parA (also known as str246C) is a tobacco (Nicotiana tabacum) member of the plant tau (U) class of glutathione S-transferases (GST superfamily; PANTHER PTHR11260:SF756, "glutathione S-transferase parA-related"). It was originally isolated as an auxin-regulated cDNA induced very rapidly (within ~30 min) by 2,4-dichlorophenoxyacetic acid during the G0-to-S transition of cultured tobacco mesophyll protoplasts (Takahashi & Nagata). The "auxin-regulated" designation refers to transcriptional induction by auxin via a cis-acting auxin-responsive promoter element, not to participation in the auxin signal-transduction machinery. The same gene was independently isolated as str246C, a defense-related gene whose transcripts accumulate upon infection by the bacterial pathogen Pseudomonas (Ralstonia) solanacearum, so parA is both auxin-inducible and stress/pathogen-inducible, typical behaviour of stress-responsive plant tau GSTs. parA has the canonical two-domain GST fold (GST N-terminal thioredoxin-like and GST C-terminal helical domains) with a glutathione-binding site, and is assigned EC 2.5.1.18. However, the parA protein itself shows only weak GST activity (<1/30 that of the closely related parB/Nt103 GST) and one study reported nuclear localization for parA, prompting the suggestion that parA may have a function distinct from a conventional cytosolic detoxification GST. Its name therefore carries "Probable", and its physiological substrate and primary role remain uncertain. Best-supported view: parA is a tau-class plant GST whose established biology is transcriptional responsiveness to auxin and to biotic stress.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0009734 auxin-activated signaling pathway | IEA GO_REF:0000043 | REMOVE | Summary: SPKW (GO_REF:0000043) keyword-derived annotation, present only in the Sept 2025 snapshot and removed from current GOA. It originates from the UniProt keyword "Auxin signaling pathway", which was attached because of the protein's historical name "Auxin-regulated protein parA". parA is a downstream auxin-responsive gene, not a component of the auxin signal-transduction pathway. Reason: This is an over-annotation that conflates "transcriptionally induced by auxin" with "component of the auxin signaling pathway". parA was isolated as an early auxin-induced transcript in cultured tobacco protoplasts [PMID:2594768], and its promoter contains a cis-acting auxin-responsive element [PMID:2236015]. Being an auxin-responsive target gene is distinct from being part of the GO:0009734 pathway, which is defined as the series of events from binding of auxin to a receptor through downstream output and is reserved for receptor/signal-transduction components (TIR1/AFB receptors, SCF-TIR1, Aux/IAA repressors, ARF transcription factors). parA is a tau-class plant GST and a downstream effector, not a signaling component. The keyword-to-GO mapping propagated the misleading "auxin" keyword into a pathway-component term. GOA's removal of this annotation when it retired the keyword2GO (GO_REF:0000043) pipeline was JUSTIFIED: a correct annotation was not lost. If a process term capturing the auxin relationship is desired, the appropriate term is "response to auxin" (GO:0009733), which covers auxin-responsive gene expression without implying signal-transduction-component status (see the NEW entry below). Proposed replacements: response to auxin Supporting Evidence: PMID:2594768 The mRNA of the par gene is approximately 900 bases long and its accumulation was detected in cultured mesophyll protoplasts as early as 30 min after the addition of 2,4-dichlorophenoxyacetic acid to the culture medium. The par mRNA was not detected in leaves or freshly prepared protoplasts or in protoplasts in the absence of 2,4-dichlorophenoxyacetic acid. PMID:2236015 deletion of a 111-base-pair (bp) direct repeat in the 5' flanking sequences of the par gene abolished the auxin-induced GUS activity, it is deduced that in the 111-bp direct repeat of the par gene promoter is localized an auxin-responsive region, which regulates auxin-mediated activation of transcription. |
