YGR117C encodes a 476-amino-acid cytoplasmic protein of unknown function in Saccharomyces cerevisiae. The protein contains an N-terminal LisH dimerization motif (residues 7-39) and a C-terminal WD40-repeat beta-propeller domain (residues 125-472), suggesting it may function as a scaffold or adaptor mediating protein-protein interactions. It belongs to the conserved UCP007778 family (IPR016520/PIRSF007778). Despite being expressed at moderate levels (~1280-2276 molecules/cell) and being conserved across Saccharomycetaceae, no gene-specific functional study has been published. GFP-fusion protein localizes to the cytoplasm (PMID:14562095). Large-scale phenotypic screens of the null mutant show pleiotropic effects including decreased competitive fitness, abnormal vacuolar morphology, altered stress resistance, and decreased endocytosis, but these do not point to a single pathway. The domain architecture (LisH + WD40) is shared with Gid7/YCL039W, a subunit of the GID E3 ubiquitin ligase complex, but there is no evidence that YGR117C is a GID complex member. Falcon deep research (2026) found no peer-reviewed gene-specific study; the only functional signal it could retrieve is from a 2014 PhD thesis reporting that ygr117c-delta cells show increased premature stop-codon readthrough and decreased reporter protein synthesis (a possible role in translation termination fidelity), plus an unvalidated listing among 446 candidates in a 2017 nonstop-decay genomic screen. These remain weak, non-peer-reviewed, and mechanistically unresolved, so the protein is best regarded as uncharacterized.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0005737
cytoplasm
|
HDA
PMID:14562095 Global analysis of protein localization in budding yeast. |
ACCEPT |
Summary: HDA annotation from Huh et al. (2003) global GFP-fusion protein localization study. YGR117C-GFP fusion was classified as cytoplasmic. This is the only informative annotation for this protein and is well supported by the large-scale localization study covering 75% of the yeast proteome.
Reason: Cytoplasmic localization is the only experimentally determined attribute of YGR117C. The Huh et al. study is a well-established, high-quality large-scale localization resource. The protein has no predicted signal peptide or transmembrane domains, consistent with cytoplasmic localization.
Supporting Evidence:
PMID:14562095
A fundamental goal of cell biology is to define the functions of proteins in the context of compartments that organize them in the cellular environment. Here we describe the construction and analysis of a collection of yeast strains expressing full-length, chromosomally tagged green fluorescent protein fusion proteins. We classify these proteins, representing 75% of the yeast proteome, into 22 distinct subcellular localization categories
file:yeast/YGR117C/YGR117C-deep-research-falcon.md
The gene product is reported as **cytoplasmic** based on cited GFP-localization work
|
|
GO:0003674
molecular_function
|
ND
GO_REF:0000015 |
ACCEPT |
Summary: ND (No Data) annotation indicating that no molecular function is known for YGR117C. This is appropriate given that no gene-specific functional study has been published. The BioReason deep research file (YGR117C-deep-research-bioreason-sft.md) predicts myosin V binding and scaffold functions based on domain architecture alone, but these predictions are fabricated without experimental support.
Reason: The ND annotation correctly reflects the current state of knowledge. No molecular function has been experimentally determined for YGR117C. While the LisH and WD40 domains suggest a potential role in protein-protein interactions, no specific binding partner or activity has been demonstrated. The BioReason predictions of myosin V binding (using incorrect GO:0032033 instead of GO:0031489) and heterochromatin formation are unsupported by any published evidence. Falcon deep research (2026) independently confirms that no molecular function has been experimentally established: the strongest gene-specific evidence retrievable (a 2014 PhD thesis) links YGR117C deletion to increased stop-codon readthrough and decreased reporter protein synthesis, but identifies no enzymatic activity, substrate, or validated binding partner, and explicitly flags the LisH/WD40 scaffold hypothesis as an inference not supported by direct evidence. The ND molecular_function annotation therefore remains appropriate.
Supporting Evidence:
file:yeast/YGR117C/YGR117C-deep-research-bioreason-sft.md
[BioReason predicts myosin V binding and heterochromatin formation based on domain architecture alone. These predictions are fabricated -- see YGR117C-bioreason-sft-review.md for details.]
file:yeast/YGR117C/YGR117C-deep-research-falcon.md
No direct enzymatic activity, substrate specificity, or validated binding partners/complex membership were identified for YGR117C in the retrieved evidence
file:yeast/YGR117C/YGR117C-deep-research-falcon.md
WD40 repeat proteins often function as scaffolds/adaptors in multiprotein complexes, and LisH motifs can mediate dimerization
|
|
GO:0008150
biological_process
|
ND
GO_REF:0000015 |
ACCEPT |
Summary: ND (No Data) annotation indicating that no biological process is known for YGR117C. This is appropriate given that no gene-specific functional study has been published. Falcon deep research surfaces a weak, thesis-level signal linking YGR117C deletion to a translation phenotype (increased stop-codon readthrough; decreased reporter protein synthesis) and a candidate listing in a nonstop-decay screen, but none of this rises to the level of a validated biological process assignment.
Reason: The ND annotation correctly reflects the current state of knowledge. Large-scale deletion screens show pleiotropic phenotypes (altered stress resistance, decreased fitness, abnormal vacuolar morphology) but these do not implicate a specific biological process. No gene-specific study has characterized the biological role of YGR117C. Falcon deep research identifies a possible role in translation termination fidelity / protein synthesis, but the only supporting evidence is a 2014 PhD thesis (reporter assays in a deletion strain, DOI:10.22215/etd/2014-10376) and an unvalidated candidate listing in a 2017 nonstop-decay genomic screen thesis (DOI:10.22215/etd/2017-12159). Falcon itself characterizes the NSD/autophagy link as not currently supported beyond candidate-list inclusion and treats it as speculative. Because there is no peer-reviewed, gene-specific primary publication and no validated mechanism, the evidence remains genuinely insufficient to assign a biological process term; ND is retained pending experimental validation (see suggested_experiments).
Supporting Evidence:
file:yeast/YGR117C/YGR117C-deep-research-falcon.md
deletion of **YGR117C** was reported to **increase translational stop-codon readthrough** of premature stop codons
file:yeast/YGR117C/YGR117C-deep-research-falcon.md
Assignment to NSD/autophagy is **not currently supported** beyond candidate-list inclusion and should be treated as speculative pending gene-specific validation
|
Q: What are the physical interaction partners of YGR117C? Systematic Y2H and AP-MS studies report 9 physical interactors, but these have not been individually validated. Focused co-IP or proximity labeling experiments could identify genuine binding partners.
