CCT3

UniProt ID: P39077
Organism: Saccharomyces cerevisiae
Review Status: COMPLETE
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Gene Description

CCT3 encodes the gamma subunit of the cytosolic group II chaperonin TRiC/CCT. As one of eight obligate paralogous subunits in each ring, Cct3 contributes ATPase and substrate-contact surfaces to the hetero-oligomeric folding chamber that matures actin, tubulin, and other cytosolic clients. Its curated core function is complex-level ATP-dependent protein folding, not nonspecific protein binding.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0006457 protein folding
IBA
GO_REF:0000033
ACCEPT
Summary: CCT3 participates in protein folding as an obligate subunit of TRiC/CCT, the cytosolic chaperonin that folds actin, tubulin, and other clients.
Reason: Protein folding is the correct biological-process context for the chaperonin complex, supported by direct yeast CCT actin-folding assays and PANTHER/InterPro family evidence.
Supporting Evidence:
file:yeast/CCT3/CCT3-deep-research-falcon.md
The CCT/TRiC complex is a double-ring ATP-driven folding machine
GO:0005832 chaperonin-containing T-complex
IBA
GO_REF:0000033
ACCEPT
Summary: CCT3 is a named subunit of the chaperonin-containing T-complex.
Reason: Complex membership is central to the gene product function and is supported by yeast CCT complex literature and family evidence.
GO:0051082 unfolded protein binding
IBA
GO_REF:0000033
MODIFY
Summary: unfolded protein binding reflects substrate engagement by TRiC/CCT, but it is less informative than the ATP-dependent folding chaperone function of the complex.
Reason: Replace generic substrate-binding language with the specific chaperonin activity supported by yeast CCT actin-folding assays and domain evidence.
GO:0000166 nucleotide binding
IEA
GO_REF:0000043
MARK AS OVER ANNOTATED
Summary: nucleotide binding is a true but overly broad family/keyword annotation for CCT3; ATP binding, ATP hydrolysis, and ATP-dependent chaperone annotations capture the specific chemistry.
Reason: Generic nucleotide binding does not add useful functional information beyond the more specific ATP-related chaperonin annotations already present.
GO:0005524 ATP binding
IEA
GO_REF:0000120
KEEP AS NON CORE
Summary: CCT3 contains a conserved chaperonin ATP-binding site, but ATP binding alone is a domain property rather than the core biological function.
Reason: Keep as a valid supporting molecular property of the CCT ATPase cycle, while treating ATP hydrolysis and complex-level protein folding as the core function.
GO:0005737 cytoplasm
IEA
GO_REF:0000044
ACCEPT
Summary: CCT3 functions as part of the cytosolic TRiC/CCT chaperonin.
Reason: Cytoplasm is the established location of the CCT/TRiC folding machine.
GO:0005832 chaperonin-containing T-complex
IEA
GO_REF:0000117
ACCEPT
Summary: CCT3 is a named subunit of the chaperonin-containing T-complex.
Reason: Complex membership is central to the gene product function and is supported by yeast CCT complex literature and family evidence.
GO:0006457 protein folding
IEA
GO_REF:0000120
ACCEPT
Summary: CCT3 participates in protein folding as an obligate subunit of TRiC/CCT, the cytosolic chaperonin that folds actin, tubulin, and other clients.
Reason: Protein folding is the correct biological-process context for the chaperonin complex, supported by direct yeast CCT actin-folding assays and PANTHER/InterPro family evidence.
GO:0016887 ATP hydrolysis activity
IEA
GO_REF:0000002
ACCEPT
Summary: CCT3 is a TCP-1/CCT chaperonin subunit with conserved ATPase machinery that powers TRiC/CCT conformational cycling.
Reason: ATP hydrolysis is a defensible subunit-level molecular function for CCT family members and is directly tied to the chaperonin folding cycle.
GO:0051082 unfolded protein binding
IEA
GO_REF:0000120
MODIFY
Summary: unfolded protein binding reflects substrate engagement by TRiC/CCT, but it is less informative than the ATP-dependent folding chaperone function of the complex.
Reason: Replace generic substrate-binding language with the specific chaperonin activity supported by yeast CCT actin-folding assays and domain evidence.
GO:0140662 ATP-dependent protein folding chaperone
IEA
GO_REF:0000002
ACCEPT
Summary: CCT3 is an obligate subunit of the ATP-dependent TRiC/CCT folding machine.
Reason: The term is appropriate as a complex-level chaperonin function; in the synthesized core function it is modeled as a contributed-to molecular function rather than a standalone activity of an isolated subunit.
Supporting Evidence:
PMID:16762366
The eukaryotic cytosolic chaperonin CCT is an essential ATP-dependent protein folding machine whose action is required for folding the cytoskeletal proteins actin and tubulin
GO:0005515 protein binding
IPI
PMID:19536198
An atlas of chaperone-protein interactions in Saccharomyces ...
MARK AS OVER ANNOTATED
Summary: protein binding is too generic for a CCT subunit and does not describe the chaperonin mechanism or substrate class.
Reason: Physical-interaction datasets are useful evidence context, but generic protein binding should not stand as a functional annotation when the specific TRiC/CCT chaperonin role is known.
Supporting Evidence:
PMID:19536198
It should be emphasized that the interactions presented are indirect TAP-tag based interactions and not direct binary interactions.
GO:0005515 protein binding
IPI
PMID:37968396
The social and structural architecture of the yeast protein ...
MARK AS OVER ANNOTATED
Summary: protein binding is too generic for a CCT subunit and does not describe the chaperonin mechanism or substrate class.
Reason: Physical-interaction datasets are useful evidence context, but generic protein binding should not stand as a functional annotation when the specific TRiC/CCT chaperonin role is known.
GO:0006457 protein folding
IDA
PMID:16762366
Quantitative actin folding reactions using yeast CCT purifie...
ACCEPT
Summary: CCT3 participates in protein folding as an obligate subunit of TRiC/CCT, the cytosolic chaperonin that folds actin, tubulin, and other clients.
Reason: Protein folding is the correct biological-process context for the chaperonin complex, supported by direct yeast CCT actin-folding assays and PANTHER/InterPro family evidence.
Supporting Evidence:
PMID:16762366
The eukaryotic cytosolic chaperonin CCT is an essential ATP-dependent protein folding machine whose action is required for folding the cytoskeletal proteins actin and tubulin
GO:0005832 chaperonin-containing T-complex
IPI
PMID:15704212
Physiological effects of unassembled chaperonin Cct subunits...
ACCEPT
Summary: CCT3 is a named subunit of the chaperonin-containing T-complex.
Reason: Complex membership is central to the gene product function and is supported by yeast CCT complex literature and family evidence.
Supporting Evidence:
PMID:16762366
The eukaryotic cytosolic chaperonin CCT is an essential ATP-dependent protein folding machine whose action is required for folding the cytoskeletal proteins actin and tubulin
GO:0005832 chaperonin-containing T-complex
IDA
PMID:16762366
Quantitative actin folding reactions using yeast CCT purifie...
ACCEPT
Summary: CCT3 is a named subunit of the chaperonin-containing T-complex.
Reason: Complex membership is central to the gene product function and is supported by yeast CCT complex literature and family evidence.
Supporting Evidence:
PMID:15704212
Eukaryotic chaperonins, the Cct complexes, are assembled into two rings, each of which is composed of a stoichiometric array of eight different subunits
GO:0051082 unfolded protein binding
IDA
PMID:16762366
Quantitative actin folding reactions using yeast CCT purifie...
MODIFY
Summary: unfolded protein binding reflects substrate engagement by TRiC/CCT, but it is less informative than the ATP-dependent folding chaperone function of the complex.
Reason: Replace generic substrate-binding language with the specific chaperonin activity supported by yeast CCT actin-folding assays and domain evidence.
Supporting Evidence:
PMID:16762366
The eukaryotic cytosolic chaperonin CCT is an essential ATP-dependent protein folding machine whose action is required for folding the cytoskeletal proteins actin and tubulin

