SIR (At5g04590) is the plastid siroheme/[4Fe-4S] sulfite reductase that converts sulfite to sulfide for assimilatory sulfur metabolism. Reducing its activity limits sulfur flux and growth, while altered expression also changes resistance to excess sulfite. The enzyme is assigned to the ferredoxin-dependent class and is predominantly stromal. Unlike pea and bean sulfite reductases, native Arabidopsis SIR lacks preferential chloroplast-nucleoid localization in the tested imaging experiments.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000103 sulfate assimilation | IBA GO_REF:0000033 | ACCEPT | Summary: SIR catalyzes the sulfite-to-sulfide step of sulfate assimilation. Reason: Native reduction of SIR activity strongly reduces sulfur flux into cysteine, glutathione and protein; the enzyme itself performs the reduction step. Supporting Evidence: PMID:23221833 Plant sulfite reductase (SiR; Enzyme Commission 1.8.7.1) catalyzes the reduction of sulfite to sulfide in the reductive sulfate assimilation pathway. PMID:20424176 The 28-fold decrease of incorporation of (35)S label into Cys, glutathione, and protein in sir1-1 showed that the decreased activity of SiR generated a severe bottleneck in the assimilatory sulfate reduction pathway. |
| GO:0003677 DNA binding | ISS GO_REF:0000024 | MARK AS OVER ANNOTATED | Summary: DNA binding is a demonstrated property of pea and maize sulfite reductases, but its transfer to Arabidopsis SIR over-annotates a nucleoid-compaction role that AtSiR does not show in vivo. Reason: The ISS rows transfer DNA binding from the pea (O23813) and maize (Q9AWB2) enzymes. Maize SiR binds DNA in vitro even though it is not preferentially nucleoid-localized, so some DNA affinity may be a conserved property of plant sulfite reductases and the term is not judged false. In pea, DNA binding underlies nucleoid compaction, and nucleoid-type SiRs carry a C-terminal peptide predicted to form a ribbon-helix-helix DNA-binding motif that the non-nucleoid land-plant SiRs, including AtSiR, lack. AtSiR-YFP is mainly stromal and not nucleoid-associated, and no DNA-binding assay has been reported for the Arabidopsis protein. DNA binding is therefore an untested, peripheral transfer for this gene, not part of its sulfite-reductase function. The residual question is recorded as a knowledge gap with a proposed direct assay. Supporting Evidence: PMID:27189994 The DAPI staining of isolated cps showed that AtSiR-YFP is not preferentially colocalized with cp nucleoids, indicating that AtSiR is mainly localized to the stroma PMID:17371503 ZmSiR does indeed have DNA-binding activity |
| GO:0003677 DNA binding | ISS GO_REF:0000024 | MARK AS OVER ANNOTATED | Summary: DNA binding is a demonstrated property of pea and maize sulfite reductases, but its transfer to Arabidopsis SIR over-annotates a nucleoid-compaction role that AtSiR does not show in vivo. Reason: The ISS rows transfer DNA binding from the pea (O23813) and maize (Q9AWB2) enzymes. Maize SiR binds DNA in vitro even though it is not preferentially nucleoid-localized, so some DNA affinity may be a conserved property of plant sulfite reductases and the term is not judged false. In pea, DNA binding underlies nucleoid compaction, and nucleoid-type SiRs carry a C-terminal peptide predicted to form a ribbon-helix-helix DNA-binding motif that the non-nucleoid land-plant SiRs, including AtSiR, lack. AtSiR-YFP is mainly stromal and not nucleoid-associated, and no DNA-binding assay has been reported for the Arabidopsis protein. DNA binding is therefore an untested, peripheral transfer for this gene, not part of its sulfite-reductase function. The residual question is recorded as a knowledge gap with a proposed direct assay. Supporting Evidence: PMID:27189994 The DAPI staining of isolated cps showed that AtSiR-YFP is not preferentially colocalized with cp nucleoids, indicating that AtSiR is mainly localized to the stroma PMID:17371503 ZmSiR does indeed have DNA-binding activity |
