| Citation | Evidence Type | Supports/Refutes/Qualifies | Claim Tested | Key Finding | Organism/Assay Context | Confidence & Limitations |
|---|---|---|---|---|---|---|
| Fukumori & Kishii 2001 (pqac-00000026, pqac-00000027, pqac-00000028, pqac-00000032) | Direct molecular/genetic characterization | Qualifies | Does P. putida AhpC directly function as a peroxiredoxin, and what reductant system is it paired with? | P. putida ahpC and ahpF are co-transcribed in an operon; AhpC is a 186 aa/24 kDa AhpC-family peroxiredoxin with conserved catalytic cysteines at positions 47 and 166; AhpC overexpression increases resistance to organic hydroperoxide (BHP); AhpF regenerates oxidized AhpC. | P. putida KT2442/KT2440 cloning, transcription mapping, heterologous expression in E. coli, peroxide-resistance assays. | High for AhpC/AhpF partnership and peroxide-defense role in P. putida; limitation: no purified-enzyme kinetic assay directly testing thioredoxin vs AhpF as reductant in P. putida. |
| Hishinuma et al. 2008 (pqac-00000031) | Regulatory/proteomic study | Qualifies | Is AhpC part of the classical OxyR-controlled peroxide defense system in P. putida, and how does this relate to thioredoxin? | OxyR regulates AhpC, AhpF, KatA, KatB, and also affects TrxB; AhpF is explicitly described as the peroxiredoxin reductase increased with AhpC. This supports an AhpC-AhpF antioxidant module distinct from generic thioredoxin dependence. | P. putida KT2442 proteome and transcriptional analysis under oxidative stress. | High for regulatory linkage; limitation: indirect for catalytic electron donor specificity. |
| Bojanovic et al. 2017 (pqac-00000015) | Transcriptomics | Qualifies | Are ahpC and ahpF co-induced under peroxide stress in P. putida? | Under H2O2 stress, ahpC (PP_2439) and ahpF (PP_2440) are both strongly induced, with ahpF showing very large early induction, consistent with a coupled AhpCF peroxide-defense system. | P. putida KT2440 RNA-seq / transcriptional profiling under H2O2 stress. | High for stress-responsive co-expression; limitation: transcript data do not by themselves prove enzymatic donor usage. |
| Ellis & Poole 1997 (pqac-00000000, pqac-00000001, pqac-00000004) | Direct biochemical mutagenesis | Supports | Are the catalytic residues required for active AhpC peroxiredase function conserved in the query protein? | In S. typhimurium AhpC, Cys46 is the essential peroxidatic cysteine and Cys165 the resolving cysteine; mutagenesis established both as central to catalysis. P. putida AhpC conserves the corresponding residues as Cys47/Cys166. | Purified S. typhimurium AhpC mutants; peroxide-reduction biochemistry. | High for catalytic mechanism and residue assignment; limitation: assay is in homolog, not the P. putida protein itself. |
| Poole et al. 2000 (pqac-00000006, pqac-00000008, pqac-00000013, pqac-00000035) | Biochemical/mechanistic review and assay synthesis | Refutes | Is classical AhpC best described as a thioredoxin peroxidase? | Classical bacterial AhpC is reduced by AhpF, a dedicated NADH:peroxiredoxin oxidoreductase whose N-terminal thioredoxin-like redox center directly reduces AhpC. This argues that AhpC in AhpCF systems is not best annotated with a term that explicitly names thioredoxin as donor. | Bacterial AhpF/AhpC systems, especially Salmonella and related species. | High for classical AhpCF systems; limitation: not P. putida-specific, though P. putida has the same ahpCF organization. |
| Wong et al. 2017 (pqac-00000002) | Direct biochemical/structural characterization | Competing | Can some AhpC proteins truly have thioredoxin peroxidase activity? | Mycobacterial AhpC uses thioredoxin-C as a reducing partner; catalytic cysteines are typical of AhpC-family proteins, but reductant usage differs from classical AhpF-dependent systems. | Mycobacterium bovis/BCG structural and partner-interaction studies. | High for this lineage; limitation: demonstrates subfamily plasticity rather than P. putida function. |
| Parsonage et al. 2010 (pqac-00000017, pqac-00000020, pqac-00000037) | Direct biochemical characterization | Competing | Can AhpC-like proteins be thioredoxin-dependent when AhpF is absent? | T. pallidum AhpC-like peroxiredoxin uses thioredoxin as electron donor in an organism lacking the usual AhpF partner. This validates GO:0008379 for some AhpC-like proteins but also shows donor usage is context-dependent. | T. pallidum purified antioxidant system biochemistry. | High for thioredoxin-dependent AhpC-like enzymes; limitation: exceptional genomic context, unlike P. putida which encodes ahpF. |
| Zhang et al. 2019 (pqac-00000007, pqac-00000019, pqac-00000003) | Direct biochemical characterization | Competing/Qualifies | Can AhpC use multiple reductants, and is thioredoxin always primary? | B. thailandensis AhpC can be reduced by both AhpD and thioredoxin, but AhpD shows higher catalytic efficiency. This demonstrates that thioredoxin compatibility does not mean thioredoxin is the physiologically preferred reductant. | Purified B. thailandensis AhpC with kinetic comparison of AhpD vs TrxC. | High; limitation: species-specific, but highly informative for interpreting donor-specific GO terms. |
| Gretes et al. 2012 (pqac-00000016, pqac-00000018) | Evolutionary/structural classification | Supports | Is the query correctly placed within the AhpC/Prx1 typical 2-Cys peroxiredoxin family? | AhpC belongs to the Prx1/AhpC subfamily of typical 2-Cys peroxiredoxins. This supports the general peroxiredoxin assignment and argues against misplacement into another peroxiredoxin subfamily. | Cross-species Prx classification/review. | High for family placement; limitation: does not specify donor usage for the P. putida enzyme. |
| Rhee 2016; Yang et al. 2025 (pqac-00000033, pqac-00000036) | Authoritative review/nomenclature history | Refutes/Qualifies | Does the label “thioredoxin peroxidase” generally fit all peroxiredoxins/AhpCs? | “Thioredoxin peroxidase/TPx” was an early name, but the family was renamed “peroxiredoxin” because not all members use thioredoxin as electron donor. This directly cautions against assigning thioredoxin-specific MF terms solely from family membership. | Broad peroxiredoxin nomenclature and mechanistic reviews. | Moderate-high; limitation: not experimental on P. putida, but directly relevant to GO term granularity. |


*Table: This table summarizes the key experimental, mechanistic, and evolutionary evidence used to assess whether Pseudomonas putida AhpC (Q88K52) directly has GO:0008379 thioredoxin peroxidase activity. It is useful for separating the supported peroxiredoxin function from the likely incorrect donor-specific assignment to thioredoxin rather than AhpF.*