eddB (PA3909) encodes EddB (extracellular DNA degradation protein B), the main secreted deoxyribonuclease of Pseudomonas aeruginosa. The 779-residue protein has a signal peptide, an N-terminal lamin-tail domain and a DNase I-like endonuclease/exonuclease/phosphatase domain of the ExeM/NucH family. It is exported across the outer membrane by the Xcp type II secretion system and needs Mg2+ and Ca2+ for stable activity in culture supernatants. EddB degrades extracellular DNA so that the bacterium can use it as a source of carbon, nitrogen and phosphate. It is expressed from the eddA-eddB operon, with the PhoD-type phosphatase/phosphodiesterase EddA, and the operon is induced by phosphate limitation, extracellular DNA and neutrophil extracellular traps. EddB also degrades the DNA backbone of neutrophil extracellular traps and helps P. aeruginosa survive NET killing.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0006308 DNA catabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN001684760 (3 leaf IBAs: P. aeruginosa EddB, Shewanella oneidensis ExeS, Xanthomonas campestris XCC0255), whose IBD has one seed, this gene's PseudoCAP IMP to PMID:20370819. The target appearing in its own WITH/FROM is expected. Reason: Soundly seeded and correct. EddB is the secreted DNase that hydrolyses extracellular DNA for nutrient use, so it catalyses the breakdown rather than merely being required for it. The node is a small clade of secreted ExeM/NucH-family nucleases, and the Shewanella leaf ExeS is independently shown to degrade extracellular DNA. Supporting Evidence: PMID:20370819 PA3909 encodes an extracellular deoxyribonuclease (DNase), which is required for degradation of DNA and utilization of DNA as a source of carbon, nitrogen and phosphate. PMID:21705528 Mutants lacking exeS and/or exeM exhibit decreased eDNA degradation |
| GO:0006308 DNA catabolic process | IMP PMID:20370819 Pseudomonas aeruginosa produces an extracellular deoxyribonu... | ACCEPT | Summary: PseudoCAP IMP; sole seed of the PTN001684760 IBD. Mulcahy et al. (2010) show that PA3909 is required for extracellular DNA degradation and for growth on DNA as a carbon, nitrogen or phosphate source. Reason: Sound seed. The mutant loses supernatant DNase activity and DNA use, and in a later study complementation with eddB restores DNA degradation. The gene product carries the nuclease domain, so the phenotype reflects its own catalytic role in the process. Supporting Evidence: PMID:20370819 This study identifies an extracellular DNase produced by P. aeruginosa that enables degradation of extracellular DNA into an accessible source of carbon, nitrogen and phosphate. PMID:29967090 Complementation with pEddB restored the capacity of P. aeruginosa eddB :: lux to degrade eDNA, with a slight delay in the degradation kinetics |
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping of IPR005135 (endonuclease/exonuclease/phosphatase) to catalytic activity. Reason: Correct but uninformative; DNA nuclease activity (GO:0004536), a descendant already on the gene with experimental support, is the specific activity. Proposed replacements: DNA nuclease activity Supporting Evidence: file:PSEAE/eddB/eddB-uniprot.txt NCBIfam; NF033681; ExeM_NucH_DNase; 1. |
| GO:0004536 DNA nuclease activity | IDA PMID:20370819 Pseudomonas aeruginosa produces an extracellular deoxyribonu... | ACCEPT | Summary: PseudoCAP IDA; DNase activity in culture supernatants that depends on PA3909 and on Mg2+/Ca2+ stabilisation. Reason: Core activity. The assays use culture supernatants rather than purified protein, but the activity depends on eddB, is restored by eddB in trans, and EddB carries an ExeM/NucH-family DNase I-like nuclease domain. Endo- versus exonucleolytic mode is not established, so the general DNA nuclease term is as precise as the evidence allows. Supporting Evidence: PMID:20370819 Stabilization of PA3909 by the addition of excess Mg(2+) and Ca(2+) was required for DNase activity in culture supernatants. PMID:29967090 Bacterial supernatants from P. aeruginosa lacking either the Xcp type II secretion system or PA3909 ( eddB ) were strongly impaired for the degradation of Sytox green-labeled extracellular salmon sperm DNA, relative to the control |
| GO:0005576 extracellular region | IDA PMID:20370819 Pseudomonas aeruginosa produces an extracellular deoxyribonu... | NEW | Summary: Proposed location: EddB is secreted by the Xcp type II secretion system and active in cell-free culture supernatants. Reason: Three independent lines agree: a SignalP signal peptide, dependence of the activity on the Xcp type II secretion system, and DNase activity in cell-free supernatants. The location is also where the core activity acts, on extracellular DNA. Supporting Evidence: PMID:20370819 The primary Xcp type II secretion system but not the Hxc type II secretion system is required for DNase activity and the ability to use DNA as a source of nutrients. file:PSEAE/eddB/eddB-uniprot.txt SIGNAL 1..23 |
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Download this section (compressed HTML)Q: Is EddB an endonuclease or an exonuclease, and what are its products? Do they feed directly into EddA-dependent phosphate release?
Q: Which other secreted nuclease(s) account for the residual extracellular DNase activity of eddB mutants?
Experiment: Purify the mature EddB (residues 24-779) and characterise its nuclease mode on circular and linear, single- and double-stranded DNA, its product sizes and its Mg2+/Ca2+ requirements; test active-site mutants of the endo/exonuclease/phosphatase domain for loss of supernatant DNase activity and NET degradation.
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