| GO:0004364 glutathione transferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Family-level molecular-function annotation (InterPro IPR045074 Tau-class GST signature, RHEA:16437, EC 2.5.1.18, PANTHER PTN004250175). parA has the canonical two-domain GST fold and a glutathione-binding site, and the closely related parB/Nt103 was directly shown to be a functional GST [PMID:1729717]. A direct assay of the parA protein detected GST activity, although at a low level (<1/30 that of parB) [PMID:7767232]. Reason: parA belongs to the plant tau (U) class of the GST superfamily (PANTHER PTHR11260:SF756; CDD GST_N_Tau/GST_C_Tau; InterPro tau-class signatures). Tau and phi classes are the plant-specific GST classes that catalyse glutathione-dependent conjugation reactions [PMID:21425939]. GST activity has been directly detected for the parA recombinant protein, so this generic molecular-function term is supported, even though parA's activity is weak relative to its paralog parB and its preferred physiological substrate is unknown (hence UniProt names it "Probable glutathione S-transferase"). The IEA term is at an appropriate level of generality for a family-based assignment. Supporting Evidence: PMID:7767232 we detected a low level of GST activity in the parA products, whose value was below 1/30 of that of parB products encoding tobacco (Nicotiana tabacum L.) GST. PMID:1729717 When we introduced expression vector pKK233-2, which retains parB cDNA, into Escherichia coli, we could detect GST activity in the parB gene product. file:TOBAC/PARA/PARA-deep-research-falcon.md Therefore, enzyme-function annotation for P25317 as an active EC 2.5.1.18 catalyst should be phrased as **“probable”** and supported by (i) family placement and (ii) proteomics annotation rather than an unambiguous parA-only enzymology experiment |
| GO:0005737 cytoplasm | IEA GO_REF:0000118 | KEEP AS NON CORE | Summary: TreeGrafter (GO_REF:0000118) phylogenetic transfer of the cytoplasm location from the PTHR11260 GST family. Plant GSTs are predominantly cytosolic enzymes [PMID:11897031], so this is the family-typical location. However, the one direct study of parA protein localization reported parA in the nucleus of tobacco protoplasts and BY-2 cells, contrasting with conventional cytoplasmic GSTs including parB [PMID:7767232]. Reason: The cytoplasm assignment is a reasonable family-level call: plant GSTs "are predominantly expressed in the cytosol" [PMID:11897031] and parA has no predicted targeting/transit peptide. However, there is a genuine experimental discrepancy: immunofluorescence and confocal imaging reported the parA protein confined to the nucleus (excluded from the nucleolus), unlike the cytoplasmic parB GST [PMID:7767232]. Because the cellular location of parA is not robustly established and the only direct evidence argues against a purely cytoplasmic localization, this term is retained (it is not clearly wrong for a GST-fold protein) but marked as non-core rather than accepted as a confirmed core localization. The nuclear-localization observation is from a single 1995 study using overexpressed/tagged protein and could be artefactual, so neither cytoplasm nor nucleus can be asserted with confidence. Supporting Evidence: PMID:11897031 GSTs are predominantly expressed in the cytosol, where their GSH-dependent catalytic functions include the conjugation and resulting detoxification of herbicides PMID:7767232 Immunofluorescence studies using an antibody against parA protein revealed that the subcellular location of parA protein is the nucleus in cultured tobacco mesophyll protoplasts, while conventional GSTs' including the parB product were primarily located in the cytoplasm. file:TOBAC/PARA/PARA-deep-research-falcon.md the plastid-preparation detection supports association with plastid fractions but does not alone prove true plastid residency (common issue in organelle proteomics); together with a nuclear-localization report, it underscores that **P25317 localization is not settled** |
| GO:0006749 glutathione metabolic process | IEA GO_REF:0000120 | ACCEPT | Summary: Family-level biological-process annotation accompanying the glutathione transferase activity call (InterPro IPR045074, PANTHER PTN004250175). Glutathione transferases use glutathione as cosubstrate/coenzyme in conjugation reactions, which constitutes glutathione-utilizing metabolism. Reason: As a tau-class GST that uses glutathione as a cosubstrate (the EC 2.5.1.18 reaction RX + glutathione = an S-substituted glutathione + a halide anion + H+), parA participates in glutathione metabolism. Plant GSTs are central to glutathione-dependent conjugation chemistry [PMID:21425939, PMID:11897031]. This generic process term is the standard partner of the GST molecular-function annotation and is appropriate at the IEA family-inference level, consistent with the directly demonstrated (if weak) GST activity of the parA protein [PMID:7767232]. Supporting Evidence: PMID:21425939 the numerous and plant-specific phi (F) and tau (U) classes are largely responsible for catalyzing glutathione-dependent reactions with xenobiotics, notably conjugation leading to detoxification PMID:7767232 we detected a low level of GST activity in the parA products, whose value was below 1/30 of that of parB products encoding tobacco (Nicotiana tabacum L.) GST. |
