Bacterial 23S rRNA U747/U1939 C5 methylation

A paired rRNA modification program producing 5-methyluridine at positions corresponding to Escherichia coli 23S rRNA U747 and U1939. In E. coli, RlmC and RlmD divide these two activities; in the characterized Bacillus subtilis and Streptococcus pneumoniae implementations, RlmCD modifies both sites. The reactions share SAM-dependent C5 chemistry but act on distinct RNA regions. Their coexistence does not establish a required order or dependence between the two reactions. This comparison covers the named bacterial examples rather than universal bacterial conservation.

MODULE:bacterial_23s_rrna_m5u747_methylationDRAFTCONCRETEBiological Processmodules/bacterial_23s_rrna_m5u747_methylation.yaml
rRNA base methylationGO:0070475
PMID:12907714
Two dedicated E. coli enzymes provide the paired-site implementation.
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. ... A purified recombinant version of YgcA retains its activity and specificity, and methylates U1939 in an RNA transcript in vitro.
PMID:21824914
B. subtilis uses a dual-specific enzyme.
Transforming this latter strain with an active copy of yefA on a plasmid restored to a significant degree the methylation at both U747 (Figure 2G) and U1939 (Figure 2H).
PMID:26365244
S. pneumoniae independently establishes a dual-specific implementation.
U747 and another nucleotide, U1939, were methylated by the dual-specific methyltransferase RlmCD encoded by SP_1029 in S. pneumoniae.
PMID:32290235
Surveyed mollicutes lack U747 modification and delimit the paired-site scope.
Consistent with this, MS analyses of the G725-C772 in domain II of the mollicutes 23S rRNAs confirmed that there was no modification at U747, or at any other nucleotide in this region (not shown).

The existing U747 module identifier is retained while its one-reaction boundary is expanded to the experimentally linked U747/U1939 specificity program. Each native variant contains two substantive activities. No PRECEDES or regulatory edge is asserted because the sources do not establish an obligatory ordering between these sites. RlmAII-dependent G748 methylation, Erm(B)-dependent antibiotic phenotypes, tRNA TrmA activity and U1939-only RlmFO implementations are outside this boundary. Broad family identifiers ground membership; they do not assert that all family members or all bacteria execute these reactions.

10Nodes
6Parts
1Variant Sets
3Variants
6Annotons
0Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:bacterial_23s_rrna_m5u747_methylation deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Function consistency and core coverage

6 gene-function check(s) reflected in core functions · 0 conflict(s) · 6 evidence or coverage gap(s) (12 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
ec_c_u747 rlmC (ECOLI)
UniProtKB:P75817
Gene 		rRNA (uridine-C5-)-methyltransferase activity
GO:0070041 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ec_d_u1939 rlmD (ECOLI)
UniProtKB:P55135
Gene 		rRNA (uridine-C5-)-methyltransferase activity
GO:0070041 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
bs_u747 rlmCD (BACSU)
UniProtKB:O31503
Gene 		rRNA (uridine-C5-)-methyltransferase activity
GO:0070041 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
bs_u1939 rlmCD (BACSU)
UniProtKB:O31503
Gene 		rRNA (uridine-C5-)-methyltransferase activity
GO:0070041 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
sp_u747 rlmCD / SP_1029 (STRPN)
UniProtKB:Q97R12
Gene 		rRNA (uridine-C5-)-methyltransferase activity
GO:0070041 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
sp_u1939 rlmCD / SP_1029 (STRPN)
UniProtKB:Q97R12
Gene 		rRNA (uridine-C5-)-methyltransferase activity
GO:0070041 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ec_c_u747 RlmC site-specific rRNA methyltransferase lineage
PANTHER:PTHR11061
Family 		rRNA (uridine-C5-)-methyltransferase activity
GO:0070041 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR11061.
ec_d_u1939 RlmD site-specific rRNA methyltransferase lineage
PANTHER:PTHR11061
Family 		rRNA (uridine-C5-)-methyltransferase activity
GO:0070041 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR11061.
bs_u747 RlmCD dual-specific rRNA methyltransferase lineage
PANTHER:PTHR11061
Family 		rRNA (uridine-C5-)-methyltransferase activity
GO:0070041 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR11061.
bs_u1939 RlmCD dual-specific rRNA methyltransferase lineage
PANTHER:PTHR11061
Family 		rRNA (uridine-C5-)-methyltransferase activity
GO:0070041 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR11061.
sp_u747 RlmCD dual-specific rRNA methyltransferase lineage
PANTHER:PTHR11061
Family 		rRNA (uridine-C5-)-methyltransferase activity
GO:0070041 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR11061.
sp_u1939 RlmCD dual-specific rRNA methyltransferase lineage
PANTHER:PTHR11061
Family 		rRNA (uridine-C5-)-methyltransferase activity
GO:0070041 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR11061.

