TRUB2 is a nuclear-encoded pseudouridine synthase of the TruB family that is imported into the mitochondrial matrix, where it is concentrated in mitochondrial RNA granules and co-sediments with the large mitoribosomal subunit. Recombinant TRUB2 isomerizes uridine-55 of tRNA to pseudouridine, and it accounts for the tRNA Psi55 synthase activity of mitochondria, consistent with modification of the T-loop of the subset of mitochondrial tRNAs that carry Psi55. It also contributes, apparently as a minor enzyme alongside RPUSD3, to pseudouridylation of specific sites in the COX1 and COX3 mitochondrial mRNAs. TRUB2 associates with RPUSD3, RPUSD4, NGRN, RCC1L (WBSCR16), FASTKD2 and MTERF3 in a mitochondrial RNA-granule module that supports 16S rRNA stability, mitoribosome assembly and mitochondrial translation; its depletion impairs mitochondrial protein synthesis, particularly of ATP8/ATP6, and oxidative phosphorylation, and it is essential for viability in several human cell lines.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0001522 pseudouridine synthesis | IEA GO_REF:0000120 | MODIFY | Summary: Electronic (ARBA/InterPro) assignment of the generic process pseudouridine synthesis from TruB-family membership. Reason: Correct but general. TRUB2 is a TruB-family pseudouridine synthase whose experimentally supported process roles are pseudouridylation of mitochondrial tRNA (Psi55) and, as a minor contributor, mitochondrial mRNA. Replace with the specific child terms the gene already carries. Proposed replacements: mitochondrial tRNA pseudouridine synthesis mRNA pseudouridine synthesis Supporting Evidence: file:human/TRUB2/TRUB2-uniprot.txt Belongs to the pseudouridine synthase TruB family. PMID:33023933 We show here that all three human recombinant proteins, TRUB1, PUS10, and TRUB2, have Ξ¨55 synthase activities, but differ slightly in their tRNA structural requirements. PMID:33023933 Knockdown of TRUB1, TRUB2, and PUS10 reduced Ξ¨55 synthesis by the nuclear, mitochondrial, and cytoplasmic extracts, respectively, in both tRNATrp and tRNAAla |
| GO:0003723 RNA binding | HDA PMID:22658674 Insights into RNA biology from an atlas of mammalian mRNA-bi... | KEEP AS NON CORE | Summary: TRUB2 was recovered in high-throughput UV-crosslinking/oligo(dT) mRNA interactome capture in human cells. Reason: RNA binding is inherent to a pseudouridine synthase that acts on tRNA and mRNA substrates, and interactome capture supports direct RNA contact. It is not the informative description of the gene's activity (that is the catalytic activity), and the specific RNA ligands are not defined by these screens, so it is retained as non-core. Supporting Evidence: PMID:22658674 to define the mRNA interactome of proliferating human HeLa cells |
| GO:0003723 RNA binding | HDA PMID:22681889 The mRNA-bound proteome and its global occupancy profile on ... | KEEP AS NON CORE | Summary: TRUB2 was recovered in high-throughput UV-crosslinking/oligo(dT) mRNA interactome capture in human cells. Reason: RNA binding is inherent to a pseudouridine synthase that acts on tRNA and mRNA substrates, and interactome capture supports direct RNA contact. It is not the informative description of the gene's activity (that is the catalytic activity), and the specific RNA ligands are not defined by these screens, so it is retained as non-core. Supporting Evidence: PMID:22681889 to identify the mRNA-bound proteome using quantitative proteomics |
| GO:0003723 RNA binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO assignment of RNA binding from the pseudouridine synthase catalytic domain superfamily (IPR020103). Reason: Consistent with the HDA interactome-capture rows and with the enzyme's RNA substrates; true but peripheral to the catalytic function, retained as non-core. Supporting Evidence: PMID:33023933 We show here that all three human recombinant proteins, TRUB1, PUS10, and TRUB2, have Ξ¨55 synthase activities, but differ slightly in their tRNA structural requirements. |
