caryoynencin

naturalproductmech:mibig-d02aa1e8bc MINTED SEEDED

Grounding review: No 3-star ChEBI entry shares this structure, so the record keeps a content-hashed identifier.

What these status tags mean

Curation status describes a workflow state. SEEDED means the record entered through the source-seeding workflow; it does not imply that no later curation occurred. PROPOSED marks an addition awaiting review; REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record. These are workflow decisions, not independently verified human review. Agent-assisted contributions may appear in the record history.

Grounding describes the identifier mapping: EXACT uses an ontology identity asserted by the source; MINTED keeps a local identifier when no defensible ontology identity is available; REVIEW_NEEDED flags an exact structure whose ontology identity needs adjudication. The grounding note retains any unresolved alternatives. These tags do not establish the strength of producer or activity evidence.

Structure

Standard InChIKey	GOOGOKNSXZDSND-QDCWQMMGSA-N
SMILES	C#CC#CC#CC#C/C=C/C=C/C(CCCCC(=O)O)O
Stereochemistry	undefined stereocentres — the InChIKey does not distinguish this compound from its stereoisomers
Cross-references	pubchem:6474912

Filing pathway

Fatty acids — computed by NPClassifier npclassifier.gnps2.org@2026-09-07, which is why it is pinned rather than recomputed. The gene cluster's asserted class is other, from MIBiG.

Producer organisms 1

A claim that this taxon makes the compound. The basis says what the evidence addressed — a knockout and a database assertion are not the same claim.

Taxon	Basis	Cluster	Evidence
Burkholderia gladioli BSR3 NCBITaxon:999541	SOURCE_ASSERTION	mibig:BGC0000892	PMID:24898429, https://mibig.secondarymetabolites.org/repository/BGC0000892.4/index.html

Occurrences 1

Somebody found the compound in this organism and cited it. That is not a claim that the organism makes it, and nothing here promotes one to the other.

Taxon	Source	Reference
Burkholderia caryophylli NCBITaxon:28094	LOTUS	DOI:10.1016/S0040-4039(00)96437-2

Biosynthetic gene clusters 1

Accession	Host	Locus evidence	Genome
mibig:BGC0000892	Burkholderia gladioli BSR3 NCBITaxon:999541	CLUSTER_UNSTATED	genbank:CP002599.1

A locus claim and a taxon claim are different questions. Heterologous expression settles the first and leaves the second where the isolation report left it.

Mechanism & Biosynthesis Overview

Causal graph — biosynthesis 11 nodes, 10 edges

Caryoynencin-related CayG/CayL assay evidence, not an exact-isomer yield or native complex. Current CayG sequence example, tagged preparations and isomer-containing products remain distinct. No CayK biochemical success, catalytic channeling or detailed reaction sequence asserted. The later DOI:10.1021/acs.joc.3c01789 abstract reports a different sequence in a Cab57 context; its full methods are unread. Imported BSR3 attribution remains a separate issue622, not validated by this graph. No antimicrobial-target claim or full-record sign-off.

