PA0906 (Q9I551) notes — AlpR

Identity

PA0906 is alpR (McFarland et al. 2015, PMID:26100878), a lambda CI/LexA-like repressor: Cro/C1-type
HTH (PF01381, PS50943) plus a peptidase S24 (LexA-like) C-terminal domain (PF00717, IPR039418).
PANTHER PTHR40661:SF2 is named after PrtR (PA0611), the pyocin repressor, a different paralog.
Divergent from alpABCDE (PA0907-PA0911), a lysis cassette.

Literature (full text cached, PMC4500232)

PMID:26100878
PMID:26100878 — DNA-damage
induced autocleavage dependent on the Ser-Lys dyad serine.
PMID:26100878
PMID:26100878
PMID:26100878
So AlpR is a direct, DNA-damage-inactivated repressor of alpR and alpA; lysis is executed by the AlpBCDE
proteins (holin-like AlpB etc.), not by AlpR.

Annotation decisions

GO:0045892 negative regulation of DNA-templated transcription (IDA PseudoCAP): ACCEPT, core.
GO:0006355 regulation of DNA-templated transcription (IBA PTN002221379; IEA): MODIFY to GO:0045892.
GO:0003677 DNA binding (IEA): MODIFY to GO:0000976 transcription cis-regulatory region binding (ChIP-seq
to the two promoter-containing intergenic regions).
GO:0006351 DNA-templated transcription (IEA): MARK_AS_OVER_ANNOTATED.
GO:0006974 DNA damage response (IDA PseudoCAP): ACCEPT; AlpR is itself cleaved in response to DNA damage
(ciprofloxacin, H2O2), which is its signal-transduction step.
GO:0001896 autolysis (IMP PseudoCAP): MODIFY to GO:0043069 negative regulation of programmed cell death.
AlpR does not execute lysis; it represses the lysis genes, and its removal/cleavage de-represses them.
GO has no "regulation of autolysis" term; autolysis is_a programmed cell death. Not a PAINT seed.
NEW GO:0001217 DNA-binding transcription repressor activity (IDA): core MF, not in GOA.
NEW GO:0016540 protein autoprocessing (IMP): S153A abolishes DNA-damage-induced cleavage; by analogy to
LexA/CI this is RecA-stimulated self-cleavage. Self-catalysis is not shown in vitro in this paper, so
this is moderate.

PseudoCAP IBA-seed assessment

QuickGO (2026-10-28) shows 10 IBA leaves for PTN002221379 (matches the worklist): PA0906, P. aeruginosa
PrtR (Q06553), S. oneidensis prophage cI/C repressors, S. typhimurium STM0898, H. influenzae HI_1476,
N. meningitidis NMB0910/NMB0556 and others — all CI/LexA-like HTH-S24 repressors.

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN002221379	GO:0006355 regulation of DNA-templated transcription	1 (sole)	10 (6 taxa)	GO:0045892, IDA, PMID:26100878 (PseudoCAP)	SOUND	ChIP-seq places AlpR on the alpR-alpA and alpA-alpB promoter regions, ectopic AlpR represses the promoter fusions, and blocking its cleavage blocks induction: direct evidence for transcriptional repression. The generic regulation term (the IBD did not propagate the negative sign) is appropriate for a clade of CI/LexA-like phage and pyocin repressors.