Q: Is YGR117C a member of or functionally related to the GID/CTLH E3 ubiquitin ligase complex? Its LisH + WD40 domain architecture is shared with Gid7/YCL039W, a known GID complex subunit.
Q: What is the basis for the pleiotropic null mutant phenotypes (altered stress resistance, abnormal vacuolar morphology, decreased endocytosis)? Do these reflect a single underlying molecular function or multiple independent activities?
Q: Does YGR117C genuinely function in translation termination fidelity? A 2014 PhD thesis (DOI:10.22215/etd/2014-10376) reported increased stop-codon readthrough and decreased reporter protein synthesis in ygr117c-delta cells, but this has never been validated in a peer-reviewed, gene-specific study, and it is unclear whether any effect is direct (e.g. via association with the translation/termination machinery) or indirect (e.g. via protein homeostasis).
Experiment: Perform tandem affinity purification followed by mass spectrometry (TAP-MS) under multiple growth conditions (log phase, stationary phase, stress) to identify stable protein complexes containing YGR117C. Compare to published GID complex composition.
Hypothesis: YGR117C functions as a scaffold protein mediating specific protein-protein interactions
Type: affinity purification-mass spectrometry
Experiment: Independently reproduce and validate the translation phenotypes reported in the 2014 thesis using dual-luciferase stop-codon readthrough reporters across all three stop codons in ygr117c-delta cells, with isogenic controls and polysome profiling to distinguish a global translation defect from a specific termination-fidelity effect. If confirmed, test for physical or genetic interaction with the eRF1/eRF3 (Sup45/Sup35) termination machinery and ribosome-associated quality control factors to determine whether any role is direct or indirect.
Hypothesis: YGR117C contributes to translation termination fidelity
Type: reporter assay and genetic interaction
Experiment: The null mutant shows abnormal vacuolar morphology and decreased endocytosis. Perform detailed vacuolar staining (FM4-64 pulse-chase) and endocytic trafficking assays in ygr117c-delta cells to characterize the trafficking defect. Combine with genetic interaction analysis focusing on vacuolar and endosomal genes.
Hypothesis: YGR117C may be involved in vacuolar function or membrane trafficking
Type: fluorescence microscopy and genetic interaction
I begin with the domain architecture. The polypeptide is almost entirely covered by two family-level signatures: IPR016520 (Uncharacterised conserved protein UCP007778 family, residues 4β471) and IPR060045 (Uncharacterised conserved protein UCP007778-like family, residues 10β469). These broad family marks indicate a conserved, non-enzymatic scaffold-like role. At the extreme N-terminus lies IPR006594 (LIS1 homology motif, residues 7β39), a short conserved site classically associated with microtubule- and dynein-linked regulation and known to mediate contacts with cytoskeletal machinery. The C-terminal two-thirds are encompassed by IPR036322 (WD40-repeat-containing domain superfamily, residues 125β472), which denotes a beta-propeller platform optimized for multivalent proteinβprotein interactions rather than catalysis. The ordered layoutβan N-terminal LIS1-like regulatory motif feeding into a large WD40 propeller embedded within a conserved UCP007778 scaffoldβcreates a modular adaptor that can couple motor proteins to specific macromolecular assemblies.
This architecture causes a molecular function centered on binding rather than enzymatic activity. The WD40 superfamily domain provides a rigid, solvent-exposed propeller surface for docking multiple partners, while the LIS1-like motif supplies a regulatory handle that can engage cytoskeletal motors or their adaptors. Such a composite scaffold is well-suited to bind class V myosins that drive nuclear positioning in yeast, supporting the molecular function formalized as GO:0032033 myosin V binding. The lack of catalytic domains and the dominance of interaction-centric folds further argue that the protein acts as a cargo/adaptor or assembly factor for motor complexes.
From this binding activity, a biological process emerges. In budding yeast, positioning of the nucleus (binuclearcytoskeleton-driven nuclear migration) requires coupling the nuclear envelope to actomyosin forces. A WD40/LIS1-like scaffold that binds myosin V can organize or stabilize the motorβcargo interface at the nuclear periphery, thereby enabling efficient nuclear translocation. The same scaffold can also influence chromatin states by recruiting or positioning silencing factors. WD40 propellers commonly serve as hubs for chromatin-modifying complexes; by assembling repressors at specific loci, the protein can promote formation of silent chromatin at the silent mating-type cassette, aligning with GO:0030466 silent mating-type cassette heterochromatin formation. Thus, the domain architecture causally links myosin V binding to two processes: force-coupling for nuclear movement and organization of repressive chromatin at the HMR locus.
Cellular location follows from these roles. The absence of transmembrane segments and the presence of interaction-centric domains indicate a soluble protein. Its function in nuclear migration implies association with the nuclear envelope and perinuclear cytoskeleton, while its role in heterochromatin formation implies nuclear access. Therefore, a primary residence in the cytoplasm with dynamic enrichment at the nuclear periphery is expected, consistent with GO:0005737 cytoplasm and a likely association with the nucleus.
Mechanistically, I hypothesize that the N-terminal LIS1-like motif tunes engagement with myosin V motors, while the WD40 propeller presents docking sites for both motor adaptors and nuclear-envelope tethers. This would create a force-transmission module that links the nuclear outer membrane to myosin V tracks, driving nuclear migration. In parallel, the same propeller could scaffold silencing assemblies at the HMR locusβrecruiting chromatin readers and writers to nucleate heterochromatin. Likely interaction partners include the myosin V motor and its adaptors at the nuclear periphery, nuclear-envelope tethers, and chromatin-silencing factors that deposit or recognize histone modifications at mating-type loci.
## Functional Summary
A cytoplasmic scaffold in bakerβs yeast that binds myosin V to couple actomyosin forces to the nuclear periphery during nuclear migration, while also assembling silencing factors to promote formation of silent chromatin at the mating-type locus. Its N-terminal regulatory motif likely modulates motor engagement, and its beta-propeller core provides a multivalent platform to tether nuclear-envelope components and chromatin modifiers, enabling coordinated nuclear positioning and transcriptional repression.
## UniProt Summary
Involved in nuclear migration. Also involved in transcriptional silencing at the HMR locus.
