SUR1 (SUPERROOT1; also ALF1/HLS3/RTY1, At2g20610) is the pyridoxal 5'-phosphate-dependent C-S lyase of core glucosinolate biosynthesis. It belongs to the class-I (tyrosine aminotransferase-like) fold of PLP enzymes but has diverged to cleave the C-S bond of S-(alkylacetohydroximoyl)-L-cysteine conjugates, derived from the glutathione conjugates of aldoxime-derived aci-nitro/nitrile oxide intermediates, releasing the thiohydroximate that UGT74 enzymes then S-glucosylate. It is a major cytosolic enzyme of the Arabidopsis pathway. Loss-of-function mutants accumulate C-S lyase substrates and have severe glucosinolate defects, but residual indolic glucosinolate formation demonstrates additional C-S lyase capacity. Because indole-3-acetaldoxime is then shunted into indole-3-acetic acid, sur1 mutants overproduce auxin and show the pleiotropic "superroot" phenotype (excess adventitious and lateral roots, epinastic cotyledons, no apical hook, sterility), so SUR1 indirectly buffers auxin homeostasis at the IAOx branch point.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0001560 regulation of cell growth by extracellular stimulus | IMP PMID:15851402 Auxin, ethylene and brassinosteroids: tripartite control of ... | MARK AS OVER ANNOTATED | Summary: Hypocotyl growth study in which sur1 (hls3) was used as an auxin-overproducing mutant to analyse auxin/ethylene/brassinosteroid interactions in hypocotyl elongation and apical hook formation. Reason: The growth effect of sur1 is a downstream consequence of IAA overproduction after IAOx is diverted from the blocked glucosinolate pathway; SUR1 does not execute any step of growth regulation by an extracellular stimulus. The phenotype is real (abstract-only cache, so not removed) but does not describe SUR1 function. Supporting Evidence: PMID:15851402 our results indicate that HLS1, SUR1/HLS3/RTY1/ALF1 and AMP1/HPT/COP2/HLS2/PT act on the auxin-ethylene interaction PMID:14871316 This suggests that the "high-auxin" phenotype of sur1 is caused by accumulation of endogenous C-S lyase substrates as well as aldoximes, including indole-3-acetaldoxime (IAOx) that is channeled into the main auxin indole-3-acetic acid (IAA). |
| GO:0004838 L-tyrosine:2-oxoglutarate transaminase activity | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: Tyrosine aminotransferase activity propagated from the PTN000202983 node of the PTHR45744 tyrosine aminotransferase family (donors include human TAT and Arabidopsis TAT7/AT5G53970). SUR1 sits in its own subfamily (PTHR45744:SF15, S-alkyl-thiohydroximate lyase SUR1). Reason: SUR1 has neofunctionalized to a C-S lyase acting on S-alkylthiohydroximate cysteine conjugates; no tyrosine transaminase activity has been reported for SUR1, and the closely related SUR1-like C-S lyase from Taraxacum showed no in vitro TyrAT activity. Residual transamination by this PLP fold cannot be excluded (the Taraxacum homolog has alanine aminotransferase activity), so this is marked as over-annotation rather than removed. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN000202983 · PTN000202983 SUPPORTS SOURCE BUT NOT TARGET Tyrosine aminotransferase function is well supported for the donor TATs (human TAT, Arabidopsis TAT7), but SUR1 lies in the neofunctionalized SUR1 subfamily (PTHR45744:SF15) with demonstrated C-S lyase activity and no reported TAT activity. Supporting Evidence: PMID:23073363 It is homologous to tyrosine and alanine aminotransferases (AlaATs) as well as to an Arabidopsis thaliana carbon-sulfur lyase (C-S lyase) (SUR1) PMID:23073363 However, we detected no in vitro tyrosine aminotransferase (TyrAT) activity PMID:14871316 We report characterization of SUPERROOT1 (SUR1) as the C-S lyase in glucosinolate biosynthesis. |
| GO:0005515 protein binding | IPI PMID:32612234 Extensive signal integration by the phytohormone protein net... | REMOVE | Summary: Binary Y2H interaction with At5g37478 (F4K773) from a systems-level phytohormone interactome map. Reason: Generic protein binding is uninformative about SUR1 function; no functional consequence of the interaction is known. Removal does not imply the interaction is false. Supporting Evidence: PMID:32612234 we experimentally generated a systems-level map of the Arabidopsis phytohormone signalling network, consisting of more than 2,000 binary protein-protein interactions |