| GO:0005507 copper ion binding | HDA PMID:20018591 Divalent metal ions in plant mitochondria and their role in ... | MARK AS OVER ANNOTATED | Summary: Retention on Cu2+-IMAC resin in a mitochondrial metal-affinity proteomic screen; not a physiological copper-binding function of a siroheme/[4Fe-4S] enzyme. Reason: PMID:20018591 captured proteins from Arabidopsis mitochondrial extracts on immobilized-metal affinity resin. The curator's identification of SIR in that screen is not disputed, but retention on Cu2+-IMAC reflects surface histidine or cysteine affinity for an immobilized ion, not a copper cofactor or a copper-dependent activity. The authors themselves treat IMAC binding as an in vitro proxy for susceptibility to metal-induced damage. SIR's cofactors are siroheme and a [4Fe-4S] cluster. The same judgement is applied to the other proteins annotated from this screen in sibling reviews (mtLPD1, mtLPD2, CAT2). Supporting Evidence: file:ARATH/SIR/SIR-uniprot.txt Note=Binds 1 siroheme per subunit. file:ARATH/SIR/SIR-uniprot.txt Note=Binds 1 [4Fe-4S] cluster per subunit. PMID:20018591 The interaction of metal ions with mitochondrial proteins that might be responsible for these toxic effects was investigated in vitro using IMAC to trap metal-binding proteins. |
| GO:0005737 cytoplasm | ISM GO_REF:0000122 | MODIFY | Summary: Refine the general cellular location to chloroplast stroma. Reason: Independent target imaging demonstrates diffuse stromal SIR. The broad cytoplasm/plastid/chloroplast term is correct but the existing chloroplast-stroma term is more precise. Proposed replacements: chloroplast stroma Supporting Evidence: PMID:27189994 The DAPI staining of isolated cps showed that AtSiR-YFP is not preferentially colocalized with cp nucleoids, indicating that AtSiR is mainly localized to the stroma |
| GO:0005829 cytosol | RCA NOT PMID:21166475 Analysis of the Arabidopsis cytosolic proteome highlights su... | ACCEPT | Summary: SIR is a plastid-stromal enzyme and not a cytosolic protein; the NOT-cytosol assertion is consistent with all target-specific localization evidence. Reason: The curator assigned NOT cytosol from the Arabidopsis cytosolic-proteome study (PMID:21166475), whose purpose was to define proteins that are not targeted to organelles. Every independent target-specific observation places SIR in the plastid. Full-length AtSiR-YFP is mainly stromal in stable lines (PMID:27189994), and SIR is detected in the chloroplast stroma proteome (UniProt, PMID:18431481). No study reports a cytosolic SIR isoform or alternative translation start; the single gene encodes a transit-peptide-bearing precursor. The negative claim is accepted, consistent with the NOT-cytosol rows for other plastid enzymes from this study in sibling reviews (GLO1, GGAT1, PGLP1). Fluorescence imaging cannot exclude a trace cytosolic pool, but no evidence for one exists. Supporting Evidence: PMID:27189994 The DAPI staining of isolated cps showed that AtSiR-YFP is not preferentially colocalized with cp nucleoids, indicating that AtSiR is mainly localized to the stroma PMID:21166475 defines an experimental set of plant protein sequences that are not targeted to subcellular locations following translation and folding file:ARATH/SIR/SIR-uniprot.txt Plastid, chloroplast stroma {ECO:0000269|PubMed:18431481}. |
| GO:0005886 plasma membrane | HDA PMID:28887381 Global Analysis of Membrane-associated Protein Oligomerizati... | MARK AS OVER ANNOTATED | Summary: Microsomal profiling does not establish a plasma-membrane location for SIR. Reason: Full PMID:28887381 and its deposited supplemental tables were inspected. SIR appears in Table S1 Mapp row 1215 as AT5G04590.1, with SUBAcon localization plastid and blank True membrane and Dual Localized flags; it was not found in their predicted membrane-complex/dual-localized lists. The broad microsomal proteome includes organellar and soluble proteins. This detection does not warrant the specific plasma-membrane term, and does not prove absolute absence of every membrane-associated SIR pool. Supporting Evidence: PMID:28887381 our proteomic data set included many uncharacterized cytosolic, chloroplast, and mitochondrial proteins. file:ARATH/SIR/SIR-source-analysis/README.md The `True membrane` and `Dual Localized` fields are both empty. |