Core Functions

CCT3 is the gamma subunit of the cytosolic TRiC/CCT chaperonin. The subunit contributes ATPase and substrate-contact surfaces to the hetero-oligomeric double-ring complex, whose ATP-dependent conformational cycle folds actin, tubulin, and other cytosolic client proteins. The synthesized function is modeled as subunit ATP hydrolysis contributing to the complex-level ATP-dependent protein folding chaperone activity.

Molecular Function:
ATP hydrolysis activity
Directly Involved In:
Cellular Locations:
Supporting Evidence:
  • PMID:16762366
    The eukaryotic cytosolic chaperonin CCT is an essential ATP-dependent protein folding machine whose action is required for folding the cytoskeletal proteins actin and tubulin
  • PMID:15704212
    Eukaryotic chaperonins, the Cct complexes, are assembled into two rings, each of which is composed of a stoichiometric array of eight different subunits

References

Gene Ontology annotation through association of InterPro records with GO terms
Annotation inferences using phylogenetic trees
Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
Electronic Gene Ontology annotations created by ARBA machine learning models
Combined Automated Annotation using Multiple IEA Methods
Physiological effects of unassembled chaperonin Cct subunits in the yeast Saccharomyces cerevisiae.
  • Yeast CCT is a double-ring complex with a stoichiometric set of eight distinct Cct subunits.
    "Eukaryotic chaperonins, the Cct complexes, are assembled into two rings, each of which is composed of a stoichiometric array of eight different subunits"
Quantitative actin folding reactions using yeast CCT purified via an internal tag in the CCT3/gamma subunit.
  • Purified yeast CCT, tagged through CCT3, catalyzes ATP-dependent actin folding; this supports protein-folding and chaperonin activity annotations for CCT3 as a TRiC/CCT subunit.
    "The eukaryotic cytosolic chaperonin CCT is an essential ATP-dependent protein folding machine whose action is required for folding the cytoskeletal proteins actin and tubulin"
An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell.
  • The chaperone interactome study is useful context for CCT contacts but reports indirect TAP-tag interactions rather than a specific molecular activity.
    "It should be emphasized that the interactions presented are indirect TAP-tag based interactions and not direct binary interactions."
The social and structural architecture of the yeast protein interactome.
file:yeast/CCT3/CCT3-deep-research-falcon.md
Falcon deep research report for CCT3
  • The Falcon report was reviewed and synthesized into the CCT3 curation, including core-function framing, family/PANTHER context, and evidence limitations.

Suggested Questions for Experts

Q: Which yeast client proteins depend specifically on Cct3 apical-domain contacts rather than on generic TRiC/CCT chamber activity?

Suggested Experiments

Experiment: Profile client aggregation, solubility, and folding reporter behavior in conditional CCT3 mutants under permissive and restrictive conditions, with actin and tubulin reporters as controls.

Hypothesis: Cct3 contributes subunit-specific contacts for a subset of aggregation-prone or Q/N-rich clients.

Type: conditional mutant proteostasis profiling

📚 Additional Documentation

Deep Research Falcon

(CCT3-deep-research-falcon.md)

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gene_id: CCT3
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protein_description: 'RecName: Full=T-complex protein 1 subunit gamma; Short=TCP-1-gamma;
AltName: Full=CCT-gamma;'
gene_info: Name=CCT3; Synonyms=BIN2, TCP3; OrderedLocusNames=YJL014W; ORFNames=J1336;
organism_full: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
protein_family: Belongs to the TCP-1 chaperonin family. .
protein_domains: Chap_CCT_gamma. (IPR012719); Chaperone_TCP-1. (IPR017998); Chaperonin_TCP-1_CS.
(IPR002194); Cpn60/GroEL/TCP-1. (IPR002423); GroEL-like_apical_dom_sf. (IPR027409)
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Question

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.

Target Gene/Protein Identity (from UniProt):

  • UniProt Accession: P39077
  • Protein Description: RecName: Full=T-complex protein 1 subunit gamma; Short=TCP-1-gamma; AltName: Full=CCT-gamma;
  • Gene Information: Name=CCT3; Synonyms=BIN2, TCP3; OrderedLocusNames=YJL014W; ORFNames=J1336;
  • Organism (full): Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  • Protein Family: Belongs to the TCP-1 chaperonin family. .
  • Key Domains: Chap_CCT_gamma. (IPR012719); Chaperone_TCP-1. (IPR017998); Chaperonin_TCP-1_CS. (IPR002194); Cpn60/GroEL/TCP-1. (IPR002423); GroEL-like_apical_dom_sf. (IPR027409)

MANDATORY VERIFICATION STEPS:

  1. Check if the gene symbol "CCT3" matches the protein description above
  2. Verify the organism is correct: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  3. Check if protein family/domains align with what you find in literature
  4. If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'CCT3' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information

Research Target:

Please provide a comprehensive research report on the gene CCT3 (gene ID: CCT3, UniProt: P39077) in yeast.

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.

Output

Question: You are an expert researcher providing comprehensive, well-cited information.

Provide detailed information focusing on:
1. Key concepts and definitions with current understanding
2. Recent developments and latest research (prioritize 2023-2024 sources)
3. Current applications and real-world implementations
4. Expert opinions and analysis from authoritative sources
5. Relevant statistics and data from recent studies

Format as a comprehensive research report with proper citations. Include URLs and publication dates where available.
Always prioritize recent, authoritative sources and provide specific citations for all major claims.

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.

Target Gene/Protein Identity (from UniProt):

  • UniProt Accession: P39077
  • Protein Description: RecName: Full=T-complex protein 1 subunit gamma; Short=TCP-1-gamma; AltName: Full=CCT-gamma;
  • Gene Information: Name=CCT3; Synonyms=BIN2, TCP3; OrderedLocusNames=YJL014W; ORFNames=J1336;
  • Organism (full): Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  • Protein Family: Belongs to the TCP-1 chaperonin family. .
  • Key Domains: Chap_CCT_gamma. (IPR012719); Chaperone_TCP-1. (IPR017998); Chaperonin_TCP-1_CS. (IPR002194); Cpn60/GroEL/TCP-1. (IPR002423); GroEL-like_apical_dom_sf. (IPR027409)

MANDATORY VERIFICATION STEPS:

  1. Check if the gene symbol "CCT3" matches the protein description above
  2. Verify the organism is correct: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  3. Check if protein family/domains align with what you find in literature
  4. If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'CCT3' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information

Research Target:

Please provide a comprehensive research report on the gene CCT3 (gene ID: CCT3, UniProt: P39077) in yeast.