| GO:0009733 response to auxin | IEP PMID:2594768 Isolation of an auxin-regulated gene cDNA expressed during t... | NEW | Summary: parA is one of the best-characterized auxin-responsive genes in tobacco. Its mRNA accumulates within 30 min of 2,4-D treatment in cultured mesophyll protoplasts and is absent without auxin [PMID:2594768], and a defined cis-acting auxin-responsive element in its promoter is required for this induction [PMID:2236015]. Reason: This term replaces the incorrect retired "auxin-activated signaling pathway" (GO:0009734) annotation. "Response to auxin" (GO:0009733) correctly captures the well-documented biology of parA: it is a downstream auxin-responsive target gene, transcriptionally induced by auxin, without implying that it is a component of the auxin signal-transduction pathway. The evidence is expression-based (auxin-dependent mRNA accumulation and a mapped auxin-responsive promoter element), so IEP is the appropriate evidence code. Supporting Evidence: PMID:2594768 The mRNA of the par gene is approximately 900 bases long and its accumulation was detected in cultured mesophyll protoplasts as early as 30 min after the addition of 2,4-dichlorophenoxyacetic acid to the culture medium. The par mRNA was not detected in leaves or freshly prepared protoplasts or in protoplasts in the absence of 2,4-dichlorophenoxyacetic acid. PMID:2236015 a chimeric gene, in which a reporter gene for bacterial beta-glucuronidase (GUS) was placed downstream of the 5' flanking sequences of the par gene ... elicited auxin-regulated expression of GUS activity. |
| GO:0009617 response to bacterium | IEP PMID:7948901 Structural organization of str 246C and str 246N, plant defe... | NEW | Summary: parA is identical in sequence to str246C, a defense-related gene whose transcripts accumulate in tobacco leaves upon inoculation with the bacterial pathogen Pseudomonas (Ralstonia) solanacearum, in both compatible and incompatible interactions [PMID:7948901]. Reason: The independent isolation of parA as the pathogen-inducible defense gene str246C documents that parA is transcriptionally responsive to bacterial infection. This is a distinct, experimentally supported aspect of parA biology not captured by any current or retired annotation. "Response to bacterium" (GO:0009617) accurately reflects the expression-based evidence (IEP). It also illustrates that parA is a general stress-inducible tau GST rather than an auxin-pathway-specific gene. Supporting Evidence: PMID:7948901 We have previously identified a cDNA clone, pNt246, whose corresponding transcripts accumulate in leaves in response to inoculation by compatible and incompatible isolates of the phytopathogenic bacterium Pseudomonas solanacearum file:TOBAC/PARA/PARA-deep-research-falcon.md Deletion analysis identifies a **bacterial response element (BRE)** between **−184 and −101** required for infection inducibility |
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Download this section (compressed HTML)Q: Does the parA protein have a genuine physiological glutathione transferase substrate (e.g. a xenobiotic, herbicide, oxidized lipid, or secondary metabolite), or is its weak GST activity vestigial?
Q: Is the reported nuclear localization of parA a real feature with functional significance, or an artefact of overexpression/tagging in protoplasts?
Q: Why is parA induced by both auxin and bacterial pathogens - does it have a role in linking growth-hormone signaling to stress/defense responses, as is seen for other stress-inducible plant tau GSTs?
Experiment: Purify recombinant parA protein and assay activity against a panel of standard GST substrates (CDNB), organic hydroperoxides (GPOX activity), and candidate physiological substrates, comparing kinetics to parB to determine whether parA is a catalytically competent GST or a divergent ligandin/regulatory protein.
Hypothesis: parA retains GST-fold but has weak/altered catalysis and may function primarily as a ligand-binding (ligandin) protein rather than a conjugating enzyme.
Experiment: Re-examine parA subcellular localization using a native-promoter fluorescent-protein fusion or immuno-electron microscopy in stably transformed tobacco, under both auxin and pathogen induction, to resolve the cytoplasm-versus-nucleus discrepancy.
Hypothesis: The previously reported nuclear localization of parA reflects a genuine, possibly stress-regulated, partitioning distinct from cytosolic GSTs such as parB.
Experiment: Generate parA loss-of-function and overexpression lines in tobacco and challenge them with auxin, oxidative stress, herbicides, and Ralstonia solanacearum to test whether parA contributes to detoxification, oxidative stress tolerance, or disease resistance.
Hypothesis: parA functions as a stress-inducible detoxification/antioxidant tau GST contributing to defense responses rather than to auxin signal transduction.
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