| GO:0005739 mitochondrion | HTP PMID:34800366 Quantitative high-confidence human mitochondrial proteome an... | MODIFY | Summary: TRUB2 is in the MitoCoP high-confidence human mitochondrial proteome. Reason: Correct but general. The protein has a predicted N-terminal mitochondrial transit peptide and is experimentally placed in the mitochondrial matrix and in matrix-located mitochondrial RNA granules, so the specific term mitochondrial matrix (already carried by the gene) is preferred. Proposed replacements: mitochondrial matrix Supporting Evidence: PMID:34800366 mitochondrial high-confidence proteome of >1,100 proteins (MitoCoP) file:human/TRUB2/TRUB2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion matrix |
| GO:0005739 mitochondrion | IDA PMID:28082677 The Pseudouridine Synthase RPUSD4 Is an Essential Component ... | MODIFY | Summary: Immunofluorescence localizes TRUB2 to mitochondria, enriched in mitochondrial RNA granules. Reason: Correct but general. The protein has a predicted N-terminal mitochondrial transit peptide and is experimentally placed in the mitochondrial matrix and in matrix-located mitochondrial RNA granules, so the specific term mitochondrial matrix (already carried by the gene) is preferred. Proposed replacements: mitochondrial matrix Supporting Evidence: PMID:28082677 We observed a clear enrichment of RPUSD3, RPUSD4, and TRUB2 in MRGs, whereas neither PUS1 nor PUSL1 appeared to be specifically enriched in discrete foci file:human/TRUB2/TRUB2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion matrix |
| GO:0005759 mitochondrial matrix | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of mitochondrial matrix activity. The IBA derives from a PAINT IBD at Bilateria node PTN000324318, seeded solely by human TRUB2 (O95900); TRUB2's appearance in its own WITH/FROM reflects its experimental grounding, not circularity. Reason: TRUB2 localizes to the mitochondrial matrix, concentrated in mitochondrial RNA granules where it co-sediments with the large mitoribosomal subunit and associates with the RPUSD3/RPUSD4/NGRN/RCC1L/FASTKD2 module. The PAINT placement at the Bilateria TRUB2-subfamily node is consistent with the conserved transit peptide and with human experimental data. Supporting Evidence: PMID:27974379 we identified a protein module in mitochondrial RNA granules file:human/TRUB2/TRUB2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion matrix file:human/TRUB2/TRUB2-uniprot.txt PTHR13195:SF0; PSEUDOURIDYLATE SYNTHASE TRUB2, MITOCHONDRIAL |
| GO:0005759 mitochondrial matrix | IDA PMID:27974379 A pseudouridine synthase module is essential for mitochondri... | ACCEPT | Summary: BioID proximity labelling and immunofluorescence place TRUB2 in mitochondrial RNA granules within the matrix. Reason: TRUB2 localizes to the mitochondrial matrix, concentrated in mitochondrial RNA granules where it co-sediments with the large mitoribosomal subunit and associates with the RPUSD3/RPUSD4/NGRN/RCC1L/FASTKD2 module. Supporting Evidence: PMID:27974379 we identified a protein module in mitochondrial RNA granules PMID:27974379 Using BioID, we reciprocally confirmed the specific interaction of TRUB2 with all these proteins |
| GO:0005759 mitochondrial matrix | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping (SL-0170, mitochondrion matrix), curated from experimental papers. Reason: TRUB2 localizes to the mitochondrial matrix, concentrated in mitochondrial RNA granules where it co-sediments with the large mitoribosomal subunit and associates with the RPUSD3/RPUSD4/NGRN/RCC1L/FASTKD2 module. Supporting Evidence: file:human/TRUB2/TRUB2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion matrix |
