Aliphatic glucosinolate biosynthesis and myrosinase activation (glucosinolate-myrosinase defense system)

This module describes the chain-elongated methionine glucosinolate pathway and classical myrosinase activation in characterized Brassicaceae. It is not a universal pathway for all glucosinolate-producing plants. Methionine-derived (aliphatic) glucosinolates are made in three phases: (1) side-chain elongation, a cycle recruited from leucine biosynthesis that runs partly in the cytosol and partly in the chloroplast: methionine is deaminated to its 2-oxo acid in the cytosol (BCAT4), and after import into the chloroplast the 2-oxo acid is condensed with acetyl-CoA (MAM), isomerized (IPMI), oxidatively decarboxylated (IPMDH1) and transaminated back to a chain-elongated methionine homolog (BCAT3), each turn adding one methylene group; (2) formation of the core glucosinolate structure, in which CYP79F converts the chain-elongated amino acid to an aldoxime, CYP83A1 activates the aldoxime for glutathione conjugation, the conjugate is trimmed by gamma-glutamyl peptidase (GGP1) and cleaved by the C-S lyase SUR1 to a thiohydroximate, which is S-glucosylated (UGT74C1/UGT74B1) and finally sulfated from PAPS by desulfoglucosinolate sulfotransferases (SOT16-18); and (3) side-chain modification, in which flavin monooxygenases (FMO GS-OX) S-oxygenate methylthioalkyl to methylsulfinylalkyl glucosinolates and the 2-oxoglutarate-dependent dioxygenase AOP2 converts these to alkenyl glucosinolates such as allylglucosinolate (sinigrin). The classical damage-activated defense chemistry depends on hydrolysis of the stored glucosinolate. On tissue damage, thioglucosidases (myrosinases, TGG1/TGG2) hydrolyze it to an unstable aglucone that rearranges by default to an isothiocyanate; Fe(II)-dependent specifier proteins (ESP, NSPs, TFP) instead redirect the aglucone to epithionitriles, simple nitriles or organic thiocyanates. Natural variation at MAM, AOP and ESP loci accounts for much of the glucosinolate and breakdown-product diversity between accessions and species. Transcriptional regulation (MYB28/MYB29 with MYC2-4), glucosinolate transport (GTR1/GTR2), indole and aromatic glucosinolates, and sulfate activation to PAPS are outside this module's boundary. BCAT3 is a characterized short-chain exit route rather than the sole exit enzyme for all chain lengths. Native transport between compartments is required; transport proteins are outside this module. Decoration and specifier branches vary among species, accessions and tissues.

MODULE:aliphatic_glucosinolate_myrosinase_defenseDRAFTABSTRACTMetabolic Pathwaymodules/aliphatic_glucosinolate_myrosinase_defense.yaml

glucosinolate biosynthetic processGO:0019761 glucosinolate catabolic processGO:0019762

PMID:20303821

Biosynthesis of glucosinolates--gene discovery and beyond.

The biosynthetic pathway has three phases, chain elongation, core structure and side-chain decoration.

Recent progress includes genes in all three phases of the pathway, i.e. side-chain elongation of precursor amino acids, formation of the core glucosinolate structure and side-chain decoration.

PMID:19224919

Nitrile-specifier proteins involved in glucosinolate hydrolysis in Arabidopsis thaliana.

Myrosinase hydrolysis gives isothiocyanates by default; specifier proteins divert the products.

The degradation of glucosinolates is catalyzed by thioglucosidases called myrosinases and leads by default to the formation of isothiocyanates.

PMID:21783213

A thiocyanate-forming protein generates multiple products upon allylglucosinolate breakdown in Thlaspi arvense.

Allylglucosinolate is the major glucosinolate of field pennycress, whose specifier protein TFP yields allylthiocyanate and the corresponding epithionitrile.

this protein promotes the formation of allylthiocyanate as well as the corresponding epithionitrile upon myrosinase-catalyzed hydrolysis of allylglucosinolate, the major glucosinolate of T. arvense.

file:projects/THLAR_OILSEED/ortholog_mapping/CALLS.md

Pennycress ortholog calls (THLAR_OILSEED project)

Sequence-based Thlaspi candidates are mapped with forward and reverse phmmer searches. These include MAM1/3 and SSU2/3 co-orthologs and incomplete models; they are inferred exemplars, not direct native biochemical assays or uniformly one-to-one orthologs.

PMID:20457641

Production of the cancer-preventive glucoraphanin in tobacco.

Methionine chain elongation is split between the cytosol (BCAT4 deamination) and the chloroplast.

a chain-elongation pathway that takes place partly in the cytosol and partly in the chloroplast

DOI:10.1016/j.bse.2025.105033

Restrict this chain-elongated methionine template to Brassicaceae; glucosinolate occurrence alone does not establish the elongation pathway.

Taxon and reaction scope are evidence-bounded. Thlaspi members include co-orthologs and incomplete models; sequence similarity is not direct target chemistry. Exact specialized MF terms are lacking for several steps (CYP83A1, AOP2, IPMDH1, terminal elongated-Met transamination); free-text activities or accurate broader terms are used rather than substrate-mismatched GO IDs. GST native conjugation and GGP-to-SUR1 conjugate processing remain biological gaps. Family memberships and all 35 individual member reviews have been checked, including a direct Brassica MAM exemplar and nine inferred Thlaspi proteins. Full repository validation and PR review remain outstanding.

25Nodes

19Parts

2Variant Sets

5Variants

20Annotons

18Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✓ present

aliphatic_glucosinolate_myrosinase_defense-deep-research-falcon.md (falcon)

Leaf nodes lacking representative members

✓ representative grounding skipped for abstract module.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Function consistency and core coverage

24 gene-function check(s) reflected in core functions · 0 conflict(s) · 43 evidence or coverage gap(s) (69 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