| GO:0006790 sulfur compound metabolic process | IEA GO_REF:0000117 | MODIFY | Summary: Refine sulfur metabolism to the established sulfate-assimilation step. Reason: SIR performs sulfite reduction within sulfate assimilation; its protective response to excess sulfite uses the same catalytic chemistry. Proposed replacements: sulfate assimilation Supporting Evidence: PMID:23221833 Plant sulfite reductase (SiR; Enzyme Commission 1.8.7.1) catalyzes the reduction of sulfite to sulfide in the reductive sulfate assimilation pathway. PMID:20424176 The 28-fold decrease of incorporation of (35)S label into Cys, glutathione, and protein in sir1-1 showed that the decreased activity of SiR generated a severe bottleneck in the assimilatory sulfate reduction pathway. |
| GO:0006790 sulfur compound metabolic process | IMP PMID:23221833 Sulfite reductase protects plants against sulfite toxicity. | MODIFY | Summary: Refine sulfur metabolism to the established sulfate-assimilation step. Reason: SIR performs sulfite reduction within sulfate assimilation; its protective response to excess sulfite uses the same catalytic chemistry. Proposed replacements: sulfate assimilation Supporting Evidence: PMID:23221833 Plant sulfite reductase (SiR; Enzyme Commission 1.8.7.1) catalyzes the reduction of sulfite to sulfide in the reductive sulfate assimilation pathway. PMID:20424176 The 28-fold decrease of incorporation of (35)S label into Cys, glutathione, and protein in sir1-1 showed that the decreased activity of SiR generated a severe bottleneck in the assimilatory sulfate reduction pathway. |
| GO:0009409 response to cold | IEP PMID:16923014 The chloroplast lumen and stromal proteomes of Arabidopsis t... | MARK AS OVER ANNOTATED | Summary: A change in stromal SIR abundance during cold acclimation is an expression response, not evidence that SIR participates in the cold response. Reason: PMID:16923014 compared stromal and lumenal proteomes by DIGE during cold shock and short- and long-term acclimation, and the TAIR curator recorded SIR among the proteins whose abundance changed (IEP). That observation is not disputed. But an abundance change of a sulfate-assimilation enzyme during acclimation shows that its level responds to cold, not that SIR performs any step of the cold response; no cold-related phenotype of sir mutants is reported. The same IEP set from this paper is treated as over-annotation in sibling reviews (CAT2, SHM1). Supporting Evidence: PMID:16923014 we have taken a proteomic approach (difference gel electrophoresis) to identify proteins that changed in abundance in Arabidopsis chloroplasts during cold shock (1 day), and short- (10 days) and long-term (40 days) acclimation to 5 degrees C. |
| GO:0009507 chloroplast | HDA PMID:18431481 Sorting signals, N-terminal modifications and abundance of t... | MODIFY | Summary: Refine the general cellular location to chloroplast stroma. Reason: Independent target imaging demonstrates diffuse stromal SIR. The broad cytoplasm/plastid/chloroplast term is correct but the existing chloroplast-stroma term is more precise. Proposed replacements: chloroplast stroma Supporting Evidence: PMID:27189994 The DAPI staining of isolated cps showed that AtSiR-YFP is not preferentially colocalized with cp nucleoids, indicating that AtSiR is mainly localized to the stroma |
| GO:0009507 chloroplast | HDA PMID:25293756 A proteomic strategy for global analysis of plant protein co... | MODIFY | Summary: Refine the general cellular location to chloroplast stroma. Reason: Independent target imaging demonstrates diffuse stromal SIR. The broad cytoplasm/plastid/chloroplast term is correct but the existing chloroplast-stroma term is more precise. Proposed replacements: chloroplast stroma Supporting Evidence: PMID:27189994 The DAPI staining of isolated cps showed that AtSiR-YFP is not preferentially colocalized with cp nucleoids, indicating that AtSiR is mainly localized to the stroma |
