Superoxide dismutase [Cu-Zn] 2, chloroplastic (CSD2, AT2G28190) is the plastid-localized copper/zinc superoxide dismutase in Arabidopsis thaliana. Synthesized with a 62-residue N-terminal chloroplast transit peptide, mature CSD2 functions in the chloroplast stroma (with peripheral association reported at the stromal surface of thylakoid membranes) as part of the water-water (Mehler-peroxidase) cycle, catalyzing the disproportionation of photochemically generated superoxide radicals into molecular oxygen and hydrogen peroxide. Plastidic CSD2 activation depends on copper import across the chloroplast envelope and thylakoid membranes by the P-type ATPases PAA1 and PAA2, while CSD2 mRNA abundance is post-transcriptionally controlled by miR398-guided cleavage in response to copper availability, sucrose, and oxidative stress.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004784 superoxide dismutase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Core enzymatic activity of CSD2 catalyzing the dismutation of superoxide radicals into hydrogen peroxide and molecular oxygen. Reason: Supported by phylogenetic conservation across eukaryotic Cu/Zn superoxide dismutases (PTN000000113) and direct biochemical characterization in Arabidopsis chloroplasts (PMID:9765550; PMID:15772282). Supporting Evidence: uniprot:O78310 Reaction=2 superoxide + 2 H(+) = H2O2 + O2; Xref=Rhea:RHEA:20696, |
| GO:0004784 superoxide dismutase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Core superoxide dismutase activity of CSD2. Reason: Consistent with the accepted IBA and IDA annotations for GO:0004784. Supporting Evidence: uniprot:O78310 Reaction=2 superoxide + 2 H(+) = H2O2 + O2; Xref=Rhea:RHEA:20696, |
| GO:0004784 superoxide dismutase activity | IDA PMID:9765550 Superoxide dismutase in Arabidopsis: an eclectic enzyme fami... | ACCEPT | Summary: Direct biochemical assay of chloroplastic Cu/Zn superoxide dismutase activity encoded by CSD2. Reason: Kliebenstein et al. (1998, PMID:9765550) demonstrated CSD2 enzymatic activity and chloroplastic localization using native PAGE SOD activity assays and CSD2-specific antibodies. Supporting Evidence: PMID:9765550 Using these antisera and nondenaturing-polyacrylamide gel electrophoresis enzyme assays, we identified protein and activity for two CuZnSODs and for FeSOD and MnSOD in Arabidopsis rosette tissue. |
| GO:0019430 removal of superoxide radicals | IBA GO_REF:0000033 | ACCEPT | Summary: Core biological process of scavenging superoxide radicals in the chloroplast. Reason: Directly entailed by CSD2's superoxide dismutase activity in the chloroplast water-water cycle (PMID:9765550; PMID:15772282; PMID:16861386). Supporting Evidence: PMID:16861386 Superoxide dismutases (SODs) constitute the first line of defense against highly toxic superoxide radicals by rapidly converting superoxide to hydrogen peroxide (H 2 O 2 ) and molecular oxygen |
| GO:0019430 removal of superoxide radicals | IC PMID:9765550 Superoxide dismutase in Arabidopsis: an eclectic enzyme fami... | ACCEPT | Summary: Curator inference from superoxide dismutase activity (GO:0004784) to removal of superoxide radicals. Reason: Consistent with the accepted IBA annotation for GO:0019430. Supporting Evidence: PMID:9765550 A number of environmental stresses can lead to enhanced production of superoxide within plant tissues, and plants are believed to rely on the enzyme superoxide dismutase (SOD) to detoxify this reactive oxygen species. |
| GO:0005507 copper ion binding | IBA GO_REF:0000033 | ACCEPT | Summary: CSD2 binds a catalytic copper ion per subunit at His108, His110, His125, and His182. Reason: Conserved catalytic cofactor binding site of Cu/Zn superoxide dismutases (InterPro IPR024134) and experimentally demonstrated requirement for PAA1/PAA2-mediated plastid copper delivery (PMID:15772282). Supporting Evidence: uniprot:O78310 Name=Cu cation; Xref=ChEBI:CHEBI:23378; Evidence={ECO:0000250}; |