Annoton	Participant	Function	Assessment
bcat4_activity	BCAT4 (Arabidopsis) UniProtKB:Q9LE06 Family Representative	L-methionine:oxo-acid transaminase activity GO:0010326	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
bcat4_activity	TAV2_LOCUS10345 (Thlaspi arvense; inferred homolog) UniProtKB:A0AAU9S298 Family Representative	L-methionine:oxo-acid transaminase activity GO:0010326	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
mam_activity	MAM1 (Arabidopsis; first two elongation cycles) UniProtKB:Q9FG67 Family Representative	methylthioalkylmalate synthase activity GO:0010177	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
mam_activity	MAM3 (Arabidopsis; long-chain cycles) UniProtKB:Q9FN52 Family Representative	methylthioalkylmalate synthase activity GO:0010177	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
mam_activity	TAV2_LOCUS6842 (Thlaspi arvense; inferred homolog) UniProtKB:A0AAU9RP64 Family Representative	methylthioalkylmalate synthase activity GO:0010177	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
mam_activity	gsl-elong-A1 / BjMAM1-A (Brassica juncea) UniProtKB:C5J4P1 Family Representative	methylthioalkylmalate synthase activity GO:0010177	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ipmi_activity	PROTEIN_COMPLEX Gene	2-(omega-methylthio)alkylmalate dehydratase activity GO:0120528	Participant Unchecked No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
ipmi_activity/ipmi_large_subunit	IIL1 / LSU1 (Arabidopsis; IPMI large subunit) UniProtKB:Q94AR8 Family Representative	contribution to glucosinolate-chain-elongation IPMI activity No function ID	No Function Id A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
ipmi_activity/ipmi_large_subunit	TAV2_LOCUS24872 (Thlaspi arvense; inferred homolog) UniProtKB:A0AAU9T4X1 Family Representative	contribution to glucosinolate-chain-elongation IPMI activity No function ID	No Function Id A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
ipmi_activity/ipmi_small_subunit	SSU3 (Arabidopsis; IPMI small subunit) UniProtKB:Q9LYT7 Family Representative	contribution to glucosinolate-chain-elongation IPMI activity No function ID	No Function Id A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
ipmi_activity/ipmi_small_subunit	TAV2_LOCUS13090 (Thlaspi arvense; inferred homolog) UniProtKB:A0AAU9S4C4 Family Representative	contribution to glucosinolate-chain-elongation IPMI activity No function ID	No Function Id A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
ipmdh1_activity	IPMDH1 (Arabidopsis) UniProtKB:Q9FMT1 Family Representative	3-(omega-methylthio)alkylmalate oxidative decarboxylation No function ID	No Function Id A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
ipmdh1_activity	TAV2_LOCUS20462 (Thlaspi arvense; inferred homolog) UniProtKB:A0AAU9SYX6 Family Representative	3-(omega-methylthio)alkylmalate oxidative decarboxylation No function ID	No Function Id A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
ipmdh1_activity:required_function	IPMDH1 (Arabidopsis) UniProtKB:Q9FMT1 Family Representative	3-(omega-methylthio)alkylmalate oxidative decarboxylation No function ID	No Function Id A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
ipmdh1_activity:required_function	TAV2_LOCUS20462 (Thlaspi arvense; inferred homolog) UniProtKB:A0AAU9SYX6 Family Representative	3-(omega-methylthio)alkylmalate oxidative decarboxylation No function ID	No Function Id A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
bcat3_activity	BCAT3 (Arabidopsis) UniProtKB:Q9M401 Family Representative	transamination of chain-elongated methionine oxo-acid homologs No function ID	No Function Id A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
bcat3_activity	TAV2_LOCUS15930 (Thlaspi arvense; inferred homolog) UniProtKB:A0AAU9SEL1 Family Representative	transamination of chain-elongated methionine oxo-acid homologs No function ID	No Function Id A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
bcat3_activity:required_function	BCAT3 (Arabidopsis) UniProtKB:Q9M401 Family Representative	transamination of chain-elongated methionine oxo-acid homologs No function ID	No Function Id A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
bcat3_activity:required_function	TAV2_LOCUS15930 (Thlaspi arvense; inferred homolog) UniProtKB:A0AAU9SEL1 Family Representative	transamination of chain-elongated methionine oxo-acid homologs No function ID	No Function Id A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
cyp79f_activity	CYP79F1 (Arabidopsis; short- and long-chain) UniProtKB:Q949U1 Family Representative	homomethionine N-monooxygenase activity GO:0120526	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
cyp79f_activity	CYP79F2 (Arabidopsis; long-chain) UniProtKB:Q9FUY7 Family Representative	homomethionine N-monooxygenase activity GO:0120526	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
cyp83a1_activity	CYP83A1 / REF2 (Arabidopsis) UniProtKB:P48421 Family Representative	(methylsulfanyl)alkanaldoxime N-monooxygenase activity (proposed new GO term; EC 1.14.14.43); parent shown GO:0016712	Function Unreviewed No retained annotation or core molecular function supports this GO assertion. Missing or broader evidence is a coverage gap, not proof the activity is absent.
gstu20_activity	GSTU20 (Arabidopsis; major contributor) UniProtKB:Q8L7C9 Family Representative	glutathione transferase activity GO:0004364	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
gstf11_activity	GSTF11 (Arabidopsis) UniProtKB:Q96324 Family Representative	glutathione transferase activity GO:0004364	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ggp1_activity	GGP1 (Arabidopsis) UniProtKB:Q9M0A7 Family Representative	gamma-glutamyl-peptidase activity GO:0034722	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ggp1_activity	TAV2_LOCUS24348 (Thlaspi arvense; inferred homolog) UniProtKB:A0AAU9T3M3 Family Representative	gamma-glutamyl-peptidase activity GO:0034722	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
sur1_activity	SUR1 (Arabidopsis) UniProtKB:Q9SIV0 Family Representative	S-alkylthiohydroximate lyase activity GO:0080108	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
sur1_activity	TAV2_LOCUS11381 (Thlaspi arvense; inferred homolog) UniProtKB:A0AAU9RX80 Family Representative	S-alkylthiohydroximate lyase activity GO:0080108	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ugt74b1_activity	UGT74B1 (Arabidopsis) UniProtKB:O48676 Family Representative	thiohydroximate beta-D-glucosyltransferase activity GO:0047251	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ugt74_activity	UGT74C1 (Arabidopsis) UniProtKB:Q9SKC1 Family Representative	thiohydroximate beta-D-glucosyltransferase activity GO:0047251	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
sot_activity	SOT18 (Arabidopsis) UniProtKB:Q9C9C9 Family Representative	aliphatic desulfoglucosinolate sulfotransferase activity GO:0120527	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
sot_activity	SOT17 (Arabidopsis) UniProtKB:Q9FZ80 Family Representative	aliphatic desulfoglucosinolate sulfotransferase activity GO:0120527	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
sot_activity	TAV2_LOCUS415 (Thlaspi arvense; inferred homolog) UniProtKB:A0AAU9RDZ2 Family Representative	aliphatic desulfoglucosinolate sulfotransferase activity GO:0120527	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fmo_gsox_activity	FMOGS-OX1 (Arabidopsis) UniProtKB:Q9SS04 Family Representative	methylthioalkyl glucosinolate S-oxygenase activity No function ID	No Function Id A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
aop2_activity	AOP2 (Arabidopsis Cvi-0; functional allele) UniProtKB:Q945B5 Family Representative	alkenyl glucosinolate synthase activity (proposed new GO term); parent GO:0016706 shown GO:0016706	Annotation Supported A retained annotation or curated replacement supports this function, but core_functions does not yet reflect it.
aop2_activity:required_function	AOP2 (Arabidopsis Cvi-0; functional allele) UniProtKB:Q945B5 Family Representative	conversion of methylsulfinylalkyl to alkenyl glucosinolates No function ID	No Function Id A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
tgg_activity	TGG1 (Arabidopsis) UniProtKB:P37702 Family Representative	thioglucosidase activity GO:0019137	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
tgg_activity	TGG2 (Arabidopsis) UniProtKB:Q9C5C2 Family Representative	thioglucosidase activity GO:0019137	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
