SWS2 (YNL081C) encodes uS13m, a 143-residue nuclear-encoded protein of the universal uS13 ribosomal protein family that is a structural component of the 37S small subunit of the mitochondrial ribosome. The 3.25-angstrom cryo-EM structure of the yeast 74S mitoribosome (Desai et al. 2017) models Sws2 as uS13m in the mt-SSU, where residues contributed by uS13m form several of the mitochondria-specific intersubunit bridges (mB8, mB9, mB10, mB13) with the large-subunit proteins mL46 and uL5m and 21S rRNA helix H62; the classical bacterial uS13 bridge B1b is absent in the yeast mitoribosome. GFP fusions localize the protein to mitochondria. Deletion causes respiratory deficiency (a high-confidence pet gene) and loss of mitochondrial DNA ([rho0]), as is typical for mitoribosomal protein mutants, and slow growth on fermentable medium. The gene was named in a synthetic genetic array screen in which sws2 deletion was sick in combination with loss of securin (pds1); the basis of that interaction is unknown. The protein acts in mitochondrial translation, the synthesis of the mitochondrially encoded respiratory-chain and ATP synthase subunits on inner-membrane-tethered mitoribosomes.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003676 nucleic acid binding | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping from the uS13-like H2TH domain. The nucleic acid partner of uS13-family proteins is ribosomal RNA (and tRNA in bacteria), so the generic term is correct but less specific than RNA binding, which the gene also carries from InterPro. Reason: True but too general. The uS13 family contacts rRNA within the ribosome; the more specific term RNA binding (GO:0003723), already assigned to this gene from the uS13 family signature, is the appropriate refinement. Neither term is core: the RNA contacts serve the structural-constituent role. Proposed replacements: RNA binding Supporting Evidence: file:yeast/SWS2/SWS2-uniprot.txt CC -!- SIMILARITY: Belongs to the universal ribosomal protein uS13 family. file:yeast/SWS2/SWS2-28154081-supplement.txt mB13! uS13m:!34,!37B38,!41! H62:!1657B1658! |
| GO:0003723 RNA binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO mapping from the uS13 family signatures. In the cryo-EM structure uS13m residues 34-41 contact 21S rRNA helix H62 in intersubunit bridge mB13, so direct RNA contact is structurally supported. RNA binding is a component of its structural role rather than a separable activity. Reason: Correct at the level the evidence supports (rRNA contacts in the mitoribosome structure; family-wide rRNA binding), but peripheral to the core structural-constituent function; no isolated RNA-binding assay exists for the yeast protein. Supporting Evidence: file:yeast/SWS2/SWS2-28154081-supplement.txt mB13! uS13m:!34,!37B38,!41! H62:!1657B1658! |
| GO:0003735 structural constituent of ribosome | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBD at the PTHR10871 root node PTN000093238, seeded by experimental annotations including this gene's own (SGD:S000005025). Structural constituent of ribosome is the ancestral function of the entire uS13 family (bacterial, cytosolic uS13/RPS18, and mitochondrial uS13m), and SWS2 is directly confirmed as a mitoribosomal protein. Reason: Core function. The node placement is appropriate (the function predates the split into cytosolic and mitochondrial lineages), and the presence of SGD:S000005025 among the seeds reflects the gene's own IDA grounding. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000093238 SUPPORTS TRANSFER Root node of PTHR10871; seeds include SGD:S000005025 itself, so the target carries its own experimental grounding for this term. Supporting Evidence: PMID:28154081 The mitoribosomal small subunit has been built de novo and includes 15S ribosomal RNA (rRNA) and 34 proteins file:yeast/SWS2/SWS2-28154081-supplement.txt uS13m! Sws2! P53937! |
| GO:0003735 structural constituent of ribosome | IDA PMID:28154081 The structure of the yeast mitochondrial ribosome. | ACCEPT | Summary: The cryo-EM structure of the yeast mitoribosome models Sws2 (P53937, chain MM, residues 2-121) as uS13m within the mt-SSU, where it also contributes residues to mitochondria-specific intersubunit bridges. Reason: Direct structural evidence that Sws2 is a built-in protein component of the mitoribosome small subunit; this is the core molecular function. Supporting Evidence: file:yeast/SWS2/SWS2-28154081-supplement.txt uS13m! Sws2! P53937! file:yeast/SWS2/SWS2-28154081-supplement.txt mB9! uS13m:!70! uL5:!253B254! file:yeast/SWS2/SWS2-uniprot.txt CC -!- SUBUNIT: Component of the mitochondrial small ribosomal subunit (mt- |