## InterPro Domains
- IPR016520: Uncharacterised conserved protein UCP007778 (family) [4-471]
- IPR006594: LIS1 homology motif (conserved_site) [7-39]
- IPR060045: Uncharacterised conserved protein UCP007778-like (family) [10-469]
- IPR036322: WD40-repeat-containing domain superfamily (homologous_superfamily) [125-472]
## GO Term Predictions
### Molecular Function
### Biological Process
### Cellular Component
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
YGR117C (UniProt P53270; S. cerevisiae S288c) remains poorly characterized in the peerβreviewed literature retrievable in this run. The strongest gene-specific experimental evidence located links YGR117C to translation fidelity/termination and overall protein synthesis, based on reporter assays in a YGR117C deletion strain; the same work cites prior GFP-tag localization placing the protein in the cytoplasm. Inclusion of YGR117C as a candidate in a genome-wide nonstop-decay (NSD) screen provides only weak, unvalidated support for involvement in mRNA surveillance-related biology.
Uncharacterized protein / ORF gene. In budding yeast, many loci are historically designated by systematic ORF names (e.g., YGR117C) before a molecular function is established. In the evidence retrieved here, YGR117C is treated as a yeast ORF with limited prior functional characterization (tan2014identificationofnovel pages 86-90).
Translation termination fidelity and stop-codon readthrough. Stop-codon readthrough assays measure the propensity for ribosomes to continue translation past a stop codon, typically using reporter constructs (e.g., Ξ²-galactosidase) engineered with premature termination codons. Increased readthrough in a deletion mutant indicates a defect (direct or indirect) in translation termination fidelity or related quality-control processes (tan2014identificationofnovel pages 86-90).
Nonstop decay (NSD). NSD is an mRNA surveillance pathway targeting transcripts lacking stop codons; genome-wide deletion screens can identify candidate genes whose deletion alters NSD reporter behavior, but candidate lists require gene-specific validation before assigning function (kazmirchuk2017agenomicscreen pages 114-117).
Limitations for 2023β2024 YGR117C-specific literature in this run. Searches targeting YGR117C/P53270 did not retrieve YGR117C-focused primary studies from 2023β2024. A 2023 Nucleic Acids Research paper was retrieved in the search results set for yeast (Msn2/G4 DNA) but did not yield YGR117C-specific evidence in the text-extraction step; therefore it cannot be used to support YGR117C functional annotation here (duy2023yeasttranscriptionfactor; no relevant evidence returned).
Most informative available study (2014). The most substantive evidence retrievable in this run comes from a 2014 doctoral thesis that experimentally tested YGR117C deletion phenotypes in translation assays (tan2014identificationofnovel pages 86-90).
In a targeted follow-up of candidate genes affecting translation fidelity, deletion of YGR117C was reported to increase translational stop-codon readthrough of premature stop codons in Ξ²-galactosidase reporter assays, and accompanying qRT-PCR controls supported that the effect was not explained by altered reporter mRNA abundance (i.e., consistent with a translation-level effect) (tan2014identificationofnovel pages 86-90). The authors interpret these results as consistent with YGR117C being involved in the translation pathway (tan2014identificationofnovel pages 86-90).
Interpretation. Increased readthrough is compatible with YGR117C contributingβdirectly (e.g., via a physical role in translation termination) or indirectly (e.g., via protein homeostasis affecting termination factors)βto maintaining termination fidelity. However, no biochemical activity, binding partner, or complex membership for YGR117C was established in the retrieved text (tan2014identificationofnovel pages 86-90).
Using a GAL1-driven Ξ²-galactosidase assay as a proxy for protein synthesis/translation efficiency, YGR117C deletion was reported among strains showing decreased protein synthesis, again with qRT-PCR indicating that mRNA levels did not account for the observed effect (tan2014identificationofnovel pages 86-90).
Interpretation. This provides convergent (though still indirect) evidence that YGR117C impacts translation output in vivo. Whether the decreased reporter output reflects reduced global translation, altered translation initiation/elongation, or altered protein stability cannot be resolved from the retrieved excerpt alone (tan2014identificationofnovel pages 86-90).
In a genome-wide investigation designed to identify genes linked to nonstop decay and its potential relationship to autophagy, YGR117C appears in an appendix table as one of 446 candidates; no gene-specific validation, effect size, or mechanistic interpretation was provided for YGR117C in the retrieved pages (kazmirchuk2017agenomicscreen pages 114-117).
Interpretation. Candidate-list inclusion alone is insufficient to assign YGR117C a role in NSD or autophagy; at most, it motivates follow-up testing (kazmirchuk2017agenomicscreen pages 114-117).
The translation-focused thesis cites prior large-scale GFP-tag localization work (Huh et al., 2003) reporting YGR117C localization in the cytoplasm (tan2014identificationofnovel pages 86-90). No additional localization experiments for YGR117C were retrieved in this run.
Interpretation. Cytoplasmic localization is consistent with translation-related roles (ribosomes and many translation factors are cytoplasmic), but does not specify association with ribosomes, stress granules, or other subcompartments.
The user-supplied UniProt/InterPro context indicates YGR117C/P53270 contains LisH and WD40-related domains (InterPro IDs IPR006594; IPR036322). However, these domain annotations could not be independently verified from retrievable database text in this run (no UniProt/InterPro pages were available in evidence), and none of the retrieved publications provided domain-level experimental characterization of YGR117C.
Interpretation (conservative). WD40 repeat proteins often function as scaffolds/adaptors in multiprotein complexes, and LisH motifs can mediate dimerization and/or regulate microtubule-associated functions in some proteins. These are plausible hypotheses for YGR117C mechanism, but they remain inferences not supported by direct evidence in the retrieved corpus, and therefore should not be treated as established function here.
No direct evidence of physical interactions, genetic interaction partners, specific stress phenotypes, or defined pathway membership for YGR117C was retrieved beyond the translation reporter phenotypes and the unvalidated NSD screen-candidate listing (tan2014identificationofnovel pages 86-90, kazmirchuk2017agenomicscreen pages 114-117).
A dissertation appendix listing yeast ORFs includes YGR117C only as an identifier without annotation, and thus provides no interpretable functional evidence (hog2014functionalstudiesof pages 95-97).
Within the retrieved literature, YGR117Cβs primary βreal-worldβ usage is as a functional genomics screening hit/candidate:
No industrial strain engineering, fermentation trait optimization, or biotechnology implementations specifically involving manipulation of YGR117C were retrieved in this run.
Quantitative effect sizes (e.g., fold change in readthrough or reporter activity) were not present in the retrieved excerpts; therefore, this report cannot provide numeric magnitudes for YGR117Cβs translation-related phenotypes without additional source access.
