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.
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.
Parent term: rRNA (adenine) methyltransferase activity
Mappings:
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: Technically true but too broad to be useful for Cfr. 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. Supporting Evidence: file:genes/STAWA/cfr/cfr-uniprot.txt Specifically methylates position 8 of adenine 2503 in 23S |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: Correct location for a bacterial rRNA-modifying enzyme. Reason: The UniProt record carries cytoplasm as the subcellular-location-derived GO annotation. Supporting Evidence: file:genes/STAWA/cfr/cfr-uniprot.txt DR GO; GO:0005737; C:cytoplasm |
| GO:0006364 rRNA processing | IEA GO_REF:0000002 | MODIFY | Summary: Broad process annotation that should be replaced by rRNA base methylation for Cfr. Reason: Cfr performs a base methylation on mature 23S rRNA. GO:0070475 is the better process-level representation than generic rRNA processing. Proposed replacements: rRNA base methylation Supporting Evidence: file:genes/STAWA/cfr/cfr-uniprot.txt Specifically methylates position 8 of adenine 2503 in 23S |
| GO:0006400 tRNA modification | IEA GO_REF:0000002 | REMOVE | Summary: Incorrect electronic carryover from broad methylthiotransferase signatures. Reason: The Cfr record and Cfr mechanism literature identify 23S rRNA A2503 as the substrate. This review found no support that Cfr modifies tRNA. Supporting Evidence: file:genes/STAWA/cfr/cfr-uniprot.txt Specifically methylates position 8 of adenine 2503 in 23S |
| GO:0008173 RNA methyltransferase activity | IEA GO_REF:0000002 | MODIFY | Summary: Correct but broad; replace with rRNA (adenine) methyltransferase activity. Reason: Cfr is an rRNA adenine methyltransferase, not a generic RNA methyltransferase. GO still lacks the exact C8/A2503 child term. Proposed replacements: rRNA (adenine) methyltransferase activity Supporting Evidence: PMID:19144912 Cfr catalyzes formation of 8-methyladenosine. |
| GO:0016433 rRNA (adenine) methyltransferase activity | IEA GO_REF:0000104 | ACCEPT | Summary: Correct core molecular-function parent for Cfr, but missing the C8/A2503 specificity. 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. Supporting Evidence: file:genes/STAWA/cfr/cfr-uniprot.txt AltName: Full=23S rRNA (adenine(2503)-C(8))-methyltransferase PMID:19144912 Cfr catalyzes formation of 8-methyladenosine. |
| GO:0016740 transferase activity | IEA GO_REF:0000002 | MODIFY | Summary: Correct but too broad; replace with rRNA (adenine) methyltransferase activity. Reason: Generic transferase activity is a weak representation of Cfr compared with GO:0016433. Proposed replacements: rRNA (adenine) methyltransferase activity Supporting Evidence: file:genes/STAWA/cfr/cfr-uniprot.txt Ribosomal RNA large subunit methyltransferase Cfr |
| GO:0019843 rRNA binding | IEA GO_REF:0000104 | KEEP AS NON CORE | Summary: Plausible substrate-binding annotation, but secondary to catalytic methyltransferase activity. Reason: Cfr acts on 23S rRNA, but substrate binding is not the core evolved function. Supporting Evidence: file:genes/STAWA/cfr/cfr-uniprot.txt adenosine(2503) in 23S rRNA |
| GO:0030488 tRNA methylation | IEA GO_REF:0000118 | REMOVE | Summary: Incorrect TreeGrafter propagation for Cfr. Reason: Cfr's supported substrate is 23S rRNA A2503, not tRNA. The tRNA methylation annotation likely comes from broader radical-SAM methylthiotransferase family context. Supporting Evidence: PMID:19144912 The Cfr-mediated modification has previously been shown to occur on nucleotide A2503 of 23S rRNA |
| GO:0051536 iron-sulfur cluster binding | IEA GO_REF:0000002 | MODIFY | Summary: Broad cofactor-binding term; the 4Fe-4S child is more informative and already annotated. Reason: Replace broad iron-sulfur cluster binding with the specific 4Fe-4S cluster binding annotation for Cfr. Proposed replacements: 4 iron, 4 sulfur cluster binding Supporting Evidence: file:genes/STAWA/cfr/cfr-uniprot.txt Name=[4Fe-4S] cluster |
| GO:0051539 4 iron, 4 sulfur cluster binding | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: Correct cofactor-binding annotation for a radical SAM Cfr enzyme. Reason: The 4Fe-4S cluster is required for the radical SAM mechanism but is secondary to methyltransferase activity. Supporting Evidence: file:genes/STAWA/cfr/cfr-uniprot.txt Binds 1 [4Fe-4S] cluster. |
| GO:0070475 rRNA base methylation | IEA GO_REF:0000120 | ACCEPT | Summary: Correct process annotation for the Cfr-catalyzed rRNA A2503 methylation. Reason: Cfr directly methylates a base in 23S rRNA; the process term is appropriate. Supporting Evidence: PMID:19144912 Antibiotic susceptibility data confirm that the antibiotic resistance conferred by Cfr is provided by methylation at the 8 position |
| GO:0046677 response to antibiotic | RCA PMID:19144912 Identification of 8-methyladenosine as the modification cata... | NEW | Summary: NEW high-level process annotation for Cfr-mediated multidrug resistance. 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. Supporting Evidence: PMID:19144912 The Cfr methyltransferase confers combined resistance to five different classes file:genes/STAWA/cfr/cfr-uniprot.txt Confers resistance to some classes of antibiotics. |
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Download this section (compressed HTML)Q: Should GO add a Cfr-specific C8 term as a sibling of the existing RlmN/C2 23S rRNA methyltransferase term?
Experiment: 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.
Type: in vitro enzyme assay
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