id: A2AXI2
gene_symbol: cfr
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:1292
  label: Staphylococcus warneri
description: >-
  cfr encodes a radical SAM 23S rRNA methyltransferase that methylates carbon 8
  of adenine 2503 in bacterial 23S rRNA. This A2503 C8 modification confers
  cross-resistance to multiple antibiotic classes that bind near the peptidyl
  transferase center. Cfr is related to RlmN, but the clinically relevant Cfr
  activity is C8 methylation rather than the housekeeping C2 methyltransferase
  activity represented by existing GO specificity terms.
existing_annotations:
- term:
    id: GO:0003824
    label: catalytic activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: Technically true but too broad to be useful for Cfr.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The specific Cfr activity is radical-SAM 23S rRNA A2503 C8
      methyltransferase activity. Generic catalytic activity should not be the
      retained molecular-function representation where better terms exist.
    supported_by:
    - reference_id: file:genes/STAWA/cfr/cfr-uniprot.txt
      supporting_text: "Specifically methylates position 8 of adenine 2503 in 23S"
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: located_in
  review:
    summary: Correct location for a bacterial rRNA-modifying enzyme.
    action: ACCEPT
    reason: The UniProt record carries cytoplasm as the subcellular-location-derived GO annotation.
    supported_by:
    - reference_id: file:genes/STAWA/cfr/cfr-uniprot.txt
      supporting_text: "DR   GO; GO:0005737; C:cytoplasm"
- term:
    id: GO:0006364
    label: rRNA processing
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    summary: Broad process annotation that should be replaced by rRNA base methylation for Cfr.
    action: MODIFY
    reason: >-
      Cfr performs a base methylation on mature 23S rRNA. GO:0070475 is the
      better process-level representation than generic rRNA processing.
    proposed_replacement_terms:
    - id: GO:0070475
      label: rRNA base methylation
    supported_by:
    - reference_id: file:genes/STAWA/cfr/cfr-uniprot.txt
      supporting_text: "Specifically methylates position 8 of adenine 2503 in 23S"
- term:
    id: GO:0006400
    label: tRNA modification
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    summary: Incorrect electronic carryover from broad methylthiotransferase signatures.
    action: REMOVE
    reason: >-
      The Cfr record and Cfr mechanism literature identify 23S rRNA A2503 as the
      substrate. This review found no support that Cfr modifies tRNA.
    supported_by:
    - reference_id: file:genes/STAWA/cfr/cfr-uniprot.txt
      supporting_text: "Specifically methylates position 8 of adenine 2503 in 23S"
- term:
    id: GO:0008173
    label: RNA methyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: Correct but broad; replace with rRNA (adenine) methyltransferase activity.
    action: MODIFY
    reason: >-
      Cfr is an rRNA adenine methyltransferase, not a generic RNA
      methyltransferase. GO still lacks the exact C8/A2503 child term.
    proposed_replacement_terms:
    - id: GO:0016433
      label: rRNA (adenine) methyltransferase activity
    supported_by:
    - reference_id: PMID:19144912
      supporting_text: "Cfr catalyzes formation of 8-methyladenosine."
- term:
    id: GO:0016433
    label: rRNA (adenine) methyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000104
  qualifier: enables
  review:
    summary: Correct core molecular-function parent for Cfr, but missing the C8/A2503 specificity.
    action: ACCEPT
    reason: >-
      Cfr methylates adenine in 23S rRNA. The existing term is the best current
      GO parent; a Cfr-specific A2503 C8 term is proposed below.
    supported_by:
    - reference_id: file:genes/STAWA/cfr/cfr-uniprot.txt
      supporting_text: "AltName: Full=23S rRNA (adenine(2503)-C(8))-methyltransferase"
    - reference_id: PMID:19144912
      supporting_text: "Cfr catalyzes formation of 8-methyladenosine."
