CYP71A13 (At2g30770, UniProt O49342) — curation notes

Identity

• Cytochrome P450 71A13, Arabidopsis thaliana; N-terminal single-pass membrane anchor (UniProt FT TRANSMEM 2..20), heme-thiolate Cys (BINDING 439). PANTHER PTHR47955:SF15 (CYP71A2-like). Tandem paralog of CYP71A12 (At2g30750), ~90% identity PMID:24151049.

Catalytic function

• Original characterization: recombinant CYP71A13 converts indole-3-acetaldoxime (IAOx) to indole-3-acetonitrile (IAN); cyp71A13 mutants make greatly reduced camalexin; IAN feeding rescues [PMID:17573535 "CYP71A13 expressed in Escherichia coli converted IAOx to indole-3-acetonitrile (IAN)"; "Exogenously supplied IAN restored camalexin production in cyp71A13 mutant plants"]. Basis of EC 4.8.1.3 / RHEA:23156 / GO:0047720.
• Klein et al. 2013 (yeast microsomes with ATR1): reaction is strictly NADPH-dependent and also oxidative; CYP71A13 produces, in the presence of Cys/GSH, Cys-IAN, via a proposed alpha-hydroxy-IAN (cyanohydrin) -> dehydro-IAN electrophile [PMID:24151049 "the formation of both IAN and IAL is strictly dependent on the presence of both CYP71A13 and the cofactor NADPH"; "These data establish that CYP71A13 catalyzes the conversion of IAOx to an electrophile capable of accepting the thiol group of L-cysteine or glutathione"]. Three P450s (CYP79B2, CYP71A13, CYP71B15) suffice to reconstitute camalexin in vitro. So CYP71A13 is a genuine heme monooxygenase, not only a dehydratase; the IAOx-dehydratase term captures the IAN-forming part of the reaction only.
• Mucha et al. 2019 (abstract): indole-3-cyanohydrin "is synthesized by CYP71A12 and especially CYP71A13" PMID:31511315.
• Kinetics: catalytic efficiency on IAOx ~0.029 uM-1 s-1 for CYP71A13 vs ~0.066 for CYP71A12 PMID:25953104.
• No GO MF term exists for the oxidative IAOx -> cyanohydrin/dehydro-IAN step (OLS search for "indoleacetaldoxime" returns only GO:0047720). Mechanism still partly proposed, so no new-term proposal made; raised as a question.

Biological process

• Camalexin biosynthesis: cyp71a13 ~2.2% of WT camalexin after UV; cyp71a12 cyp71a13 double KO essentially camalexin-deficient PMID:25953104. CYP71A13 is the dominant isoform for camalexin in leaves; CYP71A12 for ICOOH derivatives PMID:31411742.
• Defense: cyp71A13 susceptible to Alternaria brassicicola PMID:17573535; UV-C-induced resistance to Botrytis lost in cyp71A13 PMID:19154205; infection defects with P. cucumerina / C. tropicale PMID:31411742. All downstream of camalexin production — the enzyme acts upstream of defense by making the phytoalexin.
• Rhizobacterium (P. fluorescens SS101) induced resistance to Pst requires camalexin; cyp71A13 among tested mutants PMID:23073694. Root-specific camalexin also controls PGPR growth promotion (CYP71A27 paper, cyp71A12/A13 as comparators) PMID:31311863.

Complex / localization

• Camalexin metabolon: co-IP and FRET-FLIM show CYP71A13 associates with CYP79B2, CYP71B15 (PAD3), ATR1 and GSTU4; CYP71A13 allosterically increases CYP79B2 substrate affinity PMID:31511315. Supports ComplexPortal "catalytic complex" NAS; the three IPI "protein binding" rows (CYP71B15, GSTU4, 14-3-3 omega/GRF2 At1g78300 from TAP proteomics PMID:19452453) are uninformative and removed per policy.
• Localization: P450 N-terminal anchor; ER membrane expected (plant class II P450), cytosolic-facing catalytic domain. GOA has "ER lumen" IDA from PMID:33831160 (TAIR) — this PMID does not resolve in NCBI E-utilities ("cannot get document summary") or Europe PMC (0 hits); PubMed web page served a JS challenge so no redirection notice could be checked. No canonical replacement established; per docs/reference_curation.md not guessed. Same row exists for CYP71A12. Topologically, "lumen" is unexpected for a signal-anchored P450, but paper unreadable -> UNDECIDED.
• Mitochondrion ISM (AtSubP prediction) — contradicted by the ER-type N-terminal anchor; removed.