The following table consolidates the directly retrievable evidence supporting YGR117C functional inference.
| Study/source | Publication year/date and URL/DOI | Experimental system/assay | Key finding related to YGR117C | Supported aspect | Notes/limitations |
|---|---|---|---|---|---|
| Tan, Identification of Novel Translation Related Genes in S. cerevisiae | 2014; DOI: 10.22215/etd/2014-10376; URL: https://doi.org/10.22215/etd/2014-10376 | Yeast deletion strain analyses; Ξ²-galactosidase stop-codon readthrough reporter; GAL1-driven Ξ²-galactosidase protein-synthesis assay; qRT-PCR controls; localization citation to Huh et al. 2003 | Deletion of YGR117C increased premature stop-codon readthrough and was also associated with decreased overall protein synthesis in reporter assays; qRT-PCR suggested effects were at the translation level rather than due to altered mRNA abundance. The thesis also cites prior GFP-localization work placing YGR117C in the cytoplasm. Authors conclude YGR117C may participate in the translation pathway. (tan2014identificationofnovel pages 86-90) | Putative function in translation/translation fidelity; cellular process: protein synthesis; localization: cytoplasm | Primary evidence is from a thesis rather than a peer-reviewed paper focused on YGR117C; mechanistic target, binding partners, and direct biochemical activity remain unresolved. Cytoplasmic localization is secondary attribution from earlier GFP-localization work, not newly demonstrated in the thesis. |
| Kazmirchuk, A Genomic Screen of S. cerevisiae Reveals a Potential Link Between Nonstop Decay and Autophagy | 2017; DOI: 10.22215/etd/2017-12159; URL: https://doi.org/10.22215/etd/2017-12159 | Genome-wide deletion-based nonstop decay (NSD) screen; appendix candidate table | YGR117C appears as one of 446 candidate genes from the NSD screen, but no gene-specific validation or mechanistic interpretation for YGR117C is provided in the retrieved text. (kazmirchuk2017agenomicscreen pages 114-117) | Very weak support for a possible link to mRNA surveillance/NSD-related screening context | Candidate-list inclusion alone is insufficient to assign function; no phenotype size, validation assay, localization, or pathway placement for YGR117C was reported in the retrieved excerpt. |
| HΓΆg, Functional studies of RNA polymerase II recruitment to promoter DNA and impact of BRF1 mutations on RNA polymerase III-dependent transcription | 2014; Jan 2014; DOI: 10.5282/edoc.17932; URL: https://doi.org/10.5282/edoc.17932 | Appendix/listing of yeast ORFs in dissertation | YGR117C is mentioned only as an ORF identifier in an appendix list; no functional, phenotypic, localization, or pathway data are given. (hog2014functionalstudiesof pages 95-97) | No substantive support; negative/neutral evidence | Useful mainly to document that this source does not provide interpretable annotation for YGR117C. |
Table: This table summarizes the small amount of directly retrievable evidence for S. cerevisiae YGR117C/P53270. It distinguishes comparatively informative translation-related evidence from sources where YGR117C is only listed without gene-specific validation.
This report is constrained to evidence retrievable via the provided tools in this run. Curated database pages (UniProt/SGD/InterPro) and 2023β2024 gene-specific studies for YGR117C were not retrievable here; consequently, domain architecture, orthology, interaction networks, and updated annotations could not be independently confirmed from authoritative databases, and recent developments could not be substantiated with YGR117C-specific citations.
References
(tan2014identificationofnovel pages 86-90): Identification of Novel Translation Related Genes in Saccharomyces Cerevisiae
(kazmirchuk2017agenomicscreen pages 114-117): Thomas Kazmirchuk. A genomic screen of saccharomyces cerevisiae reveals a potential link between nonstop decay and autophagy. ArXiv, 2017. URL: https://doi.org/10.22215/etd/2017-12159, doi:10.22215/etd/2017-12159. This article has 0 citations.
(hog2014functionalstudiesof pages 95-97): Friederike HΓΆg. Functional studies of rna polymerase ii recruitment to promoter dna and impact of brf1 mutations on rna polymerase iii-dependent transcription. Dissertation, Jan 2014. URL: https://doi.org/10.5282/edoc.17932, doi:10.5282/edoc.17932. This article has 0 citations.
From UniProt and InterPro:
- LisH motif (IPR006594, PROSITE PS50896): residues 7-39. The LIS1 homology motif is a short alpha-helical domain involved in protein dimerization. Originally identified in the LIS1 (lissencephaly-1) protein.
- WD40-repeat-containing domain superfamily (IPR036322, SUPFAM SSF50978): residues 125-472. A beta-propeller fold commonly serving as a protein-protein interaction platform.
- Uncharacterised conserved protein UCP007778 (IPR016520, PIRSF007778): residues 4-471. A broad family-level signature. Also IPR060045 (UCP007778-like, residues 10-469).
The combination of an N-terminal LisH motif plus a C-terminal WD40 propeller is found in several yeast proteins, notably GID7/YCL039W, a subunit of the GID E3 ubiquitin ligase complex. However, YGR117C is NOT Gid7 -- they are distinct proteins with distinct systematic names.
"Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm" [PMID:14562095, Huh et al. 2003]
Only 3 annotations:
1. GO:0005737 cytoplasm (HDA, PMID:14562095) -- GFP-fusion localization
2. GO:0003674 molecular_function (ND, GO_REF:0000015) -- No Data
3. GO:0008150 biological_process (ND, GO_REF:0000015) -- No Data
This is an extremely poorly annotated gene. The ND annotations explicitly indicate that no molecular function or biological process is known.
The ygr117c-delta null mutant is viable and shows:
- Decreased competitive fitness
- Decreased endocytosis
- Decreased hyperosmotic stress resistance
- Increased innate thermotolerance
- Increased oxidative stress resistance
- Increased mitotic recombination
- Abnormal vacuolar morphology
- Decreased utilization of nitrogen source (decreased rate)
- Variable chemical resistance (both increased and decreased reported)
- Haploinsufficient
These are all from large-scale surveys and are not gene-specific studies. The phenotype profile is broad and does not point to a single pathway.
9 physical interactors detected via:
- Affinity Capture-MS: 3 experiments
- Affinity Capture-RNA: 2 experiments
- Co-localization: 1 experiment
- Co-purification: 1 experiment
- Two-hybrid: 2 experiments
Specific interactors not individually available from web scraping, but the total is 9 physical and 29 genetic interactors.