esp_activity	ESP (Arabidopsis) UniProtKB:Q8RY71 Family Representative	carbon-sulfur lyase activity (epithionitrile-forming sulfolyase) GO:0016846	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
nsp_activity	NSP1 (Arabidopsis) UniProtKB:Q9SDM9 Family Representative	carbon-sulfur lyase activity (nitrile-forming sulfolyase) GO:0016846	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
nsp_activity:required_function	NSP1 (Arabidopsis) UniProtKB:Q9SDM9 Family Representative	simple nitrile formation from myrosinase-generated glucosinolate aglucones No function ID	No Function Id A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
tfp_activity	TaTFP (field pennycress) UniProtKB:G1FNI6 Family Representative	carbon-sulfur lyase activity (thiocyanate-forming sulfolyase) GO:0016846	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
tfp_activity:required_function	TaTFP (field pennycress) UniProtKB:G1FNI6 Family Representative	thiocyanate-forming specifier activity on allylglucosinolate aglucone No function ID	No Function Id A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
bcat4_activity	BCAT4 methionine aminotransferase subfamily PANTHER:PTHR42825:SF8 Family	L-methionine:oxo-acid transaminase activity GO:0010326	Family Supported Family review supports GO:0010326 for PANTHER:PTHR42825:SF8. This GO term describes unelongated L-methionine transamination. It is established for cytosolic BCAT4 (SF8) and a plastidial backup capacity of Arabidopsis BCAT3 (SF2), supported by recombinant activity and bcat3/bcat4 metabolite genetics. BCAT3 also transaminates chain-elongated methionine homologs, but that distinct substrate range is not covered by GO:0010326. Within heterogeneous SF2 this assessment concerns the characterized plant BCAT3 lineage; bacterial IlvE and fungal members do not inherit this specialized claim merely through SF2 membership.
mam_activity	methylthioalkylmalate synthase homologs PANTHER:PTHR10277 Family	methylthioalkylmalate synthase activity GO:0010177	Family Function Unreviewed Family review leaves GO:0010177 UNRESOLVED. MAM chemistry is established for Arabidopsis MAM1/MAM3 in SF60 and directly for Brassica juncea BjMAM1-A (C5J4P1; gsl-elong-A1) in SF73. The target is linked to the assayed protein by GenBank FM161920/CAQ56040.1 and PDB6E1J. An exclusive SF60 boundary would exclude this demonstrated enzyme; extending the claim to all SF73 would exceed the evidence. The exact complete subfamily/node boundary therefore remains unresolved. Specific experimentally characterized members remain supported, and functional constraints are needed when selecting from the broader family.
ipmi_large_subunit	IPMI large-subunit homologs PANTHER:PTHR43822:SF2 Family	contribution to glucosinolate-chain-elongation IPMI activity No function ID	No Function Id The family function has no GO identifier for comparison; prose is not matched.
ipmi_small_subunit	glucosinolate-type IPMI small-subunit homologs PANTHER:PTHR43345 Family	contribution to glucosinolate-chain-elongation IPMI activity No function ID	No Function Id The family function has no GO identifier for comparison; prose is not matched.
ipmdh1_activity	IPMDH1 subfamily PANTHER:PTHR42979:SF5 Family	3-(omega-methylthio)alkylmalate oxidative decarboxylation No function ID	No Function Id The family function has no GO identifier for comparison; prose is not matched.
ipmdh1_activity:required_function	IPMDH1 subfamily PANTHER:PTHR42979:SF5 Family	3-(omega-methylthio)alkylmalate oxidative decarboxylation No function ID	No Function Id The family function has no GO identifier for comparison; prose is not matched.
bcat3_activity	BCAT3 plastid branched-chain aminotransferase subfamily PANTHER:PTHR42825:SF2 Family	transamination of chain-elongated methionine oxo-acid homologs No function ID	No Function Id The family function has no GO identifier for comparison; prose is not matched.
bcat3_activity:required_function	BCAT3 plastid branched-chain aminotransferase subfamily PANTHER:PTHR42825:SF2 Family	transamination of chain-elongated methionine oxo-acid homologs No function ID	No Function Id The family function has no GO identifier for comparison; prose is not matched.
cyp79f_activity	CYP79F cytochrome P450 subfamily PANTHER:PTHR24298:SF684 Family	homomethionine N-monooxygenase activity GO:0120526	Family Review Missing No supported structured family review is available for PANTHER:PTHR24298:SF684.
cyp83a1_activity	CYP83A1 cytochrome P450 subfamily PANTHER:PTHR47956:SF11 Family	(methylsulfanyl)alkanaldoxime N-monooxygenase activity (proposed new GO term; EC 1.14.14.43); parent shown GO:0016712	Family Review Missing No supported structured family review is available for PANTHER:PTHR47956:SF11.
gstu20_activity	GLUTATHIONE S-TRANSFERASE U20 PANTHER:PTHR11260:SF601 Family	glutathione transferase activity GO:0004364	Family Review Missing No supported structured family review is available for PANTHER:PTHR11260:SF601.
gstf11_activity	GLUTATHIONE S-TRANSFERASE F11 PANTHER:PTHR43900:SF64 Family	glutathione transferase activity GO:0004364	Family Review Missing No supported structured family review is available for PANTHER:PTHR43900:SF64.
ggp1_activity	GGP1 subfamily PANTHER:PTHR42695:SF14 Family	gamma-glutamyl-peptidase activity GO:0034722	Family Review Missing No supported structured family review is available for PANTHER:PTHR42695:SF14.
sur1_activity	SUR1 subfamily PANTHER:PTHR45744:SF15 Family	S-alkylthiohydroximate lyase activity GO:0080108	Family Review Missing No supported structured family review is available for PANTHER:PTHR45744:SF15.
ugt74b1_activity	UGT74B1 subfamily PANTHER:PTHR11926:SF727 Family	thiohydroximate beta-D-glucosyltransferase activity GO:0047251	Family Review Missing No supported structured family review is available for PANTHER:PTHR11926:SF727.
ugt74_activity	UGT74C1 subfamily PANTHER:PTHR11926:SF1356 Family	thiohydroximate beta-D-glucosyltransferase activity GO:0047251	Family Review Missing No supported structured family review is available for PANTHER:PTHR11926:SF1356.
sot_activity	desulfoglucosinolate sulfotransferases (SOT16-18) PANTHER:PTHR11783 Family	aliphatic desulfoglucosinolate sulfotransferase activity GO:0120527	Family Review Missing No supported structured family review is available for PANTHER:PTHR11783.
fmo_gsox_activity	crucifer-specific FMO GS-OX subclade Family	methylthioalkyl glucosinolate S-oxygenase activity No function ID	No Function Id The family function has no GO identifier for comparison; prose is not matched.
aop2_activity	AOP 2-oxoglutarate-dependent dioxygenase family PANTHER:PTHR47990 Family	alkenyl glucosinolate synthase activity (proposed new GO term); parent GO:0016706 shown GO:0016706	Family Review Missing No supported structured family review is available for PANTHER:PTHR47990.
aop2_activity:required_function	AOP 2-oxoglutarate-dependent dioxygenase family PANTHER:PTHR47990 Family	conversion of methylsulfinylalkyl to alkenyl glucosinolates No function ID	No Function Id The family function has no GO identifier for comparison; prose is not matched.
tgg_activity	classical myrosinase subfamily (glycoside hydrolase family 1) PANTHER:PTHR10353:SF218 Family	thioglucosidase activity GO:0019137	Family Review Missing No supported structured family review is available for PANTHER:PTHR10353:SF218.
esp_activity	epithiospecifier protein PANTHER:PTHR47435:SF2 Family	carbon-sulfur lyase activity (epithionitrile-forming sulfolyase) GO:0016846	Family Review Missing No supported structured family review is available for PANTHER:PTHR47435:SF2.
nsp_activity	nitrile-specifier proteins (kelch-repeat specifier family) PANTHER:PTHR47435 Family	carbon-sulfur lyase activity (nitrile-forming sulfolyase) GO:0016846	Family Review Missing No supported structured family review is available for PANTHER:PTHR47435.
nsp_activity:required_function	nitrile-specifier proteins (kelch-repeat specifier family) PANTHER:PTHR47435 Family	simple nitrile formation from myrosinase-generated glucosinolate aglucones No function ID	No Function Id The family function has no GO identifier for comparison; prose is not matched.
tfp_activity	thiocyanate-forming protein PANTHER:PTHR47435:SF7 Family	carbon-sulfur lyase activity (thiocyanate-forming sulfolyase) GO:0016846	Family Review Missing No supported structured family review is available for PANTHER:PTHR47435:SF7.
tfp_activity:required_function	thiocyanate-forming protein PANTHER:PTHR47435:SF7 Family	thiocyanate-forming specifier activity on allylglucosinolate aglucone No function ID	No Function Id The family function has no GO identifier for comparison; prose is not matched.