| GO:0009532 plastid stroma | IEA GO_REF:0000044 | MODIFY | Summary: Refine the general cellular location to chloroplast stroma. Reason: Independent target imaging demonstrates diffuse stromal SIR. The broad cytoplasm/plastid/chloroplast term is correct but the existing chloroplast-stroma term is more precise. Proposed replacements: chloroplast stroma Supporting Evidence: PMID:27189994 The DAPI staining of isolated cps showed that AtSiR-YFP is not preferentially colocalized with cp nucleoids, indicating that AtSiR is mainly localized to the stroma |
| GO:0009536 plastid | IEA GO_REF:0000117 | MODIFY | Summary: Refine the general cellular location to chloroplast stroma. Reason: Independent target imaging demonstrates diffuse stromal SIR. The broad cytoplasm/plastid/chloroplast term is correct but the existing chloroplast-stroma term is more precise. Proposed replacements: chloroplast stroma Supporting Evidence: PMID:27189994 The DAPI staining of isolated cps showed that AtSiR-YFP is not preferentially colocalized with cp nucleoids, indicating that AtSiR is mainly localized to the stroma |
| GO:0009536 plastid | TAS PMID:9661674 Isolation and characterization of a gene for assimilatory su... | MODIFY | Summary: Refine the general cellular location to chloroplast stroma. Reason: Independent target imaging demonstrates diffuse stromal SIR. The broad cytoplasm/plastid/chloroplast term is correct but the existing chloroplast-stroma term is more precise. Proposed replacements: chloroplast stroma Supporting Evidence: PMID:27189994 The DAPI staining of isolated cps showed that AtSiR-YFP is not preferentially colocalized with cp nucleoids, indicating that AtSiR is mainly localized to the stroma |
| GO:0009570 chloroplast stroma | HDA PMID:18633119 Quantitative proteomics of a chloroplast SRP54 sorting mutan... | ACCEPT | Summary: Native Arabidopsis SIR is predominantly in chloroplast stroma. Reason: Independent AtSiR-YFP imaging and DAPI comparison directly support stromal localization; repeated proteomic/phylogenetic rows refer to this same established claim. Supporting Evidence: PMID:27189994 The DAPI staining of isolated cps showed that AtSiR-YFP is not preferentially colocalized with cp nucleoids, indicating that AtSiR is mainly localized to the stroma |
| GO:0009570 chloroplast stroma | HDA PMID:20061580 AT_CHLORO, a comprehensive chloroplast proteome database wit... | ACCEPT | Summary: Native Arabidopsis SIR is predominantly in chloroplast stroma. Reason: Independent AtSiR-YFP imaging and DAPI comparison directly support stromal localization; repeated proteomic/phylogenetic rows refer to this same established claim. Supporting Evidence: PMID:27189994 The DAPI staining of isolated cps showed that AtSiR-YFP is not preferentially colocalized with cp nucleoids, indicating that AtSiR is mainly localized to the stroma |
| GO:0009570 chloroplast stroma | IBA GO_REF:0000033 | ACCEPT | Summary: Native Arabidopsis SIR is predominantly in chloroplast stroma. Reason: Independent AtSiR-YFP imaging and DAPI comparison directly support stromal localization; repeated proteomic/phylogenetic rows refer to this same established claim. Supporting Evidence: PMID:27189994 The DAPI staining of isolated cps showed that AtSiR-YFP is not preferentially colocalized with cp nucleoids, indicating that AtSiR is mainly localized to the stroma |
| GO:0009570 chloroplast stroma | IEA GO_REF:0000044 | ACCEPT | Summary: Native Arabidopsis SIR is predominantly in chloroplast stroma. Reason: Independent AtSiR-YFP imaging and DAPI comparison directly support stromal localization; repeated proteomic/phylogenetic rows refer to this same established claim. Supporting Evidence: PMID:27189994 The DAPI staining of isolated cps showed that AtSiR-YFP is not preferentially colocalized with cp nucleoids, indicating that AtSiR is mainly localized to the stroma |