| GO:0005759 mitochondrial matrix | IMP PMID:33023933 Mammalian nuclear TRUB1, mitochondrial TRUB2, and cytoplasmi... | ACCEPT | Summary: Psi55 synthase activity of mitochondrial extracts is lost on TRUB2 knockdown, locating TRUB2 activity in mitochondria. Reason: Knockdown specifically reduced Psi55 synthesis by mitochondrial extracts, supporting is_active_in the mitochondrial matrix. TRUB2 localizes to the mitochondrial matrix, concentrated in mitochondrial RNA granules where it co-sediments with the large mitoribosomal subunit and associates with the RPUSD3/RPUSD4/NGRN/RCC1L/FASTKD2 module. Supporting Evidence: PMID:33023933 Knockdown of TRUB1, TRUB2, and PUS10 reduced Ξ¨55 synthesis by the nuclear, mitochondrial, and cytoplasmic extracts, respectively, in both tRNATrp and tRNAAla |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-9936243 | ACCEPT | Summary: Reactome places TRUB2, as part of the mitochondrial pseudouridylation module, in the mitochondrial matrix. Reason: TRUB2 localizes to the mitochondrial matrix, concentrated in mitochondrial RNA granules where it co-sediments with the large mitoribosomal subunit and associates with the RPUSD3/RPUSD4/NGRN/RCC1L/FASTKD2 module. Supporting Evidence: Reactome:R-HSA-9936243 which binds 16S rRNA file:human/TRUB2/TRUB2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion matrix |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-9937369 | ACCEPT | Summary: Reactome places TRUB2, as part of the mitochondrial pseudouridylation module, in the mitochondrial matrix. Reason: TRUB2 localizes to the mitochondrial matrix, concentrated in mitochondrial RNA granules where it co-sediments with the large mitoribosomal subunit and associates with the RPUSD3/RPUSD4/NGRN/RCC1L/FASTKD2 module. Supporting Evidence: Reactome:R-HSA-9937369 Either RPUSD3 or TRUB2 in the module can catalyze the conversion of uridine-390 of MT-CO1 mRNA and uridine-697 of MT-CO3 mRNA to pseudouridine residues file:human/TRUB2/TRUB2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion matrix |
| GO:0006396 RNA processing | IEA GO_REF:0000120 | MODIFY | Summary: Electronic assignment of the very general process RNA processing from the TruB N-terminal domain (IPR002501). Reason: Uninformative for an RNA-modifying enzyme. Replace with the specific pseudouridylation processes the gene already carries. Proposed replacements: mitochondrial tRNA pseudouridine synthesis mRNA pseudouridine synthesis Supporting Evidence: PMID:33023933 We show here that all three human recombinant proteins, TRUB1, PUS10, and TRUB2, have Ξ¨55 synthase activities, but differ slightly in their tRNA structural requirements. file:human/TRUB2/TRUB2-uniprot.txt Belongs to the pseudouridine synthase TruB family. |
| GO:0009451 RNA modification | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO assignment of RNA modification from the pseudouridine synthase catalytic domain superfamily. Reason: Correct but general. The supported specific processes are mitochondrial tRNA pseudouridine synthesis and mRNA pseudouridine synthesis, both already annotated. Proposed replacements: mitochondrial tRNA pseudouridine synthesis mRNA pseudouridine synthesis Supporting Evidence: PMID:33023933 We show here that all three human recombinant proteins, TRUB1, PUS10, and TRUB2, have Ξ¨55 synthase activities, but differ slightly in their tRNA structural requirements. PMID:27974379 Depletion of both TRUB2 and RPUSD3 resulted in decreased pseudouridylation in the COXI |
| GO:0009982 pseudouridine synthase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of pseudouridine synthase activity. The IBA derives from a PAINT IBD at Bilateria node PTN000324318, seeded solely by human TRUB2 (O95900); TRUB2's appearance in its own WITH/FROM reflects its experimental grounding, not circularity. Reason: Recombinant human TRUB2 converts U55 to pseudouridine in tRNA transcripts in vitro and also modified one mRNA site in an in vitro mRNA pool, so pseudouridine synthase activity is directly established. The tRNA-specific child (tRNA pseudouridine(55) synthase activity) is annotated separately; no mRNA-specific pseudouridine synthase activity term exists in GO, so this general term is as precise as the mRNA-directed evidence allows and is kept. TRUB2 retains the TruB fold and the predicted catalytic aspartate (by similarity). Supporting Evidence: PMID:33023933 We show here that all three human recombinant proteins, TRUB1, PUS10, and TRUB2, have Ξ¨55 synthase activities, but differ slightly in their tRNA structural requirements. file:human/TRUB2/TRUB2-uniprot.txt Belongs to the pseudouridine synthase TruB family. file:human/TRUB2/TRUB2-uniprot.txt PTHR13195:SF0; PSEUDOURIDYLATE SYNTHASE TRUB2, MITOCHONDRIAL |
