Phr (PA4660) is the class I cyclobutane pyrimidine dimer (CPD) DNA photolyase of Pseudomonas aeruginosa, a member of the photolyase/cryptochrome family with an N-terminal photolyase domain and a C-terminal FAD-binding domain. By homology to E. coli PhrB it binds FAD as the catalytic cofactor and a folate antenna chromophore, recognizes CPDs formed between adjacent pyrimidines by UV light, and uses blue/near-UV light energy to split the dimer back to two pyrimidines (EC 4.1.99.3), a direct reversal repair called photoreactivation. The cloned PAO1 gene complements a photolyase-deficient E. coli strain, and phr insertion mutants survive UV-B irradiation less well than wild type when allowed to recover in light, an effect that is much larger in a nucleotide-excision-repair (uvrA) background.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000719 photoreactive repair | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA prediction, but correct for this gene: phr complements a photolyase mutant and its loss lowers UV survival only under photoreactivating light. Reason: Core process; supported by the gene's own genetic evidence, not only the rule. Supporting Evidence: PMID:11282583 shown to complement a known phr mutation following expression in Escherichia coli SY2 PMID:11282583 followed by a recovery period under photoreactivating conditions |
| GO:0003677 DNA binding | IBA GO_REF:0000033 | MODIFY | Summary: IBA from the deep photolyase/cryptochrome node PTN000155848. DNA binding is true of a photolyase, and generic DNA binding is the right level for a node that includes cryptochromes; for this gene the substrate is CPD-damaged DNA. Reason: Correct but general for Phr. A CPD photolyase binds UV-damaged DNA, so GO:0003684 damaged DNA binding (is_a GO:0003677) is the specific term. The node-level claim is not disputed. Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000155848 · PTN000155848 SUPPORTS TRANSFER Deep node spanning class I photolyases and cryptochromes; generic DNA binding suits it. Phr is a class I CPD photolyase inside the clade. UniProtKB:P00914 · E. coli PhrB SUPPORTS TRANSFER Closest characterized seed, a CPD photolyase of the same class. Proposed replacements: damaged DNA binding Supporting Evidence: PMID:11282583 shown to complement a known phr mutation following expression in Escherichia coli SY2 |
| GO:0003904 deoxyribodipyrimidine photo-lyase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN000155848, seeded by experimentally characterized photolyases including E. coli PhrB and yeast PHR1. Phr carries the class I photolyase domains and complements an E. coli photolyase mutant. Reason: Core molecular function; family membership plus functional complementation. Supporting Evidence: PMID:11282583 shown to complement a known phr mutation following expression in Escherichia coli SY2 |
| GO:0003904 deoxyribodipyrimidine photo-lyase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Automated EC mapping; agrees with the IBA and with the complementation data. Reason: Consistent with the IBA row on the same term. Supporting Evidence: PMID:11282583 shown to complement a known phr mutation following expression in Escherichia coli SY2 |
| GO:0009416 response to light stimulus | IBA GO_REF:0000033 | TOO GENERAL | Summary: IBA from PTN000155970, seeded by E. coli PhrB and by this gene's own PseudoCAP UV protection row (self-seed, expected). The node term is true of a light-driven repair enzyme and suits the clade. Reason: True but uninformative here: GO:0009650 UV protection, kept in this review, is_a GO:0009411 response to UV is_a GO:0009416. |
| GO:0009650 UV protection | IMP PMID:11282583 Construction and analysis of photolyase mutants of Pseudomon... | KEEP AS NON CORE | Summary: PseudoCAP seed of PTN000155970. phr mutants survive UV-B less well under photoreactivating conditions, and complementation restores survival. The mechanism is photoreactive repair, accepted separately. Reason: Directly shown and correctly coded; it is the organism-level outcome of the core photoreactive repair activity rather than the activity itself. Supporting Evidence: PMID:11282583 These mutants showed a decrease in survival compared to the wild type of as much as 19-fold after irradiation at UV-B doses of 1,000 to 1,550 |
| GO:0071949 FAD binding | IBA GO_REF:0000033 | ACCEPT | Summary: FAD is the catalytic cofactor of the whole photolyase/cryptochrome family; Phr carries the FAD-binding domain. Reason: Cofactor binding inherited across the family and required for the core activity. Supporting Evidence: PMID:11282583 shown to complement a known phr mutation following expression in Escherichia coli SY2 |
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Download this section (compressed HTML)Q: The PhrB seed of PTN000155970 is annotated to GO:0007603 phototransduction, visible light (IDA, PMID:6325459). Is a signalling term appropriate for a DNA repair photolyase, or should that row be photoreactive repair?
Experiment: Purify P. aeruginosa Phr and measure light-dependent CPD repair in vitro and its chromophore content (FAD and antenna folate).
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