| GO:0009941 chloroplast envelope | HDA PMID:12938931 Proteomic study of the Arabidopsis thaliana chloroplastic en... | MARK AS OVER ANNOTATED | Summary: Detection of a soluble stromal enzyme in a "mixed" chloroplast envelope preparation; the envelope is not a functional location of SIR. Reason: PMID:12938931 identified 392 proteins in "mixed" envelope fractions prepared on sucrose step gradients. The detection of SIR in that preparation is not disputed. SIR has no transmembrane segment or envelope-targeting signal, full-length AtSiR-YFP is diffusely stromal (PMID:27189994), and no envelope-associated role is known; abundant stromal enzymes routinely co-purify with envelope membranes. The envelope term therefore over-annotates a soluble stromal protein, as judged for other stromal enzymes from this proteome in sibling reviews (GLDP1, GLN2, GLU1). Supporting Evidence: PMID:12938931 "mixed" envelopes were subsequently isolated using sucrose step gradients PMID:27189994 The DAPI staining of isolated cps showed that AtSiR-YFP is not preferentially colocalized with cp nucleoids, indicating that AtSiR is mainly localized to the stroma |
| GO:0010319 stromule | IDA PMID:16923014 The chloroplast lumen and stromal proteomes of Arabidopsis t... | MODIFY | Summary: The paper measured the stromal fraction of isolated chloroplasts; stromule is a mapping of that fraction, and the location the evidence supports is chloroplast stroma. Reason: PMID:16923014 fractionated isolated chloroplasts into stroma and lumen and compared them by DIGE. Stromules cannot be separated from bulk stroma by that fractionation, and the abstract does not mention them. As documented in the RCA review, TAIR applied this IDA stromule annotation to all proteins curated from the paper, including peroxisomal and mitochondrial ones, so the term records the stromal fraction rather than an observation of stromules. A stromal protein will also occupy stromules, which are stroma-filled, so the claim is not false. The supported location is chloroplast stroma (GO:0009570), which SIR already carries from imaging and stromal proteomics. Proposed replacements: chloroplast stroma Supporting Evidence: PMID:16923014 To understand how the stroma and the lumen proteomes adapt to low temperatures, we have taken a proteomic approach (difference gel electrophoresis) PMID:27189994 The DAPI staining of isolated cps showed that AtSiR-YFP is not preferentially colocalized with cp nucleoids, indicating that AtSiR is mainly localized to the stroma |
| GO:0016491 oxidoreductase activity | IEA GO_REF:0000002 | MODIFY | Summary: Refine redox activity to ferredoxin-type sulfite reductase. Reason: The target’s sulfite-reduction chemistry, catalytic family and curated donor class support the specific existing activity. Reduced-dye extract assays in the perturbation papers establish substrate activity, not a directly identified native ferredoxin partner. Proposed replacements: sulfite reductase (ferredoxin) activity Supporting Evidence: PMID:23221833 Plant sulfite reductase (SiR; Enzyme Commission 1.8.7.1) catalyzes the reduction of sulfite to sulfide in the reductive sulfate assimilation pathway. PMID:20424176 The 28-fold decrease of incorporation of (35)S label into Cys, glutathione, and protein in sir1-1 showed that the decreased activity of SiR generated a severe bottleneck in the assimilatory sulfate reduction pathway. |
| GO:0019418 sulfide oxidation | ISS GO_REF:0000024 | REMOVE | Summary: Assimilatory SIR reduces sulfite; it is not assigned the sulfide-oxidation pathway. Reason: Live GO:0019418 defines conversion of sulfide to sulfite or sulfate. The native perturbation studies establish the opposite physiological role: sulfite reduction to assimilatory sulfide. A reversible display of an enzyme reaction does not establish participation in the sulfide-oxidation process. Supporting Evidence: PMID:23221833 Plant sulfite reductase (SiR; Enzyme Commission 1.8.7.1) catalyzes the reduction of sulfite to sulfide in the reductive sulfate assimilation pathway. PMID:20424176 The 28-fold decrease of incorporation of (35)S label into Cys, glutathione, and protein in sir1-1 showed that the decreased activity of SiR generated a severe bottleneck in the assimilatory sulfate reduction pathway. |