Gene-review completeness (4/4 grounded genes reviewed)

4 complete review(s) · 1 with deep research · 0 missing review · 3 reviewed but lacking deep research

Gene Review Complete Deep research
rlmC P75817 ✓ ✓ ✓
rlmCD O31503 ✓ ✓ ✗
rlmCD Q97R12 ✓ ✓ ✗
rlmD P55135 ✓ ✓ ✗

Details

Context
BacteriaNCBITaxon:2
Paired U747/U1939 rRNA C5 methylationBiological Processbacterial_23s_rrna_m5u747_methylation
rRNA base methylationGO:0070475
Context
BacteriaNCBITaxon:2
Variant set: Native paired-site implementations by taxon and division of substrate specificity (Exactly One)

A chosen native species implementation must include both site activities. This structural requirement defines the paired-site program; it does not mean that deleting one enzyme abolishes the other reaction.

Escherichia coli K-12 paired-site implementationBiological Processecoli_paired_sites

Two distinct RNA-site modifications are installed by two dedicated enzymes, RlmC and RlmD.

Context
Escherichia coli K-12NCBITaxon:83333
PMID:12907714
Establishes the paired sites in this named bacterial implementation.
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. ... A purified recombinant version of YgcA retains its activity and specificity, and methylates U1939 in an RNA transcript in vitro.
Part: U747 C5 methylation
U747 C5 methylationReactionecoli_u747_step

Annotons

E. coli RlmC U747 C5 methylation
ec_c_u747
Participant: Gene Product: rlmC (ECOLI)
Gene Product:
rlmC (ECOLI)UniProtKB:P75817
Family:
RlmC site-specific rRNA methyltransferase lineagePANTHER:PTHR11061 PTHR11061 is the verified broad RNA m5U methyltransferase family. The substrate specificity asserted here is restricted to this characterized exemplar; membership alone does not distinguish rRNA U747, rRNA U1939 or tRNA U54.
Representative Members: rlmC (ECOLI)UniProtKB:P75817

Function

rRNA (uridine-C5-)-methyltransferase activityGO:0070041 C5 methyl transfer at the indicated RNA position; numbering follows the E. coli reference convention, not a claim that every bacterial rRNA has both modifications.
Substrates: uridine 747 in 23S rRNA S-adenosyl-L-methionine
Products: 5-methyluridine 747 in 23S rRNA S-adenosyl-L-homocysteine

Processes

rRNA base methylationGO:0070475

Installs m5U at the U747 site. RlmC is assigned by native genetic loss of this modification, with no active recombinant preparation in the original study.

PMID:12907714
E. coli RlmC is experimentally assigned to the U747 reaction.
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.
Part: U1939 C5 methylation
U1939 C5 methylationReactionecoli_u1939_step

Annotons

E. coli RlmD U1939 C5 methylation
ec_d_u1939
Participant: Gene Product: rlmD (ECOLI)
Gene Product:
rlmD (ECOLI)UniProtKB:P55135
Family:
RlmD site-specific rRNA methyltransferase lineagePANTHER:PTHR11061 PTHR11061 is the verified broad RNA m5U methyltransferase family. The substrate specificity asserted here is restricted to this characterized exemplar; membership alone does not distinguish rRNA U747, rRNA U1939 or tRNA U54.
Representative Members: rlmD (ECOLI)UniProtKB:P55135

Function

rRNA (uridine-C5-)-methyltransferase activityGO:0070041 C5 methyl transfer at the indicated RNA position; numbering follows the E. coli reference convention, not a claim that every bacterial rRNA has both modifications.
Substrates: uridine 1939 in 23S rRNA S-adenosyl-L-methionine
Products: 5-methyluridine 1939 in 23S rRNA S-adenosyl-L-homocysteine

Processes

rRNA base methylationGO:0070475

Installs m5U at the U1939 site. RlmD is distinct from the RlmC enzyme acting at U747.