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.

Comprehensive research report: Saccharomyces cerevisiae CCT3 (UniProt P39077; ORF YJL014W) — functional annotation

Executive summary

CCT3 encodes T-complex protein 1 subunit gamma (CCTγ; TRiC/CCT subunit 3), one of eight essential subunits comprising the eukaryotic cytosolic group II chaperonin CCT/TRiC. The CCT/TRiC complex is a double-ring ATP-driven folding machine that is required for proteostasis, including folding of key cytoskeletal proteins such as actin and tubulin. Yeast-specific evidence indicates that CCT3 has detectable subunit-specific client preferences, particularly affecting Q/N-rich proteins and P-body-associated proteins, and that perturbing CCT3 function produces broad stress sensitivities including ethanol and cell-wall integrity–associated phenotypes. (grantham2020themolecularchaperone pages 1-2, nadlerholly2012interactionsofsubunit pages 2-2, narayanan2016defectsinprotein pages 4-6)

1) Gene/protein identity verification (critical disambiguation)

The literature summarized here pertains to Saccharomyces cerevisiae (S288C) CCT3/YJL014W, encoding a subunit of the CCT/TRiC chaperonin complex. This is consistent with the UniProt description for P39077 as a TCP-1 chaperonin family member (CCTγ) and with yeast genetics studies that explicitly mutate CCT3 and assay phenotypes in yeast (e.g., CCT3 D91E; cct3-1). (nadlerholly2012interactionsofsubunit pages 2-2, narayanan2016defectsinprotein pages 2-4)

2) Key concepts and definitions (current understanding)

2.1 What is CCT/TRiC, and where does CCT3 fit?

CCT/TRiC (chaperonin-containing TCP-1; tailless complex polypeptide 1 ring complex) is a eukaryotic ATP-dependent chaperonin. It is an obligate hetero-oligomer composed of two rings, each containing eight distinct subunits (commonly denoted CCT1–CCT8 or α–θ), generating a central chamber where client proteins fold. (grantham2020themolecularchaperone pages 1-2)

CCT3 is one of these eight distinct subunits. Structural/mechanistic work synthesized in the literature places CCT3 as part of a subunit pairing/grouping (e.g., CCT1–CCT3) and within a lower ATP-affinity hemisphere of the ring (CCT3/6/7/8) relative to a higher-affinity hemisphere (CCT1/2/4/5), implying subunit-specialized contributions to the ATPase cycle. (kelly2020structuralandfunctional pages 42-48)

2.2 Mechanism of action: ATP-driven conformational cycle and substrate folding

CCT/TRiC operates via a coordinated ATPase-driven conformational cycle: substrate binds to apical domains, ATP binding/hydrolysis drives ring closure and encapsulation, and conformational changes promote folding. This general mechanism and architecture are described in authoritative reviews emphasizing the complex’s role as an essential proteostasis component. (grantham2020themolecularchaperone pages 1-2, que2024theroleof pages 1-2)

A mechanistic quantitative detail highlighted in structural/functional synthesis is that, on average, ~4 subunits per ring are occupied under saturating ATP, consistent with asymmetric ATP usage across subunits and supporting the view that not all subunits contribute equivalently to nucleotide binding/hydrolysis at a given time. CCT3 is categorized among lower ATP-affinity subunits in this model. (kelly2020structuralandfunctional pages 42-48)

3) Primary biological function of yeast CCT3

3.1 Core function: proteostasis via folding/assembly of complex cytosolic proteins

CCT/TRiC is described as required for folding of the abundant cytoskeletal proteins actin and tubulin, which are central to microfilament and microtubule assembly. These clients are repeatedly treated as key/obligate substrates of the complex in reviews and in yeast stress-phenotype work that links impaired folding to cytoskeleton-mediated stress adaptation. (grantham2020themolecularchaperone pages 1-2, narayanan2016defectsinprotein pages 4-6)

3.2 Subunit-specific client interactions: Q/N-rich proteins and P-body biology (yeast-specific)

A yeast-focused PNAS study directly probed subunit specialization using ATP-site mutations in CCT3 vs CCT6 and high-throughput microscopy. A CCT3 mutant (D91E; “MA3”) produced a strong, specific phenotype: dramatic accumulation of P-bodies, with multiple known P-body proteins forming prominent cytoplasmic puncta that colocalize with an established P-body marker. (nadlerholly2012interactionsofsubunit pages 2-2, nadlerholly2012interactionsofsubunit media 88c0bc6b)

Quantitatively, the same study reported that in MA3 relative to wild type, 46 proteins increased and 18 decreased at P < 0.01, and that the screen involved ~5,100 GFP-tagged strains, supporting a large-scale systematic assessment of proteome-level changes in a CCT3-perturbed background. (nadlerholly2012interactionsofsubunit pages 2-2)

The authors further concluded that subunit CCT3 shows a stronger in vivo interaction with Q/N-rich proteins than CCT6 and proposed that CCT3 contains features compatible with binding Q/N-rich segments, linking CCT3 activity to proteostasis of aggregation-prone regions commonly enriched in P-body components. (nadlerholly2012interactionsofsubunit pages 2-2, nadlerholly2012interactionsofsubunit pages 4-5)

4) Subcellular localization and where CCT3 carries out its function

4.1 Cytosolic role (dominant/established)

CCT/TRiC is classically treated as a cytosolic chaperonin that acts on cytosolic proteins, consistent with its canonical substrates (actin/tubulin) and broad role in folding newly synthesized proteins. (grantham2020themolecularchaperone pages 1-2, que2024theroleof pages 1-2)

4.2 Nuclear roles (emerging, yeast-relevant)

A 2024 yeast preprint reports that TRiC/CCT governs RNA polymerase II activity in the nucleus to support RNA homeostasis, indicating that in yeast the complex has functionally relevant nuclear activity beyond canonical cytosolic folding. The study used yeast TRiC purification and nuclear extract transcription assays (including 100 ng immobilized DNA template and 100 µg nuclear extract), supporting mechanistic investigation of nuclear transcription outputs in a TRiC-compromised condition (cct1-2). Although this is not CCT3-specific, it is a recent yeast development expanding the functional landscape in which CCT subunits operate. (gvozdenov2024triccctchaperoningoverns pages 30-33)

5) Phenotypes and essentiality

5.1 Essentiality

CCT/TRiC subunits are encoded by essential yeast genes, consistent with the central role of TRiC/CCT in folding core cellular proteins and maintaining homeostasis. (grantham2020themolecularchaperone pages 1-2)

5.2 Stress tolerance, ethanol tolerance, and cell wall integrity phenotypes (cct3 alleles)

A focused phenotyping study of yeast folding-machinery mutants reports that the cct3-1 mutant shows sensitivity to diverse stressors. In the authors’ categorical scoring, cct3-1 was sensitive/supersensitive across multiple conditions including ethanol, NaCl, DTT, arsenate, H2O2, SDS (cell-wall integrity proxy), and methanol, and was supersensitive to TBZ (a microtubule/actin-related stressor used in the study). (narayanan2016defectsinprotein pages 2-4)