Expression (project context, not annotation grounds)

• Tang et al. 2023 (Colletotrichum higginsianum single-cell atlas; full text user-supplied): "CYP71A12 was induced mainly in the epidermis, whereas CYP71A13 was almost exclusively induced in the vasculature cells" at infection sites. Expression only; no GO annotation follows. [PMID:37741284, cached abstract only]
• UniProt: induced by Pst DC3000, B. cinerea, flagellin, BTH, UV-C; repressed by WRKY18/WRKY40.

PMID:33831160 investigation

• just fetch-gene-pmids failed; esummary returns error "cannot get document summary"; Europe PMC EXT_ID query hitCount 0; WebSearch no hits. Treated as unresolvable/likely deleted PMID; annotation set UNDECIDED; reference kept with original id for provenance, flagged in reference_review.

Deep research provenance

• just deep-research-falcon ARATH CYP71A13 --fallback perplexity-lite: the just recipe reported failure (perplexity provider unavailable as fallback), but the falcon client process completed later and wrote CYP71A13-deep-research-falcon.md (on-topic; consistent with this review).
• just deep-research ARATH CYP71A13 --provider asta: returned only off-topic papers (database/genome-assembly papers, none on CYP71A13); file deleted.
• just deep-research ARATH CYP71A13 --provider openscientist: completed, on-topic (CYP71A13-deep-research-openscientist.md).
• Both reports state (from Mucha et al. 2019 full text, not in our abstract-only cache) that fluorescent CYP71A13 fusions localize to the ER in N. benthamiana and that CYP71A13 co-IPs with ATR1 and CYP71B15. Not independently verified here (PMC full text could not be retrieved), so ER membrane was not added as a NEW annotation; it is flagged in suggested questions/experiments.

Synthesis approach

• Function inferred from convergent lines: (1) enzyme assays (E. coli, yeast microsomes: IAOx -> IAN, NADPH-dependent oxidative products, Cys-IAN with thiol donor, in vitro camalexin reconstitution) [PMID:17573535, PMID:24151049, PMID:25953104]; (2) mutant metabolite phenotypes (single ~2% camalexin, double KO traces; IAN rescue) [PMID:17573535, PMID:25953104]; (3) resistance phenotypes (A. brassicicola, B. cinerea UV-C-induced resistance, P. cucumerina/C. tropicale) [PMID:17573535, PMID:19154205, PMID:31411742]; (4) UniProt/Rhea (RHEA:23156, EC 4.8.1.3); (5) P450 family context (heme-thiolate, N-anchor) and paralog CYP71A12 (partially redundant, biased to ICOOH); (6) PAINT IBA node PTN005384924 for ISR is the CYP71A12/A13 clade, grounded in their own IMPs. Tang 2023 single-cell data used only as expression context.
• Consistent with sibling CYP71A12 review: ER lumen IDA (PMID:33831160) UNDECIDED with topology caveat; ISR IBA and IMP KEEP_AS_NON_CORE (camalexin-dependent, SA-dependent ISR by P. fluorescens SS101).

PMID:33831160 follow-up (coordinator check, 2026-10-02)

Rechecked directly: NCBI esummary returns "cannot get document summary", efetch returns an
empty PubmedArticleSet, and Europe PMC (EXT_ID:33831160) has 0 hits. The PubMed web page
(pubmed.ncbi.nlm.nih.gov/33831160/) serves a bot challenge, so any duplicate/redirect notice
could not be read; the record is therefore unidentified, not shown to be deleted.
QuickGO lists six TAIR annotations citing it, all dated 2022-02-03: GO:0005788 ER lumen (IDA)
on CYP71A12, CYP71A13 and CYP71B15; GO:0005783 ER (IDA) on CYP71B15; and two GO:0005515 IPI
rows on CYP71B15. This content resembles Mucha et al. 2019 (PMID:31511315, camalexin
metabolon), but per docs/reference_curation.md no replacement is recorded from similarity
alone. Someone with browser access to PubMed, or TAIR, can settle it in one lookup.