| GO:0005737 cytoplasm | ISM GO_REF:0000122 | MODIFY | Summary: The supported cytoplasmic compartment is the cytosol. Reason: Refine the true general cytoplasm location to cytosol, already supported elsewhere in this review. This refinement does not exclude distinct secondary compartments reported under other terms. Proposed replacements: cytosol Supporting Evidence: PMID:25293756 Applying this approach to the crude cytosolic fraction of Arabidopsis thaliana leaves using size exclusion chromatography, we identified hundreds of cytosolic proteins |
| GO:0005739 mitochondrion | HDA PMID:28887381 Global Analysis of Membrane-associated Protein Oligomerizati... | MARK AS OVER ANNOTATED | Summary: The microsome experiment does not independently establish mitochondrion localization. Reason: Full-text inspection of PMID:28887381 shows that washed microsomes were profiled by chromatography and sucrose gradients, while subcellular labels were taken from SUBAcon and prior GFP data. The authors explicitly report that no organelle occupied a single gradient cluster. Detection or membrane association is meaningful, but assigning SUR1 specifically to mitochondrion exceeds the spatial resolution of this experiment. This is not a claim that the detected protein is absent or that all additional localization is impossible; the unsupported compartment assignment, rather than the proteomic observation, is marked as over-annotated. Supporting Evidence: PMID:28887381 The proteins with known localizations had scattered distributions across the entire gradient and no organelle fell in a single cluster. PMID:28887381 We used SUBAcon localization predictions to analyze oligomerization as a function of subcellular localization (Fig. 7C). |
| GO:0005829 cytosol | HDA PMID:25293756 A proteomic strategy for global analysis of plant protein co... | ACCEPT | Summary: Detected in size-exclusion profiling of the crude leaf cytosolic fraction. Reason: Consistent with the cytosolic location of the core glucosinolate pathway and with the IBA; cytosol is the location of SUR1 activity. Supporting Evidence: PMID:25293756 Applying this approach to the crude cytosolic fraction of Arabidopsis thaliana leaves using size exclusion chromatography, we identified hundreds of cytosolic proteins |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of cytosolic activity within the plant TAT/SUR1 clade. Reason: Consistent with the HDA cytosol data and with cytosolic localization of the Taraxacum SUR1 homolog. Supporting Evidence: PMID:23073363 TbCSL is in vivo localized in the cytosol |
| GO:0006520 amino acid metabolic process | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: InterPro2GO mapping from the tyrosine/nicotianamine aminotransferase signature (IPR005958). Reason: The mapping reflects the ancestral aminotransferase family, not SUR1's role. SUR1 cleaves S-substituted cysteine conjugates in glucosinolate biosynthesis; this is better described by glucosinolate biosynthetic process. Supporting Evidence: PMID:14871316 We report characterization of SUPERROOT1 (SUR1) as the C-S lyase in glucosinolate biosynthesis. |
| GO:0006572 L-tyrosine catabolic process | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: A tyrosine-catabolic role is not established for specialized glucosinolate C-S lyase SUR1. Reason: The target has a directly demonstrated glucosinolate-pathway role, whereas the inherited tyrosine-catabolism claim relies on its broader PLP-enzyme lineage. Comparator Taraxacum assays do not establish loss of every possible transaminase activity in Arabidopsis SUR1. Retain this as an unsupported physiological extension, without claiming that lack of a reported phenotype proves evolutionary loss. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN000202983 · PTN000202983 SUPPORTS SOURCE BUT NOT TARGET Tyrosine aminotransferase function is well supported for the donor TATs (human TAT, Arabidopsis TAT7), but SUR1 lies in the neofunctionalized SUR1 subfamily (PTHR45744:SF15) with demonstrated C-S lyase activity and no reported TAT activity. Supporting Evidence: PMID:14871316 The abolishment of glucosinolates in sur1 indicates that the SUR1 function is not redundant and thus SUR1 constitutes a single gene family. PMID:23073363 However, we detected no in vitro tyrosine aminotransferase (TyrAT) activity |