Gene-review completeness (35/35 grounded genes reviewed)

25 complete review(s) · 21 with deep research · 0 missing review · 14 reviewed but lacking deep research

Gene	Review	Complete	Deep research
AOP2 Q945B5	✓	✓	✓
BCAT3 Q9M401	✓	✓	✓
BCAT4 Q9LE06	✓	✓	✓
CYP79F1 Q949U1	✓	✓	✗
CYP79F2 Q9FUY7	✓	✓	✓
CYP83A1 P48421	✓	✓	✓
ESP Q8RY71	✓	✓	✓
FMOGS-OX1 Q9SS04	✓	13/14	✓
GGP1 Q9M0A7	✓	✓	✓
gsl-elong-A1 C5J4P1	✓	7/8	✗
GSTF11 Q96324	✓	9/11	✓
GSTU20 Q8L7C9	✓	22/25	✓
IIL1 Q94AR8	✓	✓	✓
IMDH1 Q9FMT1	✓	31/32	✓
MAM1 Q9FG67	✓	✓	✗
MAM3 Q9FN52	✓	✓	✗
NSP1 Q9SDM9	✓	17/18	✓
SOT17 Q9FZ80	✓	✓	✓
SOT18 Q9C9C9	✓	✓	✓
SSU3 Q9LYT7	✓	✓	✓
SUR1 Q9SIV0	✓	✓	✓
TAV2_LOCUS10345 A0AAU9S298	✓	✓	✗
TAV2_LOCUS11381 A0AAU9RX80	✓	5/6	✗
TAV2_LOCUS13090 A0AAU9S4C4	✓	✓	✗
TAV2_LOCUS15930 A0AAU9SEL1	✓	✓	✗
TAV2_LOCUS20462 A0AAU9SYX6	✓	✓	✗
TAV2_LOCUS24348 A0AAU9T3M3	✓	✓	✗
TAV2_LOCUS24872 A0AAU9T4X1	✓	✓	✗
TAV2_LOCUS415 A0AAU9RDZ2	✓	✓	✗
TAV2_LOCUS6842 A0AAU9RP64	✓	6/7	✗
TFP G1FNI6	✓	7/8	✓
TGG1 P37702	✓	✓	✓
TGG2 Q9C5C2	✓	✓	✓
UGT74B1 O48676	✓	10/14	✗
UGT74C1 Q9SKC1	✓	✓	✓

Tree

Aliphatic glucosinolate-myrosinase defense systemMetabolic Pathwayaliphatic_glucosinolate_myrosinase_defense

Parts
1. 1. methionine side-chain elongation
2. Methionine chain-elongation cycleMetabolic Pathwaychain_elongation
  
  Parts
  1. 1. deamination of methionine
  2. Methionine deamination (BCAT4)Reactionmet_deamination
    
    Annotons
    
    BCAT4: methionine:oxo-acid transaminase Family: BCAT4 methionine aminotransferase subfamily
  3. 2. condensation with acetyl-CoA
  4. Methylthioalkylmalate synthase (MAM)Reactionmam_condensation
    
    Annotons
    
    MAM1/MAM3: methylthioalkylmalate synthase Family: methylthioalkylmalate synthase homologs
  5. 3. isomerization
  6. Isopropylmalate isomerase (IPMI, glucosinolate-type small subunit)Reactionipmi_isomerization
    
    Annotons
    
    IPMI heterodimer (LSU1 + SSU2/SSU3): 2-(omega-methylthio)alkylmalate dehydratase Protein Complex: glucosinolate-chain-elongation isopropylmalate isomerase heterodimer
  7. 4. oxidative decarboxylation
  8. Isopropylmalate dehydrogenase (IPMDH1)Reactionipmdh_decarboxylation
    
    Annotons
    
    IPMDH1: 3-(omega-methylthio)alkylmalate dehydrogenase Family: IPMDH1 subfamily
  9. 5. transamination to the chain-elongated amino acid
  10. Terminal transamination (BCAT3)Reactionbcat3_transamination
    
    Annotons
    
    BCAT3: transamination of elongated 2-oxo acids Family: BCAT3 plastid branched-chain aminotransferase subfamily
3. 2. core glucosinolate structure
4. Core glucosinolate structure formationMetabolic Pathwaycore_structure
  
  Parts
  1. 1. aldoxime formation
  2. CYP79F aldoxime formationReactionaldoxime_formation
    
    Annotons
    
    CYP79F1/F2: homomethionine N-monooxygenase Family: CYP79F cytochrome P450 subfamily
  3. 2. aldoxime activation for glutathione conjugation
  4. CYP83A1 aldoxime oxidationReactionaldoxime_oxidation
    
    Annotons
    
    CYP83A1: aliphatic aldoxime oxidation Family: CYP83A1 cytochrome P450 subfamily
  5. 3. candidate GST contributions to required sulfur conjugation optional
  6. Glutathione conjugation (GSTU20/GSTF11)Reactiongsh_conjugation
    
    Annotons
    
    GLUTATHIONE S-TRANSFERASE U20 (candidate native conjugation role) Family: GLUTATHIONE S-TRANSFERASE U20
    
    GLUTATHIONE S-TRANSFERASE F11 (candidate native conjugation role) Family: GLUTATHIONE S-TRANSFERASE F11
  7. 4. removal of the gamma-glutamyl residue
  8. Gamma-glutamyl peptidase (GGP1)Reactionggp_cleavage
    
    Annotons
    
    GGP1: gamma-glutamyl peptidase Family: GGP1 subfamily
  9. 5. C-S cleavage to thiohydroximate
  10. C-S lyase (SUR1)Reactioncs_lyase
    
    Annotons
    
    SUR1: S-alkylthiohydroximate lyase Family: SUR1 subfamily
  11. 6. S-glucosylation
  12. Thiohydroximate S-glucosylationReactions_glucosylation
    
    Variants
    
    Major and accessory thiohydroximate glucosyltransferases (One Or More)
    
    UGT74B1 routeReactionugt74b1_route
    
    Annotons
    
    UGT74B1 major thiohydroximate glucosylation route Family: UGT74B1 subfamily
    
    UGT74C1 accessory routeReactionugt74c1_route
    
    Annotons
    
    UGT74C1: thiohydroximate S-glucosyltransferase (aliphatic) Family: UGT74C1 subfamily
  13. 7. sulfation
  14. Desulfoglucosinolate sulfotransferase (SOT17/SOT18)Reactionsulfation
    
    Annotons
    
    SOT17/SOT18: aliphatic desulfoglucosinolate sulfotransferase Family: desulfoglucosinolate sulfotransferases (SOT16-18)
5. 3. side-chain modification optional
6. Side-chain S-oxygenation and alkenylationMetabolic Pathwayside_chain_modification
  
  Parts
  1. 1. S-oxygenation
  2. Flavin monooxygenase S-oxygenation (FMO GS-OX)Reactions_oxygenation
    
    Annotons
    
    FMO GS-OX1-5: methylthioalkyl glucosinolate S-oxygenase Family: crucifer-specific FMO GS-OX subclade
  3. 2. alkenylation optional
  4. AOP2 alkenyl glucosinolate formationReactionalkenylation
    
    Annotons
    
    AOP2: 2-oxoglutarate-dependent dioxygenase (methylsulfinylalkyl -> alkenyl) Family: AOP 2-oxoglutarate-dependent dioxygenase family
7. 4. damage-triggered hydrolysis
8. Myrosinase (thioglucosidase) hydrolysisReactionmyrosinase_hydrolysis
  
