Camalexin biosynthesisMetabolic Pathwaycamalexin_biosynthesis
Boundary. Parts 1-4 are the biosynthetic pathway (GO:0010120); part 5 is kept as an explicit regulatory part with its own concept (GO:1901183) so that the enzyme-versus-regulator split made in the MPK3 and WRKY33 gene reviews is visible: MPK3/MPK6 and WRKY33 regulate the pathway and are not parts of it. Upstream perception (CERK1, FLS2, MKK4/MKK5), the MPK4-MKS1 sequestration of WRKY33, other transcriptional inputs, tryptophan supply, camalexin export (ABCG36/PDR8) and the indole glucosinolate, auxin and 4-hydroxy-ICN branches from IAOx are outside this module. Metabolon. CYP79B2, CYP71A12, CYP71A13 and CYP71B15 co-purify and interact (co-IP, FRET-FLIM) with each other and with P450 reductase ATR1 at the ER (PMID:31511315). This is recorded in prose rather than as a complex part because the complex has no GO term beyond generic catalytic complex and the soluble steps (GST, GGP) are not shown to be in it. GSTU4 binds the complex but is not a pathway enzyme. Gene reviews. CYP79B2, CYP79B3, CYP71A13, CYP71A12, GSTF6, CYP71B15, GGP1, WRKY33 and MPK3 have completed reviews (genes/ARATH/) and the annoton functions and locations follow their core functions; MPK6's review is also complete. GGP3 and GSTU4 have no gene review yet and are grounded by UniProt only. CYP71A13 and CYP71A12 are modelled as separate annotons. Both reviews now use GO:0047720 as the core molecular function, but CYP71A12 contributes little to camalexin and releases more cyanohydrin breakdown products, and its review proposes a cyanohydrin-forming term. PANTHER. Only GGP1 is in the local PANTHER member index, so the other family descriptors carry no PANTHER id. Ontology follow-ups (not knowledge gaps). GO has no molecular-function term for the first PAD3 reaction (Cys(IAN) to dihydrocamalexic acid with cyanide release, RHEA:10452; proposed in the CYP71B15 review as dihydrocamalexate synthase activity), and GO:0010298 describes the second reaction as a simple decarboxylation although it is an O2-dependent oxidative decarboxylation (RHEA:34807, EC 1.14.19.52). The MPK6 review now uses positive regulation of camalexin biosynthetic process, matching MPK3, so the paralogs are treated alike.
Connections
IAOx is the CYP71A13 substrate (channelled within the P450 metabolon).
The CYP71A13-derived electrophile (dehydro-IAN, formed via indole-3-cyanohydrin) is captured by glutathione.
Cys(IAN) is the PAD3 substrate.
WRKY33 binds and activates the CYP71A13 promoter.
WRKY33 binds and activates the PAD3 promoter.
Part 1: tryptophan to indole-3-acetaldoxime (CYP79B2/B3)
Part 2: indole-3-acetaldoxime to the reactive cyanohydrin / dehydro-IAN intermediate (CYP71A13, minor CYP71A12)
Part 3: glutathione conjugation and processing to the cysteine conjugate (GSTF6, GGP1/GGP3)
Glutathione conjugation and processingMetabolic Pathwaygsh_conjugation
Glutathione, not free cysteine, supplies the thiazole sulfur. The activated IAN intermediate is conjugated to glutathione (GS-IAN); the gamma-glutamyl residue is removed in the cytosol by GGP1 (and GGP3), and glycine is then removed by an unidentified peptidase to give Cys(IAN). The extracellular gamma-glutamyl transpeptidases GGT1/GGT2 were proposed for the gamma-glutamyl step but the intermediate-accumulation, localization and enzyme-activity evidence favours GGP1.
Connections
GS-IAN is the GGP substrate; the Cys(IAN)-Gly product is trimmed to Cys(IAN) by an unidentified peptidase before PAD3.
Part 1: glutathione conjugation of the activated IAN intermediate
Glutathione conjugation (GSTF6)Reactiongst_conjugation
Annotons
GSTF6: glutathione transferase (implicated)
gstf6_activity
Participant: Gene Product: GSTF6 (Arabidopsis)
Function
glutathione transferase activity (conjugation of activated IAN)GO:0004364
Substrates:
indole-3-cyanohydrin / activated IAN intermediate
glutathione
Products:
GS-IAN (gamma-Glu-Cys(IAN)-Gly)
Locations
The 'implicated' framing follows the GSTF6 gene review, which keeps glutathione transferase activity as core but treats GSTF6 as one of several redundant contributors to GS-IAN formation: single-gene knockout and overexpression effects are modest (Su et al. 2011), camalexin is normal in gstf2 gstf3 gstf6 triple and gstf2 gstf3 gstf6 gstf7 knockdown lines, 41 of 54 Arabidopsis GSTs supported GS-IAN formation with CYP71A13 in engineered yeast (Mucha et al. 2019, as reported in the GSTF6 deep research), and the CYP71A13-derived electrophile reacts with thiols without an enzyme (PMID:24151049). GOA has no camalexin annotation for GSTF6. GSTU4 (UniProtKB:Q9ZW27) is recruited to the metabolon but is not a pathway enzyme (camalexin rises in gstu4 knockouts; PMID:31511315) and is deliberately not modelled as a participant.
