PGLP1 (2-phosphoglycolate phosphatase 1; UniProt name PGLP1A; At5g36700) is the chloroplast-stromal haloacid dehalogenase (HAD)-superfamily phosphatase that hydrolyses 2-phosphoglycolate to glycolate and phosphate (EC 3.1.3.18). 2-Phosphoglycolate is made in large amounts by the oxygenase reaction of Rubisco and inhibits Calvin-Benson cycle enzymes such as triose-phosphate isomerase and sedoheptulose-1,7-bisphosphatase, so PGLP1 catalyses the entry reaction of the photorespiratory C2 cycle that salvages this carbon back to 3-phosphoglycerate. The nuclear-encoded precursor carries an N-terminal chloroplast transit peptide that is removed on import. Knockout of PGLP1, like the classical EMS mutant CS119 (a splice-site allele of the same gene), abolishes almost all leaf phosphoglycolate phosphatase activity and is lethal in normal air but viable in CO2-enriched air. The close paralog PGLP2 (At5g47760) is an active, putatively cytosolic enzyme without a photorespiratory role. PGLP1 activity is inhibited by H2O2-dependent sulfenylation of Cys-86 under heat stress, and altered PGLP1 levels change plant thermotolerance through their effect on 2-phosphoglycolate levels.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | MODIFY | Summary: Phylogenetic inference that PGLP1 is active in the cytoplasm, propagated from a PANTHER node whose experimentally characterized members (yeast, E. coli, mammalian and Plasmodium HAD phosphatases, Arabidopsis At3g58830) are largely cytosolic. Reason: In GO the chloroplast is part of the cytoplasm, so the statement is not false, but it is far less specific than the evidence. PGLP1 is a nuclear-encoded precursor with a chloroplast transit peptide, is found in the stromal proteome, and acts on the 2-phosphoglycolate generated by Rubisco in the stroma; TAIR also records it as NOT cytosolic. The PAINT node's cytoplasmic placement fits the clade's soluble non-plastid members but not this plastid-targeted member. The correct specific location, already carried by PGLP1 from several HDA rows, is chloroplast stroma. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: COMPARTMENT OR COMPLEX MISMATCH GRANULARITY MISMATCH Sources checked: PANTHER:PTN002711682 Β· PTN002711682 SUPPORTS SOURCE BUT NOT TARGET Cytoplasm fits the soluble non-plastid members of this HAD-IIA phosphatase node; PGLP1 is transit-peptide targeted to the chloroplast stroma, which GO places within cytoplasm, so the transferred term is only true at a much coarser level. Proposed replacements: chloroplast stroma Supporting Evidence: PMID:17478634 The protein harbors a predicted 62-amino acid chloroplast-targeting peptide PMID:17478634 Most recently, protein At5g36700 has been detected in the chloroplast proteome ( Peltier et al., 2006 ), which fully supports our conclusion. PMID:38409783 its N-terminal chloroplast transit peptide is removed when the protein is transported into chloroplasts |
| GO:0005829 cytosol | RCA NOT PMID:21166475 Analysis of the Arabidopsis cytosolic proteome highlights su... | ACCEPT | Summary: NOT annotation: TAIR records that PGLP1 is not located in the cytosol, based on the Arabidopsis cytosolic proteome study, which separated true cytosolic proteins from organelle-targeted ones. Reason: The negative statement agrees with everything else known about PGLP1: it has a cleavable chloroplast transit peptide and acts in the stroma, where Rubisco makes its substrate. The photorespiratory paper names the paralog PGLP2, not PGLP1, as the putatively cytosolic phosphoglycolate phosphatase. The cached record for PMID:21166475 is abstract-only, so the gene-level reasoning of the curator cannot be checked, but it is consistent with the evidence. Supporting Evidence: PMID:21166475 defines an experimental set of plant protein sequences that are not targeted to subcellular locations following translation and folding in the cytosol PMID:17478634 It encodes a putatively cytosolic enzyme, AtPGLP2, which shows PGLP activity. |
| GO:0008150 biological_process | ND GO_REF:0000015 | MODIFY | Summary: Root-term placeholder stating that no biological process data were available when the annotation was made. Reason: Out of date. Knockout and point-mutant data establish PGLP1 as the enzyme that catalyses the first step of the photorespiratory C2 cycle, and GOA has no photorespiration row for P0DKC3. PGLP1 itself performs this step of the process (it dephosphorylates 2-phosphoglycolate), so it meets the participation test, and the comparator enzymes of the same pathway (GLYK, PLGG1) carry photorespiration. Proposed replacements: photorespiration Supporting Evidence: PMID:17478634 The chloroplastidal enzyme 2-phosphoglycolate phosphatase (PGLP), PGLP1, catalyzes the first reaction of the photorespiratory C 2 cycle, a major pathway of plant primary metabolism. PMID:17478634 These combined data establish At5g36700 as the gene encoding the photorespiratory PGLP, PGLP1. PMID:22303256 Thus, At5g36700 encodes the photorespiratory PGLP in Arabidopsis. |