  Annotons
  - TGG1/TGG2: myrosinase Family: classical myrosinase subfamily (glycoside hydrolase family 1)
9. 5. product specification optional
10. Specifier-protein redirection of the agluconeMetabolic Pathwayproduct_specification
  
  Variants
  1. Epithionitrile, simple nitrile or thiocyanate formation by specifier protein / product class (Zero Or More)
    
    Epithiospecifier protein (epithionitriles and simple nitriles)Reactionesp_route
    
    Annotons
    
    ESP: epithionitrile-forming specifier Family: epithiospecifier protein
    
    Nitrile-specifier proteins (simple nitriles)Reactionnsp_route
    
    Annotons
    
    NSP1-5: nitrile-forming specifier Family: nitrile-specifier proteins (kelch-repeat specifier family)
    
    Thiocyanate-forming protein (organic thiocyanates)Reactiontfp_route
    
    Annotons
    
    TFP: thiocyanate-forming specifier Family: thiocyanate-forming protein

Details

Context

BrassicaceaeNCBITaxon:3700

DOI:10.1016/j.bse.2025.105033

The critical review concludes that chain-elongated methionine glucosinolates are conclusively known in Brassicaceae; scattered reports outside the family require independent confirmation.

Aliphatic glucosinolate-myrosinase defense systemMetabolic Pathwayaliphatic_glucosinolate_myrosinase_defense

glucosinolate biosynthetic processGO:0019761 glucosinolate catabolic processGO:0019762

Context

BrassicaceaeNCBITaxon:3700

DOI:10.1016/j.bse.2025.105033

The critical review concludes that chain-elongated methionine glucosinolates are conclusively known in Brassicaceae; scattered reports outside the family require independent confirmation.

Arabidopsis exemplars ground each step; field pennycress TFP (G1FNI6) grounds the thiocyanate route. Pennycress seed is dominated by allylglucosinolate (sinigrin), which requires one elongation turn and a functional AOP2. The domestication work reducing pennycress seed glucosinolate targets the regulators MYB28 and MYC3 (PMID:41578087), which are outside this module. Obsolete GO terms avoided: GO:0033506 (glucosinolate biosynthesis from homomethionine), GO:0103092/GO:0103093 (methylthioalkylmalate isomerase/dehydrogenase), GO:0103096 (CYP79F1 dihomomethionine monooxygenase). CYP83A1 and AOP2 have no reaction-specific GO term. All Arabidopsis exemplars have completed gene reviews (genes/ARATH/<GENE>/); annoton locations follow their core functions. Several exemplars have roles outside this module that are recorded only in their reviews: BCAT3 and IMDH1 in leucine biosynthesis, GGP1 in glutathione catabolism and camalexin biosynthesis, and TGG1 in stomatal regulation.

Connections

chain_elongation -> core_structure Provides Input For

Chain-elongated methionine homologs are the CYP79F substrates.

PMID:20457641

Chain-elongated methionine homologs are the CYP79F substrates.

core_structure -> side_chain_modification Provides Input For

Methylthioalkyl glucosinolates are S-oxygenated and alkenylated. This describes a common route, not an obligatory order: some FMO reactions also accept desulfoglucosinolates.

PMID:36823985

Methylthioalkyl glucosinolates are S-oxygenated and alkenylated.

core_structure -> myrosinase_hydrolysis Provides Input For

Intact glucosinolates (modified or not) are myrosinase substrates on tissue damage.

PMID:36823985

Intact glucosinolates (modified or not) are myrosinase substrates on tissue damage.

side_chain_modification -> myrosinase_hydrolysis Provides Input For

Alkenyl glucosinolates such as sinigrin are hydrolyzed by myrosinase.

PMID:36823985

Alkenyl glucosinolates such as sinigrin are hydrolyzed by myrosinase.

myrosinase_hydrolysis -> product_specification Provides Input For

The aglucone is redirected by specifier proteins where present; otherwise it forms an isothiocyanate.

PMID:19224919

The aglucone is redirected by specifier proteins where present; otherwise it forms an isothiocyanate.

Part 1: methionine side-chain elongation

Methionine chain-elongation cycleMetabolic Pathwaychain_elongation

A cycle recruited from leucine biosynthesis that adds one methylene group per turn to methionine. The deamination is cytosolic; the condensation, isomerization, oxidative decarboxylation and terminal transamination run in the chloroplast. The number of turns (set mainly by MAM paralogs) determines side-chain length; one turn yields homomethionine, the precursor of C3 (propyl/allyl) glucosinolates.

Connections

met_deamination -> mam_condensation Provides Input For

PMID:20457641

The cytosolic oxo acid enters plastid elongation. Transport is required but outside this module; the edge does not imply passive diffusion.

mam_condensation -> ipmi_isomerization Provides Input For

PMID:19597944

The condensed 2-malate derivative is isomerized to the 3-malate derivative by the heterodimer.

ipmi_isomerization -> ipmdh_decarboxylation Provides Input For

PMID:21697089

The methylthioalkyl 3-malate substrate undergoes NAD-dependent oxidative decarboxylation.

ipmdh_decarboxylation -> mam_condensation Provides Input For

PMID:14740211

The elongated oxo acid can enter another condensation cycle according to MAM substrate specificity; repeated cycles are not mandatory for every molecule.

ipmdh_decarboxylation -> bcat3_transamination Provides Input For

PMID:18162591

Transamination provides a characterized short-chain exit route rather than the exclusive exit for all chain lengths.

Part 1: deamination of methionine

Methionine deamination (BCAT4)Reactionmet_deamination

Annotons

BCAT4: methionine:oxo-acid transaminase

bcat4_activity

Participant: Family: BCAT4 methionine aminotransferase subfamily

Family:

BCAT4 methionine aminotransferase subfamilyPANTHER:PTHR42825:SF8

Representative Members: BCAT4 (Arabidopsis)UniProtKB:Q9LE06 TAV2_LOCUS10345 (Thlaspi arvense; inferred homolog)UniProtKB:A0AAU9S298

Function

L-methionine:oxo-acid transaminase activityGO:0010326

Substrates: L-methionine

Products: 4-methylthio-2-oxobutanoate

Locations

cytosolGO:0005829

Part 2: condensation with acetyl-CoA

Methylthioalkylmalate synthase (MAM)Reactionmam_condensation

Annotons

MAM1/MAM3: methylthioalkylmalate synthase

mam_activity

Participant: Family: methylthioalkylmalate synthase homologs

Family:

methylthioalkylmalate synthase homologsPANTHER:PTHR10277 The verified parent family includes substrate-diverse condensation enzymes. Required methylthioalkylmalate synthase activity selects the pathway role; Arabidopsis/Thlaspi SF60 and Brassica MAM1-A SF73 are not asserted as one substrate-uniform subfamily.