| GO:0005507 copper ion binding | IEA GO_REF:0000002 | ACCEPT | Summary: CSD2 binds a catalytic copper ion. Reason: Consistent with the accepted IBA annotation for GO:0005507. Supporting Evidence: uniprot:O78310 Name=Cu cation; Xref=ChEBI:CHEBI:23378; Evidence={ECO:0000250}; |
| GO:0006801 superoxide metabolic process | IEA GO_REF:0000002 | MODIFY | Summary: Broad InterPro2GO mapping for Cu/Zn superoxide dismutase domain (IPR001424). Reason: GO:0006801 (superoxide metabolic process) is less specific than GO:0019430 (removal of superoxide radicals), which CSD2 already carries via IBA and IC. Proposed replacements: removal of superoxide radicals Supporting Evidence: PMID:16861386 Superoxide dismutases (SODs) constitute the first line of defense against highly toxic superoxide radicals by rapidly converting superoxide to hydrogen peroxide (H 2 O 2 ) and molecular oxygen |
| GO:0009507 chloroplast | IEA GO_REF:0000120 | ACCEPT | Summary: Plastid/chloroplast localization of CSD2. Reason: Consistent with the experimental IDA and HDA annotations confirming chloroplast localization of CSD2 (PMID:9765550; PMID:18431481; PMID:25293756). Supporting Evidence: uniprot:O78310 SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000269|PubMed:18431481, ECO:0000269|PubMed:9765550}. |
| GO:0009507 chloroplast | HDA PMID:18431481 Sorting signals, N-terminal modifications and abundance of t... | ACCEPT | Summary: Chloroplast proteome analysis confirming plastid localization and N-terminal transit peptide processing of CSD2. Reason: Zybailov et al. (2008, PMID:18431481) identified mature CSD2 in purified Arabidopsis chloroplasts. Supporting Evidence: uniprot:O78310 SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000269|PubMed:18431481, ECO:0000269|PubMed:9765550}. |
| GO:0009507 chloroplast | IDA PMID:9765550 Superoxide dismutase in Arabidopsis: an eclectic enzyme fami... | ACCEPT | Summary: Subcellular fractionation and immunoblot confirmation of CSD2 in Arabidopsis chloroplasts. Reason: Kliebenstein et al. (1998, PMID:9765550) directly demonstrated CSD2 localization in isolated intact chloroplasts. Supporting Evidence: PMID:9765550 Additionally, subcellular fractionation studies revealed the presence of CSD2 and FeSOD protein within Arabidopsis chloroplasts. |
| GO:0009507 chloroplast | HDA PMID:25293756 A proteomic strategy for global analysis of plant protein co... | ACCEPT | Summary: High-throughput proteomic identification of CSD2 in chloroplast protein fractions. Reason: Consistent with the accepted IDA and HDA annotations for GO:0009507. Supporting Evidence: PMID:9765550 Additionally, subcellular fractionation studies revealed the presence of CSD2 and FeSOD protein within Arabidopsis chloroplasts. |
| GO:0009507 chloroplast | ISM GO_REF:0000122 | ACCEPT | Summary: Sequence-based prediction of chloroplast localization via N-terminal transit peptide. Reason: Consistent with the accepted IDA and HDA annotations for GO:0009507. Supporting Evidence: uniprot:O78310 SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000269|PubMed:18431481, ECO:0000269|PubMed:9765550}. |
| GO:0046872 metal ion binding | IEA GO_REF:0000002 | MODIFY | Summary: Broad InterPro2GO mapping for metal ion binding. Reason: GO:0046872 (metal ion binding) is too general; CSD2 specifically binds one catalytic copper ion (GO:0005507, already present) and one structural zinc ion (GO:0008270) per subunit. Proposed replacements: copper ion binding zinc ion binding Supporting Evidence: uniprot:O78310 Note=Binds 1 copper ion per subunit. {ECO:0000250}; uniprot:O78310 Note=Binds 1 zinc ion per subunit. {ECO:0000250}; |
| GO:0009651 response to salt stress | IEP PMID:34260941 EGY3 mediates chloroplastic ROS homeostasis and promotes ret... | MODIFY | Summary: CSD2 stability and chloroplastic superoxide scavenging are promoted by EGY3 in response to salt stress. Reason: GO:0009651 (response to salt stress) is less specific than GO:0071472 (cellular response to salt stress), which CSD2 already carries. Proposed replacements: cellular response to salt stress Supporting Evidence: PMID:34260941 EGY3 interacts with chloroplastic Cu/Zn-SOD2 (CSD2) and promotes CSD2 stability under stress conditions. |
