Caffeoyl-CoA O-methyltransferase that methylates caffeoyl-CoA and 5-hydroxyferuloyl-CoA in phenylpropanoid/lignin metabolism.
The preferred accession for this review is O65862. These relationships are manually assessed.
REFERENCE PROTEOME EQUIVALENT · Reviewed 2026-10-19
Reference proteome: UP000006729
Retain O65862 as the preferred Swiss-Prot accession. A0A2K1Z5Q2 represents the same protein sequence at the corresponding reference-proteome locus, supported by exact sequence identity and a shared Gramene identifier. The source cultivars differ; this relationship does not assert that all GO annotations can be transferred automatically.
The current Swiss-Prot and TrEMBL records have identical full-length 247-residue sequences and share UniParc UPI00000ACCF9.
file:POPTR/CCOAOMT1/CCOAOMT1-record-evidence.yaml
sequence_identical: true primary_sequence_length: 247 alternative_sequence_length: 247 shared_uniparc_id: UPI00000ACCF9
Both current records cross-reference Gramene Potri.009G099800.2.v4.1; the Swiss-Prot record also has this EnsemblPlants identifier, and the reference-proteome entry names locus POPTR_009G099800. This independently supports the counterpart assignment.
file:POPTR/CCOAOMT1/CCOAOMT1-record-evidence.yaml
database: Gramene id: Potri.009G099800.2.v4.1
file:POPTR/CCOAOMT1/CCOAOMT1-record-evidence.yaml
value: POPTR_009G099800
The live UniProt records and proteome metadata place A0A2K1Z5Q2, but not O65862, in reference proteome UP000006729 for the same taxon (NCBITaxon:3694).
file:POPTR/CCOAOMT1/CCOAOMT1-record-evidence.yaml
reference_proteome: UP000006729 proteome_is_reference: true proteome_taxon_matches: true primary_in_reference_proteome: false alternative_in_reference_proteome: true
UniSave entry versions 94 (2015), 122 (2020), and 132 (2024) have no Proteomes cross-reference. These samples establish longstanding absence at those dates, not a recent dropout or uninterrupted absence between samples; they do not explain why UniProt omitted the association.
file:POPTR/CCOAOMT1/CCOAOMT1-record-evidence.yaml
sampled_history_versions: - 94 - 122 - 132 sampled_versions_with_proteome_links: []
The Swiss-Prot source material is cultivar Trichobel, whereas the reference proteome represents cultivar Nisqually. This provides context for separate records but does not establish UniProt's reason for keeping the Swiss-Prot accession outside the proteome.
file:POPTR/CCOAOMT1/CCOAOMT1-record-evidence.yaml
RC STRAIN=cv. Trichobel; TISSUE=Xylem;
file:POPTR/CCOAOMT1/CCOAOMT1-record-evidence.yaml
strain: cv. Nisqually
Definition: The chemical reactions and pathways resulting in the formation of polysaccharides modified with feruloyl groups in the plant cell wall.
Justification: The reviewed UniProt entry states that Populus CCoAOMT plays a role in synthesis of feruloylated polysaccharides, but existing GO lignin and broad phenylpropanoid terms do not capture this wall-polysaccharide feruloylation role.
Parent term: phenylpropanoid biosynthetic process
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0008171 O-methyltransferase activity | IEA GO_REF:0000002 | MODIFY | Summary: O-methyltransferase activity is correct but too broad for a characterized caffeoyl-CoA O-methyltransferase. Reason: Use the specific EC/Rhea-supported caffeoyl-CoA O-methyltransferase term. UniProt names the protein with the specific EC 2.1.1.104, and the falcon deep research confirms it is a SAM-dependent O-methyltransferase acting on hydroxycinnamoyl-CoA esters, so the generic O-methyltransferase term should be replaced with the specific activity. Proposed replacements: caffeoyl-CoA O-methyltransferase activity Supporting Evidence: file:POPTR/CCOAOMT1/CCOAOMT1-uniprot.txt RecName: Full=Caffeoyl-CoA O-methyltransferase 1; file:POPTR/CCOAOMT1/CCOAOMT1-uniprot.txt EC=2.1.1.104; file:POPTR/CCOAOMT1/CCOAOMT1-deep-research-falcon.md catalyzing methylation of |
| GO:0042409 caffeoyl-CoA O-methyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Caffeoyl-CoA O-methyltransferase activity is the core molecular function. Reason: The UniProt entry and EC assignment match this term directly, and the falcon deep research independently confirms this as the best molecular-function annotation for O65862, describing it as a SAM-dependent hydroxycinnamoyl-CoA O-methyltransferase that methylates caffeoyl-CoA. The original IEA is mapped from RHEA:16925/EC:2.1.1.104, consistent with the curated catalytic-activity statement. Supporting Evidence: file:POPTR/CCOAOMT1/CCOAOMT1-uniprot.txt Reaction=(E)-caffeoyl-CoA + S-adenosyl-L-methionine = (E)-feruloyl-CoA file:POPTR/CCOAOMT1/CCOAOMT1-uniprot.txt EC=2.1.1.104; file:POPTR/CCOAOMT1/CCOAOMT1-deep-research-falcon.md CCoAOMT is described as methylating file:POPTR/CCOAOMT1/CCOAOMT1-deep-research-falcon.md placing it in the phenylpropanoid/monolignol pathway where methylation is required for monolignol formation and lignification. |
| GO:0009699 phenylpropanoid biosynthetic process | IEA GO_REF:0000041 | MODIFY | Summary: Phenylpropanoid biosynthesis is correct but less specific than the experimentally supported lignin-biosynthesis role of Populus CCoAOMT. Reason: The Populus xylem down-regulation study directly links CCoAOMT to lignin amount, and the falcon deep research reinforces that the strongest Populus evidence places CCoAOMT activity in xylem lignification/secondary-wall formation rather than only the broad phenylpropanoid pathway. Reducing CCoAOMT lowers Klason lignin and shifts S/G ratio in poplar wood, so the more specific lignin-biosynthesis term better captures the experimentally supported role. Proposed replacements: lignin biosynthetic process Supporting Evidence: PMID:10934215 To clarify the in vivo role of CCoAOMT in lignin biosynthesis, transgenic poplars with 10% residual CCoAOMT protein levels in the stem xylem were generated. PMID:10934215 the affected transgenic lines had a 12% reduced Klason lignin content file:POPTR/CCOAOMT1/CCOAOMT1-uniprot.txt DR GO; GO:0009809; P:lignin biosynthetic process; IEA:UniProtKB-KW. file:POPTR/CCOAOMT1/CCOAOMT1-deep-research-falcon.md it is direct experimental evidence in Populus wood that reducing CCoAOMT activity changes lignin amount and composition in xylem, file:POPTR/CCOAOMT1/CCOAOMT1-deep-research-falcon.md supporting the functional assignment of Populus CCOAOMT enzymes (including PtrCCOAOMT1) as lignin-pathway O-methyltransferases. |
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Download this section (compressed HTML)Q: How much does CCOAOMT1 contribute to lignin composition relative to CCOAOMT2 in xylem?
Q: What fraction of CCOAOMT1 activity supports monolignol biosynthesis versus feruloylated polysaccharide synthesis in Populus xylem?
Experiment: Create isoform-specific knockdowns and measure lignin monomer composition and wall-bound ferulate.
Type: targeted functional assay
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Download this section (compressed HTML)CCOAOMT1-uniprot.txt and CCOAOMT1-goa.tsv.Loading supporting content…
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