Low-confidence interactions only:
- ISW1 (YBR245C): score 0.412 -- chromatin remodeling ATPase
- PHO81 (YGR233C): score 0.410 -- CDK inhibitor in phosphate signaling
- GDE1 (YPL110C): score 0.403 -- glycerophosphocholine phosphodiesterase
All scores are near the 0.4 threshold, indicating weak/low-confidence associations. These likely reflect genomic context or text-mining co-mentions rather than functional interactions.
Only 1 primary reference and 3 additional references per SGD. No gene-specific functional study has been published. All annotations derive from large-scale genomic/proteomic surveys:
- PMID:8905931 -- sequencing of chr VII region (Hansen et al. 1996)
- PMID:9169869 -- chr VII complete sequence (Tettelin et al. 1997)
- PMID:24374639 -- genome reannotation (Engel et al. 2014)
- PMID:14562106 -- protein expression (Ghaemmaghami et al. 2003)
- PMID:14562095 -- protein localization (Huh et al. 2003)
There is NO published paper that specifically investigates YGR117C function. All information comes from genome-wide surveys. The protein is genuinely uncharacterized.
The BioReason deep research file makes several specific claims that need verification:
FABRICATED.
- The correct GO term for myosin V binding is GO:0031489, not GO:0032033. GO:0032033 does not exist as a myosin V binding term.
- There is NO evidence linking YGR117C to myosin V or any myosin. No published study reports this interaction.
- BioReason appears to reason: LisH domain -> "classically associated with microtubule- and dynein-linked regulation" -> nuclear positioning -> myosin V binding. This chain of reasoning is speculative and unsupported.
- While LisH domains ARE found in some cytoskeletal-associated proteins (LIS1 itself), having a LisH domain does not imply myosin V binding. LisH domains are found in diverse contexts including the GID/CTLH E3 ligase complex.
FABRICATED.
- No evidence links YGR117C to nuclear migration. No published study reports this.
- The BioReason UniProt Summary section states "Involved in nuclear migration. Also involved in transcriptional silencing at the HMR locus." -- this text does NOT appear in the actual UniProt entry for P53270. The UniProt entry says "Uncharacterized protein YGR117C" with NO functional description.
- This is a clear fabrication in the "UniProt Summary" section of the BioReason output.
FABRICATED.
- No evidence links YGR117C to heterochromatin formation or mating-type silencing.
- The BioReason reasoning: WD40 propeller -> "commonly serve as hubs for chromatin-modifying complexes" -> "recruiting or positioning silencing factors" -> HMR heterochromatin. This is pure speculation.
- While WD40 proteins DO participate in chromatin complexes (e.g., WDR5 in COMPASS), having WD40 repeats does not imply a role in chromatin silencing.
PARTIALLY CORRECT.
- The InterPro domain assignments (IPR016520, IPR006594, IPR060045, IPR036322) are accurate.
- The description of LisH as an alpha-helical motif and WD40 as a beta-propeller is correct.
- However, the functional extrapolation from domains to specific biological roles is unfounded.
FABRICATED.
- BioReason's "UniProt Summary" states: "Involved in nuclear migration. Also involved in transcriptional silencing at the HMR locus."
- The actual UniProt record for P53270 contains NO functional description. The protein is listed as "Uncharacterized protein YGR117C".
- This is the most concerning fabrication because it masquerades as an authoritative source.
YGR117C encodes a cytoplasmic protein of unknown function containing LisH and WD40 domains. Its function is genuinely unknown. The BioReason predictions are almost entirely fabricated from domain architecture extrapolation, with a fabricated "UniProt Summary" that does not match the actual UniProt record.
Source: YGR117C-deep-research-bioreason-sft.md
The BioReason functional summary describes YGR117C as:
A cytoplasmic scaffold in baker's yeast that binds myosin V to couple actomyosin forces to the nuclear periphery during nuclear migration, while also assembling silencing factors to promote formation of silent chromatin at the mating-type locus. Its N-terminal regulatory motif likely modulates motor engagement, and its beta-propeller core provides a multivalent platform to tether nuclear-envelope components and chromatin modifiers, enabling coordinated nuclear positioning and transcriptional repression.
This summary is almost entirely fabricated. YGR117C is a genuinely uncharacterized protein with no published functional study. The BioReason model has constructed an elaborate narrative from domain architecture alone, presenting speculation as established fact.
Fabricated claims:
"Binds myosin V" is fabricated. No published study or database entry links YGR117C to myosin V or any myosin motor protein. The BioReason thinking trace reasons from "LisH motif" to "classically associated with microtubule- and dynein-linked regulation" to "myosin V binding." This chain of inference is unsupported. LisH domains are found in diverse protein families including the GID/CTLH E3 ubiquitin ligase complex (Gid7/YCL039W also has LisH + WD40 domains), transcriptional corepressor complexes, and other non-cytoskeletal contexts. Having a LisH domain does not imply motor protein binding.
"Nuclear migration" is fabricated. No evidence links YGR117C to nuclear migration. Nuclear migration in budding yeast is mediated by the Kar9-Myo2 pathway and the dynein pathway, neither of which involves YGR117C. The thinking trace constructs this claim by chaining domain-level generalizations without any gene-specific evidence.
"Silent mating-type cassette heterochromatin formation" (GO:0030466) is fabricated. No evidence links YGR117C to heterochromatin formation, chromatin silencing, or the HMR locus. The reasoning in the thinking trace -- "WD40 propellers commonly serve as hubs for chromatin-modifying complexes" leading to "recruiting or positioning silencing factors" -- is a generic domain-level speculation applied without justification. While some WD40 proteins do participate in chromatin complexes (e.g., WDR5 in COMPASS, Gid7 in GID complex), the vast majority of WD40 proteins have unrelated functions.
The "UniProt Summary" is fabricated. The BioReason output includes a "UniProt Summary" section stating: "Involved in nuclear migration. Also involved in transcriptional silencing at the HMR locus." This text does NOT appear in the actual UniProt entry for P53270. The real UniProt record describes the protein as "Uncharacterized protein YGR117C" with no functional annotation. This fabrication is particularly problematic because it appears to attribute invented claims to an authoritative database, lending false credibility.
GO:0032033 "myosin V binding" is an incorrect GO term ID. The actual GO term for myosin V binding is GO:0031489. GO:0032033 does not correspond to myosin V binding, suggesting the model hallucinated both the function and the GO identifier.