- term:
    id: GO:0016740
    label: transferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: Correct but too broad; replace with rRNA (adenine) methyltransferase activity.
    action: MODIFY
    reason: Generic transferase activity is a weak representation of Cfr compared with GO:0016433.
    proposed_replacement_terms:
    - id: GO:0016433
      label: rRNA (adenine) methyltransferase activity
    supported_by:
    - reference_id: file:genes/STAWA/cfr/cfr-uniprot.txt
      supporting_text: "Ribosomal RNA large subunit methyltransferase Cfr"
- term:
    id: GO:0019843
    label: rRNA binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000104
  qualifier: enables
  review:
    summary: Plausible substrate-binding annotation, but secondary to catalytic methyltransferase activity.
    action: KEEP_AS_NON_CORE
    reason: Cfr acts on 23S rRNA, but substrate binding is not the core evolved function.
    supported_by:
    - reference_id: file:genes/STAWA/cfr/cfr-uniprot.txt
      supporting_text: "adenosine(2503) in 23S rRNA"
- term:
    id: GO:0030488
    label: tRNA methylation
  evidence_type: IEA
  original_reference_id: GO_REF:0000118
  qualifier: involved_in
  review:
    summary: Incorrect TreeGrafter propagation for Cfr.
    action: REMOVE
    reason: >-
      Cfr's supported substrate is 23S rRNA A2503, not tRNA. The tRNA
      methylation annotation likely comes from broader radical-SAM
      methylthiotransferase family context.
    supported_by:
    - reference_id: PMID:19144912
      supporting_text: "The Cfr-mediated modification has previously been shown to occur on nucleotide A2503 of 23S rRNA"
- term:
    id: GO:0051536
    label: iron-sulfur cluster binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: Broad cofactor-binding term; the 4Fe-4S child is more informative and already annotated.
    action: MODIFY
    reason: Replace broad iron-sulfur cluster binding with the specific 4Fe-4S cluster binding annotation for Cfr.
    proposed_replacement_terms:
    - id: GO:0051539
      label: 4 iron, 4 sulfur cluster binding
    supported_by:
    - reference_id: file:genes/STAWA/cfr/cfr-uniprot.txt
      supporting_text: "Name=[4Fe-4S] cluster"
- term:
    id: GO:0051539
    label: 4 iron, 4 sulfur cluster binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: Correct cofactor-binding annotation for a radical SAM Cfr enzyme.
    action: KEEP_AS_NON_CORE
    reason: The 4Fe-4S cluster is required for the radical SAM mechanism but is secondary to methyltransferase activity.
    supported_by:
    - reference_id: file:genes/STAWA/cfr/cfr-uniprot.txt
      supporting_text: "Binds 1 [4Fe-4S] cluster."
- term:
    id: GO:0070475
    label: rRNA base methylation
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: involved_in
  review:
    summary: Correct process annotation for the Cfr-catalyzed rRNA A2503 methylation.
    action: ACCEPT
    reason: Cfr directly methylates a base in 23S rRNA; the process term is appropriate.
    supported_by:
    - reference_id: PMID:19144912
      supporting_text: "Antibiotic susceptibility data confirm that the antibiotic resistance conferred by Cfr is provided by methylation at the 8 position"
- term:
    id: GO:0046677
    label: response to antibiotic
  evidence_type: RCA
  original_reference_id: PMID:19144912
  qualifier: involved_in
  review:
    summary: NEW high-level process annotation for Cfr-mediated multidrug resistance.
    action: NEW
    reason: >-
      Cfr-mediated A2503 C8 methylation provides resistance to multiple
      peptidyl-transferase-center antibiotic classes. This is a high-level
      process annotation, while the core curation need remains the C8-specific
      molecular-function term.
    additional_reference_ids:
    - PMID:17145796
    - file:genes/STAWA/cfr/cfr-uniprot.txt
    supported_by:
    - reference_id: PMID:19144912
      supporting_text: "The Cfr methyltransferase confers combined resistance to five different classes"
    - reference_id: file:genes/STAWA/cfr/cfr-uniprot.txt
      supporting_text: "Confers resistance to some classes of antibiotics."
