trm4b

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0002127 tRNA wobble base cytosine methylation	IBA GO_REF:0000033	REMOVE	Summary: Trm4b does not carry out physiological tRNA wobble C34 methylation. Reason: GO:0002127 specifies methylation of tRNA anticodon position 34. The direct paralog-resolved study assigns this in vivo process to Trm4a and explicitly excludes Trm4b, despite its C34 activity in vitro. This is target-specific divergence from the budding-yeast Trm4 ancestral function, not an objection to donor count or self-inclusion in PAINT evidence. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN000516076 SUPPORTS SOURCE BUT NOT TARGET Budding-yeast Trm4 supplies physiological wobble C34 methylation; paralog-resolved S. pombe knockout/methylome experiments assign that physiological role to Trm4a, while Trm4b supplies C49/C50. Supporting Evidence: PMID:30646830 Trm4b methylates both C34 and C49 in vitro, even though it does not methylate C34 in vivo. file:SCHPO/trm402/trm402-deep-research-falcon.md It does not overturn the in-vivo assignment of C34 to Trm4a.
GO:0002127 tRNA wobble base cytosine methylation	ISO GO_REF:0000024	REMOVE	Summary: Trm4b does not carry out physiological tRNA wobble C34 methylation. Reason: GO:0002127 specifies methylation of tRNA anticodon position 34. The direct paralog-resolved study assigns this in vivo process to Trm4a and explicitly excludes Trm4b, despite its C34 activity in vitro. This is target-specific divergence from the budding-yeast Trm4 ancestral function, not an objection to donor count or self-inclusion in PAINT evidence. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: SGD:S000000120 SUPPORTS SOURCE BUT NOT TARGET Budding-yeast Trm4 supplies physiological wobble C34 methylation; paralog-resolved S. pombe knockout/methylome experiments assign that physiological role to Trm4a, while Trm4b supplies C49/C50. Supporting Evidence: PMID:30646830 Trm4b methylates both C34 and C49 in vitro, even though it does not methylate C34 in vivo. file:SCHPO/trm402/trm402-deep-research-falcon.md It does not overturn the in-vivo assignment of C34 to Trm4a.
GO:0003723 RNA binding	IEA GO_REF:0000002	ACCEPT	Summary: Retain the broad RNA binding annotation. Reason: Trm4b directly recognizes and methylates tRNA using SAM. The characterized reaction supports RNA binding and the broader RNA methyltransferase/methyltransferase classes. A narrower existing catalytic annotation does not make these accurate ancestor or substrate-recognition annotations incorrect. Supporting Evidence: PMID:30646830 Trm4b showed robust in vitro activity on wild-type tRNAProCGG.
GO:0005634 nucleus	HDA PMID:16823372 ORFeome cloning and global analysis of protein localization ...	ACCEPT	Summary: Trm4b has nuclear localization. Reason: PomBase HDA localization and the experiment-attributed UniProt record agree with nuclear tRNA modification. The underlying localization atlas is abstract-only in the cache; this accepts the curator’s target-level observation without claiming independent inspection of its microscopy. Supporting Evidence: PMID:30646830 However, both enzymes are localized to the nucleus
GO:0005634 nucleus	IBA GO_REF:0000033	ACCEPT	Summary: Trm4b has nuclear localization. Reason: PomBase HDA localization and the experiment-attributed UniProt record agree with nuclear tRNA modification. The underlying localization atlas is abstract-only in the cache; this accepts the curator’s target-level observation without claiming independent inspection of its microscopy. Supporting Evidence: PMID:30646830 However, both enzymes are localized to the nucleus
GO:0005634 nucleus	IEA GO_REF:0000044	ACCEPT	Summary: Trm4b has nuclear localization. Reason: PomBase HDA localization and the experiment-attributed UniProt record agree with nuclear tRNA modification. The underlying localization atlas is abstract-only in the cache; this accepts the curator’s target-level observation without claiming independent inspection of its microscopy. Supporting Evidence: PMID:30646830 However, both enzymes are localized to the nucleus