| GO:0008967 phosphoglycolate phosphatase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic annotation from the UniProt catalytic activity (Rhea:14369, EC 3.1.3.18), which is itself backed by experimental evidence from PMID:17478634. Reason: The EC/Rhea mapping is correct and matches the experimentally demonstrated activity of recombinant PGLP1 and the loss of leaf activity in the knockout. Core molecular function. Supporting Evidence: PMID:17478634 Both semipurified proteins showed PGLP activity, 420 ΞΌ mol min β1 mg β1 for PGPL1 and 690 ΞΌ mol min β1 mg β1 for PGPL2. |
| GO:0008967 phosphoglycolate phosphatase activity | IMP PMID:17478634 Identification of the photorespiratory 2-phosphoglycolate ph... | ACCEPT | Summary: T-DNA knockout of At5g36700 reduces leaf phosphoglycolate phosphatase activity by 97%, and the recombinant mature protein (and a G260S variant) is active in vitro. Reason: Directly supported by the cited paper, which combines loss of leaf activity in the knockout with activity of the recombinant protein. This is the core molecular function of PGLP1. Supporting Evidence: PMID:17478634 Enzyme measurements with protein extracts from mutant plants grown under 0.9% CO 2 revealed a 97% reduction of leaf PGLP activity in Atpglp1-1 plants PMID:17478634 Both semipurified proteins showed PGLP activity, 420 ΞΌ mol min β1 mg β1 for PGPL1 and 690 ΞΌ mol min β1 mg β1 for PGPL2. |
| GO:0009507 chloroplast | HDA PMID:18431481 Sorting signals, N-terminal modifications and abundance of t... | ACCEPT | Summary: Detected in a large-scale MS analysis of purified Arabidopsis chloroplasts. Reason: Consistent with the transit peptide (mapped by proteomics) and with the stromal location of the photorespiratory entry step. Chloroplast stroma is the more precise compartment, but a chloroplast assignment from an organelle proteome is still informative and correct. Supporting Evidence: PMID:18431481 we present a large scale analysis by nanoLC-Q-TOF and nanoLC-LTQ-Orbitrap mass spectrometry (MS) of ten independent chloroplast preparations from Arabidopsis thaliana which unambiguously identified 1325 proteins PMID:17478634 The protein harbors a predicted 62-amino acid chloroplast-targeting peptide |
| GO:0009507 chloroplast | HDA PMID:25293756 A proteomic strategy for global analysis of plant protein co... | ACCEPT | Summary: Chloroplast assignment from a leaf protein-complex profiling study that fractionated Arabidopsis leaf extracts by size-exclusion chromatography. Reason: The gene-level assignment is in supplementary data not in the cached text, but the chloroplast location is independently established for PGLP1 (transit peptide, chloroplast and stromal proteomes), so the annotation is correct. Supporting Evidence: PMID:17478634 Most recently, protein At5g36700 has been detected in the chloroplast proteome ( Peltier et al., 2006 ), which fully supports our conclusion. |
| GO:0009507 chloroplast | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping (Plastid, chloroplast). Reason: Correct; supported by the transit peptide and organelle proteomics. Supporting Evidence: PMID:17478634 The protein harbors a predicted 62-amino acid chloroplast-targeting peptide |
| GO:0009507 chloroplast | ISM GO_REF:0000122 | ACCEPT | Summary: AtSubP sequence-based prediction of chloroplast location. Reason: The prediction agrees with the experimentally supported chloroplast location. Supporting Evidence: PMID:17478634 Two of these proteins, At5g36700 and At5g36790, harbor predicted chloroplast-targeting sequences. |
| GO:0009536 plastid | HDA PMID:28887381 Global Analysis of Membrane-associated Protein Oligomerizati... | ACCEPT | Summary: Plastid assignment from a large-scale size-exclusion profiling study of membrane-associated and soluble leaf proteins. Reason: True and consistent with the chloroplast stroma location; plastid is broad, but as a proteomic-screen assignment it still conveys the correct organelle. The precise compartment is captured by the chloroplast stroma rows. Supporting Evidence: PMID:28887381 Our method identified proteins from all of the major organelles, with more than 50% of them predicted to be part of a stable complex. PMID:17478634 The protein harbors a predicted 62-amino acid chloroplast-targeting peptide |