Part 2: removal of the gamma-glutamyl residue from GS-IAN
Gamma-glutamyl removal (GGP1/GGP3)Reactionggp_step
Annotons
GGP1 (and GGP3): gamma-glutamyl peptidase
ggp1_activity
Participant: Family: GGP1 gamma-glutamyl peptidase subfamily
Function
gamma-glutamyl-peptidase activityGO:0034722
Substrates:
GS-IAN (gamma-Glu-Cys(IAN)-Gly)
Products:
Cys(IAN)-Gly
L-glutamate
Locations
GGP3 (UniProtKB:Q9M0A5) acts redundantly (the ggp1 ggp3 double mutant has less camalexin than ggp1) but is not listed as a representative member because it is not in the local PANTHER member index for the GGP1 subfamily; it has no gene review. GGP1 also acts in core glucosinolate biosynthesis and glutathione catabolism (recorded in its gene review and in the aliphatic glucosinolate module).
Part 4: cysteine conjugate to dihydrocamalexic acid and camalexin (CYP71B15/PAD3)
Thiazole ring formation (PAD3)Metabolic Pathwaypad3_steps
The bifunctional P450 CYP71B15 (PAD3) catalyses two consecutive reactions (overall RHEA:52776, EC 1.14.19.52): thiazoline ring closure of Cys(IAN) with cyanide release to dihydrocamalexic acid (RHEA:10452), and oxidative decarboxylation of dihydrocamalexic acid to camalexin (RHEA:34807).
Annotons
CYP71B15/PAD3: dihydrocamalexate synthase (no GO term yet)
pad3_dhca_synthase
Participant: Gene Product: CYP71B15 / PAD3 (Arabidopsis)
Function
dihydrocamalexate synthase activity Proposed term (see knowledge gaps), reused from the CYP71B15 gene review; corresponds to RHEA:10452.
Substrates:
Cys(IAN) (2-(L-cystein-S-yl)-2-(1H-indol-3-yl)-acetonitrile)
O2
reduced [NADPH--hemoprotein reductase]
Products:
dihydrocamalexic acid
hydrogen cyanide
Locations
CYP71B15/PAD3: dihydrocamalexic acid decarboxylase (camalexin synthase)
pad3_dhca_decarboxylase
Participant: Gene Product: CYP71B15 / PAD3 (Arabidopsis)
Function
dihydrocamalexic acid decarboxylase activity (oxidative, P450)GO:0010298
Substrates:
dihydrocamalexic acid
O2
reduced [NADPH--hemoprotein reductase]
Products:
camalexin
CO2
Locations
GO:0010298 is defined as a simple decarboxylation and sits under carboxy-lyase activity, whereas the PAD3 reaction is an O2- and reductase-dependent oxidative decarboxylation (RHEA:34807). The term is used as in the CYP71B15 review, which raises the redefinition as a suggested question.
Connections
Dihydrocamalexic acid made in the first PAD3 reaction is the substrate of the second.
Part 5: transcriptional activation of the pathway (MPK3/MPK6-WRKY33; regulatory, not catalytic)
MPK3/MPK6-WRKY33 transcriptional activationRegulatory Stepwrky33_activation
Pathogen-activated MPK3 and MPK6 phosphorylate WRKY33, which binds W-boxes in the CYP71A13 and PAD3 promoters and drives their induction. This part regulates camalexin biosynthesis; its members are annotated to positive regulation of camalexin biosynthetic process (GO:1901183), not to the biosynthetic process itself.
positive regulation of camalexin biosynthetic processGO:1901183
Annotons
MPK3/MPK6: MAP kinase phosphorylating WRKY33
mpk3_mpk6_activity
Participant: Family: MPK3/MPK6 group A MAP kinases (redundant paralogs)
Family:
MPK3/MPK6 group A MAP kinases (redundant paralogs)
Function
MAP kinase activityGO:0004707
Targets:
WRKY33 (N-terminal SP sites)
Processes
positive regulation of camalexin biosynthetic processGO:1901183 Locations
The MPK3 and MPK6 reviews both use GO:1901183 (positive regulation of camalexin biosynthetic process) for this role, so the redundant pair is treated the same way.
WRKY33: W-box-binding activator of CYP71A13 and PAD3
wrky33_activity
Participant: Gene Product: WRKY33 (Arabidopsis)
Function
transcription cis-regulatory region binding (CYP71A13 and PAD3 promoters)GO:0000976
Targets:
CYP71A13 promoter
PAD3 (CYP71B15) promoter
Processes
positive regulation of camalexin biosynthetic processGO:1901183 Locations
Connections
Phosphorylation of WRKY33 at MPK3/MPK6 sites is needed for full camalexin induction (phospho-site mutant WRKY33 complements poorly).
PMID:21498677Mutation of MPK3/MPK6 phosphorylation sites in WRKY33 compromises its ability to complement the camalexin induction in the wrky33 mutant