| GO:0020037 heme binding | IEA GO_REF:0000002 | ACCEPT | Summary: SIR binds the catalytic siroheme cofactor. Reason: The conserved siroheme-containing reductase architecture and curated cofactor assignment support this core property. Supporting Evidence: file:ARATH/SIR/SIR-uniprot.txt Note=Binds 1 siroheme per subunit. |
| GO:0042644 chloroplast nucleoid | IEA GO_REF:0000044 | REMOVE | Summary: Direct Arabidopsis imaging contradicts preferential nucleoid localization. Reason: PMID:27189994 Figure 3 directly tests stable AtSiR-YFP lines: signal is stromal without preferential DAPI colocalization. Adding the Phaseolus C-terminal extension redirects it to nucleoids. The pea-based transfer is therefore contradicted for native Arabidopsis localization in the tested system; enzyme homology does not preserve this targeting role. Supporting Evidence: PMID:27189994 The DAPI staining of isolated cps showed that AtSiR-YFP is not preferentially colocalized with cp nucleoids, indicating that AtSiR is mainly localized to the stroma |
| GO:0042644 chloroplast nucleoid | ISS GO_REF:0000024 | REMOVE | Summary: Direct Arabidopsis imaging contradicts preferential nucleoid localization. Reason: PMID:27189994 Figure 3 directly tests stable AtSiR-YFP lines: signal is stromal without preferential DAPI colocalization. Adding the Phaseolus C-terminal extension redirects it to nucleoids. The pea-based transfer is therefore contradicted for native Arabidopsis localization in the tested system; enzyme homology does not preserve this targeting role. Supporting Evidence: PMID:27189994 The DAPI staining of isolated cps showed that AtSiR-YFP is not preferentially colocalized with cp nucleoids, indicating that AtSiR is mainly localized to the stroma |
| GO:0045892 negative regulation of DNA-templated transcription | ISS GO_REF:0000024 | MARK AS OVER ANNOTATED | Summary: Pea nucleoid compaction does not establish Arabidopsis transcriptional repression. Reason: The original mechanism is biochemical DNA compaction by pea SiR. Target-specific AtSiR imaging and C-terminal divergence undermine transfer of that nucleoid-based regulatory role. This is an overextended functional inference, not proof that the Arabidopsis enzyme cannot make any DNA contact. Supporting Evidence: PMID:27189994 The DAPI staining of isolated cps showed that AtSiR-YFP is not preferentially colocalized with cp nucleoids, indicating that AtSiR is mainly localized to the stroma PMID:11997391 Pea chloroplast nucleoids have an abundant 70-kDa protein identified as sulfite reductase (SiR) that can compact DNA. |
| GO:0048046 apoplast | HDA PMID:18538804 Hydroponic isotope labelling of entire plants (HILEP) for qu... | MARK AS OVER ANNOTATED | Summary: Detection in a whole-plant labelled proteome that reported apoplast changes; an extracellular location is not plausible for this plastid-stromal enzyme. Reason: PMID:18538804 is a metabolic-labelling quantitative proteomics method paper on oxidatively stressed plants. The curator's identification of SIR there is not disputed. SIR, however, is a transit-peptide-bearing stromal enzyme with no secretion signal and no known extracellular role, and its target-specific imaging is stromal (PMID:27189994). The apoplast term over-annotates a proteomic co-detection, as for the other plastid and mitochondrial enzymes curated from this study in sibling reviews (RCA, GLDP1, SHM1, GLO1). Supporting Evidence: PMID:18538804 it was possible to show differential protein expression in the apoplast of plants submitted to oxidative stress. PMID:27189994 The DAPI staining of isolated cps showed that AtSiR-YFP is not preferentially colocalized with cp nucleoids, indicating that AtSiR is mainly localized to the stroma |