| GO:0009982 pseudouridine synthase activity | IDA PMID:31477916 mRNA structure determines modification by pseudouridine synt... | ACCEPT | Summary: Recombinant TRUB2 pseudouridylated a single site in an in vitro-transcribed pool of human mRNA fragments. Reason: Recombinant human TRUB2 converts U55 to pseudouridine in tRNA transcripts in vitro and also modified one mRNA site in an in vitro mRNA pool, so pseudouridine synthase activity is directly established. The tRNA-specific child (tRNA pseudouridine(55) synthase activity) is annotated separately; no mRNA-specific pseudouridine synthase activity term exists in GO, so this general term is as precise as the mRNA-directed evidence allows and is kept. Note that the single TRUB2 mRNA site was in a cytosolic mRNA and the authors doubt it is physiological. Supporting Evidence: PMID:31477916 TRUB1 modified the largest number of sites (61), followed by PUS7 (22), PUS1 (20), RPUSD2 (17), and TRUB2 (1). PMID:31477916 The modification of a cytosolic mRNA by TRUB2 was unexpected given the predominantly mitochondrial localization of this enzyme |
| GO:0009982 pseudouridine synthase activity | IDA PMID:33023933 Mammalian nuclear TRUB1, mitochondrial TRUB2, and cytoplasmi... | ACCEPT | Summary: Recombinant TRUB2 synthesizes Psi55 in tRNA transcripts in vitro. Reason: Recombinant human TRUB2 converts U55 to pseudouridine in tRNA transcripts in vitro and also modified one mRNA site in an in vitro mRNA pool, so pseudouridine synthase activity is directly established. The tRNA-specific child (tRNA pseudouridine(55) synthase activity) is annotated separately; no mRNA-specific pseudouridine synthase activity term exists in GO, so this general term is as precise as the mRNA-directed evidence allows and is kept. Supporting Evidence: PMID:33023933 We show here that all three human recombinant proteins, TRUB1, PUS10, and TRUB2, have Ξ¨55 synthase activities, but differ slightly in their tRNA structural requirements. |
| GO:0009982 pseudouridine synthase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic assignment from InterPro (IPR020103, IPR039048) and Rhea:56644. Reason: Recombinant human TRUB2 converts U55 to pseudouridine in tRNA transcripts in vitro and also modified one mRNA site in an in vitro mRNA pool, so pseudouridine synthase activity is directly established. The tRNA-specific child (tRNA pseudouridine(55) synthase activity) is annotated separately; no mRNA-specific pseudouridine synthase activity term exists in GO, so this general term is as precise as the mRNA-directed evidence allows and is kept. Supporting Evidence: PMID:33023933 We show here that all three human recombinant proteins, TRUB1, PUS10, and TRUB2, have Ξ¨55 synthase activities, but differ slightly in their tRNA structural requirements. file:human/TRUB2/TRUB2-uniprot.txt IPR039048; Trub2 |
| GO:0009982 pseudouridine synthase activity | TAS Reactome:R-HSA-9937369 | ACCEPT | Summary: Reactome: RPUSD3 or TRUB2 pseudouridylates MT-CO1 and MT-CO3 mRNA. Reason: Recombinant human TRUB2 converts U55 to pseudouridine in tRNA transcripts in vitro and also modified one mRNA site in an in vitro mRNA pool, so pseudouridine synthase activity is directly established. The tRNA-specific child (tRNA pseudouridine(55) synthase activity) is annotated separately; no mRNA-specific pseudouridine synthase activity term exists in GO, so this general term is as precise as the mRNA-directed evidence allows and is kept. The Reactome reaction relies on Antonicka et al., who consider RPUSD3 the major enzyme for these mt-mRNA sites. Supporting Evidence: Reactome:R-HSA-9937369 Either RPUSD3 or TRUB2 in the module can catalyze the conversion of uridine-390 of MT-CO1 mRNA and uridine-697 of MT-CO3 mRNA to pseudouridine residues PMID:33023933 We show here that all three human recombinant proteins, TRUB1, PUS10, and TRUB2, have Ξ¨55 synthase activities, but differ slightly in their tRNA structural requirements. |