| GO:0048046 apoplast | HDA PMID:18538804 Hydroponic isotope labelling of entire plants (HILEP) for qu... | REMOVE | Summary: High-throughput proteomic detection of CSD2 in apoplastic wash fluid. Reason: CSD2 possesses a canonical 62-residue N-terminal chloroplast transit peptide (uniprot:O78310), lacks a secretory signal peptide, and is imported into the chloroplast stroma (PMID:9765550; PMID:15772282; PMID:18431481). Unlike peripheral association with thylakoid membranes inside the plastid (GO:0009579), a plastid-imported stromal protein has no secretory route across the chloroplast envelope and plasma membrane into the extracellular apoplast; detection in whole-leaf apoplastic wash fluid reflects plastid lysis contamination. Supporting Evidence: PMID:15772282 CSD1 encodes a Cu/ZnSOD active in the cytosol, and CSD2 encodes a Cu/ZnSOD active in the chloroplast stroma. |
| GO:0009579 thylakoid | HDA PMID:16648217 High light response of the thylakoid proteome in arabidopsis... | KEEP AS NON CORE | Summary: Proteomic identification of CSD2 in the peripheral thylakoid proteome released from purified thylakoid membranes. Reason: Giacomelli et al. (2006, PMID:16648217) identified Cu,Zn-SOD (spot 390) in the peripheral/lumenal thylakoid proteome released by mild sonication of Percoll-purified thylakoids. While CSD2's primary compartment is the chloroplast stroma (GO:0009570), peripheral association with the stromal face of thylakoid membranes near Photosystem I (where superoxide is photoproduced in the water-water cycle) is biologically plausible within the plastid, unlike the extracellular apoplast HDA artifact (GO:0048046). Supporting Evidence: PMID:16648217 The soluble thylakoid proteome (lumen and peripherally attached proteins) were released by mild sonication (three times for 20 s at 10 W) with a Fisher Scientific membrane dismembrator (model 100) from a 3 mL thylakoid suspension at 1 mg chlorophyll mL β1 . PMID:16648217 Spot 390 contained Cu,Zn SOD that was consistently more abundant in vtc2 . |
| GO:0009570 chloroplast stroma | HDA PMID:18633119 Quantitative proteomics of a chloroplast SRP54 sorting mutan... | ACCEPT | Summary: Subplastidial proteomic identification of CSD2 in the chloroplast stroma. Reason: CSD2 is the major stromal Cu/ZnSOD in Arabidopsis chloroplasts (PMID:15772282; PMID:18633119; PMID:20061580). Supporting Evidence: PMID:15772282 CSD1 encodes a Cu/ZnSOD active in the cytosol, and CSD2 encodes a Cu/ZnSOD active in the chloroplast stroma. |
| GO:0009570 chloroplast stroma | HDA PMID:20061580 AT_CHLORO, a comprehensive chloroplast proteome database wit... | ACCEPT | Summary: Subplastidial AT_CHLORO proteome assignment of CSD2 to the chloroplast stroma. Reason: Consistent with the HDA annotation from PMID:18633119 and biochemical studies (PMID:15772282) showing CSD2 in the chloroplast stroma. Supporting Evidence: PMID:20061580 We went a step further into the knowledge of the chloroplast proteome by focusing, in the same set of experiments, on the localization of proteins in the stroma, the thylakoids, and envelope membranes. |
| GO:0034599 cellular response to oxidative stress | IEP PMID:16861386 Posttranscriptional induction of two Cu/Zn superoxide dismut... | ACCEPT | Summary: Post-transcriptional induction of CSD2 via downregulation of miR398 protects chloroplast membranes and photosynthetic apparatus during oxidative stress. Reason: Sunkar et al. (2006, PMID:16861386) showed that relief of miR398-mediated repression of CSD2 is essential for cellular oxidative stress tolerance in Arabidopsis. Supporting Evidence: PMID:16861386 Here, we show that miR398 expression is downregulated transcriptionally by oxidative stresses, and this downregulation is important for posttranscriptional CSD1 and CSD2 mRNA accumulation and oxidative stress tolerance. |
