id: A0A2I0M3K7 gene_symbol: A0A2I0M3K7 product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:8932 label: Columba livia description: >- 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. existing_annotations: - term: id: GO:0001522 label: pseudouridine synthesis evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: involved_in review: 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. action: MODIFY 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. proposed_replacement_terms: - id: GO:1990481 label: mRNA pseudouridine synthesis supported_by: - reference_id: PMID:27974379 supporting_text: >- TRUB2/RPUSD3 were similarly involved in pseudouridylating specific residues in mitochondrial mRNAs - reference_id: file:COLLI/A0A2I0M3K7/A0A2I0M3K7-bioinformatics/RESULTS.md supporting_text: >- PAINT node PTN000324318 asserts pseudouridine synthase activity (GO:0009982), mRNA pseudouridine synthesis (GO:1990481), positive regulation of mitochondrial translation (GO:0070131) and mitochondrial matrix (GO:0005759). - term: id: GO:0003723 label: RNA binding evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: enables review: 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. action: KEEP_AS_NON_CORE reason: >- True and appropriately precise for binding, but ancillary to the pseudouridine synthase activity that is the core function. supported_by: - reference_id: file:COLLI/A0A2I0M3K7/A0A2I0M3K7-uniprot.txt record_section: ["DR:InterPro"] supporting_text: DR InterPro; IPR020103; PsdUridine_synth_cat_dom_sf. - term: id: GO:0006396 label: RNA processing evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: involved_in review: 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. action: MARK_AS_OVER_ANNOTATED reason: >- Legacy domain-level mapping that does not describe what TRUB2 does; pseudouridylation is captured by the pseudouridine synthesis / mRNA pseudouridine synthesis terms. supported_by: - reference_id: PMID:27974379 supporting_text: >- Depletion of the individual enzymes produced specific mitochondrial protein synthesis and oxidative phosphorylation assembly defects without affecting mitochondrial mRNA levels. - term: id: GO:0009451 label: RNA modification evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: involved_in review: 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. action: MODIFY reason: >- Correct but general; refine to GO:1990481 mRNA pseudouridine synthesis, as supported by human TRUB2 experimental data and the bilaterian TRUB2 PAINT node. proposed_replacement_terms: - id: GO:1990481 label: mRNA pseudouridine synthesis supported_by: - reference_id: PMID:27974379 supporting_text: >- TRUB2/RPUSD3 were similarly involved in pseudouridylating specific residues in mitochondrial mRNAs - term: id: GO:0009982 label: pseudouridine synthase activity evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: enables review: 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. action: ACCEPT 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. supported_by: - reference_id: PMID:33023933 supporting_text: >- while TRUB1, PUS10, and TRUB2 all have tRNA Ψ55 synthase activities, they have different tRNA structural requirements - reference_id: file:COLLI/A0A2I0M3K7/A0A2I0M3K7-bioinformatics/RESULTS.md supporting_text: >- UniProt places A0A2I0M3K7 in PANTHER PTHR13195:SF0 (PSEUDOURIDYLATE SYNTHASE TRUB2, MITOCHONDRIAL) and InterPro IPR039048 (Trub2), the same subfamily as human TRUB2. - reference_id: file:COLLI/A0A2I0M3K7/A0A2I0M3K7-bioinformatics/RESULTS.md supporting_text: >- 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). - term: id: GO:0005759 label: mitochondrial matrix evidence_type: IBA original_reference_id: GO_REF:0000033 review: 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. action: NEW reason: >- Location supported by human experimental data and a PAINT ancestral assertion covering the TRUB2 subfamily that includes the pigeon gene. supported_by: - reference_id: PMID:27974379 supporting_text: >- 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 - reference_id: file:COLLI/A0A2I0M3K7/A0A2I0M3K7-bioinformatics/RESULTS.md supporting_text: >- PAINT node PTN000324318 asserts pseudouridine synthase activity (GO:0009982), mRNA pseudouridine synthesis (GO:1990481), positive regulation of mitochondrial translation (GO:0070131) and mitochondrial matrix (GO:0005759). references: - id: GO_REF:0000002 title: Gene Ontology annotation