| GO:0050311 sulfite reductase (ferredoxin) activity | IBA GO_REF:0000033 | ACCEPT | Summary: SIR is the ferredoxin-type assimilatory sulfite reductase. Reason: Native Arabidopsis perturbation and sulfite-turnover assays establish the catalytic role. The donor class is supported by conserved plant enzyme architecture and curated function; reduced-methyl-viologen assays should not be recast as direct native ferredoxin-pairing experiments. Independent maize SiR–Fd co-crystals and interface mutants (PMID:26920048) provide primary comparative support for the plant donor class. Supporting Evidence: PMID:23221833 Plant sulfite reductase (SiR; Enzyme Commission 1.8.7.1) catalyzes the reduction of sulfite to sulfide in the reductive sulfate assimilation pathway. PMID:20424176 The 28-fold decrease of incorporation of (35)S label into Cys, glutathione, and protein in sir1-1 showed that the decreased activity of SiR generated a severe bottleneck in the assimilatory sulfate reduction pathway. PMID:26920048 Mutational analysis of a total of seven basic residues of SiR distributed widely at the interface of the complex showed their importance for supporting an efficient Fd-dependent activity and a strong physical binding to Fd. |
| GO:0050311 sulfite reductase (ferredoxin) activity | IDA PMID:23221833 Sulfite reductase protects plants against sulfite toxicity. | ACCEPT | Summary: SIR is the ferredoxin-type assimilatory sulfite reductase. Reason: Native Arabidopsis perturbation and sulfite-turnover assays establish the catalytic role. The donor class is supported by conserved plant enzyme architecture and curated function; reduced-methyl-viologen assays should not be recast as direct native ferredoxin-pairing experiments. Independent maize SiR–Fd co-crystals and interface mutants (PMID:26920048) provide primary comparative support for the plant donor class. Supporting Evidence: PMID:23221833 Plant sulfite reductase (SiR; Enzyme Commission 1.8.7.1) catalyzes the reduction of sulfite to sulfide in the reductive sulfate assimilation pathway. PMID:20424176 The 28-fold decrease of incorporation of (35)S label into Cys, glutathione, and protein in sir1-1 showed that the decreased activity of SiR generated a severe bottleneck in the assimilatory sulfate reduction pathway. PMID:26920048 Mutational analysis of a total of seven basic residues of SiR distributed widely at the interface of the complex showed their importance for supporting an efficient Fd-dependent activity and a strong physical binding to Fd. |
| GO:0050311 sulfite reductase (ferredoxin) activity | IEA GO_REF:0000120 | ACCEPT | Summary: SIR is the ferredoxin-type assimilatory sulfite reductase. Reason: Native Arabidopsis perturbation and sulfite-turnover assays establish the catalytic role. The donor class is supported by conserved plant enzyme architecture and curated function; reduced-methyl-viologen assays should not be recast as direct native ferredoxin-pairing experiments. Independent maize SiR–Fd co-crystals and interface mutants (PMID:26920048) provide primary comparative support for the plant donor class. Supporting Evidence: PMID:23221833 Plant sulfite reductase (SiR; Enzyme Commission 1.8.7.1) catalyzes the reduction of sulfite to sulfide in the reductive sulfate assimilation pathway. PMID:20424176 The 28-fold decrease of incorporation of (35)S label into Cys, glutathione, and protein in sir1-1 showed that the decreased activity of SiR generated a severe bottleneck in the assimilatory sulfate reduction pathway. PMID:26920048 Mutational analysis of a total of seven basic residues of SiR distributed widely at the interface of the complex showed their importance for supporting an efficient Fd-dependent activity and a strong physical binding to Fd. |
