A0A2I0M3K7 is the rock pigeon (Columba livia) gene model for TRUB2, a member of the TruB family of pseudouridine synthases that convert uridine to pseudouridine in RNA. It is classified in PANTHER subfamily PTHR13195:SF0 (mitochondrial TRUB2) and InterPro Trub2 (IPR039048), together with human TRUB2. In mammals TRUB2 is a mitochondrial matrix enzyme found in mitochondrial RNA granules, where it contributes, as a minor enzyme alongside RPUSD3, to pseudouridylation of specific mitochondrial mRNA residues (in COXI and COXIII transcripts); human TRUB2 also shows tRNA pseudouridine-55 synthase activity in vitro and in mitochondrial extracts, and its depletion impairs mitochondrial protein synthesis. The pigeon entry as modelled is a 142-residue N-terminally truncated product from an unassembled whole-genome-shotgun contig. It corresponds to human TRUB2 residues 178-307 (about 73% identity) and lacks the first 177 residues, including the catalytic aspartate (human D98) and the predicted mitochondrial transit peptide, so the encoded polypeptide is not by itself a complete enzyme. The full-length pigeon TRUB2 gene is expected to carry the conserved mitochondrial pseudouridine synthase function inferred for the bilaterian TRUB2 lineage.
Summary: Pseudouridine synthesis is the correct general process for the TRUB2 gene, from Trub2/TruB family membership (IPR039048, PTHR13195:SF0). The more specific process established for the TRUB2 lineage is mRNA pseudouridine synthesis: human TRUB2 contributes to pseudouridylation of specific mitochondrial mRNA residues, and the PAINT curator placed mRNA pseudouridine synthesis (GO:1990481) on the bilaterian TRUB2 node PTN000324318, from which this pigeon gene descends via SF0 membership. The previous review replaced this term with mitochondrial tRNA pseudouridine synthesis (GO:0070902); that term is not asserted at the PAINT node even though human TRUB2 has an IMP for it, which is treated here as a deliberate decision not to project the tRNA activity across Bilateria, so it is not transferred to pigeon.
Reason: Correct but general. Refine to GO:1990481 mRNA pseudouridine synthesis, the descendant supported by human experimental data and by the PAINT ancestral assertion for the TRUB2 subfamily. The tRNA-specific term proposed previously is withdrawn because PAINT did not propagate it. Note the accession is a truncated gene model lacking the catalytic aspartate; the claim is made for the TRUB2 gene, not for the 142-aa polypeptide in isolation.
Summary: RNA binding is inherent to a TruB-family pseudouridine synthase that acts directly on RNA substrates, and the InterPro pseudouridine synthase catalytic-domain superfamily (IPR020103) supports it. No more specific binding activity (for example tRNA or mRNA binding as a separable function) is established for the TRUB2 lineage, so the term is as precise as the evidence allows, but it is a mechanistic consequence of the catalytic activity rather than an independent core function.
Reason: True and appropriately precise for binding, but ancillary to the pseudouridine synthase activity that is the core function.
Supporting Evidence:
file:COLLI/A0A2I0M3K7/A0A2I0M3K7-uniprot.txt
DR InterPro; IPR020103; PsdUridine_synth_cat_dom_sf.
Summary: This row comes from the InterPro2GO mapping of the Pfam TruB N-terminal domain (IPR002501). In the current GO structure RNA modification and pseudouridine synthesis are not classified under RNA processing (their ancestors run through RNA metabolic process and macromolecule modification), so pseudouridylation does not entail RNA processing. Human TRUB2 depletion affects mitochondrial translation without altering mitochondrial mRNA levels, and there is no evidence that TRUB2 performs cleavage, splicing or end-processing.
Reason: Legacy domain-level mapping that does not describe what TRUB2 does; pseudouridylation is captured by the pseudouridine synthesis / mRNA pseudouridine synthesis terms.
Depletion of the individual enzymes produced specific mitochondrial protein synthesis and oxidative phosphorylation assembly defects without affecting mitochondrial mRNA levels.
Summary: RNA modification is a correct but general ancestor of pseudouridine synthesis. The specific process supported for the TRUB2 lineage is mRNA pseudouridine synthesis (GO:1990481), which is an is_a descendant of RNA modification and is the refinement proposed for the pseudouridine synthesis row in this review.
Reason: Correct but general; refine to GO:1990481 mRNA pseudouridine synthesis, as supported by human TRUB2 experimental data and the bilaterian TRUB2 PAINT node.
Summary: Pseudouridine synthase activity is the core molecular function of the TRUB2 gene. The pigeon gene is placed in PTHR13195:SF0 (mitochondrial TRUB2) and IPR039048 (Trub2), the subfamily of human TRUB2, and the PAINT curator asserted exactly this general activity (GO:0009982) at the bilaterian TRUB2 node PTN000324318. The previous review replaced it with tRNA pseudouridine(55) synthase activity (GO:0160148). Human TRUB2 does show tRNA Psi55 synthase activity, but PAINT propagated only the general activity from human TRUB2, not the tRNA-specific term, and the dominant in-cell evidence for TRUB2 concerns mitochondrial mRNA sites, so the tRNA-specific refinement is not transferred here. Caveat on identity: the 142-aa gene model covers human TRUB2 residues 178-307 only and lacks the catalytic aspartate (human D98), so the modelled polypeptide is not a complete enzyme; the annotation is appropriate for the TRUB2 gene that the model represents.
Reason: As precise as the phylogenetic evidence supports (matches the PAINT node assertion for the TRUB2 subfamily); the tRNA Psi55-specific term is withdrawn because PAINT deliberately did not project it.
