RlmC (RumB/YbjF) is the Escherichia coli K-12 SAM-dependent enzyme assigned to C5 methylation of uridine 747 in 23S rRNA. Native gene disruption specifically eliminates m5U747, whereas recombinant preparations in the original study were inactive on the tested transcripts and unmethylated 23S rRNA. The physiological substrate state and the cause of that in-vitro inactivity remain unresolved. RlmC belongs to the RNA m5U methyltransferase family but differs in site specificity from RlmD (23S U1939) and TrmA (tRNA U54 and tmRNA U341). Its catalytic cysteine and Fe-S-binding features are curated sequence-based inferences, not direct RlmC mechanistic measurements.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0070041 rRNA (uridine-C5-)-methyltransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: RlmC supplies the U747-specific rRNA C5-uridine methylation activity (PMID:12907714). Reason: The PAINT rRNA-C5 activity is consistent with the native loss of m5U747 and the curated RlmC subfamily. This molecular-function term specifies the RNA and chemical position, while the nucleotide site is stated in prose. The knockout establishes the assignment without claiming successful recombinant reconstitution. Supporting Evidence: PMID:12907714 Comparison of the methylation patterns in 23S rRNAs from YbjF(+) and YbjF(-) strains showed that the latter differed only in the lack of the m(5)U747 modification PMID:12907714 We were unable to generate a recombinant version of YbjF that retained in vitro activity, so the function of this enzyme was defined in vivo by engineering a ybjF knockout strain |
| GO:0070475 rRNA base methylation | IBA GO_REF:0000033 | ACCEPT | Summary: The inherited rRNA base-methylation claim matches loss of the U747 methyl group in the rlmC mutant. Reason: MALDI-MS comparison in PMID:12907714 supplies target-specific experimental grounding for the conserved process. The annotation describes formation of a modified rRNA base, not an inferred downstream growth or antibiotic-response phenotype. Supporting Evidence: PMID:12907714 Comparison of the methylation patterns in 23S rRNAs from YbjF(+) and YbjF(-) strains showed that the latter differed only in the lack of the m(5)U747 modification |
| GO:0005506 iron ion binding | IEA GO_REF:0000104 | MODIFY | Summary: The iron-ion claim is laterally corrected to rule-supported [4Fe-4S] cluster binding. Reason: The target UniProt FT:BINDING features assign a [4Fe-4S] cluster through HAMAP MF_01012. This supports a lateral correction from iron-ion binding to cluster binding, not an is_a descendant refinement. The cluster assignment retains its rule-based sequence-inference status. PMID:15181002 measures the paralog RlmD/RumA, not RlmC; neither its spectroscopy nor its oxidative-regulation hypothesis is a direct target assay. The exact RumA CX5CGGC motif must not be asserted for the different RlmC sequence. Proposed replacements: 4 iron, 4 sulfur cluster binding Supporting Evidence: file:ECOLI/rlmC/rlmC-uniprot.txt FT BINDING 3 FT /ligand="[4Fe-4S] cluster" FT /ligand_id="ChEBI:CHEBI:49883" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01012" |
| GO:0006396 RNA processing | IEA GO_REF:0000120 | MODIFY | Summary: RlmC participates in RNA maturation by methylating the uracil base of 23S rRNA U747. Reason: RNA processing includes conversion of primary transcripts into mature RNA and does not exclude chemical modification. InterPro-based processing is therefore sound but broad; refine it to rRNA base methylation, already supported by the native mutant. This does not claim cleavage, splicing or a particular assembly intermediate. Proposed replacements: rRNA base methylation Supporting Evidence: PMID:12907714 Comparison of the methylation patterns in 23S rRNAs from YbjF(+) and YbjF(-) strains showed that the latter differed only in the lack of the m(5)U747 modification |
| GO:0008173 RNA methyltransferase activity | IEA GO_REF:0000120 | MODIFY | Summary: The RNA methyltransferase mapping is refined to rRNA uridine-C5 methyltransferase activity. Reason: RlmC is assigned to an rRNA uracil-C5 reaction by native U747 methylation loss and curated enzyme-family evidence. The original term is true, but the existing GO:0070041 expresses the supported chemistry more precisely; specificity is not a reason to demote the activity to non-core. Proposed replacements: rRNA (uridine-C5-)-methyltransferase activity Supporting Evidence: PMID:12907714 Comparison of the methylation patterns in 23S rRNAs from YbjF(+) and YbjF(-) strains showed that the latter differed only in the lack of the m(5)U747 modification |
| GO:0008757 S-adenosylmethionine-dependent methyltransferase activity | IEA GO_REF:0000117 | MODIFY | Summary: SAM-dependent methyl transfer is part of RlmC rRNA C5-uridine methylation. Reason: The ARBA row is assessed using independent curated HAMAP SAM-binding features and PMID:12907714, not the ARBA prediction itself. GO:0070041 retains SAM as methyl donor in its definition and specifies the rRNA reaction; the tested recombinant inactivity is not evidence against the native enzyme assignment. Proposed replacements: rRNA (uridine-C5-)-methyltransferase activity Supporting Evidence: file:ECOLI/rlmC/rlmC-uniprot.txt FT BINDING 212 FT /ligand="S-adenosyl-L-methionine" FT /ligand_id="ChEBI:CHEBI:59789" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01012" PMID:12907714 Comparison of the methylation patterns in 23S rRNAs from YbjF(+) and YbjF(-) strains showed that the latter differed only in the lack of the m(5)U747 modification |
