YML6 (YML025C) encodes YmL6, the yeast mitochondrial ribosomal large-subunit protein uL4m. It is a nuclear-encoded member of the universal uL4 family. A 26-residue N-terminal transit peptide targets it to mitochondria, where it is removed. The mature protein is an integral component of the 54S large subunit of the 74S mitoribosome, which makes the few mitochondrial genome-encoded proteins, mostly hydrophobic respiratory-chain subunits, at the inner membrane. YmL6 was identified by purifying the protein from the mitochondrial large subunit and sequencing it. In cryo-EM structures of the yeast mitoribosome, uL4m sits deep in the large subunit and, with uL22, forms the conserved constriction of the nascent-polypeptide exit tunnel. Its role is structural; no enzymatic or separate regulatory activity has been described.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003735 structural constituent of ribosome | IBA GO_REF:0000033 | ACCEPT | Summary: The structural-constituent role of uL4 proteins was propagated from the PTHR10746 family root node PTN000078778. YML6 is a uL4-family member and a demonstrated mtLSU subunit. Reason: The IBD sits at the root of the universal uL4 family. YML6 is inside that clade, because it belongs to the uL4 family and to PANTHER subfamily PTHR10746:SF6. Nothing suggests the structural role was lost; the yeast protein is built into the 54S subunit in the cryo-EM structure. The SGD entry in WITH/FROM is this gene's own IDA, which is one of the descendant evidences behind the IBD, and is expected. Supporting Evidence: file:yeast/YML6/YML6-uniprot.txt Belongs to the universal ribosomal protein uL4 family. PMID:24675956 Beyond the entrance, the tunnel is lined by conserved elements (Fig. 6C), including the constriction site formed by uL22 and uL4. |
| GO:0003735 structural constituent of ribosome | IDA PMID:9151978 Identification and characterization of the genes for mitocho... | ACCEPT | Summary: YmL6 was purified as a protein of the mitochondrial large ribosomal subunit and assigned to its gene by partial protein sequencing. Reason: Purifying the protein from mitochondrial large subunits and identifying its gene shows directly that YML6 is a ribosome component. Later cryo-EM structures confirm it is a core structural protein of the 54S subunit. Only the abstract is cached, but the claim is consistent with all other evidence and with the curator's reading of the full text. Supporting Evidence: PMID:9151978 We have purified 13 large subunit proteins of the mitochondrial ribosome of the yeast Saccharomyces cerevisiae and determined their partial amino acid sequences. PMID:24675956 Beyond the entrance, the tunnel is lined by conserved elements (Fig. 6C), including the constriction site formed by uL22 and uL4. |
| GO:0003735 structural constituent of ribosome | IEA GO_REF:0000002 | ACCEPT | Summary: An InterPro2GO mapping from the uL4 ribosomal-protein signatures. Reason: The uL4 signatures are diagnostic of the ribosomal protein, and the mapping agrees with the experimental (IDA) and phylogenetic (IBA) evidence for this gene. Supporting Evidence: file:yeast/YML6/YML6-uniprot.txt InterPro; IPR002136; Ribosomal_uL4. |
| GO:0005739 mitochondrion | HDA PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimen... | ACCEPT | Summary: The protein was detected in the PROMITO proteome of purified yeast mitochondria. Reason: Detection in purified mitochondria agrees with the protein's mitochondrial transit peptide and its membership of the mitoribosome. The more specific location, the mitochondrial large ribosomal subunit, is captured separately. Mitochondrion is as precise as this proteomic evidence allows, so the row is kept as it is. Supporting Evidence: PMID:16823961 A total of 851 different proteins (PROMITO dataset) were identified file:yeast/YML6/YML6-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14562095, |
| GO:0005739 mitochondrion | HDA PMID:24769239 Quantitative variations of the mitochondrial proteome and ph... | ACCEPT | Summary: The protein was detected in a quantitative proteome of isolated mitochondria from cells grown on fermentable and respiratory carbon sources. Reason: This is high-throughput detection in isolated mitochondria. It agrees with the transit peptide, with other organellar proteomics and with mitoribosome membership. Supporting Evidence: PMID:24769239 we performed an overall quantitative proteomic and phosphoproteomic study of isolated mitochondria |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | ACCEPT | Summary: A UniProt subcellular-location mapping. The UniProt location is backed by experimental proteomics and localisation papers. Reason: The SubCell statement is experimentally supported (ECO:0000269) and agrees with the HDA rows. Supporting Evidence: file:yeast/YML6/YML6-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14562095, |
