Gene Ontology annotation through association of InterPro records with GO terms

Annotation inferences using phylogenetic trees

Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features

GO_REF:0000117

Electronic Gene Ontology annotations created by ARBA machine learning models

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

PMID:12907714

Identifying the methyltransferases for m(5)U747 and m(5)U1939 in 23S rRNA using MALDI mass spectrometry.

YbjF (now RlmC/RumB) is responsible for m5U747 methylation in 23S rRNA, as demonstrated by in vivo knockout showing specific loss of this modification.

"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"
Recombinant YbjF/RlmC could not be obtained in an active form in vitro, so function was established by in vivo knockout analysis.

"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"
The three E. coli m5U RNA methyltransferases are: TrmA (tRNA U54), YbjF/RumB/RlmC (23S rRNA U747), and YgcA/RumA/RlmD (23S rRNA U1939).

"With this report, the functions of all the E.coli m(5)U RNA methyltransferases are identified"

PMID:21824914

A single methyltransferase YefA (RlmCD) catalyses both m5U747 and m5U1939 modifications in Bacillus subtilis 23S rRNA.

In B. subtilis, a single COG2265 enzyme (YefA/RlmCD) catalyzes both m5U747 and m5U1939 modifications, whereas E. coli uses separate enzymes RlmC and RlmD for these two sites.

"methylation of U747 and U1939 in B. subtilis rRNA is catalysed by a single enzyme, YefA that is a COG2265 member"

PMID:21051506

Specificity shifts in the rRNA and tRNA nucleotide targets of archaeal and bacterial m5U methyltransferases.

RNA m5U methyltransferases arose in Bacteria and spread to Archaea and Eukaryota by horizontal gene transfer. The COG2265 enzymes have undergone target specificity shifts during evolution.

"The RNA m(5)U methyltransferases appear to have arisen in Bacteria and were then dispersed by horizontal transfer of an rlmD-type gene to the Archaea and Eukaryota"

PMID:30388185

Unveiling the structural features that determine the dual methyltransferase activities of Streptococcus pneumoniae RlmCD.

Structural analysis of S. pneumoniae RlmCD in complex with U747-containing and U1939-containing RNA substrates reveals how the dual-specificity enzyme discriminates between the two substrates, providing insight into the dedicated specificity of E. coli RlmC for U747.

"RlmC is the dedicated enzyme for m5U747 in Escherichia coli"

PMID:15181002

Redox reactions of the iron-sulfur cluster in a ribosomal RNA methyltransferase, RumA: optical and EPR studies.

RumA/RlmD homologs (including RlmC) contain a conserved [4Fe-4S] cluster with a CX5CGGC binding motif. The cluster is structural rather than catalytic since the methyltransferase reaction does not involve a redox step.

"Sequence data base searches revealed that RumA homologs are widespread in various kingdoms of life and contain a conserved and unique iron-sulfur cluster binding motif, CX(5)CGGC"

PMID:17459887

Amino acid residues of the Escherichia coli tRNA(m5U54)methyltransferase (TrmA) critical for stability, covalent binding of tRNA and enzymatic activity.

Conserved residues in the COG2265 catalytic domain are shared across TrmA, RumA/RlmD, and RumB/RlmC, supporting modular evolution with a conserved catalytic domain combined with different RNA-binding domains.

"the amino acids F188, Q190, G220, D299, R302, C324 and E358, conserved in the C-terminal catalytic domain of several RNA(m5U)methyltransferases of the COG2265 family, are important for the formation of the TrmA-tRNA intermediate and/or the enzymatic activity"

file:ECOLI/rlmC/rlmC-deep-research-falcon.md

Falcon (Edison Scientific) deep research report: E. coli K-12 rlmC (UniProt P75817) - 23S rRNA m5U747 methyltransferase

RlmC is an SAM-dependent C5 uridine methyltransferase that forms m5U747 in 23S rRNA; in vivo knockout (MALDI-MS mapping) establishes it is required for this modification, with no detectable in vitro activity on naked RNA.

"These data directly support that **RlmC is required in vivo for m5U747 formation**."
RlmC is distinct from its COG2265 paralogs TrmA (tRNA U54) and RlmD/RumA (23S rRNA U1939), each with a dedicated target.

"This assignment explicitly distinguishes RlmC from the related paralogs **TrmA** (tRNA U54 methyltransferase) and **RlmD/RumA** (23S rRNA U1939 methyltransferase)."
Recombinant/purified RlmC showed no detectable activity on isolated 23S rRNA or a 694-767 nt transcript, suggesting the physiological substrate is an assembly intermediate / RNP rather than free RNA.

"This negative biochemical evidence has been interpreted as suggesting RlmC may require a **specific ribonucleoprotein (RNP) context**, such as a **ribosome assembly intermediate** or near-mature 50S particle, rather than free RNA."
The m5U747 target nucleotide lies in hairpin 35 of 23S rRNA and projects toward the large-subunit nascent peptide exit tunnel.

"Comparative analysis places **m5U747** in **hairpin 35** of 23S rRNA, where the base is described as protruding into the **large-subunit exit tunnel** and thus may influence the tunnel environment and nascent chain interactions."
RlmC acts in the rRNA chemical modification pathway, which is coupled to ribosome biogenesis and maturation, and bacterial rRNA modification enzymes act cytoplasmically on pre-rRNA / assembling ribosomal particles.

"In bacteria, these modification enzymes are generally **cytoplasmic** and act on pre-rRNA / assembling ribosomal particles"
ΔrlmC produces a generally mild but conditional phenotype, with accumulation of the 17S rRNA precursor at 20C but not 37C, indicating a subtle role in rRNA maturation/homeostasis rather than catastrophic assembly failure.

"loss of m5U747 produces **subtle/conditional defects** in rRNA maturation/homeostasis rather than catastrophic ribosome assembly failure."