TrmA is an Escherichia coli K-12 RNA methyltransferase that uses SAM to form m5U54 in tRNA and m5U341 in the tRNA-like domain of tmRNA. It also promotes tRNA folding independently of methyl-group transfer through its RNA-binding domain. TrmA forms stable covalent complexes with undermodified tRNAs and with a 3-prime fragment of 16S rRNA; this latter association does not establish rRNA methylation or stable ribosomal membership. Cytosolic localization is supported by independently curated fractionation/proteomic experiments. The physiological consequences of catalysis and RNA-chaperone function depend on growth conditions and are not interchangeable with an absolute essentiality claim.
Definition: Catalysis of transfer of a methyl group from S-adenosyl-L-methionine to carbon 5 of a uridine residue in the tRNA-like domain of transfer-messenger RNA (tmRNA), producing 5-methyluridine and S-adenosyl-L-homocysteine.
Justification: The existing tRNA U54 term excludes tmRNA, while the general RNA methyltransferase term loses the established base, methylation position and donor specificity. PMID:23603891 assigns tmRNA m5U formation to the characterized SAM-dependent enzyme TrmA. The proposed name avoids imposing E. coli residue numbering on all tmRNAs. This formalizes an already-supported substrate activity; no new gene-annotation row is proposed. Purified tRNA-enzyme evidence in PMID:6997293 establishes the SAM-dependent TrmA chemistry; the tmRNA deletion experiment does not independently measure donor dependence.
Parent term: RNA methyltransferase activity
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000049 tRNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: The inherited tRNA-binding activity is directly supported by native RNA complexes and purified-domain assays. Reason: The PAINT claim matches physical TrmA-tRNA association in PMID:8419334 and mutational/binding measurements in PMID:32597953. Binding contributes to both catalysis and folding; it is not merely a redundant name for methyltransferase activity. Supporting Evidence: PMID:8419334 After sequencing and Southern blot analyses, the RNA was identified to be a subset of undermodified tRNA species as well as the 3' terminus of 16 S rRNA. PMID:32597953 We identify two conserved residues, F106 and H125, in the RNA-binding domain of TrmA, which interact with the tRNA elbow and are critical for tRNA binding. |
| GO:0000049 tRNA binding | IDA PMID:8419334 The tRNA-(m5U54)-methyltransferase of Escherichia coli is pr... | ACCEPT | Summary: Native TrmA forms a stable complex with undermodified tRNAs. Reason: The original PMID:8419334 reports RNA identification after complex isolation, sequencing and Southern analysis. Its abstract explicitly names tRNAs; later full binding and chaperone experiments corroborate this target activity. Supporting Evidence: PMID:8419334 After sequencing and Southern blot analyses, the RNA was identified to be a subset of undermodified tRNA species as well as the 3' terminus of 16 S rRNA. PMID:32597953 We identify two conserved residues, F106 and H125, in the RNA-binding domain of TrmA, which interact with the tRNA elbow and are critical for tRNA binding. |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: The PAINT cytosol placement agrees with two independently curated E. coli fractionation studies. Reason: The ancestral-location inference is evaluated together with the target IDA rows from PMID:15911532 and PMID:18304323 and TrmA intracellular RNA interactions. A short donor set would not invalidate PAINT; no target-specific relocation or loss is established. The individual supplementary proteomic row was not independently recovered, so this is retention of convergent curator-supported location, not a new localization measurement. Supporting Evidence: PMID:15911532 3,199 protein forms were detected, and of those 2,160 were annotated and assigned to the cytosol, periplasm, inner membrane, and outer membrane by biochemical fractionation followed by two-dimensional gel electrophoresis and tandem mass spectrometry. PMID:18304323 we identified 1103 proteins from the cytosolic fraction of the Escherichia coli strain MC4100. |