| GO:0008483 transaminase activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO transfer of transaminase activity from the aminotransferase fold signature. Reason: The essence (a PLP-dependent enzyme of the aminotransferase fold) is right, but SUR1's demonstrated activity is C-S bond cleavage of S-alkylthiohydroximate cysteine conjugates; the informative term is S-alkylthiohydroximate lyase activity. Proposed replacements: S-alkylthiohydroximate lyase activity Supporting Evidence: PMID:14871316 C-S lyase activity of recombinant SUR1 heterologously expressed in Escherichia coli was demonstrated using the C-S lyase substrate djenkolic acid. |
| GO:0009684 indoleacetic acid biosynthetic process | IMP PMID:8589625 Superroot, a recessive mutation in Arabidopsis, confers auxi... | MARK AS OVER ANNOTATED | Summary: sur1 mutants have elevated free and conjugated IAA and an auxin-overproduction phenotype. Reason: SUR1 performs no step of IAA biosynthesis; loss of SUR1 increases IAA because the upstream glucosinolate intermediate IAOx is redirected into auxin. The mutant phenotype therefore reflects metabolic shunting (SUR1 acting, if anything, to limit IAA production), not participation. Abstract-only cache and experimental code, so marked as over-annotation rather than removed. Supporting Evidence: PMID:8589625 Analysis by gas chromatography coupled to mass spectrometry indicated increased levels of both free and conjugated indole-3-acetic acid. PMID:14871316 This suggests that the "high-auxin" phenotype of sur1 is caused by accumulation of endogenous C-S lyase substrates as well as aldoximes, including indole-3-acetaldoxime (IAOx) that is channeled into the main auxin indole-3-acetic acid (IAA). |
| GO:0016846 carbon-sulfur lyase activity | IDA PMID:14871316 Arabidopsis mutants in the C-S lyase of glucosinolate biosyn... | MODIFY | Summary: SUR1 is the substrate-specific S-alkylthiohydroximate C-S lyase. Reason: Refine the general carbon-sulfur lyase class to the specific activity already annotated. The original study combines in vivo labeled-precursor accumulation with recombinant C-S lyase activity on djenkolic acid; it is not represented as a purified native Cys-Gly-conjugate assay. Proposed replacements: S-alkylthiohydroximate lyase activity Supporting Evidence: PMID:14871316 C-S lyase activity of recombinant SUR1 heterologously expressed in Escherichia coli was demonstrated using the C-S lyase substrate djenkolic acid. |
| GO:0019761 glucosinolate biosynthetic process | IMP PMID:14871316 Arabidopsis mutants in the C-S lyase of glucosinolate biosyn... | ACCEPT | Summary: sur1 is completely devoid of aliphatic and indole glucosinolates, and in vivo feeding of p-hydroxyphenylacetaldoxime leads to accumulation of the C-S lyase substrate. Reason: Core process; SUR1 catalyzes the C-S cleavage step of the core glucosinolate pathway. A recent report that sur1 retains some indolic glucosinolate suggests a minor additional C-S lyase for indolic substrates, but does not alter SUR1's role. Supporting Evidence: PMID:14871316 This is evidenced by selective metabolite profiling of sur1, which is completely devoid of aliphatic and indole glucosinolates. PMID:41819465 sur1 plants are still able to accumulate significant indolic GL amounts as compared with wild type plants, indicating that additional C-S lyase is involved in the biosynthesis of these specialized metabolites |
| GO:0030170 pyridoxal phosphate binding | IEA GO_REF:0000002 | ACCEPT | Summary: PLP binding inferred from the class-I aminotransferase domain; UniProt records PLP as cofactor. Reason: C-S lyases of this fold are PLP-dependent; cofactor binding is correct and mechanistically required, though not a standalone function. Supporting Evidence: PMID:23073363 We isolated a novel pyridoxal-5-phosphate-dependent l-cystine lyase from the dandelion Taraxacum brevicorniculatum. |
| GO:0048830 adventitious root development | TAS PMID:16377752 Proteomic analysis of different mutant genotypes of Arabidop... | MARK AS OVER ANNOTATED | Summary: Proteomic comparison of sur1-3 and other adventitious-rooting mutants; sur1 spontaneously forms adventitious roots because it overproduces auxin. Reason: Excess adventitious rooting is an indirect consequence of auxin overproduction in the absence of SUR1's glucosinolate-pathway activity; SUR1 does not function in root development per se. Supporting Evidence: PMID:16377752 The auxin overproducers sur1-3 and sur2-1 spontaneously develop adventitious roots on the hypocotyl PMID:14871316 This suggests that the "high-auxin" phenotype of sur1 is caused by accumulation of endogenous C-S lyase substrates |