Subject	Predicate	Object	Notes	Evidence
Ballard 720 reference locus on FXAH01000012.1	encodes_native_reference	Native CayG sequence reference	FXAH01000012.1 CDS65666..66862(-),1-based inclusive; SMF59989.1,398aa. CDS-aware table11=GenPept=UniProt sequencev1,unreviewed entry40. Also equals the historical DSM50341 CayG/AIG53832.1 translation in partial KJ815057.1; the historical nucleotide sequence lacks the complete CDS stop codon. CCUG20834 lists Ballard720 and DSM50341 as collection designations. Neither the strain lineage nor sequence equality identifies a tagged assay stock.	https://www.ncbi.nlm.nih.gov/nuccore/FXAH01000012.1 https://www.ncbi.nlm.nih.gov/protein/SMF59989.1 https://www.ncbi.nlm.nih.gov/nuccore/KJ815057.1 https://www.ccug.se/strain?id=20834 https://www.uniprot.org/uniprotkb/A0A075T858 reference https://www.ncbi.nlm.nih.gov/nuccore/FXAH01000012.1 evidence type DATABASE_ASSERTION notes Source and complete native CDS inspected. retrieved on 2026-10-06 reference https://www.ncbi.nlm.nih.gov/protein/SMF59989.1 evidence type DATABASE_ASSERTION notes Independent versioned GenPept inspected. retrieved on 2026-10-06 reference https://www.ncbi.nlm.nih.gov/nuccore/KJ815057.1 evidence type DATABASE_ASSERTION notes Historical cayG gene/DSM50341 and partial annotation inspected. retrieved on 2026-10-06 reference https://www.ccug.se/strain?id=20834 evidence type DATABASE_ASSERTION notes Culture collection designations inspected. retrieved on 2026-10-06 reference https://www.uniprot.org/uniprotkb/A0A075T858 evidence type CURATOR_INFERENCE notes Exact four-way sequence comparison; reference only. retrieved on 2026-10-06
Study N-His6 CayG preparation	has_native_sequence_example	Native CayG sequence reference	An explicitly selected same-species/gene reference, not verified study-strain, allele or full construct identity. Main text names T.caryophylli; detailed construct methods remain unread. Do not assign UniProt directly to the tagged preparation.	DOI:10.1002/anie.202203264 https://www.ncbi.nlm.nih.gov/nuccore/KJ815057.1 https://www.uniprot.org/uniprotkb/A0A075T858 reference DOI:10.1002/anie.202203264 evidence type CURATOR_INFERENCE notes Retained main PDF and Figures 1-5 inspected; detailed SI methods unread. Native gene/species context only. retrieved on 2026-10-06 reference https://www.ncbi.nlm.nih.gov/nuccore/KJ815057.1 evidence type DATABASE_ASSERTION notes Native DSM50341 cayG reference. retrieved on 2026-10-06 reference https://www.uniprot.org/uniprotkb/A0A075T858 evidence type CURATOR_INFERENCE notes Deliberate native sequence example, not assay-stock grounding. retrieved on 2026-10-06
Study N-His6 CayG preparation	was_included_in	Reported CayG/CayL in-vitro assay	Soluble N-terminal His6 preparation expressed in BL21(DE3); exact vector, linker and full stock sequence unverified. No direct protein association asserted.	DOI:10.1002/anie.202203264 reference DOI:10.1002/anie.202203264 evidence type PRIMARY_EXPERIMENT notes Retained main PDF and Figures 1-5 inspected; detailed SI methods unread. Main page3 and Figure3A trace a. retrieved on 2026-10-06
Study N-His6 CayL preparation	was_included_in	Reported CayG/CayL in-vitro assay	Soluble tagged CayL expressed in BL21(DE3). No exact native CayL accession selected; a neighboring rubredoxin or FDR homolog must not substitute for the tested reagent.	DOI:10.1002/anie.202203264 reference DOI:10.1002/anie.202203264 evidence type PRIMARY_EXPERIMENT notes Retained main PDF and Figures 1-5 inspected; detailed SI methods unread. Main page3 and Figure3A trace a. retrieved on 2026-10-06 snippet N-His6-tagged CayL