The same work reports ethanol-specific findings: cct3-1 is noted as sensitive at 3% ethanol, and while all tested cct mutants failed to grow at 8% ethanol, many recovered tolerance to 6% ethanol by 48 h—with cct1 and cct3 mutants highlighted as exceptions in this recovery pattern. The authors also used Congo Red and zymolyase sensitivity and SEM morphology changes to support that defects in the folding machinery correlate with cell wall integrity defects, providing a plausible mechanistic link between CCT3 impairment, actin/cytoskeletal dysfunction, and cell-wall biosynthetic/maintenance pathways. (narayanan2016defectsinprotein pages 4-6)

5.3 CCT3 perturbation and RNA granules/P-bodies

The yeast CCT3 D91E mutant (MA3) triggers prominent P-body formation and altered abundance/localization of multiple P-body components; this is consistent with the hypothesis that CCT3 function supports folding/stability of specific aggregation-prone/QN-rich components that influence ribonucleoprotein granule formation. (nadlerholly2012interactionsofsubunit pages 2-2, nadlerholly2012interactionsofsubunit media 88c0bc6b)

6) Signaling/biochemical pathways and process-level placement

6.1 Proteostasis network positioning

CCT/TRiC is positioned as a major node in cellular proteostasis, supporting folding and suppressing aggregation, and it participates in protein biogenesis processes that intersect with translation. (grantham2020themolecularchaperone pages 1-2, que2024theroleof pages 1-2)

6.2 Translation coupling (recent synthesis)

A 2024 review synthesizes evidence that CCT/TRiC has multiple roles related to translation elongation, including interacting with emerging peptides to protect them from aggregation/degradation and facilitating proper folding programs during protein synthesis. This provides a modern conceptual framework for interpreting CCT3 function as part of a chaperonin machine integrated with translation and nascent-chain quality control (even when the review is not yeast-exclusive). (que2024theroleof pages 1-2)

7) Recent developments (prioritizing 2023–2024)

7.1 2024: CCT/TRiC in translation elongation (review)

Que et al. (Heliyon; available online 1 Apr 2024) frame CCT/TRiC as an essential molecular chaperone in the elongation phase of eukaryotic translation and summarize how it contributes to maintaining balance among synthesis, folding, assembly, and degradation—an updated synthesis of field consensus relevant to interpreting yeast CCT3 phenotypes in conditions that stress protein biogenesis. URL: https://doi.org/10.1016/j.heliyon.2024.e29029 (que2024theroleof pages 1-2)

7.2 2024: Nuclear TRiC activity in yeast transcription (preprint)

Gvozdenov et al. (bioRxiv; posted 26 Sep 2024) report that TRiC/CCT supports RNA polymerase II activity in the yeast nucleus, expanding the apparent functional reach of TRiC beyond canonical cytosolic folding and suggesting that TRiC perturbation can impact RNA homeostasis. URL: https://doi.org/10.1101/2024.09.26.615188 (gvozdenov2024triccctchaperoningoverns pages 30-33)

7.3 2023: Subunit-resolved substrate contacts (CCT3 involvement)

A 2023 structural study of TRiC-mediated tubulin folding reports that near-natively folded tubulin engages mainly with the CCT3/6/8 subunits through electrostatic/hydrophilic interactions in the closed chamber (in a human TRiC system). While not yeast-specific, this provides current mechanistic support for why CCT3 subunits can contribute specialized binding surfaces for key cytoskeletal clients—consistent with long-standing yeast genetics emphasizing actin/tubulin dependence on TRiC. URL: https://doi.org/10.1038/s42003-023-04915-x (gvozdenov2024triccctchaperoningoverns pages 33-36)

8) Current applications and real-world implementations

8.1 Structural biology tool development (yeast CCT3 as an engineering handle)

A practical implementation in yeast structural biology is the use of CCT3 as a subunit for internal tagging: Zang et al. (Scientific Reports; Feb 2018) describe a yeast internal-subunit eGFP labeling strategy (YISEL) and note purification of yeast CCT via an internal tag in the CCT3/γ subunit to enable cryo-EM subunit assignment. This is a concrete experimental application leveraging the endogenous yeast CCT3 locus. URL: https://doi.org/10.1038/s41598-017-18962-y (zang2018developmentofa pages 7-8)

8.2 Industrially relevant stress tolerance phenotyping

Ethanol tolerance and cell wall integrity are central to industrial yeast performance. The observation that cct3-1 mutants show ethanol sensitivity and cell-wall-related phenotypes suggests that CCT3/TRiC integrity is a factor to consider in strain robustness under high-ethanol fermentations or other envelope-stressing conditions (noting that the cited study is phenotyping-focused rather than an industrial deployment report). URL: https://doi.org/10.1007/s00284-016-1024-x (narayanan2016defectsinprotein pages 4-6)

9) Expert opinions and analysis (authoritative interpretation of evidence)

  1. Subunit specialization is biologically meaningful. The yeast CCT3 D91E study demonstrates that perturbing different TRiC subunits can yield qualitatively different cellular phenotypes, supporting the view that TRiC is not merely an eightfold-redundant machine but has subunit-specific substrate interfaces and cellular roles. (nadlerholly2012interactionsofsubunit pages 2-2)
  2. CCT3 links folding capacity to RNP granule dynamics. The strong P-body phenotype in CCT3 mutant yeast provides a plausible mechanistic bridge between proteostasis and post-transcriptional RNA regulation, aligning with 2024 yeast work implicating TRiC in nuclear RNA homeostasis (though via a different experimental angle). (nadlerholly2012interactionsofsubunit pages 2-2, gvozdenov2024triccctchaperoningoverns pages 30-33)
  3. Stress phenotypes likely reflect multiple downstream failures. Broad cct3-1 sensitivity (ethanol, SDS, oxidative/reductive stressors) is consistent with a folding-factor deficit affecting cytoskeletal organization, membrane/cell-wall maintenance, and generalized proteostasis under stress. The cell-wall integrity assays (SDS, Congo Red, zymolyase) provide process-level evidence that CCT perturbation couples protein folding to envelope robustness. (narayanan2016defectsinprotein pages 2-4, narayanan2016defectsinprotein pages 4-6)

10) Key statistics and data points (from cited studies)

  • TRiC/CCT architecture: 2 rings × 8 distinct subunits (16 total subunits per complex). (grantham2020themolecularchaperone pages 1-2)
  • ATP occupancy asymmetry (model/synthesis): ~4 subunits per ring occupied under saturating ATP; CCT3 in low ATP-affinity hemisphere. (kelly2020structuralandfunctional pages 42-48)
  • Yeast CCT3 mutant proteome changes: 46 upregulated, 18 downregulated proteins in CCT3 D91E (MA3) vs wild type at P < 0.01; screen size ~5,100 GFP-tagged strains. (nadlerholly2012interactionsofsubunit pages 2-2)
  • Ethanol tolerance phenotypes: cct3-1 sensitive at 3% ethanol; all cct mutants fail at 8% ethanol in the cited study; differential recovery to 6% by 48 h reported with cct1/cct3 as exceptions. (narayanan2016defectsinprotein pages 4-6)
  • Nuclear transcription assay conditions in yeast TRiC study (supporting methods transparency): 100 ng DNA template and 100 µg nuclear extract per reaction. (gvozdenov2024triccctchaperoningoverns pages 30-33)