| GO:0016556 mRNA modification | TAS Reactome:R-HSA-9937008 | MODIFY | Summary: Reactome includes TRUB2 in mitochondrial mRNA modification via pseudouridylation of MT-CO1/MT-CO3 mRNA. Reason: Correct in direction but general; the specific modification is pseudouridylation, captured by mRNA pseudouridine synthesis (already annotated and treated as non-core because TRUB2's contribution to mt-mRNA pseudouridylation appears secondary to RPUSD3). Proposed replacements: mRNA pseudouridine synthesis Supporting Evidence: Reactome:R-HSA-9937369 Either RPUSD3 or TRUB2 in the module can catalyze the conversion of uridine-390 of MT-CO1 mRNA and uridine-697 of MT-CO3 mRNA to pseudouridine residues PMID:27974379 Depletion of both TRUB2 and RPUSD3 resulted in decreased pseudouridylation in the COXI |
| GO:0035770 ribonucleoprotein granule | IDA PMID:28082677 The Pseudouridine Synthase RPUSD4 Is an Essential Component ... | ACCEPT | Summary: Immunofluorescence shows TRUB2 enrichment in mitochondrial RNA granules (MRGs). Reason: Mitochondrial RNA granules are matrix ribonucleoprotein foci; GO has no mitochondrion-specific RNA granule term, so ribonucleoprotein granule is the most precise available term. Independently supported by BioID with granule proteins. Supporting Evidence: PMID:28082677 We observed a clear enrichment of RPUSD3, RPUSD4, and TRUB2 in MRGs, whereas neither PUS1 nor PUSL1 appeared to be specifically enriched in discrete foci PMID:27974379 we identified a protein module in mitochondrial RNA granules |
| GO:0070131 positive regulation of mitochondrial translation | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Phylogenetic inference of positive regulation of mitochondrial translation. The IBA derives from a PAINT IBD at Bilateria node PTN000324318, seeded solely by human TRUB2 (O95900); TRUB2's appearance in its own WITH/FROM reflects its experimental grounding, not circularity. Reason: TRUB2 depletion reduces mitochondrial protein synthesis (to 76% of control), most strongly for ATP8/ATP6, and disrupts mitoribosome large-subunit assembly; CRISPR disruption of module members abolishes 16S rRNA abundance and mitochondrial translation. These are necessity data: TRUB2 is a modifying enzyme required for efficient mitochondrial translation, not a demonstrated regulator of it. The term is retained as non-core because the PAINT curator deliberately propagated it and the gene product does act on mitochondrial translation substrates, but it should not be read as a core regulatory activity. Supporting Evidence: PMID:27974379 was decreased to 76, 20, and 53% of control in cells in which TRUB2, RPUSD4, and RPUSD3 were depleted PMID:27974379 Remarkably, in TRUB2 knockdown cells, the synthesis of ATP6 and ATP8 proteins (encoded on a bicistronic transcript) was severely reduced |
| GO:0070131 positive regulation of mitochondrial translation | IMP PMID:27667664 A Genome-wide CRISPR Death Screen Identifies Genes Essential... | KEEP AS NON CORE | Summary: CRISPR disruption of TRUB2 and other module members reduces 16S rRNA and mitochondrial translation. Reason: TRUB2 depletion reduces mitochondrial protein synthesis (to 76% of control), most strongly for ATP8/ATP6, and disrupts mitoribosome large-subunit assembly; CRISPR disruption of module members abolishes 16S rRNA abundance and mitochondrial translation. These are necessity data: TRUB2 is a modifying enzyme required for efficient mitochondrial translation, not a demonstrated regulator of it. The term is retained as non-core because the PAINT curator deliberately propagated it and the gene product does act on mitochondrial translation substrates, but it should not be read as a core regulatory activity. Supporting Evidence: PMID:27667664 Finally, we used CRISPR to disrupt all members of the module and found that they were all required for 16S rRNA abundance and mitochondrial translation PMID:27667664 Using protein immunoprecipitation and mass spectrometry, we identified and confirmed the interaction of NGRN with WBSCR16, RPUSD3, RPUSD4, TRUB2, and FASTKD2. |