Representative Members: MAM1 (Arabidopsis; first two elongation cycles)UniProtKB:Q9FG67 MAM3 (Arabidopsis; long-chain cycles)UniProtKB:Q9FN52 TAV2_LOCUS6842 (Thlaspi arvense; inferred homolog)UniProtKB:A0AAU9RP64 gsl-elong-A1 / BjMAM1-A (Brassica juncea)UniProtKB:C5J4P1

Required Function:

methylthioalkylmalate synthase activityGO:0010177

Function

methylthioalkylmalate synthase activityGO:0010177

Substrates: omega-methylthio-2-oxoalkanoate acetyl-CoA

Products: 2-(omega-methylthio)alkylmalate CoA

Locations

chloroplastGO:0009507

Part 3: isomerization

Isopropylmalate isomerase (IPMI, glucosinolate-type small subunit)Reactionipmi_isomerization

Annotons

IPMI heterodimer (LSU1 + SSU2/SSU3): 2-(omega-methylthio)alkylmalate dehydratase

ipmi_activity

Participant: Protein Complex: glucosinolate-chain-elongation isopropylmalate isomerase heterodimer

Protein Complex:

glucosinolate-chain-elongation isopropylmalate isomerase heterodimerGO:0009316

Active units:

IPMI large-subunit homologs

Participant: Family: IPMI large-subunit homologs

Family:

IPMI large-subunit homologsPANTHER:PTHR43822:SF2

Representative Members: IIL1 / LSU1 (Arabidopsis; IPMI large subunit)UniProtKB:Q94AR8 TAV2_LOCUS24872 (Thlaspi arvense; inferred homolog)UniProtKB:A0AAU9T4X1

Required Function:

contribution to glucosinolate-chain-elongation IPMI activity A contributing subunit role; the complete reaction is assigned to the heterodimer.

Role: Shared catalytic large subunit; pathway specificity depends on the assembled complex.

PMID:19597944

Heterodimeric IPMI combines a shared large subunit with small subunits that distinguish leucine biosynthesis and methionine chain elongation.

PMID:32612621

Arabidopsis SSU2/3 and SSU1 complexes differ in metabolic role and plastid distribution; Thlaspi roles remain inferred.

glucosinolate-type IPMI small-subunit homologs

Participant: Family: glucosinolate-type IPMI small-subunit homologs

Family:

glucosinolate-type IPMI small-subunit homologsPANTHER:PTHR43345

Representative Members: SSU3 (Arabidopsis; IPMI small subunit)UniProtKB:Q9LYT7 TAV2_LOCUS13090 (Thlaspi arvense; inferred homolog)UniProtKB:A0AAU9S4C4

Required Function:

contribution to glucosinolate-chain-elongation IPMI activity A contributing subunit role; the complete reaction is assigned to the heterodimer.

Role: SSU2/3-type specificity subunit; the broad family also contains leucine-specialized members and requires the stated function constraint.

PMID:19597944

Heterodimeric IPMI combines a shared large subunit with small subunits that distinguish leucine biosynthesis and methionine chain elongation.

PMID:32612621

Arabidopsis SSU2/3 and SSU1 complexes differ in metabolic role and plastid distribution; Thlaspi roles remain inferred.

Function

2-(omega-methylthio)alkylmalate dehydratase activityGO:0120528

Substrates: 2-(omega-methylthio)alkylmalate

Products: 3-(omega-methylthio)alkylmalate

Locations

chloroplast stromaGO:0009570

Activity requires the heterodimeric 3-isopropylmalate dehydratase complex (GO:0009316); the gene reviews record each subunit as contributes_to this activity in that complex. LSU1 is shared with leucine biosynthesis (with SSU1); SSU2/SSU3 specialize the enzyme for methionine chain elongation.

Part 4: oxidative decarboxylation

Isopropylmalate dehydrogenase (IPMDH1)Reactionipmdh_decarboxylation

Annotons

IPMDH1: 3-(omega-methylthio)alkylmalate dehydrogenase

ipmdh1_activity

Participant: Family: IPMDH1 subfamily

Family:

IPMDH1 subfamilyPANTHER:PTHR42979:SF5

Representative Members: IPMDH1 (Arabidopsis)UniProtKB:Q9FMT1 TAV2_LOCUS20462 (Thlaspi arvense; inferred homolog)UniProtKB:A0AAU9SYX6

Required Function:

3-(omega-methylthio)alkylmalate oxidative decarboxylation Functional constraint on the selected pathway members; the verified family also contains members with other substrates or biological roles.

Taxon:

BrassicaceaeNCBITaxon:3700

Function

3-(omega-methylthio)alkylmalate oxidative decarboxylation

Substrates: 3-(omega-methylthio)alkylmalate NAD+

Products: chain-elongated omega-methylthio-2-oxoalkanoate CO2 + NADH

Locations

chloroplast stromaGO:0009570

IPMDH1 catalyzes the specialized NAD-dependent oxidative decarboxylation step. GO:0003862 describes the distinct 3-isopropylmalate reaction and is not used as a broad term for this substrate.

The precise methylthioalkylmalate reaction is described in free text and in the gene reviews as a proposed MF; the leucine-specific GO:0003862 reaction is not used as its parent.

Part 5: transamination to the chain-elongated amino acid

Terminal transamination (BCAT3)Reactionbcat3_transamination

Annotons

BCAT3: transamination of elongated 2-oxo acids

bcat3_activity

Participant: Family: BCAT3 plastid branched-chain aminotransferase subfamily

Family:

BCAT3 plastid branched-chain aminotransferase subfamilyPANTHER:PTHR42825:SF2

Representative Members: BCAT3 (Arabidopsis)UniProtKB:Q9M401 TAV2_LOCUS15930 (Thlaspi arvense; inferred homolog)UniProtKB:A0AAU9SEL1

Required Function:

transamination of chain-elongated methionine oxo-acid homologs Functional constraint on the selected pathway members; the verified family also contains members with other substrates or biological roles.

Taxon:

BrassicaceaeNCBITaxon:3700

Function

transamination of chain-elongated methionine oxo-acid homologs

Substrates: chain-elongated omega-methylthio-2-oxoalkanoate

Products: homomethionine / dihomomethionine

Locations

chloroplastGO:0009507

BCAT3 is directly supported as a short-chain terminal transaminase and also serves branched-chain amino-acid metabolism. This is not unelongated methionine activity GO:0010326 and does not assert BCAT3 as the only exit enzyme for every chain length.

Part 2: core glucosinolate structure

Core glucosinolate structure formationMetabolic Pathwaycore_structure

Conversion of the chain-elongated methionine homolog to a desulfoglucosinolate and then to the intact glucosinolate.

Connections

aldoxime_formation -> aldoxime_oxidation Provides Input For

PMID:11133994

CYP79F1 produces defined chain-elongated methionine aldoximes.

PMID:12970475

Recombinant CYP83A1 accepts aliphatic oximes derived from chain-elongated methionine.

aldoxime_oxidation -> gsh_conjugation Provides Input For

PMID:35145536

Native GST contribution and intermediate handling remain unresolved.

gsh_conjugation -> ggp_cleavage Provides Input For

PMID:19483696

Native GST contribution and intermediate handling remain unresolved.

ggp_cleavage -> cs_lyase Provides Input For

PMID:21712415

GGP cleavage yields a cysteinylglycine conjugate, whereas SUR1 is commonly modeled with a cysteine conjugate. Whether SUR1 uses Cys-Gly directly or another peptidase acts first remains unresolved.

cs_lyase -> s_glucosylation Provides Input For

PMID:14871316

Reported pathway chemistry supplies the next step; individual enzyme and substrate evidence is distinguished from whole-pathway reconstruction.

s_glucosylation -> sulfation Provides Input For

PMID:16367753

Reported pathway chemistry supplies the next step; individual enzyme and substrate evidence is distinguished from whole-pathway reconstruction.

aldoxime_oxidation -> ggp_cleavage Provides Input For

PMID:12970475

Reactive CYP83-generated products are trapped by thiols.

PMID:35145536

GST mutants affect product abundance without directly reconstituting native intermediate conjugation.