Visual evidence (figure citations)

Microscopy and quantitative panels illustrating that CCT3 mutation (MA3) causes P-body accumulation and stronger Q/N-rich protein effects than a CCT6 mutant are shown in the retrieved figure crops from Nadler-Holly et al. (PNAS, 2012). (nadlerholly2012interactionsofsubunit media 88c0bc6b, nadlerholly2012interactionsofsubunit media 61c31059, nadlerholly2012interactionsofsubunit media 27997266)

Evidence-backed annotation summary table

Aspect Key points Best supporting citations Key source URLs+publication dates
identity/synonyms • Verified target is Saccharomyces cerevisiae CCT3 / YJL014W, encoding the TRiC/CCT chaperonin subunit gamma (CCTγ). • CCT3 is one of the eight distinct paralogous subunits of the eukaryotic cytosolic chaperonin CCT/TRiC. • The literature also uses the CCT/TRiC-wide naming scheme CCT1–CCT8 / α–θ, so care is needed to avoid mixing with non-yeast CCT3 orthologs. (grantham2020themolecularchaperone pages 1-2, gvozdenov2024triccctchaperoningoverns pages 33-36, kelly2020structuralandfunctional pages 42-48) https://doi.org/10.3389/fgene.2020.00172 (Mar 2020); https://doi.org/10.1101/2024.09.26.615188 (Sep 26, 2024); https://doi.org/10.1073/pnas.1209277109 (Oct 2012)
complex • CCT3 functions as a subunit of the CCT/TRiC hetero-oligomer, a barrel-shaped chaperonin with two rings of eight distinct subunits each. • Each subunit occupies a defined position within the ring. • Structural work places CCT3 in the CCT1–CCT3 apical-domain pair and in the low-ATP-affinity hemisphere (CCT3/6/7/8). (grantham2020themolecularchaperone pages 1-2, kelly2020structuralandfunctional pages 42-48, zang2018developmentofa pages 7-8) https://doi.org/10.3389/fgene.2020.00172 (Mar 2020); https://doi.org/10.1038/s41598-017-18962-y (Feb 2018)
mechanism • CCT/TRiC is an ATP-dependent folding machine with substrate-binding apical domains and nucleotide-binding equatorial domains. • For CCT3 specifically, structural/functional characterization places it among the lower ATP-affinity subunits; under saturating ATP, an average of ~4 subunits per ring are occupied. • CCT3 contributes to the inter-ring interaction network via its N-terminus in models of ring closure. (grantham2020themolecularchaperone pages 1-2, kelly2020structuralandfunctional pages 42-48) https://doi.org/10.3389/fgene.2020.00172 (Mar 2020)
localization • The strongest supported localization for the yeast complex is the cytosol/cytoplasm, consistent with its role folding newly made cytosolic proteins. • Recent yeast work also supports a nuclear role for TRiC/CCT in RNA polymerase II activity and RNA homeostasis, though this was shown for the complex rather than CCT3 specifically. • Older cited background also notes reports of association with Golgi membranes, nuclear matrix, and heterochromatin for CCT/TRiC literature more broadly. (gvozdenov2024triccctchaperoningoverns pages 30-33, gvozdenov2024triccctchaperoningoverns pages 33-36, que2024theroleof pages 1-2) https://doi.org/10.1101/2024.09.26.615188 (Sep 26, 2024); https://doi.org/10.1016/j.heliyon.2024.e29029 (Apr 1, 2024)
substrates/clients • Canonical CCT/TRiC clients include actin and tubulin, described as major/obligate substrates of the complex. • A CCT3-specific yeast study found stronger interaction of CCT3 than CCT6 with Q/N-rich proteins, especially proteins linked to P-bodies. • In the CCT3 mutant screen, 46 proteins increased and 18 decreased relative to wild type, and 8 of 9 most-changed proteins had physical/genetic interactions with Q/N-rich proteins. (nadlerholly2012interactionsofsubunit pages 2-2, grantham2020themolecularchaperone pages 1-2, nadlerholly2012interactionsofsubunit pages 4-5, nadlerholly2012interactionsofsubunit pages 5-6) https://doi.org/10.1073/pnas.1209277109 (Oct 2012); https://doi.org/10.3389/fgene.2020.00172 (Mar 2020)
phenotypes • Yeast CCT genes are essential, and the review literature states CCT subunits are encoded by essential yeast genes. • A CCT3 ATP-site mutant (D91E/MA3) caused strong P-body accumulation; several canonical P-body proteins formed prominent puncta, and the screen covered ~5,100 GFP-tagged strains. • In stress-phenotype work, cct3-1 showed sensitivity to multiple stressors including ethanol, NaCl, DTT, arsenate, H2O2, SDS, methanol, and was reported as supersensitive to TBZ; cct3-1 was sensitive at 3% ethanol, and cct3 mutants were among strains not recovering tolerance like most others by 48 h. (nadlerholly2012interactionsofsubunit pages 2-2, grantham2020themolecularchaperone pages 1-2, narayanan2016defectsinprotein pages 2-4, narayanan2016defectsinprotein pages 4-6) https://doi.org/10.1073/pnas.1209277109 (Oct 2012); https://doi.org/10.1007/s00284-016-1024-x (Mar 2016); https://doi.org/10.3389/fgene.2020.00172 (Mar 2020)
recent 2023-2024 developments • A 2024 review emphasizes CCT/TRiC as an important regulator of translation elongation/protein synthesis coupling. • A 2023 structural study on TRiC-mediated tubulin folding captured a near-native folding intermediate engaging mainly CCT3/6/8 subunits in the closed chamber, supporting subunit-specialized substrate contacts. • A 2024 yeast preprint reports nuclear TRiC/CCT support of RNA polymerase II activity and RNA homeostasis. (gvozdenov2024triccctchaperoningoverns pages 30-33, que2024theroleof pages 1-2) https://doi.org/10.1016/j.heliyon.2024.e29029 (Apr 1, 2024); https://doi.org/10.1038/s42003-023-04915-x (May 2023); https://doi.org/10.1101/2024.09.26.615188 (Sep 26, 2024)
applications • Yeast CCT3 has been used experimentally as an anchor for internal subunit eGFP labeling to map TRiC/CCT subunit arrangement in cryo-EM studies. • CCT/TRiC is used as a model system for studying proteostasis, aggregation control, and folding of complex proteins. • Stress-sensitive yeast cct mutants, including cct3-1, provide practical models for probing cell wall integrity and ethanol tolerance relevant to industrial/biotechnology contexts. (zang2018developmentofa pages 7-8, grantham2020themolecularchaperone pages 1-2, narayanan2016defectsinprotein pages 4-6) https://doi.org/10.1038/s41598-017-18962-y (Feb 2018); https://doi.org/10.3389/fgene.2020.00172 (Mar 2020); https://doi.org/10.1007/s00284-016-1024-x (Mar 2016)

Table: This table summarizes the evidence-supported functional annotation of Saccharomyces cerevisiae CCT3/YJL014W, including complex membership, mechanism, localization, substrates, phenotypes, and recent developments. It is useful as a compact reference anchored to specific context IDs and source URLs.