| GO:0009451 RNA modification | IEA GO_REF:0000117 | MODIFY | Summary: The RNA-modification mapping is narrowed to the experimentally assigned rRNA base modification. Reason: Adding the C5 methyl group to U747 is the specific modification supported for this target. The broader ARBA-derived claim remains biologically sound, but rRNA base methylation captures it without implying other RNA substrates or modifications. Proposed replacements: rRNA base methylation Supporting Evidence: PMID:12907714 Comparison of the methylation patterns in 23S rRNAs from YbjF(+) and YbjF(-) strains showed that the latter differed only in the lack of the m(5)U747 modification |
| GO:0016070 RNA metabolic process | IEA GO_REF:0000002 | MODIFY | Summary: RlmC contributes to RNA metabolism through U747 base methylation. Reason: InterPro IPR011825 identifies the RlmC subfamily, and the native mutant establishes its particular reaction. Refine RNA metabolic process to the supported rRNA base-methylation descendant rather than retain a general term as peripheral. Proposed replacements: rRNA base methylation Supporting Evidence: PMID:12907714 Comparison of the methylation patterns in 23S rRNAs from YbjF(+) and YbjF(-) strains showed that the latter differed only in the lack of the m(5)U747 modification |
| GO:0016436 rRNA (uridine) methyltransferase activity | IEA GO_REF:0000002 | MODIFY | Summary: The InterPro uridine-methyltransferase mapping is refined to the C5-specific rRNA activity. Reason: The loss is specifically m5U747, so GO:0070041 adds chemically supported positional precision to the uridine methyltransferase term. It does not imply a purified RlmC assay or a demonstrated catalytic intermediate. Proposed replacements: rRNA (uridine-C5-)-methyltransferase activity Supporting Evidence: PMID:12907714 Comparison of the methylation patterns in 23S rRNAs from YbjF(+) and YbjF(-) strains showed that the latter differed only in the lack of the m(5)U747 modification |
| GO:0031167 rRNA methylation | IEA GO_REF:0000104 | MODIFY | Summary: RlmC methylates an rRNA base rather than a ribose group. Reason: The UniRule rRNA-methylation term is correct; the m5U747 chemistry directly supports the existing rRNA base-methylation descendant GO:0070475. This is core reaction specificity, not a peripheral function. Proposed replacements: rRNA base methylation Supporting Evidence: PMID:12907714 Comparison of the methylation patterns in 23S rRNAs from YbjF(+) and YbjF(-) strains showed that the latter differed only in the lack of the m(5)U747 modification |
| GO:0070041 rRNA (uridine-C5-)-methyltransferase activity | IEA GO_REF:0000104 | ACCEPT | Summary: The curated UniRule C5-uridine methyltransferase assignment agrees with native RlmC evidence. Reason: The independent native knockout and mass-spectrometric result in PMID:12907714 support the same claim as the phylogenetic row. Both rows are retained; their agreement is not grounds for removing a duplicate biological assertion. Supporting Evidence: PMID:12907714 Comparison of the methylation patterns in 23S rRNAs from YbjF(+) and YbjF(-) strains showed that the latter differed only in the lack of the m(5)U747 modification |
| GO:0070475 rRNA base methylation | IMP PMID:12907714 Identifying the methyltransferases for m(5)U747 and m(5)U193... | ACCEPT | Summary: The rlmC/ybjF knockout specifically removes the U747 methyl group in native 23S rRNA. Reason: This is the direct process assignment from PMID:12907714. The authors compared methylation patterns and localized the missing group to U747; the paper also reports no detectable competitive growth disadvantage under the tested conditions, so no downstream stress or growth process is inferred. Supporting Evidence: PMID:12907714 Comparison of the methylation patterns in 23S rRNAs from YbjF(+) and YbjF(-) strains showed that the latter differed only in the lack of the m(5)U747 modification PMID:12907714 in competition experiments run in rich and minimal media, we have not been able to detect any growth disadvantage for ybjF ( rumB ) knockout strains compared to the wild type |
| GO:0016436 rRNA (uridine) methyltransferase activity | IMP PMID:12907714 Identifying the methyltransferases for m(5)U747 and m(5)U193... | MODIFY | Summary: The original mutant-phenotype assignment supports rRNA uridine-C5 methylation more precisely. Reason: Retain the experimental biological conclusion from PMID:12907714 while specifying the C5 methyl group with GO:0070041. The action does not change the original IMP evidence payload or recast the experiment as purified-enzyme activity. Proposed replacements: rRNA (uridine-C5-)-methyltransferase activity Supporting Evidence: PMID:12907714 Comparison of the methylation patterns in 23S rRNAs from YbjF(+) and YbjF(-) strains showed that the latter differed only in the lack of the m(5)U747 modification PMID:12907714 We were unable to generate a recombinant version of YbjF that retained in vitro activity, so the function of this enzyme was defined in vivo by engineering a ybjF knockout strain |
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Download this section (compressed HTML)Q: Which RNA or ribonucleoprotein state supports active RlmC, and did the original recombinant purification inactivate the enzyme rather than omit a required substrate state?
Q: Can the HAMAP-inferred RlmC [4Fe-4S] cluster and its ligands be verified directly, and does it affect folding, RNA binding or another property? RlmD redox data alone do not answer this.
Q: Under which conditions, if any, does loss of m5U747 alter ribosome function or fitness beyond the negative rich/minimal competition results in PMID:12907714?
Experiment: Compare RlmC preparations with measured Fe-S occupancy and folding against defined 23S transcripts, full-length rRNA and assembly particles, using site-resolved mass spectrometry and inactive-enzyme controls. A negative assay should be distinguished from loss of enzyme integrity.
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