Part 1: aldoxime formation

CYP79F aldoxime formationReactionaldoxime_formation

Annotons

CYP79F1/F2: homomethionine N-monooxygenase

cyp79f_activity

Participant: Family: CYP79F cytochrome P450 subfamily

Family:

CYP79F cytochrome P450 subfamilyPANTHER:PTHR24298:SF684 PANTHER release classifications place both Arabidopsis exemplars in PTHR24298:SF684, while current UniProt also records PTHR47944:SF19. Both placements are retained in the member index; the declared ID follows the release-supported CYP79F grouping.

Representative Members: CYP79F1 (Arabidopsis; short- and long-chain)UniProtKB:Q949U1 CYP79F2 (Arabidopsis; long-chain)UniProtKB:Q9FUY7

Function

homomethionine N-monooxygenase activityGO:0120526

Substrates: chain-elongated methionine homolog

Products: omega-methylthioalkanaldoxime

Locations

endoplasmic reticulum membraneGO:0005789

Part 2: aldoxime activation for glutathione conjugation

CYP83A1 aldoxime oxidationReactionaldoxime_oxidation

Annotons

CYP83A1: aliphatic aldoxime oxidation

cyp83a1_activity

Participant: Family: CYP83A1 cytochrome P450 subfamily

Family:

CYP83A1 cytochrome P450 subfamilyPANTHER:PTHR47956:SF11 PANTHER release classifications place CYP83A1 in PTHR47956:SF11, while current UniProt also records PTHR47955:SF22. Both placements are retained in the member index; neither surprising alternate family name is used as substrate evidence.

Representative Members: CYP83A1 / REF2 (Arabidopsis)UniProtKB:P48421

Function

(methylsulfanyl)alkanaldoxime N-monooxygenase activity (proposed new GO term; EC 1.14.14.43); parent shownGO:0016712

Substrates: omega-methylthioalkanaldoxime

Products: activated aci-nitro compound (conjugated to glutathione)

Locations

endoplasmic reticulum membraneGO:0005789

Part 3: candidate GST contributions to required sulfur conjugation (optional)

Sulfur incorporation is required chemistry, but the relative native roles of GSTU20, GSTF11 and spontaneous conjugation are unresolved. These candidate enzymes are therefore optional in the cross-species template rather than an asserted universally necessary two-enzyme step.

Glutathione conjugation (GSTU20/GSTF11)Reactiongsh_conjugation

Candidate GST contributions to sulfur incorporation. Two distinct GST families contribute genetically; their native intermediate reaction has not been reconstituted.

Annotons

GLUTATHIONE S-TRANSFERASE U20 (candidate native conjugation role)

gstu20_activity

Participant: Family: GLUTATHIONE S-TRANSFERASE U20

Family:

GLUTATHIONE S-TRANSFERASE U20PANTHER:PTHR11260:SF601

Representative Members: GSTU20 (Arabidopsis; major contributor)UniProtKB:Q8L7C9

Function

glutathione transferase activityGO:0004364

Locations

cytosolGO:0005829

Genetics and GST-family evidence support a candidate conjugation role. Native-intermediate catalysis and its quantitative contribution relative to spontaneous conjugation remain unresolved.

GLUTATHIONE S-TRANSFERASE F11 (candidate native conjugation role)

gstf11_activity

Participant: Family: GLUTATHIONE S-TRANSFERASE F11

Family:

GLUTATHIONE S-TRANSFERASE F11PANTHER:PTHR43900:SF64

Representative Members: GSTF11 (Arabidopsis)UniProtKB:Q96324

Function

glutathione transferase activityGO:0004364

Locations

cytosolGO:0005829

Genetics and GST-family evidence support a candidate conjugation role. Native-intermediate catalysis and its quantitative contribution relative to spontaneous conjugation remain unresolved.

Part 4: removal of the gamma-glutamyl residue

Gamma-glutamyl peptidase (GGP1)Reactionggp_cleavage

Annotons

GGP1: gamma-glutamyl peptidase

ggp1_activity

Participant: Family: GGP1 subfamily

Family:

GGP1 subfamilyPANTHER:PTHR42695:SF14

Representative Members: GGP1 (Arabidopsis)UniProtKB:Q9M0A7 TAV2_LOCUS24348 (Thlaspi arvense; inferred homolog)UniProtKB:A0AAU9T3M3

Function

gamma-glutamyl-peptidase activityGO:0034722

Substrates: S-(alkylacetohydroximoyl)-glutathione

Products: S-(alkylacetohydroximoyl)-cysteinylglycine L-glutamate

Locations

cytosolGO:0005829

Part 5: C-S cleavage to thiohydroximate

C-S lyase (SUR1)Reactioncs_lyase

Annotons

SUR1: S-alkylthiohydroximate lyase

sur1_activity

Participant: Family: SUR1 subfamily

Family:

SUR1 subfamilyPANTHER:PTHR45744:SF15

Representative Members: SUR1 (Arabidopsis)UniProtKB:Q9SIV0 TAV2_LOCUS11381 (Thlaspi arvense; inferred homolog)UniProtKB:A0AAU9RX80

Function

S-alkylthiohydroximate lyase activityGO:0080108

Substrates: S-(alkylacetohydroximoyl)-L-cysteine

Products: thiohydroximate

Locations

cytosolGO:0005829

Part 6: S-glucosylation

Thiohydroximate S-glucosylationReactions_glucosylation

Variant set: Major and accessory thiohydroximate glucosyltransferases (One Or More)

PMID:24779768

UGT74C1 complements UGT74B1 defects; the two enzymes provide overlapping routes rather than two sequential reactions.

UGT74B1 routeReactionugt74b1_route

Annotons

UGT74B1 major thiohydroximate glucosylation route

ugt74b1_activity

Participant: Family: UGT74B1 subfamily

Family:

UGT74B1 subfamilyPANTHER:PTHR11926:SF727

Representative Members: UGT74B1 (Arabidopsis)UniProtKB:O48676

Required Function:

thiohydroximate beta-D-glucosyltransferase activityGO:0047251

Function

thiohydroximate beta-D-glucosyltransferase activityGO:0047251

Substrates: thiohydroximate UDP-glucose

Products: desulfoglucosinolate UDP

Locations

cytosolGO:0005829

A major characterized core-structure glucosyltransferase; UGT74C1 can supply an accessory route.

UGT74C1 accessory routeReactionugt74c1_route

Annotons

UGT74C1: thiohydroximate S-glucosyltransferase (aliphatic)

ugt74_activity

Participant: Family: UGT74C1 subfamily

Family:

UGT74C1 subfamilyPANTHER:PTHR11926:SF1356

Representative Members: UGT74C1 (Arabidopsis)UniProtKB:Q9SKC1

Required Function:

thiohydroximate beta-D-glucosyltransferase activityGO:0047251

Function

thiohydroximate beta-D-glucosyltransferase activityGO:0047251

Substrates: thiohydroximate UDP-glucose

Products: desulfoglucosinolate UDP

Locations

cytoplasmGO:0005737

Accessory UGT74C1 route supported by enzymology and complementation of UGT74B1 defects; it is not required in addition to UGT74B1 for every realization.

Part 7: sulfation

Desulfoglucosinolate sulfotransferase (SOT17/SOT18)Reactionsulfation

Annotons

SOT17/SOT18: aliphatic desulfoglucosinolate sulfotransferase

sot_activity

Participant: Family: desulfoglucosinolate sulfotransferases (SOT16-18)

Family:

desulfoglucosinolate sulfotransferases (SOT16-18)PANTHER:PTHR11783

Representative Members: SOT18 (Arabidopsis)UniProtKB:Q9C9C9 SOT17 (Arabidopsis)UniProtKB:Q9FZ80 TAV2_LOCUS415 (Thlaspi arvense; inferred homolog)UniProtKB:A0AAU9RDZ2

Required Function:

aliphatic desulfoglucosinolate sulfotransferase activityGO:0120527 Functional constraint on the selected pathway members; the verified family also contains members with other substrates or biological roles.

