UniProt: P25317 (GSTXA_TOBAC). "Probable glutathione S-transferase parA";
AltNames "Auxin-regulated protein parA" and "STR246C protein". EC 2.5.1.18.
220 aa, GST superfamily, tau (U) class. PANTHER PTHR11260:SF756 ("GLUTATHIONE
S-TRANSFERASE PARA-RELATED"). 220 aa, two-domain GST architecture (GST N-terminal
4-83; GST C-terminal 89-209). Reference proteome UP000790787, chromosome 2.
Evidence level PE 2 (transcript level) — no purified-protein characterization of
parA itself.
This review is part of the SPKW-PLANTS retrospective subproject: assessing whether
GOA's retirement of the keyword-to-GO (GO_REF:0000043) pipeline removed a correct
annotation or an over-annotation. The retired annotation here is
auxin-activated signaling pathway (GO:0009734).
The par ("protoplast auxin-regulated") genes were isolated by Takahashi & Nagata
from cultured tobacco mesophyll protoplasts as genes induced very rapidly by
2,4-dichlorophenoxyacetic acid (2,4-D, a synthetic auxin) during the G0→S transition.
parA was the founding clone [PMID:2594768 "A cDNA clone for an auxin-regulatedparB was isolated from the same system and was the first par gene whose productparC is another member of the family; PANTHER places parC (P49332/Q03666) inSo the par family is a cluster of auxin-inducible (and stress-inducible) tau-class
plant GSTs. The naming "auxin-regulated" refers to transcriptional induction by
auxin, established by promoter-reporter work: deletion of a 111-bp direct repeat
in the parA promoter abolished auxin-induced expression, localising a cis-acting
auxin-responsive region [PMID:2236015 (abstract) "deletion of a 111-base-pair (bp)
direct repeat in the 5' flanking sequences of the par gene abolished the
auxin-induced GUS activity ... an auxin-responsive region, which regulates
auxin-mediated activation of transcription"].
The genomic clone str246C is sequence-identical to parA PMID:7948901. str246C transcripts
accumulate in leaves on inoculation with the bacterial pathogen Pseudomonas
(Ralstonia) solanacearum PMID:7948901.
str246C/parA is therefore both auxin-inducible AND pathogen/defense-inducible —
classic behaviour of stress-responsive plant tau GSTs, which are induced by a wide
range of stimuli (auxin, herbicides, pathogens, oxidative stress, heavy metals).
A direct study of the parA protein itself found important departures from a typical
cytosolic GST PMID:7767232:
- Enzyme activity: "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 ... GST."
So parA has measurable but very weak GST activity relative to parB.
- Localization: "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." Confocal imaging of BY-2
cells showed "the parA product was confined to the nucleus, but was excluded
from the nucleolus."
- The authors note "exon/intron organization of the parA family was appreciably
different from that of conventional GSTs including parB" and that "the parA
protein is much more similar to a 24-kDa protein of Escherichia coli that is
reported to bind to RNA polymerase."
- Conclusion: "These different characteristics of parA compared with the
conventional GSTs indicate that parA protein would have distinct functions, such
as involvement in transcription, rather than functioning as a conventional GST."
Caveats: this is a single 1995 study; the "24-kDa E. coli RNA polymerase-binding
protein" comparison is weak by modern standards, and nuclear localization of an
overexpressed/tagged protein in protoplasts can be artefactual. UniProt nonetheless
retains "Probable glutathione S-transferase" (the name carries "Probable"), retains
EC 2.5.1.18 (a generic GST reaction RX + GSH), and assigns the "cytoplasm" CC term
by TreeGrafter family inference rather than experiment. The honest position: parA
has GST-family sequence/structure (tau class) and weak catalytic activity, but its
true physiological substrate and primary cellular role are not established. The
modern GOA molecular-function (glutathione transferase activity, IEA from
InterPro/RHEA/EC/PANTHER) and process (glutathione metabolic process) annotations
are family-level inferences that are reasonable but not experimentally proven for
parA specifically.
Plant GSTs (EC 2.5.1.18) are a large, plant-specific-rich superfamily; phi (F) and
tau (U) classes are plant-specific and most numerous PMID:11897031. They use GSH as cosubstrate/
coenzyme; functions include "conjugation and resulting detoxification of herbicides,
the reduction of organic hydroperoxides formed during oxidative stress and the
isomerization of maleylacetoacetate" plus non-catalytic ligandin roles "binding
flavonoid natural products in the cytosol prior to their deposition in the vacuole"
and roles "as components of ultraviolet-inducible cell signaling pathways"
PMID:11897031. "GSTs are predominantly expressed in the cytosol" PMID:11897031.
The tau/phi classes "are largely responsible for catalyzing glutathione-dependent
reactions with xenobiotics, notably conjugation leading to detoxification"; plant
GSTs use "a catalytic serine in place of a tyrosine residue" PMID:21425939.
Endogenous roles are "less well defined ... linked to a diverse range of functions,
including signaling, counteracting oxidative stress, and detoxifying and
transporting secondary metabolites" PMID:21425939.
Critical distinction for this review. The bona fide auxin signal-transduction
pathway (GO:0009734, "auxin-activated signaling pathway") consists of: auxin
perception by the TIR1/AFB F-box receptors, auxin-promoted degradation of Aux/IAA
repressors via the SCF^TIR1 ubiquitin ligase, and de-repression of ARF
transcription factors. parA/parB/parC are downstream auxin-responsive target
genes — their promoters contain auxin-responsive cis-elements and they are
transcriptionally induced when auxin signaling is active. A downstream
auxin-responsive metabolic enzyme is not a "component" of the signaling pathway.
The GO term that correctly captures "this gene is transcriptionally induced by
auxin" is "response to auxin" (GO:0009733), which is a parent that includes
auxin-responsive gene expression without implying signal-transduction-component
status. GO:0009734 (auxin-activated signaling pathway) is reserved for receptors/
Aux-IAA/ARF/SCF-TIR1 components.
The SPKW pipeline (GO_REF:0000043) generated GO:0009734 purely from the UniProt
keyword "Auxin signaling pathway", which UniProt had attached on the basis of the
historical name "Auxin-regulated protein". This is a textbook "expression ≠
function" / "downstream effector mislabeled as pathway component" over-annotation.