| GO:0035195 miRNA-mediated post-transcriptional gene silencing | IEP PMID:16861386 Posttranscriptional induction of two Cu/Zn superoxide dismut... | REMOVE | Summary: Mis-annotation of an mRNA target substrate (CSD2) to the miRNA-mediated post-transcriptional gene silencing pathway. Reason: A gene product is involved_in a biological process only if it performs part of the work of that process. Sunkar et al. (2006, PMID:16861386) showed that CSD2 mRNA is cleaved as a target substrate of miR398-loaded RISC; the chloroplastic CSD2 superoxide dismutase enzyme plays no role in executing miRNA-mediated gene silencing. Most comparator miRNA targets in Arabidopsis (e.g., SPLs, ARFs, AP2, APS1, LAC4) are not annotated to GO:0035195, and the two other TAIR protein-coding targets carrying GO:0035195 (CSD1 and PXMT1/AT1G66700) reflect the same substrate-vs-actor curation error. Supporting Evidence: PMID:16861386 After 2 d of coexpression with miR398, CSD1 and CSD2 mRNA decreased substantially, which demonstrated that the miR398 can direct the degradation of CSD1 and CSD2 mRNAs in vivo file:projects/THLAR_OILSEED/mirna_targets/goa_tair_mirna_annotations.tsv tair.gaf.gz AGI_LocusCode AT2G28190 CSD2 involved_in GO:0035195 PMID:16861386 IEP P Superoxide dismutase [Cu-Zn] 2, chloroplastic protein |
| GO:0071329 cellular response to sucrose stimulus | IEP PMID:18392778 Sucrose induction of Arabidopsis miR398 represses two Cu/Zn ... | KEEP AS NON CORE | Summary: Sucrose induces miR398 expression, post-transcriptionally decreasing CSD2 mRNA and protein abundance. Reason: Supported by Dugas & Bartel (2008, PMID:18392778); represents an upstream metabolic regulatory response rather than CSD2's core enzymatic activity. Supporting Evidence: PMID:18392778 Here we show that miR398 is positively regulated by sucrose, resulting in decreased CSD1 and CSD2 mRNA and protein accumulation. |
| GO:0071457 cellular response to ozone | IEP PMID:9765550 Superoxide dismutase in Arabidopsis: an eclectic enzyme fami... | KEEP AS NON CORE | Summary: CSD2 mRNA transiently decreases during acute ozone fumigation while CSD2 protein increases at 48-72 h post-fumigation. Reason: Supported by Kliebenstein et al. (1998, PMID:9765550); non-core environmental stress context. Supporting Evidence: PMID:9765550 Ozone fumigation caused a transient decrease in the accumulation of the CSD2 and FSD1 mRNAs, although no reproducible effect was seen on the FSD2 mRNA. |
| GO:0071472 cellular response to salt stress | IEP PMID:18275461 Long-term effects of mild salt stress on growth, ion accumul... | KEEP AS NON CORE | Summary: CSD2 transcript abundance is modulated in response to salt stress in Arabidopsis leaves. Reason: Supported by Attia et al. (2008, PMID:18275461); non-core environmental stress response. Supporting Evidence: PMID:18275461 In both accessions, the expression of CSD2 and CSD3 was lowered by salt. |
| GO:0071484 cellular response to light intensity | IEP PMID:9765550 Superoxide dismutase in Arabidopsis: an eclectic enzyme fami... | KEEP AS NON CORE | Summary: CSD2 steady-state mRNA levels increase between 60 and 125 umol m-2 s-1 PAR and gradually increase after a high-light pulse, although CSD2 protein levels remain stable across fluences in that assay. Reason: Supported by Kliebenstein et al. (1998, PMID:9765550) and Sunkar et al. (2006, PMID:16861386); represents a specific environmental stimulus context. Supporting Evidence: PMID:9765550 As shown in Figure 8 A, CSD1 and CSD2 mRNA steady-state levels increased between 60 and 125 ΞΌmol m β2 s β1 PAR, but no further increases were observed at higher fluences. |