| GO:0005829 cytosol | IDA PMID:15911532 Localization, annotation, and comparison of the Escherichia ... | ACCEPT | Summary: The original fractionation/proteome study supports the curated cytosolic TrmA assignment. Reason: PMID:15911532 assigns identified protein forms to subcellular fractions; the cached abstract describes the assay but does not expose the TrmA-specific table, which the authors offered on request. Retain the experimental curator assignment in conjunction with the independent cytosolic dataset and native RNA-binding biology; do not assert inspection of an unavailable target spot. Supporting Evidence: PMID:15911532 3,199 protein forms were detected, and of those 2,160 were annotated and assigned to the cytosol, periplasm, inner membrane, and outer membrane by biochemical fractionation followed by two-dimensional gel electrophoresis and tandem mass spectrometry. PMID:18304323 we identified 1103 proteins from the cytosolic fraction of the Escherichia coli strain MC4100. |
| GO:0005829 cytosol | IDA PMID:18304323 Protein abundance profiling of the Escherichia coli cytosol. | ACCEPT | Summary: The independent MC4100 cytosolic proteome supports TrmA cytosol localization. Reason: The full PMID:18304323 describes cytosolic fractionation and mass spectrometry. Its target-level evidence is in supplementary Table S2, which could not be independently retrieved here; the original target IDA annotation and separate fractionation study are consistent, with no evidence for an alternative exclusive location. Supporting Evidence: PMID:18304323 we identified 1103 proteins from the cytosolic fraction of the Escherichia coli strain MC4100. PMID:15911532 3,199 protein forms were detected, and of those 2,160 were annotated and assigned to the cytosol, periplasm, inner membrane, and outer membrane by biochemical fractionation followed by two-dimensional gel electrophoresis and tandem mass spectrometry. |
| GO:0006396 RNA processing | IEA GO_REF:0000120 | MODIFY | Summary: TrmA participates in RNA maturation through tRNA and tmRNA methylation. Reason: RNA processing includes chemical maturation rather than only cleavage. Refine the broad InterPro/combined process mapping to RNA methylation, which covers both demonstrated RNA substrates; restricting this row only to tRNA would lose the experimentally established tmRNA reaction. tRNA folding is independently retained under its own precise process term. Proposed replacements: RNA methylation Supporting Evidence: PMID:6997293 The tRNA-modifying enzyme, S-adenosylmethionine: tRNA (uridine-5)-methyltransferase, has been purified essentially to homogeneity from an Escherichia coli strain containing an elevated level of this enzyme. PMID:23603891 Here, we show that m (5)U formation in tmRNAs is exclusively due to TrmA and should be considered as a dual-specific enzyme. |
| GO:0008173 RNA methyltransferase activity | IEA GO_REF:0000120 | MODIFY | Summary: Resolve broad RNA methyltransferase activity into the established tRNA reaction and proposed tmRNA reaction. Reason: TrmA methylates tRNA U54 and the homologous uridine in the tRNA-like domain of tmRNA. GO:0030697 is the existing precise tRNA/SAM-dependent descendant. A separate proposed tmRNA C5-methyltransferase term captures the second experimentally supported RNA class, for which no matching term was found in the live ontology. Listing both activities preserves the substrate breadth that would be lost by refining only to tRNA; rRNA binding does not establish rRNA methylation. Proposed replacements: tRNA (uracil(54)-C5)-methyltransferase activity, S-adenosyl methionine-dependent tmRNA (uracil-C5)-methyltransferase activity, S-adenosyl methionine-dependent Supporting Evidence: PMID:6997293 The tRNA-modifying enzyme, S-adenosylmethionine: tRNA (uridine-5)-methyltransferase, has been purified essentially to homogeneity from an Escherichia coli strain containing an elevated level of this enzyme. PMID:23603891 Here, we show that m (5)U formation in tmRNAs is exclusively due to TrmA and should be considered as a dual-specific enzyme. |