| GO:0005743 mitochondrial inner membrane | NAS PMID:25609543 Organization of the mitochondrial translation machinery stud... | KEEP AS NON CORE | Summary: The Complex Portal annotation reflects that yeast mitoribosomes are tethered to the inner mitochondrial membrane. Reason: Cryo-electron tomography shows that most mitoribosomes sit right next to the inner membrane. Two membrane contacts were seen, made by the 21S rRNA expansion segment 96-ES1 and by Mba1, not by uL4m. uL4m lies deep in the large subunit, at the exit-tunnel constriction. Its association with the inner membrane is therefore indirect, through the whole mitoribosome, and peripheral. The claim is true in that complex-level sense but is not a defining location of the protein. Supporting Evidence: PMID:25609543 Most mitoribosomes reside in immediate proximity to the inner mitochondrial membrane PMID:25609543 two distinct membrane contact sites, formed by the 21S rRNA expansion segment 96-ES1 and the inner membrane protein Mba1 |
| GO:0005762 mitochondrial large ribosomal subunit | IBA GO_REF:0000033 | ACCEPT | Summary: Membership of the mitochondrial large subunit was propagated from the mitochondrial uL4m node PTN000078780. Its donors are yeast YML6, human MRPL4 and a trypanosome uL4m. Reason: The node is the mitochondrial uL4m clade, matching PANTHER subfamily PTHR10746:SF6, and YML6 is in it. The IBA agrees with this gene's own direct experimental evidence. YML6 appearing in its own WITH/FROM is expected, because its IDA is one of the descendant evidences behind the IBD. Supporting Evidence: file:yeast/YML6/YML6-uniprot.txt PANTHER; PTHR10746:SF6; LARGE RIBOSOMAL SUBUNIT PROTEIN UL4M; 1. file:yeast/YML6/YML6-uniprot.txt SUBUNIT: Component of the mitochondrial large ribosomal subunit (mt- |
| GO:0005762 mitochondrial large ribosomal subunit | IDA PMID:9151978 Identification and characterization of the genes for mitocho... | ACCEPT | Summary: YmL6 was purified from the large subunit of yeast mitochondrial ribosomes and sequenced. Reason: Direct biochemical identification as an mtLSU protein. It is confirmed by N-terminal sequencing (PMID:2060626) and by the cryo-EM structure of the 54S subunit (PMID:24675956), which UniProt cites with ECO:0000269 for the subunit statement. Supporting Evidence: PMID:9151978 we were able to identify and characterize 12 new genes for large subunit proteins of the yeast mitochondrial ribosome file:yeast/YML6/YML6-uniprot.txt SUBUNIT: Component of the mitochondrial large ribosomal subunit (mt- |
| GO:0005762 mitochondrial large ribosomal subunit | NAS PMID:28154081 The structure of the yeast mitochondrial ribosome. | ACCEPT | Summary: The Complex Portal annotation comes from the 3.3 A structure of the complete yeast mitoribosome. Reason: This agrees with the IDA and the 54S structure. The full mitoribosome structure includes the large subunit that contains uL4m. Supporting Evidence: PMID:28154081 we have determined the structure of the 75-component yeast mitoribosome to an overall resolution of 3.3 angstroms |
| GO:0005840 ribosome | IBA GO_REF:0000033 | MODIFY | Summary: The generic ribosome location was propagated from the uL4 family root PTN000078778. It is correct at the family level. Reason: Ribosome is correct but less specific than the evidence for YML6, which places it in the mitochondrial large ribosomal subunit (GO:0005762, a part_of descendant). The gene already carries that term by IDA, IBA and NAS. The family-root node has to stay general, because it covers bacterial, plastid and mitochondrial uL4 proteins. For this mitochondrial member the specific term is the right one. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000078778 SUPPORTS TRANSFER Family-root uL4 node spanning bacterial, plastid and mitochondrial ribosomes. Ribosome is correctly transferred but generic. The mitochondrial clade node PTN000078780 carries the specific mtLSU term. Proposed replacements: mitochondrial large ribosomal subunit Supporting Evidence: file:yeast/YML6/YML6-uniprot.txt SUBUNIT: Component of the mitochondrial large ribosomal subunit (mt- |
| GO:0005840 ribosome | IEA GO_REF:0000002 | MODIFY | Summary: An InterPro2GO mapping of the uL4 signatures to ribosome. Reason: Correct but general. The InterPro signatures cannot tell cytosolic, plastid and mitochondrial ribosomes apart. For YML6 the experimentally supported location is the mitochondrial large ribosomal subunit (GO:0005762), which the gene already carries. Proposed replacements: mitochondrial large ribosomal subunit Supporting Evidence: file:yeast/YML6/YML6-uniprot.txt SUBUNIT: Component of the mitochondrial large ribosomal subunit (mt- |