Limitations of the current evidence set

  • The most detailed yeast CCT3 functional specificity evidence in the retrieved set is from 2012 (PNAS). While still high-quality, yeast CCT3-specific primary literature in 2023–2024 was not directly retrieved here; recent work largely focuses on TRiC/CCT more generally or in other organisms, and should be integrated cautiously when making yeast-subunit-specific claims. (nadlerholly2012interactionsofsubunit pages 2-2, que2024theroleof pages 1-2)

Key sources (URLs and publication dates)

  • Nadler-Holly et al. 2012-10. PNAS. “Interactions of subunit CCT3 in the yeast chaperonin CCT/TRiC with Q/N-rich proteins…” https://doi.org/10.1073/pnas.1209277109 (nadlerholly2012interactionsofsubunit pages 2-2)
  • Narayanan et al. 2016-03. Current Microbiology. “Defects in Protein Folding Machinery Affect Cell Wall Integrity and Reduce Ethanol Tolerance…” https://doi.org/10.1007/s00284-016-1024-x (narayanan2016defectsinprotein pages 4-6)
  • Grantham 2020-03. Frontiers in Genetics. “The Molecular Chaperone CCT/TRiC…” https://doi.org/10.3389/fgene.2020.00172 (grantham2020themolecularchaperone pages 1-2)
  • Zang et al. 2018-02. Scientific Reports. “Development of a yeast internal-subunit eGFP labeling strategy…” https://doi.org/10.1038/s41598-017-18962-y (zang2018developmentofa pages 7-8)
  • Que et al. 2024-04-01 (online). Heliyon. “The role of molecular chaperone CCT/TRiC in translation elongation…” https://doi.org/10.1016/j.heliyon.2024.e29029 (que2024theroleof pages 1-2)
  • Gvozdenov et al. 2024-09-26 (posted). bioRxiv. “TRiC/CCT Chaperonin Governs RNA Polymerase II Activity in the Nucleus…” https://doi.org/10.1101/2024.09.26.615188 (gvozdenov2024triccctchaperoningoverns pages 30-33)

References

  1. (grantham2020themolecularchaperone pages 1-2): Julie Grantham. The molecular chaperone cct/tric: an essential component of proteostasis and a potential modulator of protein aggregation. Frontiers in Genetics, Mar 2020. URL: https://doi.org/10.3389/fgene.2020.00172, doi:10.3389/fgene.2020.00172. This article has 139 citations and is from a peer-reviewed journal.

  2. (nadlerholly2012interactionsofsubunit pages 2-2): Michal Nadler-Holly, Michal Breker, Ranit Gruber, Ariel Azia, Melissa Gymrek, Miriam Eisenstein, Keith R. Willison, Maya Schuldiner, and Amnon Horovitz. Interactions of subunit cct3 in the yeast chaperonin cct/tric with q/n-rich proteins revealed by high-throughput microscopy analysis. Proceedings of the National Academy of Sciences, 109:18833-18838, Oct 2012. URL: https://doi.org/10.1073/pnas.1209277109, doi:10.1073/pnas.1209277109. This article has 52 citations and is from a highest quality peer-reviewed journal.

  3. (narayanan2016defectsinprotein pages 4-6): Aswathy Narayanan, Dileep Pullepu, Praveen Kumar Reddy, Wasim Uddin, and M. Anaul Kabir. Defects in protein folding machinery affect cell wall integrity and reduce ethanol tolerance in s. cerevisiae. Current Microbiology, 73:38-45, Mar 2016. URL: https://doi.org/10.1007/s00284-016-1024-x, doi:10.1007/s00284-016-1024-x. This article has 7 citations and is from a peer-reviewed journal.

  4. (narayanan2016defectsinprotein pages 2-4): Aswathy Narayanan, Dileep Pullepu, Praveen Kumar Reddy, Wasim Uddin, and M. Anaul Kabir. Defects in protein folding machinery affect cell wall integrity and reduce ethanol tolerance in s. cerevisiae. Current Microbiology, 73:38-45, Mar 2016. URL: https://doi.org/10.1007/s00284-016-1024-x, doi:10.1007/s00284-016-1024-x. This article has 7 citations and is from a peer-reviewed journal.

  5. (kelly2020structuralandfunctional pages 42-48): J Kelly. Structural and functional characterisation of the group ii chaperonin cct/tric. Unknown journal, 2020.

  6. (que2024theroleof pages 1-2): Yueyue Que, Yudan Qiu, Zheyu Ding, Shanshan Zhang, Rong Wei, Jianing Xia, and Yingying Lin. The role of molecular chaperone cct/tric in translation elongation: a literature review. Heliyon, 10:e29029, Apr 2024. URL: https://doi.org/10.1016/j.heliyon.2024.e29029, doi:10.1016/j.heliyon.2024.e29029. This article has 12 citations.

  7. (nadlerholly2012interactionsofsubunit media 88c0bc6b): Michal Nadler-Holly, Michal Breker, Ranit Gruber, Ariel Azia, Melissa Gymrek, Miriam Eisenstein, Keith R. Willison, Maya Schuldiner, and Amnon Horovitz. Interactions of subunit cct3 in the yeast chaperonin cct/tric with q/n-rich proteins revealed by high-throughput microscopy analysis. Proceedings of the National Academy of Sciences, 109:18833-18838, Oct 2012. URL: https://doi.org/10.1073/pnas.1209277109, doi:10.1073/pnas.1209277109. This article has 52 citations and is from a highest quality peer-reviewed journal.

  8. (nadlerholly2012interactionsofsubunit pages 4-5): Michal Nadler-Holly, Michal Breker, Ranit Gruber, Ariel Azia, Melissa Gymrek, Miriam Eisenstein, Keith R. Willison, Maya Schuldiner, and Amnon Horovitz. Interactions of subunit cct3 in the yeast chaperonin cct/tric with q/n-rich proteins revealed by high-throughput microscopy analysis. Proceedings of the National Academy of Sciences, 109:18833-18838, Oct 2012. URL: https://doi.org/10.1073/pnas.1209277109, doi:10.1073/pnas.1209277109. This article has 52 citations and is from a highest quality peer-reviewed journal.

  9. (gvozdenov2024triccctchaperoningoverns pages 30-33): Zlata Gvozdenov, Audrey Yi Tyan Peng, Anusmita Biswas, Zeno Barcutean, Daniel Gestaut, Judith Frydman, Kevin Struhl, and Brian C. Freeman. Tric/cct chaperonin governs rna polymerase ii activity in the nucleus to support rna homeostasis. bioRxiv, Sep 2024. URL: https://doi.org/10.1101/2024.09.26.615188, doi:10.1101/2024.09.26.615188. This article has 3 citations.

  10. (gvozdenov2024triccctchaperoningoverns pages 33-36): Zlata Gvozdenov, Audrey Yi Tyan Peng, Anusmita Biswas, Zeno Barcutean, Daniel Gestaut, Judith Frydman, Kevin Struhl, and Brian C. Freeman. Tric/cct chaperonin governs rna polymerase ii activity in the nucleus to support rna homeostasis. bioRxiv, Sep 2024. URL: https://doi.org/10.1101/2024.09.26.615188, doi:10.1101/2024.09.26.615188. This article has 3 citations.