| GO:0008757 S-adenosylmethionine-dependent methyltransferase activity | IEA GO_REF:0000117 | MODIFY | Summary: Refine SAM-dependent methyl transfer to the supported tRNA and tmRNA C5-uridine reactions. Reason: Purified TrmA establishes SAM-dependent tRNA U54 methylation (PMID:6997293). GO:0030697 is an is_a descendant of GO:0008757 and is already carried by this gene, preserving both donor and substrate specificity. The separate proposed tmRNA C5-methyltransferase activity retains the second substrate established by native RNA analysis in PMID:23603891. RNA methyltransferase GO:0008173 alone is not a descendant of the SAM-dependent term and would discard its methyl-donor information. The tmRNA substrate assignment is based on loss of the modification in trmA-deleted cells, not a separately measured purified tmRNA reaction rate. Proposed replacements: tRNA (uracil(54)-C5)-methyltransferase activity, S-adenosyl methionine-dependent tmRNA (uracil-C5)-methyltransferase activity, S-adenosyl methionine-dependent Supporting Evidence: PMID:6997293 The tRNA-modifying enzyme, S-adenosylmethionine: tRNA (uridine-5)-methyltransferase, has been purified essentially to homogeneity from an Escherichia coli strain containing an elevated level of this enzyme. PMID:23603891 Here, we show that m (5)U formation in tmRNAs is exclusively due to TrmA and should be considered as a dual-specific enzyme. |
| GO:0009451 RNA modification | IEA GO_REF:0000117 | MODIFY | Summary: TrmA RNA modification is methylation of tRNA and tmRNA uridines. Reason: The ARBA-derived broad process can be refined to RNA methylation on independent target evidence. This retains both tRNA U54 and tmRNA U341 coverage without inferring participation in every downstream trans-translation or stress process. Proposed replacements: RNA methylation Supporting Evidence: PMID:6997293 The tRNA-modifying enzyme, S-adenosylmethionine: tRNA (uridine-5)-methyltransferase, has been purified essentially to homogeneity from an Escherichia coli strain containing an elevated level of this enzyme. PMID:23603891 The evidence comes from the lack of m (5)U in purified tmRNA or TLD variants recovered from an Escherichia coli mutant strain deleted of the trmA gene. |
| GO:0019843 rRNA binding | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: The inherited rRNA-binding claim is supported by TrmA association with a 16S rRNA fragment. Reason: PMID:8419334 directly identified the 3-prime terminus of 16S rRNA in the native stable TrmA-RNA complex. This supports binding but not a ribosomal catalytic substrate: the complex was not ribosome-associated, and U747/U1939 methylation belongs to distinct enzymes. The physiological role of this association is less established than tRNA/tmRNA modification and folding. Supporting Evidence: PMID:8419334 After sequencing and Southern blot analyses, the RNA was identified to be a subset of undermodified tRNA species as well as the 3' terminus of 16 S rRNA. PMID:8419334 However, the complex is not associated with the ribosome and the covalently bound RNA does not affect the tRNA methylating activity of the enzyme. |
| GO:0019843 rRNA binding | IDA PMID:8419334 The tRNA-(m5U54)-methyltransferase of Escherichia coli is pr... | KEEP AS NON CORE | Summary: TrmA binds a native 3-prime fragment of 16S rRNA in a stable RNA-protein complex. Reason: The original PMID:8419334 provides direct association evidence in its accessible abstract. Retain the precise binding claim while separating it from rRNA methylation and ribosomal structural membership; neither follows from this experiment. Supporting Evidence: PMID:8419334 After sequencing and Southern blot analyses, the RNA was identified to be a subset of undermodified tRNA species as well as the 3' terminus of 16 S rRNA. PMID:8419334 However, the complex is not associated with the ribosome and the covalently bound RNA does not affect the tRNA methylating activity of the enzyme. |
| GO:0030488 tRNA methylation | IEA GO_REF:0000104 | ACCEPT | Summary: The UniRule tRNA-methylation process agrees with TrmA target chemistry. Reason: Purified enzyme biochemistry and genetic loss of tRNA m5U independently support the process. The additional tmRNA substrate does not negate the accurate tRNA claim, and mature tRNA methylation is a direct catalytic contribution rather than a necessity-only phenotype. Supporting Evidence: PMID:6997293 The tRNA-modifying enzyme, S-adenosylmethionine: tRNA (uridine-5)-methyltransferase, has been purified essentially to homogeneity from an Escherichia coli strain containing an elevated level of this enzyme. PMID:1100618 Matched pairs of transductant strains differing by the presence of absence of 5-methyluridine (ribothymidine) (m5U) in their transfer ribonucleic acid (tRNA) were used to study the function of this modified nucleoside in Escherichia coli. |