| GO:0071493 cellular response to UV-B | IEP PMID:9765550 Superoxide dismutase in Arabidopsis: an eclectic enzyme fami... | KEEP AS NON CORE | Summary: CSD2 protein accumulation transiently decreases on days 1 and 2 of acute UV-B exposure before recovering to control levels by day 3, while CSD2 mRNA levels remain unchanged. Reason: Kliebenstein et al. (1998, PMID:9765550) reported no significant change in CSD2 mRNA under UV-B treatment (causing the IEP evidence code to be imprecise for a protein-level change), but documented a transient decrease in CSD2 protein on days 1 and 2 of UV-B exposure; retained as a non-core environmental stimulus response. Supporting Evidence: PMID:9765550 CSD2 showed the opposite response, with decreased protein accumulation on d 1 and 2 in response to the UV-B treatment. Protein levels recovered to control levels by d 3 (Fig. 11 B). |
| GO:0010039 response to iron ion | IEP PMID:16861386 Posttranscriptional induction of two Cu/Zn superoxide dismut... | KEEP AS NON CORE | Summary: Excess iron induces oxidative stress, downregulating miR398 and increasing CSD2 mRNA accumulation. Reason: Supported by Sunkar et al. (2006, PMID:16861386); non-core metal-stress response. Supporting Evidence: PMID:16861386 Here, we show that miR398 expression is downregulated transcriptionally by oxidative stresses, and this downregulation is important for posttranscriptional CSD1 and CSD2 mRNA accumulation and oxidative stress tolerance. |
| GO:0006979 response to oxidative stress | IDA PMID:15772282 Two P-type ATPases are required for copper delivery in Arabi... | MODIFY | Summary: CSD2 protects chloroplasts from oxidative stress in a copper-dependent manner. Reason: GO:0006979 (response to oxidative stress) is less specific than GO:0034599 (cellular response to oxidative stress), which CSD2 already carries. Proposed replacements: cellular response to oxidative stress Supporting Evidence: PMID:15772282 CSD1 encodes a Cu/ZnSOD active in the cytosol, and CSD2 encodes a Cu/ZnSOD active in the chloroplast stroma. |
| GO:0046688 response to copper ion | IEP PMID:15772282 Two P-type ATPases are required for copper delivery in Arabi... | KEEP AS NON CORE | Summary: CSD2 transcript and holoenzyme levels are regulated by copper supply. Reason: Abdel-Ghany et al. (2005, PMID:15772282) demonstrated that CSD2 mRNA, protein, and enzyme activity increase with exogenous copper supply and depend on plastidic copper transport by PAA1. Supporting Evidence: PMID:15772282 As with CSD1, the increase in CSD2 activity in response to Cu can be ascribed to an increase in gene expression, as increased CSD2 protein and mRNA levels were observed with increased Cu ( Figures 9B and 9C ). |
| GO:0009416 response to light stimulus | IEP PMID:9765550 Superoxide dismutase in Arabidopsis: an eclectic enzyme fami... | MODIFY | Summary: CSD2 mRNA increases in response to growth light fluence. Reason: GO:0009416 (response to light stimulus) is less specific than GO:0071484 (cellular response to light intensity), which CSD2 already carries from the same study (PMID:9765550). Proposed replacements: cellular response to light intensity Supporting Evidence: PMID:9765550 As shown in Figure 8 A, CSD1 and CSD2 mRNA steady-state levels increased between 60 and 125 ΞΌmol m β2 s β1 PAR, but no further increases were observed at higher fluences. |
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Download this section (compressed HTML)Q: What molecular mechanism governs the partitioning of mature CSD2 between the soluble chloroplast stroma and the stromal surface of thylakoid membranes near Photosystem I under high-light stress?
Experiment: Quantify the ratio of thylakoid-associated to soluble stromal CSD2 protein and specific activity across a light-intensity gradient in wild-type, paa2, and ccs mutants using rapid subplastidial fractionation.
Hypothesis: High-light-driven electron transport promotes transient electrostatic recruitment of holo-CSD2 to the stromal face of PSI-enriched thylakoid membranes where superoxide is generated.
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