eddB (PA3909, Q9HXA4) notes

No deep-research provider was available; this is a manual literature review
(PubMed search; cached publications). PMID:20370819 is abstract-only;
PMID:29967090 and PMID:21705528 have full text cached.

Identity

UniProt Q9HXA4 (TrEMBL, PE 4), 779 aa, "Extracelullar DNA degradation
protein, EddB" (submitter name). SignalP signal peptide 1..23.
Domains: lamin-tail (LTD, PF00932, 19..131), endonuclease/exonuclease/
phosphatase (PF03372, IPR005135; DNase I-like fold SSF56219, CDD cd10283
MnuA_DNase1-like), NCBIfam NF033681 ExeM_NucH_DNase, InterPro IPR047971
ExeM-like, CDD cd04486 YhcR_OBF_like, PANTHER PTHR42834.
Operon: eddA (PA3910, PhoD-type alkaline phosphatase/phosphodiesterase) -
eddB PMID:29967090.

Literature

Mulcahy et al. 2010 (PMID:20370819, PseudoCAP seed paper): "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."
Induced by phosphate limitation and by DNA; activity in culture supernatants
needs excess Mg2+/Ca2+ for stabilisation; secretion via the Xcp type II
secretion system PMID:20370819.
Wilton et al. 2018 (PMID:29967090, full text): supernatants of the eddB::lux
mutant were strongly impaired in degrading Sytox-labelled DNA and pEddB
complementation restored it PMID:29967090. EddB degrades
neutrophil extracellular trap DNA and contributes to survival against NET
killing; eDNA and NETs induce the operon. Residual activity in mutants suggests
other secreted nucleases exist.
Gödeke et al. 2011 (PMID:21705528): the Shewanella oneidensis relatives ExeS
and ExeM (ExeS is one of the other two PTN001684760 leaves) are extracellular
endonucleases needed for eDNA degradation and DNA use as a nutrient
PMID:21705528.

GO term reasoning

MF GO:0004536 DNA nuclease activity: the supernatant DNase activity depends on
eddB and is restored by eddB in trans; EddB carries the DNase I-like
endo/exonuclease/phosphatase domain of the ExeM/NucH family. The assay is on
supernatants, not purified protein, so the strict evidence is genetic, but the
gene product carrying a nuclease domain is the obvious catalyst. Endo- versus
exonucleolytic mode is not shown for EddB, so stay at DNA nuclease activity.
BP GO:0006308 DNA catabolic process: EddB hydrolyses DNA (extracellular DNA) to
provide nutrients. The gene product catalyses the breakdown, so it does the
work of the process (participation test passes). Seed SOUND.
CC: secreted through Xcp T2SS, activity in culture supernatant, SignalP
signal peptide -> GO:0005576 extracellular region (NEW). Two independent lines
agree (signal peptide + T2SS dependence + supernatant activity).
catalytic activity IEA (InterPro IPR005135): too general -> MODIFY to
GO:0004536.
Node PTN001684760: 3 leaves (EddB, Shewanella ExeS Q8EFX1, Xanthomonas
XCC0255). ExeS is independently characterised as an extracellular
endonuclease, so the node term suits the clade.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN001684760	GO:0006308 DNA catabolic process	1 (sole seed)	3 (3 taxa: P. aeruginosa EddB, S. oneidensis ExeS, X. campestris XCC0255)	GO:0006308 DNA catabolic process, IMP, PMID:20370819 (PseudoCAP)	SOUND	eddB mutant supernatants lose DNase activity and the ability to use DNA as a C/N/P source; complementation restores DNA degradation (PMID:29967090). EddB carries the ExeM/NucH DNase I-like nuclease domain, so it is the catalyst of the breakdown, not just required for it. The term suits a small clade of secreted ExeM/NucH-family nucleases; ExeS is independently shown to degrade eDNA (PMID:21705528).

Decisions summary

DNA catabolic process IBA and IMP: ACCEPT.
DNA nuclease activity IDA: ACCEPT.
catalytic activity IEA: MODIFY to GO:0004536.
NEW: GO:0005576 extracellular region (IDA, PMID:20370819).