PtrB (PA0612) is a 66-residue protein with a single DksA/TraR-type C4 zinc finger, encoded next to the pyocin repressor gene prtR at the start of the R/F pyocin cluster. Its expression is repressed by PrtR and so rises when DNA damage triggers RecA-dependent cleavage of PrtR during the SOS response. PtrB then represses the type III secretion system: ptrB deletion restores ExoS production and exoT transcription in a prtR mutant and abolishes the mitomycin C-induced shutdown of type III secretion. It does not act by binding the master activator ExsA, and how it represses type III genes is unknown. PtrB thus links the DNA-damage response, which activates pyocin synthesis through PrtN, to shutdown of type III secretion.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0008270 zinc ion binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO mapping from the DksA/TraR C4 zinc finger (IPR000962). Reason: PtrB carries the DksA/TraR C4 zinc finger with both CxxC pairs, so zinc binding is likely, but it is structural and has not been tested; the known role is repression of type III secretion. Supporting Evidence: file:PSEAE/ptrB/ptrB-uniprot.txt Pfam; PF01258; zf-dskA_traR; 1. PMID:16109947 PtrB has a prokaryotic DskA/TraR C4-type zinc-finger motif but does not directly interact with the master regulator, ExsA. |
| GO:1900378 positive regulation of secondary metabolite biosynthetic process | IBA GO_REF:0000033 | REMOVE | Summary: PAINT IBA from PTN002215317, sole seed the PseudoCAP IMP on this protein. Reason: The seed is unsupported (the cited paper shows repression of type III secretion, not regulation of any secondary metabolite), and the node's leaves (E. coli and Salmonella YbiI, a plasmid TraR, a Fels-2 prophage protein, Haemophilus HI_1497, Xanthomonas XCC1304, PA4870) are small phage- and plasmid-borne DksA/TraR-type proteins with no shared secondary-metabolite role. Propagation Review Root cause: SOURCE BAD Failure modes: SOURCE MISCITATION Sources checked: PANTHER:PTN002215317 · PTN002215317 SOURCE BAD PAINT leaf GAF (cached 2026-10-28) lists 8 GO:1900378 leaves in 5 taxa, all small DksA/TraR C4 zinc-finger proteins. UniProtKB:G3XDA6 · ptrB SOURCE BAD Sole seed; the PseudoCAP IMP is not supported by PMID:16109947. Supporting Evidence: PMID:16109947 PrtN activates the expression of pyocin synthesis genes, while PtrB represses the TTSS genes. |
| GO:1900378 positive regulation of secondary metabolite biosynthetic process | IMP PMID:16109947 PtrB of Pseudomonas aeruginosa suppresses the type III secre... | MODIFY | Summary: PseudoCAP IMP citing Wu and Jin 2005, a paper on PtrB as a repressor of type III secretion. Reason: Full text read (cached). The paper's ptrB mutant phenotypes are restored ExoS production, exoT transcription and cytotoxicity in a prtR background, and loss of mitomycin C-induced TTSS repression; it never assays a secondary metabolite. Pyocin synthesis is activated by PrtN, not PtrB, and is not secondary metabolism. The supported process is negative regulation of type III protein secretion; GO has no term for regulation of type III secretion specifically, so GO:0050709 negative regulation of protein secretion is the closest. ptrB deletion restores ExoS production and secretion and exoT transcription when PrtR is absent, and abolishes mitomycin C-mediated suppression, with PA0613 as the in-frame deletion control. Proposed replacements: negative regulation of protein secretion Supporting Evidence: 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. PMID:16109947 PrtN activates the expression of pyocin synthesis genes, while PtrB represses the TTSS genes. PMID:16109947 The above observations clearly indicated that PA0612, but not PA0613, is required for TTSS repression in the prtR mutant background. |
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Download this section (compressed HTML)Q: Does PtrB act like DksA and TraR, through the RNA polymerase secondary channel, to repress exsA-dependent promoters, or through another regulator?
Experiment: Test PtrB binding to RNA polymerase (pull-down or bacterial two-hybrid with the beta' subunit) and its effect on exsA and exoS promoter transcription in vitro, with zinc-finger cysteine mutants as controls.
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