OxyR (PP_5309) is a LysR-type transcriptional regulator (LTTR) that serves as the master sensor and regulator of the hydrogen-peroxide oxidative-stress response in Pseudomonas putida KT2440. Like other OxyR proteins, it is a cytoplasmic, constitutively expressed homotetramer that senses H2O2 directly through conserved cysteine residues; oxidation forms an intramolecular disulfide bond that triggers a conformational change altering its DNA-binding and transcription-modulating activity. OxyR binds palindromic operator sequences upstream of antioxidant genes and controls expression of the principal peroxide-detoxifying enzymes, including the two major catalases KatA and KatB and the alkyl hydroperoxide reductase/peroxiredoxin subunit AhpC. Architecturally it has the canonical LTTR organization, with an N-terminal winged helix-turn-helix DNA-binding domain and a C-terminal effector/regulatory (periplasmic-binding-protein-like) domain that mediates redox sensing and oligomerization. As a dual regulator it can both activate and repress transcription depending on target and redox state, and it autoregulates its own promoter. Through this regulon it coordinates removal of reactive oxygen species and maintenance of redox homeostasis, contributing to survival under oxidative stress.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003677 DNA binding | IEA GO_REF:0000104 | ACCEPT | Summary: OxyR is a LysR-type transcriptional regulator with an N-terminal winged helix-turn-helix domain; direct DNA binding to operator sequences upstream of katA, katB and ahpC is experimentally demonstrated (purified OxyR bound these sequences). Reason: Well-supported by the HTH domain architecture and by experimental DNA-binding data. A core molecular activity, though the more specific transcription-factor term below better captures the function. |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000120 | ACCEPT | Summary: OxyR is a sequence-specific DNA-binding transcription factor of the LysR/OxyR family that activates and represses target promoters in response to peroxide. Reason: This is the core molecular function. Strongly supported by family assignment, domain architecture, and experimental promoter binding/regulation data in P. putida. |
| GO:0006351 DNA-templated transcription | IEA GO_REF:0000104 | MARK AS OVER ANNOTATED | Summary: This term denotes the act of transcription itself (the polymerase reaction), which OxyR does not perform; OxyR regulates transcription rather than carrying it out. Reason: OxyR is a regulator, not part of the transcription machinery. The accurate process annotation is regulation of transcription, not the transcription process per se. This is a generic UniProtKB keyword-derived IEA. |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000120 | ACCEPT | Summary: OxyR regulates transcription of its peroxide-defense regulon. This high-level process term is correct but could be made more specific (positive/negative regulation). Reason: Accurate as a parent process term for a transcriptional regulator. Specific directional regulation is captured by other annotations and core_functions. |
| GO:0032993 protein-DNA complex | IEA GO_REF:0000118 | ACCEPT | Summary: As a DNA-binding transcription factor, OxyR forms part of a protein-DNA complex when bound to operator sequences. Reason: Consistent with the demonstrated sequence-specific DNA binding. Reasonable cellular-component annotation for a DNA-binding regulator, though non-core. |
| GO:0045892 negative regulation of DNA-templated transcription | EXP PMID:17107553 OxyR regulated the expression of two major catalases, KatA a... | ACCEPT | Summary: CollecTF experimental annotation. OxyR is a dual regulator; Hishinuma et al. (2006) characterized OxyR binding and regulation of the katA, katB and ahpC promoters in P. putida KT2442, and OxyR is known to repress certain targets and autorepress its own gene. The curator (CollecTF) read the full text and assigned this term from experimental binding-site evidence. Reason: Experimental annotation (EXP, two ECO codes) from CollecTF, a reliable resource, based on demonstrated operator binding. Per guidelines, do not overrule an experimental annotation whose full text the curator read. OxyR's dual activator/repressor nature makes negative regulation biologically appropriate alongside positive regulation. |
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Download this section (compressed HTML)Q: Does P. putida OxyR also regulate a nitrosative-stress (RNS) response, as the UniProt "dual regulator" name implies, or is its in vivo role restricted to peroxide defense?
Q: To what extent is the RecG helicase requirement for OxyR target induction (reported in Pseudomonas) operative for the katA/katB/ahpC regulon in KT2440?
Experiment: ChIP-seq or genome-wide DAP-seq of OxyR under peroxide stress in KT2440 to define the complete regulon and distinguish activated versus repressed targets.
Experiment: Construct a clean oxyR deletion (or cysteine point mutants) and assess H2O2 sensitivity, catalase activity, and transcriptome to confirm direct versus indirect regulatory roles.
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