent) and measure c-di-GMP hydrolysis with and without tobramycin; compare wild type with the catalytic-residue mutant used by Hoffman et al.
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: How Arr senses aminoglycosides, and why loss of a c-di-GMP phosphodiesterase blocks tobramycin-induced biofilm formation rather than enhancing it, are unknown. No purified-enzyme activity has been reported, and an overexpression lysate assay detected none.
BIOLOGY
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