GO:0005737 cytoplasm	IBA GO_REF:0000033	ACCEPT	Summary: Retain the cytoplasmic IBA without treating nuclear localization as exclusionary. Reason: The PAINT inference asserts inherited cytoplasmic residence; the target localization record establishes a nuclear pool but does not test every condition or exclude cytoplasmic shuttling during tRNA maturation. Lack of compartment-resolved experiments and broadness do not establish a non-core role or a propagation error. Supporting Evidence: file:SCHPO/trm402/trm402-deep-research-falcon.md This conclusion does not exclude transient cytoplasmic residence or modification of recycled tRNAs
GO:0006364 rRNA processing	IBA GO_REF:0000033	UNDECIDED	Summary: The additional rRNA/mitochondrial-ribosome function is not resolved for Trm4b. Reason: The direct Trm4a/Trm4b study establishes tRNA substrate specificity. It does not test or refute this separate rRNA/mitochondrial function. The cited PAINT node includes functions from other RNA-cytosine-methyltransferase branches; deciding whether this specific function is inherited by Trm4b requires its experimental substrate evidence and ancestral-node placement. Broad family membership alone does not resolve that question. Propagation Review Root cause: UNRESOLVED Sources checked: PANTHER:PTN000516076 UNRESOLVED The descendant-supported ancestral assertion remains under review for the target-specific lineage/functional scope described in the rationale; donor number and target self-inclusion are not objections. Supporting Evidence: PMID:30646830 Trm4b methylated all C49 sites on tRNAs.
GO:0008168 methyltransferase activity	IEA GO_REF:0000002	ACCEPT	Summary: Retain the broad methyltransferase activity annotation. Reason: Trm4b directly recognizes and methylates tRNA using SAM. The characterized reaction supports RNA binding and the broader RNA methyltransferase/methyltransferase classes. A narrower existing catalytic annotation does not make these accurate ancestor or substrate-recognition annotations incorrect. Supporting Evidence: PMID:30646830 Trm4b showed robust in vitro activity on wild-type tRNAProCGG.
GO:0008173 RNA methyltransferase activity	IEA GO_REF:0000002	ACCEPT	Summary: Retain the broad RNA methyltransferase activity annotation. Reason: Trm4b directly recognizes and methylates tRNA using SAM. The characterized reaction supports RNA binding and the broader RNA methyltransferase/methyltransferase classes. A narrower existing catalytic annotation does not make these accurate ancestor or substrate-recognition annotations incorrect. Supporting Evidence: PMID:30646830 Trm4b showed robust in vitro activity on wild-type tRNAProCGG.
GO:0009383 rRNA (cytosine-C5-)-methyltransferase activity	IBA GO_REF:0000033	UNDECIDED	Summary: The additional rRNA/mitochondrial-ribosome function is not resolved for Trm4b. Reason: The direct Trm4a/Trm4b study establishes tRNA substrate specificity. It does not test or refute this separate rRNA/mitochondrial function. The cited PAINT node includes functions from other RNA-cytosine-methyltransferase branches; deciding whether this specific function is inherited by Trm4b requires its experimental substrate evidence and ancestral-node placement. Broad family membership alone does not resolve that question. Propagation Review Root cause: UNRESOLVED Sources checked: PANTHER:PTN000516076 UNRESOLVED The descendant-supported ancestral assertion remains under review for the target-specific lineage/functional scope described in the rationale; donor number and target self-inclusion are not objections. Supporting Evidence: PMID:30646830 Trm4b methylated all C49 sites on tRNAs.
GO:0016428 tRNA (cytidine-N5)-methyltransferase activity	IBA GO_REF:0000033	ACCEPT	Summary: Trm4b is an experimentally demonstrated tRNA cytosine-C5 methyltransferase. Reason: Target-gene deletion and biochemical assays establish C49/C50 methylation. This directly validates the activity independently of ARBA or other annotations. The PAINT target appearing among descendant sources is legitimate experimental grounding. Supporting Evidence: PMID:30646830 Conversely, Trm4b methylates C49 and C50, which both lie in the TΨC-stem.