| GO:0070902 mitochondrial tRNA pseudouridine synthesis | IMP PMID:33023933 Mammalian nuclear TRUB1, mitochondrial TRUB2, and cytoplasmi... | ACCEPT | Summary: TRUB2 knockdown reduces tRNA Psi55 synthase activity of mitochondrial extracts. Reason: TRUB2 is the mitochondrial tRNA Psi55 synthase: recombinant enzyme makes Psi55 and its knockdown removes Psi55 activity from mitochondrial extracts. Caveat: the assay substrates were tRNA transcripts (tRNATrp, tRNAAla) rather than mitochondrial tRNAs, and the four mt-tRNAs bearing Psi55 are proposed, not shown, as in vivo TRUB2 targets. PAINT did not propagate this term to node PTN000324318, so it is human-experimental only. Supporting Evidence: PMID:33023933 Knockdown of TRUB1, TRUB2, and PUS10 reduced Ξ¨55 synthesis by the nuclear, mitochondrial, and cytoplasmic extracts, respectively, in both tRNATrp and tRNAAla PMID:33023933 TRUB2 is present in the mitochondria and is suggested to produce Ξ¨55 in all four human mitochondrial tRNAs (out of 22 total) with this modification PMID:33023933 We show here that all three human recombinant proteins, TRUB1, PUS10, and TRUB2, have Ξ¨55 synthase activities, but differ slightly in their tRNA structural requirements. |
| GO:0160148 tRNA pseudouridine(55) synthase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic assignment via Rhea:42532 / EC 5.4.99.25. Reason: Recombinant human TRUB2 has tRNA Psi55 synthase activity in vitro, requiring the U54-A58 reverse Hoogsteen pair and enhanced by m1A58, and knockdown removes Psi55 activity from mitochondrial extracts. This is the best biochemically established activity of TRUB2 and the ancestral activity of the TruB family. Supporting Evidence: PMID:33023933 We show here that all three human recombinant proteins, TRUB1, PUS10, and TRUB2, have Ξ¨55 synthase activities, but differ slightly in their tRNA structural requirements. file:human/TRUB2/TRUB2-uniprot.txt Belongs to the pseudouridine synthase TruB family. |
| GO:0160148 tRNA pseudouridine(55) synthase activity | IMP PMID:33023933 Mammalian nuclear TRUB1, mitochondrial TRUB2, and cytoplasmi... | ACCEPT | Summary: Knockdown reduces Psi55 synthesis by mitochondrial extracts. Reason: Recombinant human TRUB2 has tRNA Psi55 synthase activity in vitro, requiring the U54-A58 reverse Hoogsteen pair and enhanced by m1A58, and knockdown removes Psi55 activity from mitochondrial extracts. This is the best biochemically established activity of TRUB2 and the ancestral activity of the TruB family. PAINT did not propagate this term to the Bilateria TRUB2 node, so transfer to orthologs should treat it as an experimental human finding. Supporting Evidence: PMID:33023933 Knockdown of TRUB1, TRUB2, and PUS10 reduced Ξ¨55 synthesis by the nuclear, mitochondrial, and cytoplasmic extracts, respectively, in both tRNATrp and tRNAAla PMID:33023933 We show here that all three human recombinant proteins, TRUB1, PUS10, and TRUB2, have Ξ¨55 synthase activities, but differ slightly in their tRNA structural requirements. |