| GO:0003735 structural constituent of ribosome | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from the uS13 family signatures; consistent with the experimental structural evidence. Reason: Same claim as the IDA and IBA rows; core function. Supporting Evidence: file:yeast/SWS2/SWS2-uniprot.txt CC -!- SIMILARITY: Belongs to the universal ribosomal protein uS13 family. |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBD at the mitochondrial uS13m node PTN000093341 (seeded by Arabidopsis AT1G77750, Neurospora Q7S2C2 and this gene). SWS2 sits in the PTHR10871:SF1 (uS13m) subfamily below this node. Mitochondrial localization is independently supported by GFP-fusion studies of the yeast protein and by its presence in the purified mitoribosome. Reason: Correct organelle-level localization with direct experimental grounding in yeast; the more specific complex membership is captured by the GO:0005763 rows. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000093341 SUPPORTS TRANSFER Mitochondrial uS13m node (PTHR10871:SF1 lineage); SWS2 is a seed and descends from it. Supporting Evidence: file:yeast/SWS2/SWS2-uniprot.txt CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:10649453, PMID:10649453 Ynl080c-GFP and Ynl081c-GFP fluorescence was visible in dot-shaped and elongated structures |
| GO:0005739 mitochondrion | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic annotation from the UniProt subcellular-location vocabulary, whose Mitochondrion statement rests on experimental GFP evidence. Reason: Consistent with the IBA row and experimental localization. Supporting Evidence: file:yeast/SWS2/SWS2-uniprot.txt CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:10649453, |
| GO:0005743 mitochondrial inner membrane | NAS PMID:25609543 Organization of the mitochondrial translation machinery stud... | KEEP AS NON CORE | Summary: ComplexPortal (CPX-1603) statement applied to all subunits of the 37S mitoribosomal small subunit, based on in situ cryo-electron tomography showing that most mitoribosomes sit next to the inner membrane. The membrane contacts are made by the large subunit (21S rRNA expansion segment 96-ES1 and Mba1), not by small-subunit proteins; uS13m is not an integral or peripheral membrane protein in its own right. Reason: Defensible at the complex level (the mitoribosome is tethered to the inner membrane, so uS13m is associated with it in vivo), but this is an indirect localization of a soluble matrix-side complex subunit and is not core. 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:0005763 mitochondrial small ribosomal subunit | IDA PMID:28154081 The structure of the yeast mitochondrial ribosome. | ACCEPT | Summary: Sws2 is built as uS13m into the mt-SSU in the cryo-EM structure of the yeast mitoribosome. Reason: Direct structural evidence; core complex membership. Supporting Evidence: file:yeast/SWS2/SWS2-28154081-supplement.txt uS13m! Sws2! P53937! PMID:28154081 The mitoribosomal small subunit has been built de novo and includes 15S ribosomal RNA (rRNA) and 34 proteins |
| GO:0005763 mitochondrial small ribosomal subunit | NAS PMID:25609543 Organization of the mitochondrial translation machinery stud... | ACCEPT | Summary: ComplexPortal assignment of Sws2 to the 37S mitoribosomal small subunit; the same claim as the IDA row. Reason: Consistent with the direct structural evidence. Supporting Evidence: file:yeast/SWS2/SWS2-uniprot.txt CC -!- SUBUNIT: Component of the mitochondrial small ribosomal subunit (mt- |
| GO:0005777 peroxisome | IDA PMID:36164978 Systematic multi-level analysis of an organelle proteome rev... | UNDECIDED | Summary: From a high-content microscopy screen of the N-terminally GFP-tagged, NOP1-promoter-driven SWAT library. Sws2 is not named in the cached article text; the call is in the supplementary dataset, which we could not inspect. The method fuses GFP to the N-terminus and overexpresses from a constitutive promoter, conditions that can perturb N-terminal mitochondrial targeting. The paper itself reports that about half of its hits are dually localized, with mitochondria as one of the other compartments. A later whole-cell proteomics study lists Sws2 among multilocalized peroxisomal proteins but explicitly derives that status from database annotation, not from new localization data. Reason: An experimental call we cannot verify from the available text, for a protein whose established function is inside mitochondria as a mitoribosome component. There is no known peroxisomal role for a mitoribosomal protein, but per curation policy an IDA whose supporting data we cannot read is not removed. Flagged for expert review. Supporting Evidence: PMID:36164978 Having a GFP tag on the N′ of each protein allows proper targeting of all known proteins with either a C′ PTS1 or an N′ PTS2 motif PMID:36164978 ~50% of the proteins in our list are dually localized to peroxisomes and other compartments such as mitochondria PMID:41686312 the experimental design of our study does not allow for monitoring the subcellular localization(s) of proteins |