Study E. coli flavodoxin reductase reagent	was_included_in	Reported CayG/CayL in-vitro assay	E.coli flavodoxin reductase is a supplied reagent, not a verified native CayG partner or a fully identified stock. Other reported reagents: Tris buffer,NADPH,glucose-6-phosphate and baker's yeast glucose-6-phosphate dehydrogenase. No concentrations or kinetic constants adopted.	DOI:10.1002/anie.202203264 reference DOI:10.1002/anie.202203264 evidence type PRIMARY_EXPERIMENT notes Retained main PDF and Figures 1-5 inspected; detailed SI methods unread. Main page3 assay-reconstitution paragraph. retrieved on 2026-10-06
Source-assigned protegencin substrate 2	was_supplied_to	Reported CayG/CayL in-vitro assay	Compound2 follows Figure1, main text and Figure3 structures. Figure3's caption reverses the names for compounds1/2; that discrepancy is not silently propagated.	DOI:10.1002/anie.202203264 reference DOI:10.1002/anie.202203264 evidence type PRIMARY_EXPERIMENT notes Retained main PDF and Figures 1-5 inspected; detailed SI methods unread. Figures1 and3 visually inspected alongside main page3. retrieved on 2026-10-06
Reported CayG/CayL in-vitro assay	yielded_reported_mixture	Source-assigned assay product mixture	HPLC retention,UV and mass comparisons support source product assignments. No yield,concentration,absolute stereochemistry,physiological flux or complete pathway asserted. CayG-only control yielded small amounts of3; CayL-only control yielded no additional product under the reported conditions, not universal inactivity.	DOI:10.1002/anie.202203264 reference DOI:10.1002/anie.202203264 evidence type PRIMARY_EXPERIMENT notes Retained main PDF and Figures 1-5 inspected; detailed SI methods unread. Main page3 and Figure3A; the full reaction differs from omission controls. retrieved on 2026-10-06
Source-assigned assay product mixture	included_source_assigned_component	Source-assigned E,E-caryoynencin component	Figure3A distinguishes E,E and Z,E peaks of1. Only the E,E component relates to this owner's alkene geometry; the mixture is not the exact owner structure. No absolute alcohol stereochemistry or mixture-level quantity assigned to the stereo-incomplete owner.	DOI:10.1002/anie.202203264 reference DOI:10.1002/anie.202203264 evidence type PRIMARY_EXPERIMENT notes Retained main PDF and Figures 1-5 inspected; detailed SI methods unread. Figure3A visually inspected; caption numbering conflict retained. retrieved on 2026-10-06
Source-assigned assay product mixture	included_source_assigned_component	Source-assigned deoxycaryoynencin component 3	Time-course rise then decline supports an intermediate hypothesis, not direct proof of a bound intermediate. Isolated3 was not converted when re-added in a fresh assay.	DOI:10.1002/anie.202203264 reference DOI:10.1002/anie.202203264 evidence type PRIMARY_EXPERIMENT notes Retained main PDF and Figures 1-5 inspected; detailed SI methods unread. Main page3,Figure3C and Figure4C trace a; proposed mechanism is not asserted. retrieved on 2026-10-06
Source-assigned assay product mixture	included_source_assigned_component	Source-assigned 8-hydroxyprotegencin component 4	A source-assigned coproduct, not caryoynencin. Isolated4 was not further converted in the reported assay; no universal substrate exclusion inferred.	DOI:10.1002/anie.202203264 reference DOI:10.1002/anie.202203264 evidence type PRIMARY_EXPERIMENT notes Retained main PDF and Figures 1-5 inspected; detailed SI methods unread. Main page3 and Figure4C trace b. retrieved on 2026-10-06

