id: O65862 gene_symbol: CCOAOMT1 product_type: PROTEIN status: DRAFT taxon: id: NCBITaxon:3694 label: Populus trichocarpa description: Caffeoyl-CoA O-methyltransferase that methylates caffeoyl-CoA and 5-hydroxyferuloyl-CoA in phenylpropanoid/lignin metabolism. alternative_records: - id: A0A2K1Z5Q2 relationship: REFERENCE_PROTEOME_EQUIVALENT reference_proteome: UP000006729 reviewed_on: '2026-10-19' reason: 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. evidence: - type: SEQUENCE_COMPARISON description: The current Swiss-Prot and TrEMBL records have identical full-length 247-residue sequences and share UniParc UPI00000ACCF9. supported_by: - reference_id: file:POPTR/CCOAOMT1/CCOAOMT1-record-evidence.yaml supporting_text: |- sequence_identical: true primary_sequence_length: 247 alternative_sequence_length: 247 shared_uniparc_id: UPI00000ACCF9 - type: LOCUS_MAPPING description: 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. supported_by: - reference_id: file:POPTR/CCOAOMT1/CCOAOMT1-record-evidence.yaml supporting_text: |- database: Gramene id: Potri.009G099800.2.v4.1 - reference_id: file:POPTR/CCOAOMT1/CCOAOMT1-record-evidence.yaml supporting_text: 'value: POPTR_009G099800' - type: PROTEOME_MEMBERSHIP description: The live UniProt records and proteome metadata place A0A2K1Z5Q2, but not O65862, in reference proteome UP000006729 for the same taxon (NCBITaxon:3694). supported_by: - reference_id: file:POPTR/CCOAOMT1/CCOAOMT1-record-evidence.yaml supporting_text: |- reference_proteome: UP000006729 proteome_is_reference: true proteome_taxon_matches: true primary_in_reference_proteome: false alternative_in_reference_proteome: true - type: RECORD_HISTORY description: 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. supported_by: - reference_id: file:POPTR/CCOAOMT1/CCOAOMT1-record-evidence.yaml supporting_text: |- sampled_history_versions: - 94 - 122 - 132 sampled_versions_with_proteome_links: [] - type: CURATION_CONTEXT description: 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. supported_by: - reference_id: file:POPTR/CCOAOMT1/CCOAOMT1-record-evidence.yaml record_section: [REF] supporting_text: RC STRAIN=cv. Trichobel; TISSUE=Xylem; - reference_id: file:POPTR/CCOAOMT1/CCOAOMT1-record-evidence.yaml supporting_text: 'strain: cv. Nisqually' existing_annotations: - term: id: GO:0008171 label: O-methyltransferase activity evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: enables review: summary: O-methyltransferase activity is correct but too broad for a characterized caffeoyl-CoA O-methyltransferase. action: MODIFY 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. supported_by: - reference_id: file:POPTR/CCOAOMT1/CCOAOMT1-uniprot.txt record_section: [DE] supporting_text: 'RecName: Full=Caffeoyl-CoA O-methyltransferase 1;' - reference_id: file:POPTR/CCOAOMT1/CCOAOMT1-uniprot.txt supporting_text: EC=2.1.1.104; - reference_id: file:POPTR/CCOAOMT1/CCOAOMT1-deep-research-falcon.md supporting_text: catalyzing methylation of proposed_replacement_terms: - id: GO:0042409 label: caffeoyl-CoA O-methyltransferase activity - term: id: GO:0042409 label: caffeoyl-CoA O-methyltransferase activity evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: enables review: summary: Caffeoyl-CoA O-methyltransferase activity is the core molecular function. action: ACCEPT 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. supported_by: - reference_id: file:POPTR/CCOAOMT1/CCOAOMT1-uniprot.txt record_section: ["CC:CATALYTIC ACTIVITY"] supporting_text: Reaction=(E)-caffeoyl-CoA + S-adenosyl-L-methionine = (E)-feruloyl-CoA - reference_id: file:POPTR/CCOAOMT1/CCOAOMT1-uniprot.txt supporting_text: EC=2.1.1.104; - reference_id: file:POPTR/CCOAOMT1/CCOAOMT1-deep-research-falcon.md supporting_text: CCoAOMT is described as methylating - reference_id: file:POPTR/CCOAOMT1/CCOAOMT1-deep-research-falcon.md supporting_text: placing it in the phenylpropanoid/monolignol pathway where methylation is required for monolignol formation and lignification. - term: id: GO:0009699 label: phenylpropanoid biosynthetic process evidence_type: IEA original_reference_id: