ptrB (PA0612, G3XDA6) notes
Identity
- UniProt G3XDA6, unreviewed, 66 aa; gene ptrB, locus PA0612. Single
DksA/TraR C4-type zinc finger (Pfam PF01258, 34-65; PROSITE PS51128,
PS01102; NCBIfam TIGR02419 C4_traR_proteo); PANTHER PTHR38777 (Fels-2
prophage protein). The two CxxC pairs (CEDC, CSRC) of the C4 motif are
present in the sequence.
- Lies between prtR (PA0611, pyocin repressor) and PA0613, at the start of the
R/F pyocin gene cluster; PA0612-PA0613 form an operon repressed by PrtR.
Literature
- Wu and Jin 2005 (PMID:16109947; strain PAK; full text cached) identified
ptrB as the PrtR-repressed repressor of the type III secretion system (TTSS)
[PMID:16109947 "Expression of ptrB is specifically repressed by PrtR, and
mitomycin C-mediated suppression of the TTSS is also abolished in a ptrB
mutant strain."; "Therefore, PtrB is a new TTSS repressor that coordinates
TTSS repression and pyocin synthesis under the stress of DNA damage."].
Deleting PA0612, not PA0613, restored ExoS production in a prtNR background
PMID:16109947. PtrB does not bind ExsA in a two-hybrid
assay PMID:16109947.
Mechanism unknown PMID:16109947.
- Pyocin synthesis is the job of PrtN, not PtrB PMID:16109947. The paper never mentions secondary metabolites, and pyocins
are protein bacteriocins, not secondary metabolites.
Participation test
PtrB is a negative regulator of type III secretion; the mutant phenotype is
derepression of ExoS secretion and exoT transcription, which by GO convention
supports a negative regulation term (IMP). Nothing in the paper relates PtrB
to any secondary metabolite pathway, positively or negatively. The seeded
term is not a phenotype of PtrB loss at all; it is unsupported.
Clade check: PTN002215317 leaves are E. coli and Salmonella YbiI, a
Salmonella plasmid TraR, Salmonella Fels-2 prophage protein STM2731,
Haemophilus HI_1497, Xanthomonas XCC1304, P. aeruginosa PA4870 and PtrB:
small phage- and plasmid-borne DksA/TraR-type zinc-finger proteins with no
shared secondary-metabolite role. The term cannot be propagated across them.
GO has no "regulation of type III secretion" term; the nearest is
GO:0050709 negative regulation of protein secretion, proposed as NEW (IMP).
PseudoCAP IBA-seed assessment
| PTN node |
node term |
n_seeds |
leaf IBAs |
seed annotation (term, evidence, PMID) |
verdict |
rationale |
| PTN002215317 |
GO:1900378 positive regulation of secondary metabolite biosynthetic process |
1 (sole) |
8 (5 taxa) |
GO:1900378, IMP, PMID:16109947 (PseudoCAP) |
WRONG |
The paper shows PtrB represses type III secretion; it reports no secondary-metabolite phenotype, and pyocin genes are activated by PrtN, not PtrB. The node's phage/plasmid DksA/TraR-like leaves share no such role. Withdraw the IBD. |
Decisions summary
- REMOVE: positive regulation of secondary metabolite biosynthesis (IBA and
IMP), with PSEUDOCAP and GO_CENTRAL defects.
- KEEP_AS_NON_CORE: zinc ion binding (IEA, C4 motif).
- NEW: GO:0050709 negative regulation of protein secretion (IMP,
PMID:16109947).