The GO term predictions sections are empty. Despite the extensive narrative about myosin V binding, nuclear migration, and heterochromatin formation, the structured Molecular Function, Biological Process, and Cellular Component prediction sections at the end of the output are all blank.
What was correct:
YGR117C has only 3 GOA annotations:
- GO:0005737 cytoplasm (HDA) -- correctly identified by BioReason
- GO:0003674 molecular_function (ND) -- no molecular function known
- GO:0008150 biological_process (ND) -- no biological process known
The ND (No Data) annotations explicitly indicate that no function is known. BioReason ignores this signal and fabricates specific functional predictions without any experimental basis.
The thinking trace reveals the core failure mode clearly:
Domain-to-function extrapolation without gene-specific evidence. The entire reasoning chain proceeds from domain architecture (LisH + WD40) through generic domain-level associations ("LisH is classically associated with microtubule regulation") to specific functional claims (myosin V binding, nuclear migration, HMR silencing). At no point does the model cite a gene-specific experiment or interaction.
Circular reasoning about localization. The trace states "Its function in nuclear migration implies association with the nuclear envelope," then uses this implied association to support the nuclear migration claim. The actual data shows cytoplasmic localization only.
Fabrication of partner proteins. The trace mentions "myosin V motor and its adaptors at the nuclear periphery, nuclear-envelope tethers, and chromatin-silencing factors" as likely interaction partners. None of these interactions have been reported for YGR117C.
Misrepresentation of the LisH domain. The trace claims LisH is "classically associated with microtubule- and dynein-linked regulation." While the founding member LIS1 does regulate dynein, the LisH domain is found in many non-cytoskeletal proteins including the GID/CTLH E3 ligase complex and transcriptional corepressor complexes. The domain's primary function is mediating dimerization, not motor protein binding.
Ignoring the GID complex connection. The most notable yeast protein with LisH + WD40 architecture is Gid7/YCL039W, a subunit of the GID E3 ubiquitin ligase complex involved in catabolite-induced degradation of gluconeogenic enzymes. If domain architecture were to suggest function, the GID complex connection would be a more reasonable hypothesis than myosin V binding. BioReason completely ignores this.
The BioReason prediction for YGR117C is a case study in the failure mode of domain-based functional inference for uncharacterized proteins. The model fabricates an elaborate, mechanistically detailed narrative (myosin V binding, nuclear migration, heterochromatin formation) that has zero experimental support. Worse, the "UniProt Summary" section presents fabricated text as if it came from UniProt, creating a false attribution to an authoritative source. The only correct elements are the domain architecture description and cytoplasm localization. For a genuinely uncharacterized protein like YGR117C, the honest answer is "function unknown," and the BioReason output is actively misleading.
id: P53270
gene_symbol: YGR117C
product_type: PROTEIN
status: COMPLETE
tags:
- uncharacterized
- LisH
- WD40
- poorly-annotated
taxon:
id: NCBITaxon:559292
label: Saccharomyces cerevisiae
description: >-
YGR117C encodes a 476-amino-acid cytoplasmic protein of unknown function in Saccharomyces cerevisiae.
The protein contains an N-terminal LisH dimerization motif (residues 7-39) and a C-terminal WD40-repeat
beta-propeller domain (residues 125-472), suggesting it may function as a scaffold or adaptor mediating
protein-protein interactions. It belongs to the conserved UCP007778 family (IPR016520/PIRSF007778).
Despite being expressed at moderate levels (~1280-2276 molecules/cell) and being conserved across
Saccharomycetaceae, no gene-specific functional study has been published. GFP-fusion protein localizes
to the cytoplasm (PMID:14562095). Large-scale phenotypic screens of the null mutant show pleiotropic
effects including decreased competitive fitness, abnormal vacuolar morphology, altered stress
resistance, and decreased endocytosis, but these do not point to a single pathway. The domain
architecture (LisH + WD40) is shared with Gid7/YCL039W, a subunit of the GID E3 ubiquitin ligase
complex, but there is no evidence that YGR117C is a GID complex member. Falcon deep research (2026)
found no peer-reviewed gene-specific study; the only functional signal it could retrieve is from a
2014 PhD thesis reporting that ygr117c-delta cells show increased premature stop-codon readthrough
and decreased reporter protein synthesis (a possible role in translation termination fidelity),
plus an unvalidated listing among 446 candidates in a 2017 nonstop-decay genomic screen. These
remain weak, non-peer-reviewed, and mechanistically unresolved, so the protein is best regarded as
uncharacterized.
existing_annotations:
- term:
id: GO:0005737
label: cytoplasm
evidence_type: HDA
original_reference_id: PMID:14562095
review:
summary: >-
HDA annotation from Huh et al. (2003) global GFP-fusion protein localization study. YGR117C-GFP
fusion was classified as cytoplasmic. This is the only informative annotation for this protein
and is well supported by the large-scale localization study covering 75% of the yeast proteome.
action: ACCEPT
reason: >-
Cytoplasmic localization is the only experimentally determined attribute of YGR117C. The Huh et al.
study is a well-established, high-quality large-scale localization resource. The protein has no
predicted signal peptide or transmembrane domains, consistent with cytoplasmic localization.
supported_by:
- reference_id: PMID:14562095
supporting_text: >-
A fundamental goal of cell biology is to define the functions of proteins in the context of
compartments that organize them in the cellular environment. Here we describe the construction
and analysis of a collection of yeast strains expressing full-length, chromosomally tagged green
fluorescent protein fusion proteins. We classify these proteins, representing 75% of the yeast
proteome, into 22 distinct subcellular localization categories
- reference_id: file:yeast/YGR117C/YGR117C-deep-research-falcon.md
supporting_text: |-
The gene product is reported as **cytoplasmic** based on cited GFP-localization work
additional_reference_ids:
- file:yeast/YGR117C/YGR117C-deep-research-falcon.md
- term:
id: GO:0003674
label: molecular_function
evidence_type: ND
original_reference_id: GO_REF:0000015
review:
summary: >-
ND (No Data) annotation indicating that no molecular function is known for YGR117C. This is
appropriate given that no gene-specific functional study has been published. The BioReason deep
research file (YGR117C-deep-research-bioreason-sft.md) predicts myosin V binding and scaffold
functions based on domain architecture alone, but these predictions are fabricated without
experimental support.
action: ACCEPT
reason: >-
The ND annotation correctly reflects the current state of knowledge. No molecular function has
been experimentally determined for YGR117C. While the LisH and WD40 domains suggest a potential
role in protein-protein interactions, no specific binding partner or activity has been demonstrated.