PMID:12907714
E. coli RlmD is experimentally assigned to the U1939 reaction.
A purified recombinant version of YgcA retains its activity and specificity, and methylates U1939 in an RNA transcript in vitro.
Bacillus subtilis subsp. subtilis str. 168 paired-site implementationBiological Processbacillus_paired_sites

Two distinct RNA-site modifications are installed by one dual-specific RlmCD protein.

Context
Bacillus subtilis subsp. subtilis str. 168NCBITaxon:224308
PMID:21824914
Establishes the paired sites in this named bacterial implementation.
Transforming this latter strain with an active copy of yefA on a plasmid restored to a significant degree the methylation at both U747 (Figure 2G) and U1939 (Figure 2H).
Part: U747 C5 methylation
U747 C5 methylationReactionbacillus_u747_step

Annotons

B. subtilis RlmCD U747 C5 methylation
bs_u747
Participant: Gene Product: rlmCD (BACSU)
Gene Product:
rlmCD (BACSU)UniProtKB:O31503
Family:
RlmCD dual-specific rRNA methyltransferase lineagePANTHER:PTHR11061 PTHR11061 is the verified broad RNA m5U methyltransferase family. The substrate specificity asserted here is restricted to this characterized exemplar; membership alone does not distinguish rRNA U747, rRNA U1939 or tRNA U54.
Representative Members: rlmCD (BACSU)UniProtKB:O31503

Function

rRNA (uridine-C5-)-methyltransferase activityGO:0070041 C5 methyl transfer at the indicated RNA position; numbering follows the E. coli reference convention, not a claim that every bacterial rRNA has both modifications.
Substrates: uridine 747 in 23S rRNA S-adenosyl-L-methionine
Products: 5-methyluridine 747 in 23S rRNA S-adenosyl-L-homocysteine

Processes

rRNA base methylationGO:0070475

Installs m5U at the U747 site. The same RlmCD protein performs the other site reaction in this variant; two activities do not imply two enzyme copies or a required reaction order.

PMID:21824914
B. subtilis RlmCD is experimentally assigned to the U747 reaction.
Transforming this latter strain with an active copy of yefA on a plasmid restored to a significant degree the methylation at both U747 (Figure 2G) and U1939 (Figure 2H).
Part: U1939 C5 methylation
U1939 C5 methylationReactionbacillus_u1939_step

Annotons

B. subtilis RlmCD U1939 C5 methylation
bs_u1939
Participant: Gene Product: rlmCD (BACSU)
Gene Product:
rlmCD (BACSU)UniProtKB:O31503
Family:
RlmCD dual-specific rRNA methyltransferase lineagePANTHER:PTHR11061 PTHR11061 is the verified broad RNA m5U methyltransferase family. The substrate specificity asserted here is restricted to this characterized exemplar; membership alone does not distinguish rRNA U747, rRNA U1939 or tRNA U54.
Representative Members: rlmCD (BACSU)UniProtKB:O31503

Function

rRNA (uridine-C5-)-methyltransferase activityGO:0070041 C5 methyl transfer at the indicated RNA position; numbering follows the E. coli reference convention, not a claim that every bacterial rRNA has both modifications.
Substrates: uridine 1939 in 23S rRNA S-adenosyl-L-methionine
Products: 5-methyluridine 1939 in 23S rRNA S-adenosyl-L-homocysteine

Processes

rRNA base methylationGO:0070475

Installs m5U at the U1939 site. The same RlmCD protein performs the other site reaction in this variant; two activities do not imply two enzyme copies or a required reaction order.

PMID:21824914
B. subtilis RlmCD is experimentally assigned to the U1939 reaction.
Transforming this latter strain with an active copy of yefA on a plasmid restored to a significant degree the methylation at both U747 (Figure 2G) and U1939 (Figure 2H).
Streptococcus pneumoniae TIGR4 paired-site implementationBiological Processstreptococcus_paired_sites

Two distinct RNA-site modifications are installed by one dual-specific RlmCD protein.