| GO:0009570 chloroplast stroma | HDA PMID:16207701 The oligomeric stromal proteome of Arabidopsis thaliana chlo... | ACCEPT | Summary: Identified in the oligomeric stromal proteome of purified Arabidopsis chloroplasts (Peltier et al. 2006). Reason: Stroma is where Rubisco produces 2-phosphoglycolate and where PGLP1 acts; this is the core location. The PGLP1 discovery paper cites this proteome as confirming the chloroplast location of At5g36700. Supporting Evidence: PMID:16207701 This study presents an analysis of the stromal proteome in its oligomeric state extracted from highly purified chloroplasts of Arabidopsis thaliana. PMID:17478634 Most recently, protein At5g36700 has been detected in the chloroplast proteome ( Peltier et al., 2006 ), which fully supports our conclusion. |
| GO:0009570 chloroplast stroma | HDA PMID:18633119 Quantitative proteomics of a chloroplast SRP54 sorting mutan... | ACCEPT | Summary: Detected in quantitative chloroplast proteomics of a cpSRP54 mutant and wild type. Reason: Consistent with the other stromal proteome data and with the function. Core location. Supporting Evidence: PMID:16207701 This study presents an analysis of the stromal proteome in its oligomeric state extracted from highly purified chloroplasts of Arabidopsis thaliana. |
| GO:0009570 chloroplast stroma | HDA PMID:20061580 AT_CHLORO, a comprehensive chloroplast proteome database wit... | ACCEPT | Summary: Subplastidial assignment to the stroma in the AT_CHLORO database, based on spectral counts in stroma, thylakoid and envelope fractions. Reason: Subfractionation proteomics agrees with the stromal location expected for the soluble photorespiratory entry enzyme. Core location. Supporting Evidence: PMID:20061580 We assessed the partitioning of each protein in the three chloroplast compartments by using a semiquantitative proteomics approach (spectral count). |
| GO:0016791 phosphatase activity | IBA GO_REF:0000033 | MODIFY | Summary: Phylogenetic inference of generic phosphatase activity for the HAD-IIA phosphatase clade (PANTHER node PTN002711682); At5g36700 itself is one of the experimentally characterized members used for the node. Reason: Correct but general. The node spans phosphatases with different substrates, so the IBA is placed at the generic level, but for PGLP1 the specific substrate is established experimentally: it is a 2-phosphoglycolate phosphatase. The specific term is already carried by PGLP1 (IMP, IEA). Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN002711682 Β· PTN002711682 SUPPORTS TRANSFER Generic phosphatase activity is correctly inherited across this HAD-IIA node, whose members differ in substrate; At5g36700 is itself one of the experimental members, and its specific activity is 2-phosphoglycolate hydrolysis. Proposed replacements: phosphoglycolate phosphatase activity Supporting Evidence: PMID:17478634 Both semipurified proteins showed PGLP activity, 420 ΞΌ mol min β1 mg β1 for PGPL1 and 690 ΞΌ mol min β1 mg β1 for PGPL2. |
| GO:0016791 phosphatase activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping from IPR006349 (2-phosphoglycolate phosphatase, eukaryotic) to generic phosphatase activity. Reason: Correct but general; the experimentally supported activity is phosphoglycolate phosphatase activity, which PGLP1 already carries. Proposed replacements: phosphoglycolate phosphatase activity Supporting Evidence: PMID:17478634 T-DNA knockout of one of these genes, At5g36700, results in very low leaf PGLP activity. |
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Download this section (compressed HTML)Q: Are At5g36700 (PGLP1A, P0DKC3) and At5g36790 (PGLP1B, P0DKC4) two real loci or a genome double annotation of one gene? The PGLP1 paper reports a double annotation in this region, and the answer decides whether annotations should be split between two accessions.
Q: Does PGLP1 activity in planta depend on chloride and Mg2+ as reported for the purified spinach and tobacco enzymes, and is the stromal enzyme regulated by ribose-5-phosphate as reported for algal and spinach PGLPs?
Experiment: Determine the crystal structure of mature Arabidopsis PGLP1 with 2-phosphoglycolate and Cl-/Mg2+ to define the substrate specificity determinants that distinguish it from the broader HAD-IIA phosphatase clade.
Type: structural biology
Experiment: Express a Cys86Ser PGLP1 variant in the pglp1 background and test growth, 2-phosphoglycolate levels and photosynthesis under heat and fluctuating light, to separate redox regulation of PGLP1 from its catalytic role.
Type: genetic complementation
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