The BioReason predictions of myosin V binding (using incorrect GO:0032033 instead of GO:0031489)
and heterochromatin formation are unsupported by any published evidence. Falcon deep research (2026)
independently confirms that no molecular function has been experimentally established: the strongest
gene-specific evidence retrievable (a 2014 PhD thesis) links YGR117C deletion to increased stop-codon
readthrough and decreased reporter protein synthesis, but identifies no enzymatic activity, substrate,
or validated binding partner, and explicitly flags the LisH/WD40 scaffold hypothesis as an inference
not supported by direct evidence. The ND molecular_function annotation therefore remains appropriate.
supported_by:
- reference_id: file:yeast/YGR117C/YGR117C-deep-research-bioreason-sft.md
supporting_text: >-
[BioReason predicts myosin V binding and heterochromatin formation based on domain architecture
alone. These predictions are fabricated -- see YGR117C-bioreason-sft-review.md for details.]
- reference_id: file:yeast/YGR117C/YGR117C-deep-research-falcon.md
supporting_text: |-
No direct enzymatic activity, substrate specificity, or validated binding partners/complex membership were identified for YGR117C in the retrieved evidence
- reference_id: file:yeast/YGR117C/YGR117C-deep-research-falcon.md
supporting_text: |-
WD40 repeat proteins often function as scaffolds/adaptors in multiprotein complexes, and LisH motifs can mediate dimerization
additional_reference_ids:
- file:yeast/YGR117C/YGR117C-deep-research-bioreason-sft.md
- file:yeast/YGR117C/YGR117C-deep-research-falcon.md
- term:
id: GO:0008150
label: biological_process
evidence_type: ND
original_reference_id: GO_REF:0000015
review:
summary: >-
ND (No Data) annotation indicating that no biological process is known for YGR117C. This is
appropriate given that no gene-specific functional study has been published. Falcon deep research
surfaces a weak, thesis-level signal linking YGR117C deletion to a translation phenotype
(increased stop-codon readthrough; decreased reporter protein synthesis) and a candidate listing
in a nonstop-decay screen, but none of this rises to the level of a validated biological process
assignment.
action: ACCEPT
reason: >-
The ND annotation correctly reflects the current state of knowledge. Large-scale deletion screens
show pleiotropic phenotypes (altered stress resistance, decreased fitness, abnormal vacuolar
morphology) but these do not implicate a specific biological process. No gene-specific study
has characterized the biological role of YGR117C. Falcon deep research identifies a possible role
in translation termination fidelity / protein synthesis, but the only supporting evidence is a
2014 PhD thesis (reporter assays in a deletion strain, DOI:10.22215/etd/2014-10376) and an
unvalidated candidate listing in a 2017 nonstop-decay genomic screen thesis
(DOI:10.22215/etd/2017-12159). Falcon itself characterizes the NSD/autophagy link as not
currently supported beyond candidate-list inclusion and treats it as speculative. Because there
is no peer-reviewed, gene-specific primary publication and no validated mechanism, the evidence
remains genuinely insufficient to assign a biological process term; ND is retained pending
experimental validation (see suggested_experiments).
supported_by:
- reference_id: file:yeast/YGR117C/YGR117C-deep-research-falcon.md
supporting_text: |-
deletion of **YGR117C** was reported to **increase translational stop-codon readthrough** of premature stop codons
- reference_id: file:yeast/YGR117C/YGR117C-deep-research-falcon.md
supporting_text: |-
Assignment to NSD/autophagy is **not currently supported** beyond candidate-list inclusion and should be treated as speculative pending gene-specific validation
additional_reference_ids:
- file:yeast/YGR117C/YGR117C-deep-research-falcon.md
references:
- id: GO_REF:0000015
title: Use of the ND evidence code for Gene Ontology (GO) terms
findings: []
- id: PMID:14562095
title: Global analysis of protein localization in budding yeast.
findings:
- statement: >-
Large-scale GFP-fusion localization study classifying 75% of yeast proteome into 22 subcellular
localization categories. YGR117C-GFP fusion localizes to the cytoplasm.
supporting_text: >-
Here we describe the construction and analysis of a collection of yeast strains expressing
full-length, chromosomally tagged green fluorescent protein fusion proteins. We classify these
proteins, representing 75% of the yeast proteome, into 22 distinct subcellular localization
categories, and provide localization information for 70% of previously unlocalized proteins.
- id: PMID:14562106
title: Global analysis of protein expression in yeast.
findings:
- statement: >-
Proteome-wide protein expression quantification. YGR117C is present at approximately 1280
molecules per cell in log phase SD medium.
supporting_text: >-
we have created a Saccharomyces cerevisiae fusion library where each open reading frame is tagged
with a high-affinity epitope and expressed from its natural chromosomal location. Through
immunodetection of the common tag, we obtain a census of proteins expressed during log-phase
growth and measurements of their absolute levels.
- id: PMID:8905931
title: >-
The sequence of a 23.4 kb segment on the right arm of chromosome VII from Saccharomyces
cerevisiae reveals CLB6, SPT6, RP28A and NUP57 genes, a Ty3 element and 11 new open reading
frames.
findings:
- statement: >-
Original genomic sequencing of the chromosomal region containing YGR117C. The gene was identified
as one of 11 new open reading frames in a 23.4 kb segment on chromosome VII.
supporting_text: >-
The sequence of a 23.4 kb segment on the right arm of chromosome VII from Saccharomyces
cerevisiae reveals CLB6, SPT6, RP28A and NUP57 genes, a Ty3 element and 11 new open reading
frames.