PMID:33831160 resolved (2026-10-02)

PubMed's redirection notice (read in a browser by the project lead): "PMID: 33831160 was deleted
because it is a duplicate of PMID: 31511315" (Mucha et al. 2019, camalexin metabolon). Recorded as
replacement: {reference_id: PMID:31511315, reason: DUPLICATE_RECORD} on the reference.
Mucha's full text (read on PMC, PMC6881122; not cacheable, PMC serves abstract only) shows
CYP71A12, CYP71A13 and CYP71B15 fusions colocalizing with the ER lumenal marker RFP-HDEL
(Supplemental Figure 4), and states that eukaryotic P450s are anchored to the ER membrane with
the catalytic centre facing the cytosol. The ER lumen IDA was therefore changed from UNDECIDED to
MODIFY -> GO:0005789 endoplasmic reticulum membrane: the organelle call is sound, the lumen call
over-reads a confocal colocalization.

2026-10-09: combined with independent review

Reconciled with an independent review (PR 4451; all 24 GOA rows matched one-to-one, no GOA drift, no NEW rows in either).

Decisions changed relative to the merged review:
- GO:1902494 catalytic complex (NAS, PMID:31511315): ACCEPT -> KEEP_AS_NON_CORE, and in_complex dropped from core_functions. The metabolon association is real, but it is a dynamic, pathogen-induced assembly; CYP71A13 is active alone with reductase PMID:24151049. This matches the CYP71A12, CYP71B15 and CYP79B2 reviews.

Decisions kept from the merged review where the two differed:
- GO:0005788 ER lumen IDA (PMID:33831160 -> PMID:31511315): kept MODIFY -> GO:0005789 ER membrane. The independent review used UNDECIDED because it could not read Mucha 2019. The merged review's MODIFY rests on a later full-text reading of PMC6881122 (RFP-HDEL colocalization, Suppl. Fig. 4; the text says P450 catalytic centres face the cytosol), recorded in the 2026-10-02 section above. The sibling CYP71A12 review does the same. On 2026-10-09 the PubMed full-text tool returned the abstract only, so the full text was not re-read.
- GO:0009682 ISR (IBA and IMP): kept MARK_AS_OVER_ANNOTATED (the independent review used KEEP_AS_NON_CORE). QuickGO definition checked 2026-10-09: "...systemic resistance to disease that does not depend upon salicylic acid signaling". PMID:23073694 reports that the SS101-induced resistance is SA-dependent.
- GO:0016020 membrane (IEA, NAS): kept ACCEPT (the independent review used MODIFY -> ER membrane). The ER membrane term is already supplied by the ER lumen MODIFY.
- GO:0004497 monooxygenase (ACCEPT vs non-core), GO:0005506 iron ion binding (non-core vs over-annotated), GO:0020037 heme binding (non-core vs ACCEPT): kept the merged decisions. Both versions are defensible, and the sibling reviews are themselves mixed. Added the 18O2-incorporation quote PMID:24151049 to the monooxygenase row.

Added from the independent review:
- PMID:26352477 (Rajniak 2015, full text cached): cyp71A13 mutants are more susceptible to Pst ("Notably, the adult leaves and seedlings of the camalexin pathway mutants cyp71A13 and pad3 are also more susceptible to Pst infection compared to WT"). Added as support on the defense response to bacterium IMP row. The same paper shows 4-OH-ICN is made by CYP71A12, not CYP71A13.
- A suggested question on CYP71A12 compensation per tissue, and a kinetic product-partitioning experiment.
- Both reviews independently raised the missing GO term for the cyanohydrin/dehydro-IAN-forming activity PMID:24151049. It is kept as a single suggested question.
- The independent review's deep-research quotes cited a falcon file that is not in the repo. None were carried over.