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. Phylogenetically Trm4b sits in PANTHER PTHR22808:SF1 together with budding-yeast Trm4/Ncl1, so the PAINT node placement is sound for the clade; the exception is target-specific, arising after the recent S. pombe-specific duplication in which C34 was partitioned to Trm4a (PTHR22808:SF29). 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. PMID:30646830 they derive from a relatively recent duplication event that occurred independently of the duplication in plants
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. Phylogenetically Trm4b sits in PANTHER PTHR22808:SF1 together with budding-yeast Trm4/Ncl1, so the PAINT node placement is sound for the clade; the exception is target-specific, arising after the recent S. pombe-specific duplication in which C34 was partitioned to Trm4a (PTHR22808:SF29). 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. PMID:30646830 they derive from a relatively recent duplication event that occurred independently of the duplication in plants
GO:0003723 RNA binding	IEA GO_REF:0000002	MODIFY	Summary: RNA binding is correct but less specific than the tRNA substrate binding the activity entails. Reason: Trm4b binds and methylates tRNA directly (recombinant protein on in vitro transcribed tRNA-Pro). The InterPro-mapped RNA binding term is true but general; the supported specific term is tRNA binding. Proposed replacements: tRNA binding Supporting Evidence: PMID:30646830 Significantly, 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	KEEP AS NON CORE	Summary: Inherited cytoplasmic location is plausible but not observed for Trm4b; non-core. Reason: The PAINT inference transfers cytoplasmic residence from NSUN2-family members. The only target-level observation (localization atlas, as cited in the primary paper and UniProt) is nuclear, where the C49/C50 activity is presumed to act. Nuclear data do not exclude a cytoplasmic pool, so the row is retained but is peripheral to the core function. Supporting Evidence: PMID:30646830 However, both enzymes are localized to the nucleus 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	MARK AS OVER ANNOTATED	Summary: Flag the NSUN4-derived rRNA-processing IBA as likely family over-propagation. Reason: The focused OpenScientist follow-up resolves the donor identity but leaves the PAINT node itself unaudited. MGI:1919431 is Nsun4, whose characterized role is mitochondrial 12S rRNA methylation and mitochondrial ribosome assembly, while S. pombe Trm4b is a nuclear Trm4/NSUN2-related tRNA C49/C50 methyltransferase with no direct rRNA-processing evidence. This is likely NSUN4 donor carry-over through a broad NSUN-family node, but the same node also reaches the NSUN2 branch, so this row should be marked as over-propagated rather than removed on an unaudited node-boundary claim. Propagation Review Root cause: PROPAGATION BAD Failure modes: WRONG ORTHOLOG OR PARALOG FUNCTIONAL DIVERGENCE Sources checked: MGI:MGI:1919431 · Nsun4 SUPPORTS SOURCE BUT NOT TARGET Donor named in the GOA WITH/FROM column is mouse Nsun4, a mitochondrial 12S rRNA m5C methyltransferase and mitochondrial-ribosome assembly factor. That paralogue-specific substrate and complex support NSUN4, not nuclear Trm4/NSUN2-related Trm4b. PANTHER:PTN000516076 · PTN000516076 UNRESOLVED Family-wide NSUN node. The OpenScientist run verified the donor identity but did not audit the PAINT tree, and local NSUN2 GOA carries the same NSUN4-derived rows from this node. Supporting Evidence: PMID:30646830 Trm4b methylated all C49 sites on tRNAs. file:SCHPO/trm402/trm402-hypotheses/trm4b-rrna-mrna-and-mitochondrial-ribosome-functions/openscientist.md the rRNA-methylation, rRNA-processing, and mitochondrial-LSU-assembly claims are refuted as paralog carry-over from NSUN4.
GO:0008168 methyltransferase activity	IEA GO_REF:0000002	MODIFY	Summary: Correct but general; the specific tRNA cytosine-C5 methyltransferase activity is supported. Reason: Trm4b is a tRNA m5C methyltransferase (C49/C50) by deletion methylome and recombinant assays. This broad InterPro-mapped catalytic class is true but less specific than GO:0016428, which the gene already carries by IDA/IMP. Proposed replacements: tRNA (cytidine-N5)-methyltransferase activity Supporting Evidence: PMID:30646830 Conversely, Trm4b methylates C49 and C50, which both lie in the TΨC-stem.
GO:0008173 RNA methyltransferase activity	IEA GO_REF:0000002	MODIFY	Summary: Correct but general; the specific tRNA cytosine-C5 methyltransferase activity is supported. Reason: Trm4b is a tRNA m5C methyltransferase (C49/C50) by deletion methylome and recombinant assays. This broad InterPro-mapped catalytic class is true but less specific than GO:0016428, which the gene already carries by IDA/IMP. Proposed replacements: tRNA (cytidine-N5)-methyltransferase activity Supporting Evidence: PMID:30646830 Conversely, Trm4b methylates C49 and C50, which both lie in the TΨC-stem.