Taxon:

BrassicaceaeNCBITaxon:3700

Function

aliphatic desulfoglucosinolate sulfotransferase activityGO:0120527

Substrates: aliphatic desulfoglucosinolate 3'-phosphoadenylyl sulfate (PAPS)

Products: aliphatic glucosinolate adenosine 3',5'-bisphosphate

Locations

cytoplasmGO:0005737

Part 3: side-chain modification (optional)

Side-chain S-oxygenation and alkenylationMetabolic Pathwayside_chain_modification

Optional decoration that varies between species and accessions. S-oxygenation gives methylsulfinylalkyl glucosinolates; AOP2 then converts them to alkenyl glucosinolates (for a C3 chain, allylglucosinolate/sinigrin). AOP2 is non-functional in some Arabidopsis accessions (e.g. Columbia), which therefore accumulate methylsulfinylalkyl glucosinolates.

Connections

s_oxygenation -> alkenylation Provides Input For

Methylsulfinylalkyl glucosinolate is the AOP2 substrate.

Part 1: S-oxygenation

Flavin monooxygenase S-oxygenation (FMO GS-OX)Reactions_oxygenation

Annotons

FMO GS-OX1-5: methylthioalkyl glucosinolate S-oxygenase

fmo_gsox_activity

Participant: Family: crucifer-specific FMO GS-OX subclade

Family:

crucifer-specific FMO GS-OX subclade

Representative Members: FMOGS-OX1 (Arabidopsis)UniProtKB:Q9SS04

Function

methylthioalkyl glucosinolate S-oxygenase activity

Substrates: methylthioalkyl glucosinolate NADPH + O2

Products: methylsulfinylalkyl glucosinolate

FMO GS-OX1 S-oxygenates multiple methylthioalkyl substrates. This generic reaction is not restricted to the C3-specific GO:0080102 activity; some experimental assays also use desulfoglucosinolates.

The selected GS-OX1 protein has a generic proposed methylthioalkyl glucosinolate S-oxygenase core. Free-text module chemistry captures its substrate range; no malformed or C3-only GO label is used for the generic activity.

Part 2: alkenylation (optional)

Alkenylation depends on functional AOP2 and is optional even when S-oxygenation occurs; methylsulfinyl-only profiles are valid realizations.

AOP2 alkenyl glucosinolate formationReactionalkenylation

Annotons

AOP2: 2-oxoglutarate-dependent dioxygenase (methylsulfinylalkyl -> alkenyl)

aop2_activity

Participant: Family: AOP 2-oxoglutarate-dependent dioxygenase family

Family:

AOP 2-oxoglutarate-dependent dioxygenase familyPANTHER:PTHR47990

Representative Members: AOP2 (Arabidopsis Cvi-0; functional allele)UniProtKB:Q945B5

Required Function:

conversion of methylsulfinylalkyl to alkenyl glucosinolates Functional constraint on the selected pathway members; the verified family also contains members with other substrates or biological roles.

Taxon:

BrassicaceaeNCBITaxon:3700

Function

alkenyl glucosinolate synthase activity (proposed new GO term); parent GO:0016706 shownGO:0016706

Substrates: methylsulfinylalkyl glucosinolate 2-oxoglutarate + O2

Products: alkenyl glucosinolate (e.g. allylglucosinolate)

Field pennycress has a complete AOP2-type coding sequence (TAV2_LOCUS22152, 84% identical to Brassica rapa AOP2), but its predicted protein (A0AAU9SS97) is a fragment caused by a false intron in the gene model, so it is not listed as a representative member. See projects/THLAR_OILSEED/ortholog_mapping/CALLS.md.

Part 4: damage-triggered hydrolysis

Myrosinase (thioglucosidase) hydrolysisReactionmyrosinase_hydrolysis

Myrosinases are kept apart from glucosinolates in intact tissue; on damage they hydrolyze the thioglucoside bond to release glucose and an unstable aglucone that, without a specifier protein, rearranges spontaneously to an isothiocyanate.

Annotons

TGG1/TGG2: myrosinase

tgg_activity

Participant: Family: classical myrosinase subfamily (glycoside hydrolase family 1)

Family:

classical myrosinase subfamily (glycoside hydrolase family 1)PANTHER:PTHR10353:SF218

Representative Members: TGG1 (Arabidopsis)UniProtKB:P37702 TGG2 (Arabidopsis)UniProtKB:Q9C5C2

Function

thioglucosidase activityGO:0019137

Substrates: glucosinolate H2O

Products: D-glucose glucosinolate aglucone (thiohydroximate-O-sulfate)

Processes

glucosinolate catabolic processGO:0019762 defense response to insectGO:0002213

Locations

plant-type vacuoleGO:0000325

Part 5: product specification (optional)

Specifier-protein redirection of the agluconeMetabolic Pathwayproduct_specification

Kelch-repeat, Fe(II)-dependent specifier proteins act on the myrosinase-generated aglucone and divert it from the default isothiocyanate. Which specifier is present sets the breakdown product profile of a tissue or species.

Variant set: Epithionitrile, simple nitrile or thiocyanate formation by specifier protein / product class (Zero Or More)

Epithiospecifier protein (epithionitriles and simple nitriles)Reactionesp_route

Annotons

ESP: epithionitrile-forming specifier

esp_activity

Participant: Family: epithiospecifier protein

Family:

epithiospecifier proteinPANTHER:PTHR47435:SF2

Representative Members: ESP (Arabidopsis)UniProtKB:Q8RY71

Function

carbon-sulfur lyase activity (epithionitrile-forming sulfolyase)GO:0016846

Substrates: alkenyl glucosinolate aglucone

Products: epithionitrile or simple nitrile

Locations

cytoplasmGO:0005737

Nitrile-specifier proteins (simple nitriles)Reactionnsp_route

Annotons

NSP1-5: nitrile-forming specifier

nsp_activity

Participant: Family: nitrile-specifier proteins (kelch-repeat specifier family)

Family:

nitrile-specifier proteins (kelch-repeat specifier family)PANTHER:PTHR47435

Representative Members: NSP1 (Arabidopsis)UniProtKB:Q9SDM9

Required Function:

simple nitrile formation from myrosinase-generated glucosinolate aglucones Specifier activity is a functional restriction; a broad kelch-repeat family assignment does not establish this reaction.

Function

carbon-sulfur lyase activity (nitrile-forming sulfolyase)GO:0016846

Substrates: glucosinolate aglucone

Products: simple nitrile

Locations

cytosolGO:0005829

Thiocyanate-forming protein (organic thiocyanates)Reactiontfp_route

Annotons

TFP: thiocyanate-forming specifier

tfp_activity

Participant: Family: thiocyanate-forming protein

Family:

thiocyanate-forming proteinPANTHER:PTHR47435:SF7

Representative Members: TaTFP (field pennycress)UniProtKB:G1FNI6

Required Function:

thiocyanate-forming specifier activity on allylglucosinolate aglucone Target-specific measured product specificity; the family label ESP does not establish thiocyanate formation for every member.

Function

carbon-sulfur lyase activity (thiocyanate-forming sulfolyase)GO:0016846

Substrates: allylglucosinolate aglucone

Products: allylthiocyanate 3,4-epithiobutane nitrile

Locations

cytosolGO:0005829

PMID:21783213

Purified Thlaspi TFP directly generates allylthiocyanate and the corresponding epithionitrile in myrosinase-coupled assays.