  11. (zang2018developmentofa pages 7-8): Yunxiang Zang, Huping Wang, Zhicheng Cui, Mingliang Jin, Caixuan Liu, Wenyu Han, Yanxing Wang, and Yao Cong. Development of a yeast internal-subunit egfp labeling strategy and its application in subunit identification in eukaryotic group ii chaperonin tric/cct. Scientific Reports, Feb 2018. URL: https://doi.org/10.1038/s41598-017-18962-y, doi:10.1038/s41598-017-18962-y. This article has 22 citations and is from a peer-reviewed journal.

  12. (nadlerholly2012interactionsofsubunit media 61c31059): Michal Nadler-Holly, Michal Breker, Ranit Gruber, Ariel Azia, Melissa Gymrek, Miriam Eisenstein, Keith R. Willison, Maya Schuldiner, and Amnon Horovitz. Interactions of subunit cct3 in the yeast chaperonin cct/tric with q/n-rich proteins revealed by high-throughput microscopy analysis. Proceedings of the National Academy of Sciences, 109:18833-18838, Oct 2012. URL: https://doi.org/10.1073/pnas.1209277109, doi:10.1073/pnas.1209277109. This article has 52 citations and is from a highest quality peer-reviewed journal.

  13. (nadlerholly2012interactionsofsubunit media 27997266): Michal Nadler-Holly, Michal Breker, Ranit Gruber, Ariel Azia, Melissa Gymrek, Miriam Eisenstein, Keith R. Willison, Maya Schuldiner, and Amnon Horovitz. Interactions of subunit cct3 in the yeast chaperonin cct/tric with q/n-rich proteins revealed by high-throughput microscopy analysis. Proceedings of the National Academy of Sciences, 109:18833-18838, Oct 2012. URL: https://doi.org/10.1073/pnas.1209277109, doi:10.1073/pnas.1209277109. This article has 52 citations and is from a highest quality peer-reviewed journal.

  14. (nadlerholly2012interactionsofsubunit pages 5-6): Michal Nadler-Holly, Michal Breker, Ranit Gruber, Ariel Azia, Melissa Gymrek, Miriam Eisenstein, Keith R. Willison, Maya Schuldiner, and Amnon Horovitz. Interactions of subunit cct3 in the yeast chaperonin cct/tric with q/n-rich proteins revealed by high-throughput microscopy analysis. Proceedings of the National Academy of Sciences, 109:18833-18838, Oct 2012. URL: https://doi.org/10.1073/pnas.1209277109, doi:10.1073/pnas.1209277109. This article has 52 citations and is from a highest quality peer-reviewed journal.

Citations

  1. grantham2020themolecularchaperone pages 1-2
  2. kelly2020structuralandfunctional pages 42-48
  3. nadlerholly2012interactionsofsubunit pages 2-2
  4. gvozdenov2024triccctchaperoningoverns pages 30-33
  5. narayanan2016defectsinprotein pages 2-4
  6. narayanan2016defectsinprotein pages 4-6
  7. que2024theroleof pages 1-2
  8. gvozdenov2024triccctchaperoningoverns pages 33-36
  9. zang2018developmentofa pages 7-8
  10. nadlerholly2012interactionsofsubunit pages 4-5
  11. nadlerholly2012interactionsofsubunit pages 5-6
  12. https://doi.org/10.1016/j.heliyon.2024.e29029
  13. https://doi.org/10.1101/2024.09.26.615188
  14. https://doi.org/10.1038/s42003-023-04915-x
  15. https://doi.org/10.1038/s41598-017-18962-y
  16. https://doi.org/10.1007/s00284-016-1024-x
  17. https://doi.org/10.3389/fgene.2020.00172
  18. https://doi.org/10.1073/pnas.1209277109
  19. https://doi.org/10.3389/fgene.2020.00172,
  20. https://doi.org/10.1073/pnas.1209277109,
  21. https://doi.org/10.1007/s00284-016-1024-x,
  22. https://doi.org/10.1016/j.heliyon.2024.e29029,
  23. https://doi.org/10.1101/2024.09.26.615188,
  24. https://doi.org/10.1038/s41598-017-18962-y,