Every edge carries its own citation; an uncited edge is refused by the corpus tests.

Causal graph — biosynthesis 9 nodes, 9 edges

CayK-associated product-profile change in a P. protegens Pf-5 heterologous expression comparison. Genetic constructs, unresolved protein identities and isomer-containing products are distinct. No purified CayK catalysis, exact stock identity, direct protein association or detailed reaction sequence is asserted. This does not validate the imported BSR3 attribution tracked in issue622 or confer full-record sign-off.

Subject	Predicate	Object	Notes	Evidence
CayG component encoded in the heterologous experiment	was_encoded_by_reported_construct_in	P. protegens Pf-5 carrying the cayG construct	Main text describes cayG in pJB861 downstream of Pm and induction with m-toluic acid. This is a genetic expression assignment, not a protein abundance measurement or exact sequence/allele verification.	DOI:10.1002/anie.202203264 reference DOI:10.1002/anie.202203264 evidence type PRIMARY_EXPERIMENT notes Retained main PDF and Figure2 inspected; detailed SI methods unread. Main page2 and Figure2B trace b. retrieved on 2026-10-06
CayG component encoded in the heterologous experiment	was_encoded_by_reported_construct_in	P. protegens Pf-5 carrying the cayKG construct	Figure2B trace c depicts the KG construct; main page3 explicitly reports cayKG co-expression. Detailed insert boundaries and laboratory stock sequence remain unverified; no tagged in-vitro preparation is identified here.	DOI:10.1002/anie.202203264 reference DOI:10.1002/anie.202203264 evidence type PRIMARY_EXPERIMENT notes Retained main PDF and Figure2 inspected; detailed SI methods unread. Main page3 and Figure2B trace c. retrieved on 2026-10-06
CayK component encoded in the heterologous experiment	was_encoded_by_reported_construct_in	P. protegens Pf-5 carrying the cayKG construct	The paper calls CayK ferritin-like; that assignment is not a solved fold or a measured electron-transfer rate. No exact CayK UniProt example selected. A neighboring AurF-annotated protein is not sufficient identity evidence.	DOI:10.1002/anie.202203264 reference DOI:10.1002/anie.202203264 evidence type PRIMARY_EXPERIMENT notes Retained main PDF and Figure2 inspected; detailed SI methods unread. Abstract, main pages2-3 and Figure2B trace c. retrieved on 2026-10-06 snippet ferritin-like protein (CayK)
P. protegens Pf-5 carrying the cayG construct	was_profiled_in	Reported culture-extract product-profile comparison	The cayG-only transformant did not show the caryoynencin product peaks seen with KG and was reported unchanged from the empty-vector profile. This condition-specific result does not prove universal CayG inactivity.	DOI:10.1002/anie.202203264 reference DOI:10.1002/anie.202203264 evidence type PRIMARY_EXPERIMENT notes Retained main PDF and Figure2 inspected; detailed SI methods unread. Main page2 and Figure2B traces a-b. retrieved on 2026-10-06
P. protegens Pf-5 carrying the cayKG construct	was_profiled_in	Reported culture-extract product-profile comparison	HPLC-DAD culture-extract profiling shows source-assigned caryoynencin peaks with KG. No exact-isomer yield, protein abundance, direct binding or native T. caryophylli production rate is inferred.	DOI:10.1002/anie.202203264 reference DOI:10.1002/anie.202203264 evidence type PRIMARY_EXPERIMENT notes Retained main PDF and Figure2 inspected; detailed SI methods unread. Main page3 and Figure2B trace c. retrieved on 2026-10-06
Reported culture-extract product-profile comparison	supports_cayk_associated_product_gain	Source-assigned caryoynencin isomer mixture	The G versus KG contrast supports a CayK-associated genetic contribution in this host. Host factors remain present; this is not purified CayK turnover, a unique native redox partnership or a physical protein complex. GL and KLG also produced the reported peaks; K and KL controls did not show them. The separately described soluble N-MalE-CayK reconstitution was unsuccessful, so in-vivo support is not in-vitro success.	DOI:10.1002/anie.202203264 reference DOI:10.1002/anie.202203264 evidence type PRIMARY_EXPERIMENT notes Retained main PDF and Figure2 inspected; detailed SI methods unread. Main page3 and Figure2B traces b-g; Figure2 caption lists b-f although the displayed panel additionally contains trace g. retrieved on 2026-10-06
Source-assigned caryoynencin isomer mixture	included_source_assigned_component	Source-assigned E,E-caryoynencin component	Figure2B trace c labels an E,E peak of compound1. This component relates to the owner's alkene geometry; mixture-level evidence is not an exact structure yield or an independently validated alcohol stereochemistry.	DOI:10.1002/anie.202203264 reference DOI:10.1002/anie.202203264 evidence type PRIMARY_EXPERIMENT notes Retained main PDF and Figure2 inspected; detailed SI methods unread. Main page3 and visually inspected Figure2B trace c. retrieved on 2026-10-06
Source-assigned caryoynencin isomer mixture	included_source_assigned_component	Source-assigned Z,E-caryoynencin component	Figure2B trace c separately labels a Z,E peak of compound1. This isomer is not the owner's E,E structure and receives no owner identifier.	DOI:10.1002/anie.202203264 reference DOI:10.1002/anie.202203264 evidence type PRIMARY_EXPERIMENT notes Retained main PDF and Figure2 inspected; detailed SI methods unread. Main page3 and visually inspected Figure2B trace c. retrieved on 2026-10-06
Native CayG sequence reference	is the native sequence reference for	CayG component encoded in the heterologous experiment	UniProtKB:A0A075T858 is the native Burkholderia caryophylli CayG reference corresponding to the heterologously expressed cayG component.	https://www.uniprot.org/uniprotkb/A0A075T858 DOI:10.1021/acschembio.1c00991 reference https://www.uniprot.org/uniprotkb/A0A075T858 evidence type DATABASE_ASSERTION retrieved on 2026-10-17 notes Active UniProtKB entry A0A075T858 for native CayG. reference DOI:10.1021/acschembio.1c00991 evidence type PRIMARY_EXPERIMENT notes Heterologous expression comparison of cayG with and without cayK.

Every edge carries its own citation; an uncited edge is refused by the corpus tests.

Explore across X-Mech

AntibioticMech (caryoynencin) ↗ MediaIngredientMech (naturalproductmech:mibig-d02aa1e8bc) ↗ TaxonMech: Burkholderia gladioli BSR3 (NCBITaxon:999541) ↗ PathwayMech (mibig:BGC0000892) ↗

Provenance

Source concept	Source	Version
BGC0000892	MIBIG	4

This page is generated from data/natural_products/fatty_acids/caryoynencin.yaml, which is generated from the committed inventories. Neither is edited by hand.