- id: file:yeast/YGR117C/YGR117C-deep-research-falcon.md
title: Falcon deep research report on YGR117C (UniProt P53270)
findings:
- statement: |
YGR117C remains poorly characterized. The strongest gene-specific experimental evidence
retrievable links the protein to translation fidelity/termination and overall protein synthesis,
based on reporter assays in a YGR117C deletion strain, and cites prior GFP-tag localization
placing the protein in the cytoplasm.
supporting_text: |-
The strongest gene-specific experimental evidence located links YGR117C to **translation fidelity/termination** and **overall protein synthesis**, based on reporter assays in a YGR117C deletion strain; the same work cites prior GFP-tag localization placing the protein in the **cytoplasm**.
reference_section_type: OTHER
- statement: |
In a translation-fidelity follow-up, deletion of YGR117C increased premature stop-codon
readthrough in a beta-galactosidase reporter assay, with qRT-PCR controls indicating the effect
was at the translation level rather than due to altered reporter mRNA abundance. The authors
interpret this as YGR117C being involved in the translation pathway. Evidence is from a 2014 PhD
thesis, not a peer-reviewed gene-specific paper.
supporting_text: |-
deletion of **YGR117C** was reported to **increase translational stop-codon readthrough** of premature stop codons in Ξ²-galactosidase reporter assays, and accompanying qRT-PCR controls supported that the effect was not explained by altered reporter mRNA abundance (i.e., consistent with a translation-level effect)
reference_section_type: OTHER
- statement: |
Using a GAL1-driven beta-galactosidase protein-synthesis assay, YGR117C deletion was among
strains showing decreased protein synthesis, again with qRT-PCR indicating mRNA levels did not
account for the effect. This provides convergent but still indirect evidence of an effect on
translation output in vivo.
supporting_text: |-
YGR117C deletion was reported among strains showing **decreased protein synthesis**, again with qRT-PCR indicating that mRNA levels did not account for the observed effect
reference_section_type: OTHER
- statement: |
YGR117C appears as one of 446 candidate genes in a genome-wide nonstop-decay (NSD) screen, but
no gene-specific validation, effect size, or mechanistic interpretation was provided. Falcon
concludes that assignment to NSD/autophagy is not currently supported beyond candidate-list
inclusion and should be treated as speculative.
supporting_text: |-
Assignment to NSD/autophagy is **not currently supported** beyond candidate-list inclusion and should be treated as speculative pending gene-specific validation
reference_section_type: OTHER
- statement: |
The protein product is reported as cytoplasmic based on cited GFP-localization work (Huh et al.
2003), consistent with translation-related roles, though it does not specify association with
ribosomes, stress granules, or other subcompartments.
supporting_text: |-
Cytoplasmic localization is consistent with translation-related roles (ribosomes and many translation factors are cytoplasmic), but does not specify association with ribosomes, stress granules, or other subcompartments.
reference_section_type: OTHER
- statement: |
No direct enzymatic activity, substrate specificity, or validated binding partners/complex
membership were identified for YGR117C. The LisH/WD40 scaffold-adaptor hypothesis is explicitly
flagged as an inference not supported by direct evidence in the retrieved corpus and should not
be treated as established function.
supporting_text: |-
No direct enzymatic activity, substrate specificity, or validated binding partners/complex membership were identified for YGR117C in the retrieved evidence
reference_section_type: OTHER
core_functions:
- description: >-
YGR117C is a protein of unknown function. Its domain architecture (N-terminal LisH dimerization
motif plus C-terminal WD40 beta-propeller) suggests it may function as a scaffold or adaptor
protein mediating protein-protein interactions, but no specific molecular function has been
experimentally demonstrated. The protein is expressed at moderate levels in the cytoplasm.
The most informative structural parallel is with Gid7/YCL039W (also LisH + WD40), a subunit
of the GID E3 ubiquitin ligase complex, but membership in the GID complex has not been
established for YGR117C. Falcon deep research adds only a weak, thesis-level link to translation
termination fidelity / protein synthesis, with no validated molecular function, so no specific
molecular_function term is asserted here.
locations:
- id: GO:0005737
label: cytoplasm
supported_by:
- reference_id: PMID:14562095
supporting_text: >-
A fundamental goal of cell biology is to define the functions of proteins in the context of
compartments that organize them in the cellular environment. Here we describe the construction
and analysis of a collection of yeast strains expressing full-length, chromosomally tagged green
fluorescent protein fusion proteins.
- reference_id: file:yeast/YGR117C/YGR117C-deep-research-falcon.md
supporting_text: |-
No direct enzymatic activity, substrate specificity, or validated binding partners/complex membership were identified for YGR117C in the retrieved evidence
suggested_questions:
- question: >-
What are the physical interaction partners of YGR117C? Systematic Y2H and AP-MS studies report
9 physical interactors, but these have not been individually validated. Focused co-IP or
proximity labeling experiments could identify genuine binding partners.
- question: >-
Is YGR117C a member of or functionally related to the GID/CTLH E3 ubiquitin ligase complex?
Its LisH + WD40 domain architecture is shared with Gid7/YCL039W, a known GID complex subunit.
- question: >-
What is the basis for the pleiotropic null mutant phenotypes (altered stress resistance, abnormal
vacuolar morphology, decreased endocytosis)? Do these reflect a single underlying molecular
function or multiple independent activities?
- question: >-
Does YGR117C genuinely function in translation termination fidelity? A 2014 PhD thesis
(DOI:10.22215/etd/2014-10376) reported increased stop-codon readthrough and decreased reporter
protein synthesis in ygr117c-delta cells, but this has never been validated in a peer-reviewed,
gene-specific study, and it is unclear whether any effect is direct (e.g. via association with
the translation/termination machinery) or indirect (e.g. via protein homeostasis).
suggested_experiments:
- hypothesis: YGR117C functions as a scaffold protein mediating specific protein-protein interactions
description: >-
Perform tandem affinity purification followed by mass spectrometry (TAP-MS) under multiple
growth conditions (log phase, stationary phase, stress) to identify stable protein complexes
containing YGR117C. Compare to published GID complex composition.
experiment_type: affinity purification-mass spectrometry
- hypothesis: YGR117C contributes to translation termination fidelity
description: >-
Independently reproduce and validate the translation phenotypes reported in the 2014 thesis using
dual-luciferase stop-codon readthrough reporters across all three stop codons in ygr117c-delta
cells, with isogenic controls and polysome profiling to distinguish a global translation defect
from a specific termination-fidelity effect. If confirmed, test for physical or genetic interaction
with the eRF1/eRF3 (Sup45/Sup35) termination machinery and ribosome-associated quality control
factors to determine whether any role is direct or indirect.
experiment_type: reporter assay and genetic interaction
- hypothesis: YGR117C may be involved in vacuolar function or membrane trafficking
description: >-
The null mutant shows abnormal vacuolar morphology and decreased endocytosis. Perform
detailed vacuolar staining (FM4-64 pulse-chase) and endocytic trafficking assays in
ygr117c-delta cells to characterize the trafficking defect. Combine with genetic interaction
analysis focusing on vacuolar and endosomal genes.
experiment_type: fluorescence microscopy and genetic interaction