| GO:1990481 mRNA pseudouridine synthesis | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Phylogenetic inference of mRNA pseudouridine synthesis. The IBA derives from a PAINT IBD at Bilateria node PTN000324318, seeded solely by human TRUB2 (O95900); TRUB2's appearance in its own WITH/FROM reflects its experimental grounding, not circularity. Reason: TRUB2 depletion lowers pseudouridylation at COX1 and COX3 mt-mRNA sites, and recombinant TRUB2 modified one site in vitro. However, the authors of the in vivo study argue RPUSD3 is the major enzyme and the TRUB2 effect secondary (TRUB2 knockdown also halves RPUSD3 mRNA), and the in vitro site was a cytosolic mRNA. The process is therefore plausible but only weakly established as a direct TRUB2 activity; kept as non-core. Supporting Evidence: PMID:27974379 Depletion of both TRUB2 and RPUSD3 resulted in decreased pseudouridylation in the COXI PMID:27974379 three lines of evidence suggest that RPUSD3 is the major modifying enzyme for COXI and COXIII mRNA and that the effect of TRUB2 is secondary |
| GO:1990481 mRNA pseudouridine synthesis | IDA PMID:31477916 mRNA structure determines modification by pseudouridine synt... | KEEP AS NON CORE | Summary: Recombinant TRUB2 modified a single site in an in vitro mRNA pool. Reason: TRUB2 depletion lowers pseudouridylation at COX1 and COX3 mt-mRNA sites, and recombinant TRUB2 modified one site in vitro. However, the authors of the in vivo study argue RPUSD3 is the major enzyme and the TRUB2 effect secondary (TRUB2 knockdown also halves RPUSD3 mRNA), and the in vitro site was a cytosolic mRNA. The process is therefore plausible but only weakly established as a direct TRUB2 activity; kept as non-core. Supporting Evidence: PMID:31477916 TRUB1 modified the largest number of sites (61), followed by PUS7 (22), PUS1 (20), RPUSD2 (17), and TRUB2 (1). PMID:31477916 The modification of a cytosolic mRNA by TRUB2 was unexpected given the predominantly mitochondrial localization of this enzyme |
| GO:1990481 mRNA pseudouridine synthesis | IMP PMID:27974379 A pseudouridine synthase module is essential for mitochondri... | KEEP AS NON CORE | Summary: TRUB2 knockdown reduces pseudouridylation at COX1 and COX3 mt-mRNA sites (Psi-seq). Reason: TRUB2 depletion lowers pseudouridylation at COX1 and COX3 mt-mRNA sites, and recombinant TRUB2 modified one site in vitro. However, the authors of the in vivo study argue RPUSD3 is the major enzyme and the TRUB2 effect secondary (TRUB2 knockdown also halves RPUSD3 mRNA), and the in vitro site was a cytosolic mRNA. The process is therefore plausible but only weakly established as a direct TRUB2 activity; kept as non-core. Supporting Evidence: PMID:27974379 Depletion of both TRUB2 and RPUSD3 resulted in decreased pseudouridylation in the COXI PMID:27974379 three lines of evidence suggest that RPUSD3 is the major modifying enzyme for COXI and COXIII mRNA and that the effect of TRUB2 is secondary |
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Download this section (compressed HTML)Q: Is TRUB2 the enzyme that installs Psi55 in the four human mitochondrial tRNAs that carry it (mt-tRNA-Glu, -Gln, -Ser(UCN), -Tyr) in vivo, and if so should PAINT propagate tRNA pseudouridine(55) synthase activity to the Bilateria TRUB2 node?
Q: Does TRUB2 pseudouridylate COX1/COX3 mt-mRNA directly, or is its effect indirect through reduced RPUSD3 expression?
Q: Should GO provide a mitochondrial RNA granule cellular component term, given the number of mtRNA-processing and modification enzymes localized there?
Q: Is 'positive regulation of mitochondrial translation' the right process term for modifying enzymes whose loss reduces mitochondrial translation, or does it overstate a regulatory role?
Experiment: Map Psi55 in purified mitochondrial tRNAs (e.g. by CMC/RT stop, BID-seq or LC-MS of isolated mt-tRNAs) in TRUB2 knockout cells rescued with wild-type or catalytic Asp98 mutant TRUB2.
Experiment: Test recombinant TRUB2 on in vitro transcribed COX1 and COX3 mt-mRNA fragments, and measure COX1/COX3 Psi levels in TRUB2 knockout cells with RPUSD3 expression restored.
Experiment: Determine whether the ATP8/ATP6 translation defect of TRUB2 depletion requires catalytic activity by complementing with a catalytically dead TRUB2.
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