| GO:0005840 ribosome | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping from the uS13 family. Correct but general; the protein is specifically a component of the mitochondrial small ribosomal subunit. Reason: GO:0005763 mitochondrial small ribosomal subunit is a descendant of ribosome and is already assigned to this gene by IDA. Proposed replacements: mitochondrial small ribosomal subunit Supporting Evidence: file:yeast/SWS2/SWS2-28154081-supplement.txt uS13m! Sws2! P53937! |
| GO:0006412 translation | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping from the uS13 family. Correct but general; as a mitoribosome subunit, Sws2 acts in mitochondrial translation, not cytosolic translation. Reason: GO:0032543 mitochondrial translation is an is_a descendant of translation and is already assigned to this gene. Proposed replacements: mitochondrial translation Supporting Evidence: file:yeast/SWS2/SWS2-uniprot.txt CC -!- FUNCTION: Component of the mitochondrial ribosome (mitoribosome), a |
| GO:0015935 small ribosomal subunit | IBA GO_REF:0000033 | MODIFY | Summary: PAINT IBD at the family root node PTN000093238, inherited by all uS13 proteins. True for SWS2, but the gene is specifically part of the mitochondrial small subunit (GO:0005763, IDA). Note that PAINT curators deliberately excluded the root's cytosol annotation from the mitochondrial node (NOT cytosol IRD at PTN000093341). Reason: Correct but general; refine to GO:0005763 mitochondrial small ribosomal subunit (an is_a descendant via organellar small ribosomal subunit), which the gene already carries by IDA. Propagation Review Root cause: TERM SCOPING PROBLEM Sources checked: PANTHER:PTN000093238 SUPPORTS TRANSFER Family root node; small-subunit membership is ancestral to all uS13 proteins and transfers correctly to SWS2. The issue is only that the root-level term is less specific than the mitochondrial subunit term supported directly for the target. Proposed replacements: mitochondrial small ribosomal subunit Supporting Evidence: file:yeast/SWS2/SWS2-uniprot.txt CC -!- SUBUNIT: Component of the mitochondrial small ribosomal subunit (mt- |
| GO:0032543 mitochondrial translation | IC PMID:12392552 Tag-mediated isolation of yeast mitochondrial ribosome and m... | ACCEPT | Summary: SGD curator inference from small-ribosomal-subunit membership in the affinity-purified yeast mitoribosome. The cached record is abstract-only and does not name Sws2, but the inference (a mitoribosome SSU structural protein participates in mitochondrial translation) is sound and is now confirmed structurally. Reason: A structural constituent of the mitoribosome does part of the work of mitochondrial translation; core process. Supporting Evidence: PMID:12392552 We have constructed a yeast strain in which one of the small subunit proteins, termed Mrp4, was tagged with S-peptide and used for affinity purification of mitochondrial ribosome. PMID:32904421 MRX14YDR115WSWS2YNL081C |
| GO:0032543 mitochondrial translation | IC PMID:28154081 The structure of the yeast mitochondrial ribosome. | ACCEPT | Summary: Curator inference from the structural assignment of Sws2 to the mt-SSU. Reason: Core process; same claim as the other mitochondrial translation rows. Supporting Evidence: file:yeast/SWS2/SWS2-28154081-supplement.txt uS13m! Sws2! P53937! |
| GO:0032543 mitochondrial translation | NAS PMID:25609543 Organization of the mitochondrial translation machinery stud... | ACCEPT | Summary: ComplexPortal statement for the 37S mitoribosomal small subunit. Reason: Core process; consistent with structural and genetic evidence. Supporting Evidence: file:yeast/SWS2/SWS2-uniprot.txt CC -!- FUNCTION: Component of the mitochondrial ribosome (mitoribosome), a |
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Download this section (compressed HTML)Q: Is the peroxisome IDA (PMID:36164978) reproducible with a C-terminal or native-promoter tag, or is it an artefact of N-terminal GFP tagging and NOP1 overexpression masking mitochondrial import of uS13m?
Q: What is the basis of the synthetic sickness of sws2 deletion with pds1 (securin) deletion? Is it a general consequence of respiratory deficiency or mtDNA loss that other mitoribosome mutants share?
Experiment: Test pds1 deletion combined with deletion of other mt-SSU protein genes (and with rho0 strains) to determine whether the SWS2-PDS1 genetic interaction is specific to uS13m or a general consequence of losing mitochondrial translation.
Experiment: Localize endogenously C-terminally tagged Sws2 under oleate (peroxisome proliferating) conditions, with mitochondrial and peroxisomal markers, to test the reported peroxisomal localization.
Component of mitochondrial small ribosomal subunit; similar to E. coli S13 ribosomal protein; participates in controlling sporulation efficiency; localizes to vacuole in response to H2O2; localizes to peroxisomes in glucose-growing cells
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