| GO:0006412 translation | IEA GO_REF:0000002 | MODIFY | Summary: An InterPro2GO mapping of the uL4 signatures to translation. Reason: Correct but general. As a structural subunit of the mitoribosome, YML6 takes part specifically in mitochondrial translation (GO:0032543, an is_a descendant), which the gene already carries by IC and NAS. Proposed replacements: mitochondrial translation Supporting Evidence: file:yeast/YML6/YML6-uniprot.txt FUNCTION: Component of the mitochondrial ribosome (mitoribosome), a |
| GO:0006417 regulation of translation | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: Regulation of translation was propagated from the uL4 family root. The only experimental donor is E. coli L4 (P60723), which autogenously represses its own S10 ribosomal-protein operon. Reason: Bacterial L4 regulates translation through feedback on the leader mRNA of the S10 operon. That mechanism depends on the bacterial operon structure. YML6 is a single nuclear gene, and none of the mitochondrial uL4m donors at node PTN000078780 (YML6, human MRPL4, trypanosome uL4m) has a regulatory annotation. Notably, the PAINT curators placed the mtLSU term on the mitochondrial node, but nothing regulatory. No study of YML6 reports a regulatory activity separate from its structural role, and being a subunit of the translating ribosome is not regulation of translation. Placing the IBD at the family root over-extends a lineage-specific bacterial function to the mitochondrial clade. Propagation Review Root cause: PROPAGATION BAD Failure modes: LINEAGE OR TAXON MISMATCH ROLE CONFLATION Sources checked: PANTHER:PTN000078778 SUPPORTS SOURCE BUT NOT TARGET Family-root node whose regulation-of-translation IBD rests only on E. coli L4 (P60723) and its S10-operon autoregulation. This is valid for the bacterial donor but not supported in the mitochondrial uL4m clade. Supporting Evidence: file:yeast/YML6/YML6-uniprot.txt FUNCTION: Component of the mitochondrial ribosome (mitoribosome), a |
| GO:0032543 mitochondrial translation | IC PMID:9151978 Identification and characterization of the genes for mitocho... | ACCEPT | Summary: The curator inferred this from the protein's membership of the mitochondrial large ribosomal subunit. Reason: A structural subunit of the mitoribosome does some of the work of mitochondrial translation, because it contributes structure that the translating ribosome needs. Here that includes lining the exit-tunnel constriction with uL22. The inference from GO:0005762 is sound. Supporting Evidence: PMID:9151978 We have purified 13 large subunit proteins of the mitochondrial ribosome of the yeast Saccharomyces cerevisiae PMID:24675956 Beyond the entrance, the tunnel is lined by conserved elements (Fig. 6C), including the constriction site formed by uL22 and uL4. |
| GO:0032543 mitochondrial translation | NAS PMID:25609543 Organization of the mitochondrial translation machinery stud... | ACCEPT | Summary: A Complex Portal annotation for the 54S mitochondrial large ribosomal subunit (CPX-1602). Reason: This agrees with the IC row and with the protein's structural role in the mitoribosome. The cited tomography paper describes the mitochondrial translation machinery in situ. Supporting Evidence: PMID:25609543 This study reveals detailed insights into the supramolecular organization of the mitochondrial translation machinery |
Loading supporting content…
Download this section (compressed HTML)Q: Does YML6 initiate early assembly of the yeast mitochondrial large subunit, as bacterial L4 does by binding the 5' domain of 23S rRNA, or has the mitochondrial extension changed when it joins the subunit?
Q: Does any mitochondrial uL4m keep an extra-ribosomal regulatory role like the S10-operon autoregulation of E. coli L4? If not, should the regulation-of-translation IBD move from the family root PTN000078778 to a bacterial node?
Experiment: Profile mtLSU subassemblies in a yml6 deletion strain (sucrose gradients with quantitative mass spectrometry) to place uL4m in the 54S assembly hierarchy, and test direct binding of recombinant mature YmL6 to 21S rRNA domain I fragments.
Type: mitoribosome assembly profiling and RNA binding
Mitochondrial ribosomal protein of the large subunit; has similarity to E. coli L4 ribosomal protein and human mitoribosomal MRP-L4 protein; essential for viability, unlike most other mitoribosomal proteins
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)