| GO:0030488 tRNA methylation | IMP PMID:1100618 Physiological and biochemical studies on the function of 5-m... | ACCEPT | Summary: The original trmA comparison establishes loss of tRNA m5U. Reason: PMID:1100618 compares matched transductants with and without tRNA m5U. Ordinary growth and elongation measurements did not reveal a defect, whereas competition favored modified tRNA; retain direct methylation participation without converting those context-dependent fitness observations into a new process assertion. Supporting Evidence: PMID:1100618 Matched pairs of transductant strains differing by the presence of absence of 5-methyluridine (ribothymidine) (m5U) in their transfer ribonucleic acid (tRNA) were used to study the function of this modified nucleoside in Escherichia coli. |
| GO:0030697 tRNA (uracil(54)-C5)-methyltransferase activity, S-adenosyl methionine-dependent | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT assigns the SAM-dependent tRNA U54 C5 methyltransferase activity to TrmA. Reason: The inherited activity agrees with direct target purification and later structural/mutational studies. Its narrower tRNA specificity remains correct even though the same protein also modifies the tRNA-like region of tmRNA; homology to RlmC/RlmD does not transfer their rRNA sites. Supporting Evidence: PMID:6997293 The tRNA-modifying enzyme, S-adenosylmethionine: tRNA (uridine-5)-methyltransferase, has been purified essentially to homogeneity from an Escherichia coli strain containing an elevated level of this enzyme. |
| GO:0030697 tRNA (uracil(54)-C5)-methyltransferase activity, S-adenosyl methionine-dependent | IDA PMID:6997293 Isolation and chracterization of m5U-methyltransferase from ... | ACCEPT | Summary: Purified E. coli TrmA catalyzes SAM-dependent tRNA uridine methylation. Reason: The original PMID:6997293 reports near-homogeneous enzyme, SAM and tRNA kinetic parameters and substrate assays. Its abstract supports the direct activity; later TrmA-RNA structure and U54 assays corroborate site-specific C5 chemistry without claiming the old paper was recovered in full. Supporting Evidence: PMID:6997293 The tRNA-modifying enzyme, S-adenosylmethionine: tRNA (uridine-5)-methyltransferase, has been purified essentially to homogeneity from an Escherichia coli strain containing an elevated level of this enzyme. |
| GO:0030697 tRNA (uracil(54)-C5)-methyltransferase activity, S-adenosyl methionine-dependent | IEA GO_REF:0000120 | ACCEPT | Summary: The combined electronic TrmA assignment matches experimentally defined tRNA U54 methylation. Reason: Independent target biochemistry supports the curated reaction; this conclusion does not rest on ARBA or an EC label alone. The RNA recognition architecture distinguishes TrmA from the U747- and U1939-specific rRNA enzymes. Supporting Evidence: PMID:6997293 The tRNA-modifying enzyme, S-adenosylmethionine: tRNA (uridine-5)-methyltransferase, has been purified essentially to homogeneity from an Escherichia coli strain containing an elevated level of this enzyme. PMID:32597953 We identify two conserved residues, F106 and H125, in the RNA-binding domain of TrmA, which interact with the tRNA elbow and are critical for tRNA binding. |
| GO:0061818 tRNA folding | IDA PMID:32597953 The methyltransferase TrmA facilitates tRNA folding through ... | ACCEPT | Summary: TrmA directly facilitates tRNA folding independently of methyltransferase catalysis. Reason: Full PMID:32597953 uses a refolding/aminoacylation assay and binding-defective versus catalytic variants. The outcome measures functional tRNA folding, not merely a knockout-associated growth effect. This is a second core molecular role, distinct from methyl-group transfer. Supporting Evidence: PMID:32597953 We directly show that TrmA enhances tRNA folding in vitro independent of its catalytic activity. PMID:32597953 We identify two conserved residues, F106 and H125, in the RNA-binding domain of TrmA, which interact with the tRNA elbow and are critical for tRNA binding. |
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Q: How do TrmA catalytic and chaperone contributions to fitness vary across growth conditions, and what is the specific contribution of tmRNA U341 methylation?
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