GO:0009383 rRNA (cytosine-C5-)-methyltransferase activity	IBA GO_REF:0000033	MARK AS OVER ANNOTATED	Summary: Flag the NSUN4-derived rRNA methyltransferase IBA as likely family over-propagation. Reason: The focused OpenScientist follow-up resolves the donor identity but leaves the PAINT node itself unaudited. MGI:1919431 is Nsun4, whose characterized substrate is mitochondrial 12S rRNA, while S. pombe Trm4b is a nuclear Trm4/NSUN2-related enzyme experimentally shown to methylate tRNA C49/C50. This is likely NSUN4 donor carry-over through a broad NSUN-family node, but the same node also reaches the NSUN2 branch, so this row should be marked as over-propagated rather than removed on an unaudited node-boundary claim. Propagation Review Root cause: PROPAGATION BAD Failure modes: WRONG ORTHOLOG OR PARALOG FUNCTIONAL DIVERGENCE Sources checked: MGI:MGI:1919431 · Nsun4 SUPPORTS SOURCE BUT NOT TARGET Donor named in the GOA WITH/FROM column is mouse Nsun4, a mitochondrial 12S rRNA m5C methyltransferase and mitochondrial-ribosome assembly factor. That paralogue-specific substrate and complex support NSUN4, not nuclear Trm4/NSUN2-related Trm4b. PANTHER:PTN000516076 · PTN000516076 UNRESOLVED Family-wide NSUN node. The OpenScientist run verified the donor identity but did not audit the PAINT tree, and local NSUN2 GOA carries the same NSUN4-derived rows from this node. Supporting Evidence: PMID:30646830 Trm4b methylated all C49 sites on tRNAs. file:SCHPO/trm402/trm402-hypotheses/trm4b-rrna-mrna-and-mitochondrial-ribosome-functions/openscientist.md MGI:1919431 = Nsun4 file:SCHPO/trm402/trm402-hypotheses/trm4b-rrna-mrna-and-mitochondrial-ribosome-functions/openscientist.md These are NSUN4 (mito 12S rRNA) and, in a different family, NSUN5/NOP2 functions.
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. The donor (human NSUN2, Q08J23) is classified in PTHR22808:SF20, whereas Trm4b is in SF1 with budding-yeast Trm4; the mRNA substrate extension is therefore not a within-subfamily transfer. 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 file:SCHPO/trm402/trm402-hypotheses/trm4b-rrna-mrna-and-mitochondrial-ribosome-functions/openscientist.md The only non-tRNA function with a defensible rationale is mRNA (cytidine-5-)-methyltransferase (GO:0062152), which sits on Trm4b as an ISS projection from human NSUN2 (Q08J23).
GO:1902775 mitochondrial large ribosomal subunit assembly	IBA GO_REF:0000033	REMOVE	Summary: Remove the NSUN4-derived mitochondrial ribosome assembly IBA from Trm4b. Reason: The focused OpenScientist follow-up resolves the donor identity but leaves the PAINT node itself unaudited. MGI:1919431 is Nsun4, and NSUN4 is a short mitochondrial branch member of heterogeneous PTHR22808, while S. pombe Trm4b is a nuclear Trm4/NSUN2-related tRNA C49/C50 methyltransferase with no mitochondrial targeting. The donor identity plus the direct compartment mismatch support removal for mitochondrial large ribosomal subunit assembly without asserting a precise PAINT-node boundary. Propagation Review Root cause: PROPAGATION BAD Failure modes: WRONG ORTHOLOG OR PARALOG COMPARTMENT OR COMPLEX MISMATCH Sources checked: MGI:MGI:1919431 · Nsun4 SUPPORTS SOURCE BUT NOT TARGET Donor named in the GOA WITH/FROM column is mouse Nsun4, a mitochondrial 12S rRNA m5C methyltransferase and mitochondrial-ribosome assembly factor. That mitochondrial role supports NSUN4, not nuclear transit-peptide-free Trm4b. PANTHER:PTN000516076 · PTN000516076 UNRESOLVED Family-wide NSUN node. The OpenScientist run verified the donor identity but did not audit the PAINT tree, and local NSUN2 GOA carries the same NSUN4-derived rows from this node. Supporting Evidence: PMID:30646830 Trm4b methylated all C49 sites on tRNAs. file:SCHPO/trm402/trm402-hypotheses/trm4b-rrna-mrna-and-mitochondrial-ribosome-functions/openscientist.md Because Trm4b lacks mitochondrial targeting entirely, the mito-LSU-assembly claim cannot be a direct Trm4b function.