GO_REF:0000041 qualifier: involved_in review: summary: Phenylpropanoid biosynthesis is correct but less specific than the experimentally supported lignin-biosynthesis role of Populus CCoAOMT. action: MODIFY 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. supported_by: - reference_id: PMID:10934215 supporting_text: 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. reference_section_type: ABSTRACT - reference_id: PMID:10934215 supporting_text: the affected transgenic lines had a 12% reduced Klason lignin content reference_section_type: ABSTRACT - reference_id: file:POPTR/CCOAOMT1/CCOAOMT1-uniprot.txt record_section: ["DR:GO"] supporting_text: DR GO; GO:0009809; P:lignin biosynthetic process; IEA:UniProtKB-KW. - reference_id: file:POPTR/CCOAOMT1/CCOAOMT1-deep-research-falcon.md supporting_text: it is direct experimental evidence in Populus wood that reducing CCoAOMT activity changes lignin amount and composition in xylem, - reference_id: file:POPTR/CCOAOMT1/CCOAOMT1-deep-research-falcon.md supporting_text: supporting the functional assignment of Populus CCOAOMT enzymes (including PtrCCOAOMT1) as lignin-pathway O-methyltransferases. proposed_replacement_terms: - id: GO:0009809 label: lignin biosynthetic process references: - id: file:POPTR/CCOAOMT1/CCOAOMT1-record-evidence.yaml title: Compact archived record and sequence evidence for O65862 findings: - statement: Dated current records, reference-proteome metadata, exact sequence comparison, and three archived entry versions support the manually assessed alternative-record relationship. - id: GO_REF:0000002 title: Gene Ontology annotation through association of InterPro records with GO terms findings: - statement: GO_REF:0000002 supplied one or more source GOA annotations reviewed in this file. - id: GO_REF:0000041 title: Gene Ontology annotation based on UniPathway vocabulary mapping findings: - statement: GO_REF:0000041 supplied one or more source GOA annotations reviewed in this file. - id: GO_REF:0000120 title: Combined Automated Annotation using Multiple IEA Methods findings: - statement: GO_REF:0000120 supplied one or more source GOA annotations reviewed in this file. - id: PMID:10934215 title: Modifications in lignin and accumulation of phenolic glucosides in poplar xylem upon down-regulation of caffeoyl-coenzyme A O-methyltransferase, an enzyme involved in lignin biosynthesis. findings: - statement: Down-regulation of poplar CCoAOMT in xylem reduced lignin content and supports a lignin-biosynthesis role for the enzyme. supporting_text: Caffeoyl-coenzyme A O-methyltransferase (CCoAOMT) methylates, in vitro, caffeoyl-CoA and 5-hydroxyferuloyl-CoA, two possible precursors in monolignol biosynthesis in vivo. reference_section_type: ABSTRACT - statement: Reduced CCoAOMT lowers Klason lignin and increases the S/G ratio in xylem. supporting_text: the affected transgenic lines had a 12% reduced Klason lignin content, an 11% increased syringyl/guaiacyl ratio in the noncondensed lignin fraction reference_section_type: ABSTRACT - id: file:POPTR/CCOAOMT1/CCOAOMT1-uniprot.txt title: UniProtKB reviewed entry for CCOAOMT1 findings: - statement: UniProt identifies CCOAOMT1 as caffeoyl-CoA O-methyltransferase EC 2.1.1.104 involved in phenylpropanoid and lignin-related cell wall metabolism. record_section: ["CC:FUNCTION"] supporting_text: 'FUNCTION: Methylates caffeoyl-CoA to feruloyl-CoA' - statement: CCOAOMT1 also contributes to feruloylated polysaccharide synthesis and cell-wall reinforcement. record_section: ["CC:FUNCTION"] supporting_text: Plays a role in the synthesis of feruloylated polysaccharides. - id: file:POPTR/CCOAOMT1/CCOAOMT1-deep-research-falcon.md title: Falcon deep research report on Populus trichocarpa CCOAOMT1 (O65862) findings: - statement: CCOAOMT1 is a SAM-dependent O-methyltransferase that methylates caffeoyl-CoA in the monolignol/lignin pathway, supplying G-unit precursors. supporting_text: placing it in the phenylpropanoid/monolignol pathway where methylation is required for monolignol formation and lignification. reference_section_type: OTHER - statement: A 2024 synthetic-biology review