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings: []
- id: GO_REF:0000104
  title: Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features
  findings: []
- id: GO_REF:0000118
  title: TreeGrafter-generated GO annotations
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: file:genes/STAWA/cfr/cfr-uniprot.txt
  title: UniProt flat file for cfr (A2AXI2)
  findings:
  - statement: UniProt names Cfr as a 23S rRNA A2503 C8 methyltransferase.
    supporting_text: "23S rRNA (adenine(2503)-C(8))-methyltransferase"
- id: PMID:17145796
  title: IS21-558 insertion sequences are involved in the mobility of the multiresistance gene cfr.
  findings:
  - statement: The source-species cfr paper supports Cfr as a multiresistance gene in Staphylococcus warneri genetic context.
    supporting_text: "gene cfr for combined resistance to phenicols, lincosamides, oxazolidinones,"
- id: PMID:19144912
  title: Identification of 8-methyladenosine as the modification catalyzed by the radical SAM methyltransferase Cfr that confers antibiotic resistance in bacteria.
  findings:
  - statement: Cfr catalyzes 8-methyladenosine formation at A2503, and resistance is provided by the C8 methylation.
    supporting_text: "Cfr catalyzes formation of 8-methyladenosine."
- id: file:projects/ANTIMICROBIAL_RESISTANCE/aro2go.sssom.yaml
  title: Curated ARO to GO mapping set for AMR gene families
  findings:
  - statement: The AMR mapping records the Cfr C8/A2503 methyltransferase as a GO molecular-function gap.
    supporting_text: "Cfr methylates C8 of A2503."
core_functions:
- description: >-
    Radical-SAM 23S rRNA A2503 C8 methyltransferase activity that produces
    8-methyladenosine in 23S rRNA and confers resistance to several
    peptidyl-transferase-center antibiotic classes.
  molecular_function:
    id: GO:0016433
    label: rRNA (adenine) methyltransferase activity
  directly_involved_in:
  - id: GO:0070475
    label: rRNA base methylation
  - id: GO:0046677
    label: response to antibiotic
  locations:
  - id: GO:0005737
    label: cytoplasm
  supported_by:
  - reference_id: PMID:19144912
    supporting_text: "Cfr catalyzes formation of 8-methyladenosine."
  - reference_id: file:genes/STAWA/cfr/cfr-uniprot.txt
    supporting_text: "Specifically methylates position 8 of adenine 2503 in 23S"
proposed_new_terms:
- proposed_name: 23S rRNA A2503 C8 methyltransferase activity
  proposed_definition: >-
    Catalysis of methyl transfer to carbon 8 of adenine 2503 in bacterial 23S
    rRNA, forming 8-methyladenosine at A2503.
  justification: >-
    Existing GO specificity for this enzyme family includes the RlmN/C2
    methyltransferase activity, but Cfr's resistance-conferring activity is C8
    methylation at A2503. The AMR mapping records this as a NoTermFound gap.
  proposed_parent:
    id: GO:0016433
    label: rRNA (adenine) methyltransferase activity
  proposed_mappings:
  - predicate: skos:exactMatch
    target_term:
      id: ARO:3000202
      label: Cfr 23S ribosomal RNA methyltransferase
  supported_by:
  - reference_id: PMID:19144912
    supporting_text: "Cfr catalyzes formation of 8-methyladenosine."
  - reference_id: file:projects/ANTIMICROBIAL_RESISTANCE/aro2go.sssom.yaml
    supporting_text: "Cfr methylates C8 of A2503."
suggested_questions:
- question: Should GO add a Cfr-specific C8 term as a sibling of the existing RlmN/C2 23S rRNA methyltransferase term?
  experts: []
suggested_experiments:
- description: >-
    Compare Cfr and RlmN activity on the same 23S rRNA substrate by MS mapping
    of A2503 products to support separate C8 and C2 GO molecular functions.
  experiment_type: in vitro enzyme assay