GO:0016428 tRNA (cytidine-N5)-methyltransferase activity	IDA PMID:30646830 Division of labour: tRNA methylation by the NSun2 tRNA methy...	ACCEPT	Summary: Trm4b is an experimentally demonstrated tRNA cytosine-C5 methyltransferase. Reason: Target-gene deletion and biochemical assays establish C49/C50 methylation. This directly validates the activity independently of ARBA or other annotations. The PAINT target appearing among descendant sources is legitimate experimental grounding. Supporting Evidence: PMID:30646830 Conversely, Trm4b methylates C49 and C50, which both lie in the TΨC-stem.
GO:0016428 tRNA (cytidine-N5)-methyltransferase activity	IEA GO_REF:0000120	ACCEPT	Summary: Trm4b is an experimentally demonstrated tRNA cytosine-C5 methyltransferase. Reason: Target-gene deletion and biochemical assays establish C49/C50 methylation. This directly validates the activity independently of ARBA or other annotations. The PAINT target appearing among descendant sources is legitimate experimental grounding. Supporting Evidence: PMID:30646830 Conversely, Trm4b methylates C49 and C50, which both lie in the TΨC-stem.
GO:0016428 tRNA (cytidine-N5)-methyltransferase activity	IMP PMID:30646830 Division of labour: tRNA methylation by the NSun2 tRNA methy...	ACCEPT	Summary: Trm4b is an experimentally demonstrated tRNA cytosine-C5 methyltransferase. Reason: Target-gene deletion and biochemical assays establish C49/C50 methylation. This directly validates the activity independently of ARBA or other annotations. The PAINT target appearing among descendant sources is legitimate experimental grounding. Supporting Evidence: PMID:30646830 Conversely, Trm4b methylates C49 and C50, which both lie in the TΨC-stem.
GO:0030488 tRNA methylation	IEA GO_REF:0000117	ACCEPT	Summary: Trm4b installs m5C modifications in tRNAs. Reason: The paralog-resolved deletion and biochemical experiments establish tRNA methylation as its physiological process. Supporting Evidence: PMID:30646830 Conversely, Trm4b methylates C49 and C50, which both lie in the TΨC-stem.
GO:0030488 tRNA methylation	IMP PMID:30646830 Division of labour: tRNA methylation by the NSun2 tRNA methy...	ACCEPT	Summary: Trm4b installs m5C modifications in tRNAs. Reason: The paralog-resolved deletion and biochemical experiments establish tRNA methylation as its physiological process. Supporting Evidence: PMID:30646830 Conversely, Trm4b methylates C49 and C50, which both lie in the TΨC-stem.
GO:0062152 mRNA (cytidine-5-)-methyltransferase activity	ISS GO_REF:0000024	UNDECIDED	Summary: mRNA methylation remains an untested substrate extension for Trm4b. Reason: NSUN2-family orthology makes this plausible, but the target study explicitly leaves methylation of mRNAs and other small RNAs open. It neither validates nor refutes the additional mRNA activity. Propagation Review Root cause: UNRESOLVED Sources checked: UniProtKB:Q08J23 UNRESOLVED The transferred RNA-substrate specificity must be assessed independently of shared methyltransferase catalysis. Supporting Evidence: PMID:30646830 It will also be interesting to see whether Trm4a and Trm4b methylate mRNAs or other small RNAs in S. pombe
GO:1902775 mitochondrial large ribosomal subunit assembly	IBA GO_REF:0000033	UNDECIDED	Summary: The additional rRNA/mitochondrial-ribosome function is not resolved for Trm4b. Reason: The direct Trm4a/Trm4b study establishes tRNA substrate specificity. It does not test or refute this separate rRNA/mitochondrial function. The cited PAINT node includes functions from other RNA-cytosine-methyltransferase branches; deciding whether this specific function is inherited by Trm4b requires its experimental substrate evidence and ancestral-node placement. Broad family membership alone does not resolve that question. Propagation Review Root cause: UNRESOLVED Sources checked: PANTHER:PTN000516076 UNRESOLVED The descendant-supported ancestral assertion remains under review for the target-specific lineage/functional scope described in the rationale; donor number and target self-inclusion are not objections. Supporting Evidence: PMID:30646830 Trm4b methylated all C49 sites on tRNAs.