UniProt places A0A2I0M3K7 in PANTHER PTHR13195:SF0 (PSEUDOURIDYLATE SYNTHASE TRUB2, MITOCHONDRIAL) and InterPro IPR039048 (Trub2), the same subfamily as human TRUB2.
PAINT node PTN000324318 does not assert tRNA pseudouridine(55) synthase activity (GO:0160148) or mitochondrial tRNA pseudouridine synthesis (GO:0070902), although human TRUB2 carries both by IMP (PMID:33023933).
Summary: Proposed location for the TRUB2 gene. The PAINT curator asserted mitochondrial matrix at the bilaterian TRUB2 node PTN000324318 (seeded by human TRUB2), and human TRUB2 is a component of mitochondrial RNA granules, which lie in the matrix. The pigeon gene is in the same subfamily (PTHR13195:SF0), but the IBA was not propagated to this entry. The truncated gene model lacks the N-terminal transit peptide region, so the location is asserted for the gene, not for the modelled 142-aa product.
Reason: Location supported by human experimental data and a PAINT ancestral assertion covering the TRUB2 subfamily that includes the pigeon gene.
we identified a protein module in mitochondrial RNA granules, platforms for post-transcriptional RNA modification and ribosome assembly, containing several proteins of unknown function including three uncharacterized pseudouridine synthases, TRUB2, RPUSD3, and RPUSD4
Mitochondrial pseudouridine synthase of the TRUB2 lineage that isomerizes uridine to pseudouridine at specific sites in mitochondrial mRNAs (as a minor contributor alongside RPUSD3), acting in mitochondrial RNA granules in the matrix. Inferred for the pigeon gene from PTHR13195:SF0 membership and the bilaterian TRUB2 PAINT node; the A0A2I0M3K7 gene model itself is N-terminally truncated and lacks the catalytic aspartate and transit peptide.
Q: Does the full-length pigeon TRUB2 locus (beyond the truncated WGS model A0A2I0M3K7) encode the N-terminal catalytic region with the conserved catalytic aspartate and a mitochondrial transit peptide, as expected for a TRUB2 ortholog?
Q: Should the tRNA pseudouridine(55) synthase activity shown for human TRUB2 be asserted at the bilaterian TRUB2 PAINT node, or is it deliberately kept human-only because in-cell evidence for native mt-tRNA targets of TRUB2 is weaker than for TRUB1?
Suggested Experiments
Experiment: Resequence or reannotate the pigeon TRUB2 locus (RNA-seq-supported gene model) to recover the full-length coding sequence, then test recombinant pigeon TRUB2 for pseudouridine synthase activity on mitochondrial mRNA and tRNA substrates.
External Prediction Reviews
These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.
A0A2I0M3K7 is an N-terminally truncated 142-residue gene model of pigeon TRUB2 (PTHR13195:SF0, IPR039048) that lacks the catalytic aspartate. The gene carries general pseudouridine synthase activity by family membership and the bilaterian TRUB2 PAINT node; tRNA substrate specificity for the TRUB2 lineage is not established, because human TRUB2 tRNA Psi55 activity is seen in vitro and in mitochondrial extracts but not in a cell-wide tRNA pseudouridine map, and PAINT did not propagate it.
Prediction method: ProtNLM2 Β· Version: UniProt 2024_06 pilot
DOMAIN ARCHITECTURE MISMATCH
Review rationale: This accession, the exact sequence ProtNLM2 was given, cannot have tRNA pseudouridine synthase activity because it lacks the catalytic aspartate that every TruB-family pseudouridine synthase activity requires. The 142-residue gene model aligns to human TRUB2 residues 178-307 and has no counterpart of human residues 1-177, which contain the active-site nucleophile D98 (equivalent to E. coli TruB D48) and most of the Pseudouridine synthase II N-terminal catalytic domain; only residues 1-54 of that domain remain (UniProt DOMAIN 1..54). For the gene, GO:0106029 would be a novel refinement of the pseudouridine synthase activity (GO:0009982) it already carries, and even at gene level a tRNA-specific activity for the TRUB2 lineage is unsettled: recombinant human TRUB2 has tRNA Psi55 activity (PMID:33023933), but a cell-wide tRNA pseudouridine map found no noticeable TRUB2 activity (PMID:41136621), in-cell evidence centres on mitochondrial mRNA sites (PMID:27974379), and the bilaterian TRUB2 PAINT node asserts only the general activity.
Supporting Evidence:
file:COLLI/A0A2I0M3K7/A0A2I0M3K7-uniprot.txt: "ID A0A2I0M3K7_COLLI Unreviewed; 142 AA. ... DR InterPro; IPR039048; Trub2. ... DR PANTHER; PTHR13195:SF0; PSEUDOURIDYLATE SYNTHASE TRUB2, MITOCHONDRIAL; 1. ... FT DOMAIN 1..54 ... FT /note="Pseudouridine synthase II N-terminal""
PMID:33023933: "all three human recombinant proteins, TRUB1, PUS10, and TRUB2, have Ξ¨55 synthase activities, but differ slightly in their tRNA structural requirements"
PMID:41136621: "RPUSD3 and TRUB2 do not exhibit noticeable enzymatic activities in human"
PMID:27974379: "TRUB2/RPUSD3 were similarly involved in pseudouridylating specific residues in mitochondrial mRNAs"
file:COLLI/A0A2I0M3K7/A0A2I0M3K7-bioinformatics/RESULTS.md: "PAINT node PTN000324318 does not assert tRNA pseudouridine(55) synthase activity (GO:0160148) or mitochondrial tRNA pseudouridine synthesis (GO:0070902), although human TRUB2 carries both by IMP (PMID:33023933)."