through association of InterPro records with GO terms findings: [] - id: GO_REF:0000033 title: Annotation inferences using phylogenetic trees - id: file:COLLI/A0A2I0M3K7/A0A2I0M3K7-deep-research-falcon.md title: Deep research report on TRUB2 in Columba livia (falcon/Edison) findings: - statement: >- TRUB2 is a mitochondrial pseudouridine synthase that catalyzes Psi55 formation in mitochondrial tRNAs, localizes to mitochondrial RNA granules, and is essential for mitochondrial translation and OXPHOS complex assembly. supporting_text: >- catalyzing the formation of pseudouridine at position 55 in the TΨC loop of select mitochondrial tRNAs reference_review: relevance: MEDIUM correctness: DISPUTED review_notes: >- Retained from the earlier review but no longer used as support. The report summarizes mammalian TRUB2 literature (Antonicka et al. 2017, PMID:27974379; Mukhopadhyay et al. 2021, PMID:33023933; Jia et al. 2022), but it foregrounds tRNA Psi55 synthesis as the primary TRUB2 function, whereas the cell-based evidence centres on mitochondrial mRNA sites and the report itself notes that TRUB2's native mt-tRNA scope is unresolved. It also does not notice that the pigeon entry is an N-terminally truncated gene model. Primary papers are cited directly instead. The finding quote was corrected to verbatim report text. - id: PMID:27974379 title: A pseudouridine synthase module is essential for mitochondrial protein synthesis and cell viability. findings: - statement: >- Human TRUB2 is a mitochondrial RNA-granule pseudouridine synthase that, with RPUSD3, pseudouridylates specific residues in mitochondrial mRNAs; its depletion impairs mitochondrial protein synthesis without altering mt-mRNA levels. supporting_text: >- TRUB2/RPUSD3 were similarly involved in pseudouridylating specific residues in mitochondrial mRNAs reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Human study; abstract-only in cache. Primary source for the mRNA pseudouridylation and mitochondrial RNA granule roles of TRUB2. Transferred to pigeon via PTHR13195:SF0 membership and the PAINT node PTN000324318 that it seeds. - id: PMID:33023933 title: Mammalian nuclear TRUB1, mitochondrial TRUB2, and cytoplasmic PUS10 produce conserved pseudouridine 55 in different sets of tRNA. findings: - statement: >- Recombinant human TRUB2 and mitochondrial extracts show tRNA Psi55 synthase activity, with stricter tRNA structural requirements than TRUB1. supporting_text: >- while TRUB1, PUS10, and TRUB2 all have tRNA Ψ55 synthase activities, they have different tRNA structural requirements reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Mammalian study; abstract-only in cache. Establishes that TRUB2 is a catalytically active pseudouridine synthase. Its tRNA-specific activity was not projected by PAINT to the bilaterian node, so here it supports only the general activity. - id: file:COLLI/A0A2I0M3K7/A0A2I0M3K7-uniprot.txt title: UniProt entry A0A2I0M3K7 (Columba livia TRUB2 gene model) - id: file:COLLI/A0A2I0M3K7/A0A2I0M3K7-bioinformatics/RESULTS.md title: Sequence completeness and evolutionary placement of A0A2I0M3K7 findings: - statement: >- The pigeon entry is an N-terminally truncated TRUB2 gene model covering human TRUB2 residues 178-307 and lacking the catalytic aspartate. supporting_text: >- The catalytic aspartate position (human D98) lies outside the region covered by the pigeon sequence, so A0A2I0M3K7 lacks the catalytic aspartate. core_functions: - description: >- 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. molecular_function: id: GO:0009982 label: pseudouridine synthase activity directly_involved_in: - id: GO:1990481 label: mRNA pseudouridine synthesis locations: - id: GO:0005759 label: mitochondrial matrix supported_by: - reference_id: PMID:27974379 supporting_text: >- TRUB2/RPUSD3 were similarly involved in pseudouridylating specific residues in mitochondrial mRNAs - reference_id: file:COLLI/A0A2I0M3K7/A0A2I0M3K7-bioinformatics/RESULTS.md supporting_text: >- PAINT node PTN000324318 asserts pseudouridine synthase activity (GO:0009982), mRNA pseudouridine synthesis (GO:1990481), positive regulation of mitochondrial translation (GO:0070131) and mitochondrial matrix (GO:0005759). suggested_questions: - question: >- 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? - question: >- 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: - description: >- 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.