| GO:0050311 sulfite reductase (ferredoxin) activity | IMP PMID:20424176 Sulfite reductase defines a newly discovered bottleneck for ... | ACCEPT | Summary: SIR is the ferredoxin-type assimilatory sulfite reductase. Reason: Native Arabidopsis perturbation and sulfite-turnover assays establish the catalytic role. The donor class is supported by conserved plant enzyme architecture and curated function; reduced-methyl-viologen assays should not be recast as direct native ferredoxin-pairing experiments. Independent maize SiR–Fd co-crystals and interface mutants (PMID:26920048) provide primary comparative support for the plant donor class. Supporting Evidence: PMID:23221833 Plant sulfite reductase (SiR; Enzyme Commission 1.8.7.1) catalyzes the reduction of sulfite to sulfide in the reductive sulfate assimilation pathway. PMID:20424176 The 28-fold decrease of incorporation of (35)S label into Cys, glutathione, and protein in sir1-1 showed that the decreased activity of SiR generated a severe bottleneck in the assimilatory sulfate reduction pathway. PMID:26920048 Mutational analysis of a total of seven basic residues of SiR distributed widely at the interface of the complex showed their importance for supporting an efficient Fd-dependent activity and a strong physical binding to Fd. |
| GO:0050311 sulfite reductase (ferredoxin) activity | IMP PMID:23221833 Sulfite reductase protects plants against sulfite toxicity. | ACCEPT | Summary: SIR is the ferredoxin-type assimilatory sulfite reductase. Reason: Native Arabidopsis perturbation and sulfite-turnover assays establish the catalytic role. The donor class is supported by conserved plant enzyme architecture and curated function; reduced-methyl-viologen assays should not be recast as direct native ferredoxin-pairing experiments. Independent maize SiR–Fd co-crystals and interface mutants (PMID:26920048) provide primary comparative support for the plant donor class. Supporting Evidence: PMID:23221833 Plant sulfite reductase (SiR; Enzyme Commission 1.8.7.1) catalyzes the reduction of sulfite to sulfide in the reductive sulfate assimilation pathway. PMID:20424176 The 28-fold decrease of incorporation of (35)S label into Cys, glutathione, and protein in sir1-1 showed that the decreased activity of SiR generated a severe bottleneck in the assimilatory sulfate reduction pathway. PMID:26920048 Mutational analysis of a total of seven basic residues of SiR distributed widely at the interface of the complex showed their importance for supporting an efficient Fd-dependent activity and a strong physical binding to Fd. |
| GO:0051536 iron-sulfur cluster binding | IEA GO_REF:0000002 | MODIFY | Summary: Refine iron-sulfur binding to the [4Fe-4S] cluster. Reason: The conserved catalytic center is a [4Fe-4S] cluster; use the existing specific term. Proposed replacements: 4 iron, 4 sulfur cluster binding Supporting Evidence: file:ARATH/SIR/SIR-uniprot.txt Note=Binds 1 [4Fe-4S] cluster per subunit. |
| GO:0051539 4 iron, 4 sulfur cluster binding | IEA GO_REF:0000002 | ACCEPT | Summary: SIR contains the catalytic [4Fe-4S] cluster. Reason: Conserved cofactor-binding residues and the curated sulfite-reductase center support the cluster assignment; this is structural/family evidence rather than a new Arabidopsis cluster measurement. Supporting Evidence: file:ARATH/SIR/SIR-uniprot.txt Note=Binds 1 [4Fe-4S] cluster per subunit. |
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Download this section (compressed HTML)Q: Does Arabidopsis SIR bind DNA directly despite its predominantly stromal distribution, and does this affect chloroplast gene expression?
Experiment: Measure DNA binding by purified Arabidopsis holo-SiR and compare binding-defective variants with wild type in chloroplast localization and transcription assays.
Type: DNA-binding and in planta functional analysis
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: Whether Arabidopsis SIR directly binds DNA, and whether such binding has a physiological role, remains unresolved by the inspected species-comparative studies.
OPEN BIOLOGY RESIDUAL_SUBGAP
What is known: AtSiR is predominantly stromal without preferential nucleoid localization. Maize SiR binds DNA despite lacking preferential nucleoid localization, so the Arabidopsis localization result alone cannot exclude DNA binding.
What would resolve it: Test purified Arabidopsis holo-SiR for DNA binding with appropriate controls, then assess any binding-defective variant for nucleoid association and transcriptional effects in planta.
Provenance (the field's own admissions):
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