assigns CCoAOMT the first O-methylation step toward G-type lignin precursors, with COMT acting later toward S-units. supporting_text: CCoAOMT performs the first O‑methylation step contributing to G-unit precursor formation reference_section_type: OTHER - statement: Because the enzyme is SAM-dependent, cellular methyl-donor balance (SAM:SAH) constrains its flux; SAH inhibits SAM-dependent O-methyltransferases. supporting_text: potent inhibitor of SAM-dependent O-methyltransferases, and the reference_section_type: OTHER - statement: Antisense down-regulation of CCoAOMT in poplar wood reduced Klason lignin (~12%) and increased S/G (~11%), giving direct Populus evidence for a lignin-biosynthesis role. supporting_text: Klason lignin decreased by ~12% reference_section_type: OTHER - statement: Reducing this O-methylation step shifts lignin composition in the noncondensed fraction. supporting_text: in the noncondensed lignin fraction, indicating that reducing this O-methylation step can shift lignin composition. reference_section_type: OTHER - statement: 2023 multiplex CRISPR editing in P. trichocarpa repeatedly selected CCoAOMT family genes among lignin-pathway targets to redesign wood composition. supporting_text: to engineer wood composition for fiber production, with CCoAOMT among the repeatedly selected targets in optimal multigene strategies. reference_section_type: OTHER - statement: The strongest accessible evidence places CCoAOMT activity in intracellular phenylpropanoid/monolignol metabolism of lignifying xylem cells, though a direct subcellular localization assay was not available. supporting_text: the most consistent inference is that PtrCCOAOMT1 operates in the reference_section_type: OTHER - id: file:POPTR/CCOAOMT1/CCOAOMT1-goa.tsv title: QuickGO GOA annotations for CCOAOMT1 findings: - statement: GOA rows supplied the existing_annotations reviewed in this file. core_functions: - description: Methylates caffeoyl-CoA to feruloyl-CoA in monolignol/lignin biosynthesis, with an additional supported role in feruloylated cell-wall polysaccharide synthesis. molecular_function: id: GO:0042409 label: caffeoyl-CoA O-methyltransferase activity directly_involved_in: - id: GO:0009809 label: lignin biosynthetic process supported_by: - reference_id: file:POPTR/CCOAOMT1/CCOAOMT1-uniprot.txt record_section: ["CC:FUNCTION"] supporting_text: 'FUNCTION: Methylates caffeoyl-CoA to feruloyl-CoA' - reference_id: PMID:10934215 supporting_text: the affected transgenic lines had a 12% reduced Klason lignin content reference_section_type: ABSTRACT - reference_id: file:POPTR/CCOAOMT1/CCOAOMT1-uniprot.txt record_section: ["CC:FUNCTION"] supporting_text: Plays a role in the synthesis of feruloylated polysaccharides. Involved in the reinforcement of the plant cell wall. - reference_id: file:POPTR/CCOAOMT1/CCOAOMT1-deep-research-falcon.md supporting_text: it is direct experimental evidence in Populus wood that reducing CCoAOMT activity changes lignin amount and composition in xylem, - reference_id: file:POPTR/CCOAOMT1/CCOAOMT1-deep-research-falcon.md supporting_text: placing it in the phenylpropanoid/monolignol pathway where methylation is required for monolignol formation and lignification. proposed_new_terms: - proposed_name: feruloylated polysaccharide biosynthetic process proposed_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. proposed_parent: id: GO:0009699 label: phenylpropanoid biosynthetic process supported_by: - reference_id: file:POPTR/CCOAOMT1/CCOAOMT1-uniprot.txt record_section: ["CC:FUNCTION"] supporting_text: Plays a role in the synthesis of feruloylated polysaccharides. Involved in the reinforcement of the plant cell wall. suggested_questions: - question: How much does CCOAOMT1 contribute to lignin composition relative to CCOAOMT2 in xylem? - question: What fraction of CCOAOMT1 activity supports monolignol biosynthesis versus feruloylated polysaccharide synthesis in Populus xylem? suggested_experiments: - description: Create isoform-specific knockdowns and measure lignin monomer composition and wall-bound ferulate. experiment_type: targeted functional assay