Context
Streptococcus pneumoniae TIGR4NCBITaxon:170187
PMID:26365244
Establishes the paired sites in this named bacterial implementation.
U747 and another nucleotide, U1939, were methylated by the dual-specific methyltransferase RlmCD encoded by SP_1029 in S. pneumoniae.
Part: U747 C5 methylation
U747 C5 methylationReactionstreptococcus_u747_step

Annotons

S. pneumoniae RlmCD / SP_1029 U747 C5 methylation
sp_u747
Participant: Gene Product: rlmCD / SP_1029 (STRPN)
Gene Product:
rlmCD / SP_1029 (STRPN)UniProtKB:Q97R12
Family:
RlmCD dual-specific rRNA methyltransferase lineagePANTHER:PTHR11061 PTHR11061 is the verified broad RNA m5U methyltransferase family. The substrate specificity asserted here is restricted to this characterized exemplar; membership alone does not distinguish rRNA U747, rRNA U1939 or tRNA U54.
Representative Members: rlmCD / SP_1029 (STRPN)UniProtKB:Q97R12

Function

rRNA (uridine-C5-)-methyltransferase activityGO:0070041 C5 methyl transfer at the indicated RNA position; numbering follows the E. coli reference convention, not a claim that every bacterial rRNA has both modifications.
Substrates: uridine 747 in 23S rRNA S-adenosyl-L-methionine
Products: 5-methyluridine 747 in 23S rRNA S-adenosyl-L-homocysteine

Processes

rRNA base methylationGO:0070475

Installs m5U at the U747 site. The same RlmCD protein performs the other site reaction in this variant; two activities do not imply two enzyme copies or a required reaction order.

PMID:26365244
S. pneumoniae RlmCD / SP_1029 is experimentally assigned to the U747 reaction.
U747 and another nucleotide, U1939, were methylated by the dual-specific methyltransferase RlmCD encoded by SP_1029 in S. pneumoniae.
PMID:30388185
Biochemistry and RNA-segment structures distinguish the two substrate recognition modes.
In this research, we determined the crystal structures of RlmCD in complex with two RNA segments containing U747 and U1939.
Part: U1939 C5 methylation
U1939 C5 methylationReactionstreptococcus_u1939_step

Annotons

S. pneumoniae RlmCD / SP_1029 U1939 C5 methylation
sp_u1939
Participant: Gene Product: rlmCD / SP_1029 (STRPN)
Gene Product:
rlmCD / SP_1029 (STRPN)UniProtKB:Q97R12
Family:
RlmCD dual-specific rRNA methyltransferase lineagePANTHER:PTHR11061 PTHR11061 is the verified broad RNA m5U methyltransferase family. The substrate specificity asserted here is restricted to this characterized exemplar; membership alone does not distinguish rRNA U747, rRNA U1939 or tRNA U54.
Representative Members: rlmCD / SP_1029 (STRPN)UniProtKB:Q97R12

Function

rRNA (uridine-C5-)-methyltransferase activityGO:0070041 C5 methyl transfer at the indicated RNA position; numbering follows the E. coli reference convention, not a claim that every bacterial rRNA has both modifications.
Substrates: uridine 1939 in 23S rRNA S-adenosyl-L-methionine
Products: 5-methyluridine 1939 in 23S rRNA S-adenosyl-L-homocysteine

Processes

rRNA base methylationGO:0070475

Installs m5U at the U1939 site. The same RlmCD protein performs the other site reaction in this variant; two activities do not imply two enzyme copies or a required reaction order.

PMID:26365244
S. pneumoniae RlmCD / SP_1029 is experimentally assigned to the U1939 reaction.
U747 and another nucleotide, U1939, were methylated by the dual-specific methyltransferase RlmCD encoded by SP_1029 in S. pneumoniae.
PMID:30388185
Biochemistry and RNA-segment structures distinguish the two substrate recognition modes.
In this research, we determined the crystal structures of RlmCD in complex with two RNA segments containing U747 and U1939.