| GO:0050832 defense response to fungus | IDA PMID:32213638 REVERSAL OF RDO5 1, a Homolog of Rice Seed Dormancy4, Intera... | REMOVE | Summary: The cited paper (Liu et al. 2020, ODR1/bHLH57 control of ABA biosynthesis and seed dormancy) is about seed dormancy. Its full text (PMC7268807, now cached locally via the publication pipeline as publications/PMID_32213638.md, HTML extraction) does not mention SUR1/SUPERROOT1, At2g20610, glucosinolates, fungi or any pathogen assay. Reason: This is not a case of an abstract foregrounding another gene. The whole cached article (Results, Methods and the accession-number list) contains no SUR1 genotype and no fungal or defense experiment, so it cannot support an IDA for defense response to fungus. The Accession Numbers section lists every gene studied (ODR1, ABI3, bHLH57, NCEDs, CYP707As, ABI4, DREB2C, TTG1, MYB5, DOG1, RDO5 and the PP2A reference) and At2g20610 is not among them. A QuickGO query for PMID:32213638 (recorded in SUR1-notes.md) returns this single annotation and nothing for ODR1 or bHLH57, which points to a mis-keyed reference in the TAIR record rather than a SUR1 experiment in the paper. The row is removed as unsupported by its reference. This does not deny that SUR1-dependent indole glucosinolates contribute to antifungal defense; that role would be indirect, via SUR1's metabolic products, and should be re-annotated from a paper that tests it. Supporting Evidence: PMID:32213638 we report the characterization of two ABA-related seed dormancy regulators in Arabidopsis PMID:32213638 Sequence data from this investigation can be found in the Arabidopsis Genome Initiative or GenBank/EMBL databases under the following accession numbers: ODR1 (At1g27461), ABI3 (At3g24650), bHLH57 (At4g01460), NCED2 (At4g18350) NCED3 (At3g14440), NCED5 (At1g30100), NCED6 (At3g24220), NCED9 (At1g78390), CYP707A1 (At4g19230), CYP707A2 (At2g29090), CYP707A3 (At5g45340), CYP707A4 (At3g19270), ABI4 (At2g40220), DREB2C (At2g40340), TTG1 (At5g24520), MYB5 (At3g13540), DOG1 (At5g45830), RDO5 (At4g11040), and PP2A (At1g13320). |
| GO:0080108 S-alkylthiohydroximate lyase activity | IMP PMID:14871316 Arabidopsis mutants in the C-S lyase of glucosinolate biosyn... | ACCEPT | Summary: Core molecular function. sur1 accumulates the C-S lyase substrate after feeding labeled p-hydroxyphenylacetaldoxime, lacks glucosinolates, and recombinant SUR1 has C-S lyase activity. Reason: Combined in vivo substrate accumulation and in vitro C-S lyase activity establish SUR1 as the S-alkylthiohydroximate C-S lyase of glucosinolate biosynthesis. Supporting Evidence: PMID:14871316 Furthermore, following in vivo feeding with radiolabeled p-hydroxyphenylacetaldoxime to the sur1 mutant, the corresponding C-S lyase substrate accumulated. |
Loading supporting content…
Download this section (compressed HTML)Q: Which enzyme provides the residual C-S lyase activity for indolic glucosinolates in sur1 mutants, and is it a paralog in the PTHR45744 family?
Q: Is the physiological SUR1 substrate the Cys-Gly or the Cys conjugate produced after GGP1 action, and does SUR1 retain any aminotransferase side activity?
Q: How much of the sur1 lethality is due to auxin excess versus accumulation of toxic glucosinolate intermediates?
Q: Which paper was intended for the GO:0050832 defense response to fungus IDA keyed to PMID:32213638? That reference is a seed-dormancy study (ODR1/bHLH57) that does not mention SUR1 or any pathogen assay, so the annotation appears mis-keyed in the TAIR record.
Experiment: Assay recombinant SUR1 kinetically with synthetic S-(alkylacetohydroximoyl)-L-cysteine and -cysteinylglycine conjugates of methionine-, phenylalanine- and tryptophan-derived precursors, and with tyrosine/2-oxoglutarate, to define its native substrate and exclude residual transaminase activity.
Experiment: Profile glucosinolates and intermediates in sur1 myb34 and sur1 combined with candidate PTHR45744 paralog mutants to identify the additional indolic C-S lyase.
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)