📄 View Raw YAML

id: P39077
gene_symbol: CCT3
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:559292
  label: Saccharomyces cerevisiae
description: >-
  CCT3 encodes the gamma subunit of the cytosolic group II chaperonin TRiC/CCT. As one of eight obligate
  paralogous subunits in each ring, Cct3 contributes ATPase and substrate-contact surfaces to the hetero-oligomeric
  folding chamber that matures actin, tubulin, and other cytosolic clients. Its curated core function
  is complex-level ATP-dependent protein folding, not nonspecific protein binding.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000043
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
  findings: []
- id: GO_REF:0000044
  title: >-
    Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied
    by conservative changes to GO terms applied by UniProt
  findings: []
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:15704212
  title: Physiological effects of unassembled chaperonin Cct subunits in the yeast Saccharomyces cerevisiae.
  findings:
  - statement: Yeast CCT is a double-ring complex with a stoichiometric set of eight distinct Cct subunits.
    supporting_text: >-
      Eukaryotic chaperonins, the Cct complexes, are assembled into two rings, each of which is composed
      of a stoichiometric array of eight different subunits
- id: PMID:16762366
  title: >-
    Quantitative actin folding reactions using yeast CCT purified via an internal tag in the CCT3/gamma
    subunit.
  findings:
  - statement: >-
      Purified yeast CCT, tagged through CCT3, catalyzes ATP-dependent actin folding; this supports protein-folding
      and chaperonin activity annotations for CCT3 as a TRiC/CCT subunit.
    supporting_text: >-
      The eukaryotic cytosolic chaperonin CCT is an essential ATP-dependent protein folding machine whose
      action is required for folding the cytoskeletal proteins actin and tubulin
- id: PMID:19536198
  title: >-
    An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding
    pathways in the cell.
  findings:
  - statement: >-
      The chaperone interactome study is useful context for CCT contacts but reports indirect TAP-tag
      interactions rather than a specific molecular activity.
    supporting_text: >-
      It should be emphasized that the interactions presented are indirect TAP-tag based interactions
      and not direct binary interactions.
- id: PMID:37968396
  title: The social and structural architecture of the yeast protein interactome.
  findings: []
- id: file:yeast/CCT3/CCT3-deep-research-falcon.md
  title: Falcon deep research report for CCT3
  findings:
  - statement: >-
      The Falcon report was reviewed and synthesized into the CCT3 curation, including core-function framing,
      family/PANTHER context, and evidence limitations.
existing_annotations:
- term:
    id: GO:0006457
    label: protein folding
  qualifier: involved_in
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      CCT3 participates in protein folding as an obligate subunit of TRiC/CCT, the cytosolic chaperonin
      that folds actin, tubulin, and other clients.
    action: ACCEPT
    reason: >-
      Protein folding is the correct biological-process context for the chaperonin complex, supported
      by direct yeast CCT actin-folding assays and PANTHER/InterPro family evidence.
    supported_by:
    - reference_id: file:yeast/CCT3/CCT3-deep-research-falcon.md
      supporting_text: The CCT/TRiC complex is a double-ring ATP-driven folding machine
- term:
    id: GO:0005832
    label: chaperonin-containing T-complex
  qualifier: part_of
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: CCT3 is a named subunit of the chaperonin-containing T-complex.
    action: ACCEPT
    reason: >-
      Complex membership is central to the gene product function and is supported by yeast CCT complex
      literature and family evidence.
- term:
    id: GO:0051082
    label: unfolded protein binding
  qualifier: enables
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      unfolded protein binding reflects substrate engagement by TRiC/CCT, but it is less informative than
      the ATP-dependent folding chaperone function of the complex.
    action: MODIFY
    reason: >-
      Replace generic substrate-binding language with the specific chaperonin activity supported by yeast
      CCT actin-folding assays and domain evidence.
    proposed_replacement_terms:
    - id: GO:0140662
      label: ATP-dependent protein folding chaperone
- term:
    id: GO:0000166
    label: nucleotide binding
  qualifier: enables
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      nucleotide binding is a true but overly broad family/keyword annotation for CCT3; ATP binding, ATP
      hydrolysis, and ATP-dependent chaperone annotations capture the specific chemistry.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Generic nucleotide binding does not add useful functional information beyond the more specific ATP-related
      chaperonin annotations already present.
- term:
    id: GO:0005524
    label: ATP binding
  qualifier: enables
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      CCT3 contains a conserved chaperonin ATP-binding site, but ATP binding alone is a domain property
      rather than the core biological function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Keep as a valid supporting molecular property of the CCT ATPase cycle, while treating ATP hydrolysis
      and complex-level protein folding as the core function.
- term:
    id: GO:0005737
    label: cytoplasm
  qualifier: located_in
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: CCT3 functions as part of the cytosolic TRiC/CCT chaperonin.
    action: ACCEPT
    reason: Cytoplasm is the established location of the CCT/TRiC folding machine.
- term:
    id: GO:0005832
    label: chaperonin-containing T-complex
  qualifier: part_of
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: CCT3 is a named subunit of the chaperonin-containing T-complex.
    action: ACCEPT
    reason: >-
      Complex membership is central to the gene product function and is supported by yeast CCT complex
      literature and family evidence.
- term:
    id: GO:0006457
    label: protein folding
  qualifier: involved_in
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      CCT3 participates in protein folding as an obligate subunit of TRiC/CCT, the cytosolic chaperonin
      that folds actin, tubulin, and other clients.
    action: ACCEPT
    reason: >-
      Protein folding is the correct biological-process context for the chaperonin complex, supported
      by direct yeast CCT actin-folding assays and PANTHER/InterPro family evidence.
- term:
    id: GO:0016887
    label: ATP hydrolysis activity
  qualifier: enables
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      CCT3 is a TCP-1/CCT chaperonin subunit with conserved ATPase machinery that powers TRiC/CCT conformational
      cycling.
    action: ACCEPT
    reason: >-
      ATP hydrolysis is a defensible subunit-level molecular function for CCT family members and is directly
      tied to the chaperonin folding cycle.
- term:
    id: GO:0051082
    label: unfolded protein binding
  qualifier: enables
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      unfolded protein binding reflects substrate engagement by TRiC/CCT, but it is less informative than
      the ATP-dependent folding chaperone function of the complex.
    action: MODIFY
    reason: >-
      Replace generic substrate-binding language with the specific chaperonin activity supported by yeast
      CCT actin-folding assays and domain evidence.
    proposed_replacement_terms:
    - id: GO:0140662
      label: ATP-dependent protein folding chaperone
- term:
    id: GO:0140662
    label: ATP-dependent protein folding chaperone
  qualifier: enables
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: CCT3 is an obligate subunit of the ATP-dependent TRiC/CCT folding machine.
    action: ACCEPT
    reason: >-
      The term is appropriate as a complex-level chaperonin function; in the synthesized core function
      it is modeled as a contributed-to molecular function rather than a standalone activity of an isolated
      subunit.
    supported_by:
    - reference_id: PMID:16762366
      supporting_text: >-
        The eukaryotic cytosolic chaperonin CCT is an essential ATP-dependent protein folding machine
        whose action is required for folding the cytoskeletal proteins actin and tubulin
      reference_section_type: ABSTRACT
- term:
    id: GO:0005515
    label: protein binding
  qualifier: enables
  evidence_type: IPI
  original_reference_id: PMID:19536198
  supporting_entities:
  - UniProtKB:P32324
  review:
    summary: >-
      protein binding is too generic for a CCT subunit and does not describe the chaperonin mechanism
      or substrate class.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Physical-interaction datasets are useful evidence context, but generic protein binding should not
      stand as a functional annotation when the specific TRiC/CCT chaperonin role is known.
    supported_by:
    - reference_id: PMID:19536198
      supporting_text: >-
        It should be emphasized that the interactions presented are indirect TAP-tag based interactions
        and not direct binary interactions.
- term:
    id: GO:0005515
    label: protein binding
  qualifier: enables
  evidence_type: IPI
  original_reference_id: PMID:37968396
  supporting_entities:
  - UniProtKB:P32324
  review:
    summary: >-
      protein binding is too generic for a CCT subunit and does not describe the chaperonin mechanism
      or substrate class.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Physical-interaction datasets are useful evidence context, but generic protein binding should not
      stand as a functional annotation when the specific TRiC/CCT chaperonin role is known.
- term:
    id: GO:0006457
    label: protein folding
  qualifier: involved_in
  evidence_type: IDA
  original_reference_id: PMID:16762366
  review:
    summary: >-
      CCT3 participates in protein folding as an obligate subunit of TRiC/CCT, the cytosolic chaperonin
      that folds actin, tubulin, and other clients.
    action: ACCEPT
    reason: >-
      Protein folding is the correct biological-process context for the chaperonin complex, supported
      by direct yeast CCT actin-folding assays and PANTHER/InterPro family evidence.
    supported_by:
    - reference_id: PMID:16762366
      supporting_text: >-
        The eukaryotic cytosolic chaperonin CCT is an essential ATP-dependent protein folding machine
        whose action is required for folding the cytoskeletal proteins actin and tubulin
      reference_section_type: ABSTRACT
- term:
    id: GO:0005832
    label: chaperonin-containing T-complex
  qualifier: part_of
  evidence_type: IPI
  original_reference_id: PMID:15704212
  supporting_entities:
  - SGD:S000002596
  review:
    summary: CCT3 is a named subunit of the chaperonin-containing T-complex.
    action: ACCEPT
    reason: >-
      Complex membership is central to the gene product function and is supported by yeast CCT complex
      literature and family evidence.
    supported_by:
    - reference_id: PMID:16762366
      supporting_text: >-
        The eukaryotic cytosolic chaperonin CCT is an essential ATP-dependent protein folding machine
        whose action is required for folding the cytoskeletal proteins actin and tubulin
      reference_section_type: ABSTRACT
- term:
    id: GO:0005832
    label: chaperonin-containing T-complex
  qualifier: part_of
  evidence_type: IDA
  original_reference_id: PMID:16762366
  review:
    summary: CCT3 is a named subunit of the chaperonin-containing T-complex.
    action: ACCEPT
    reason: >-
      Complex membership is central to the gene product function and is supported by yeast CCT complex
      literature and family evidence.
    supported_by:
    - reference_id: PMID:15704212
      supporting_text: >-
        Eukaryotic chaperonins, the Cct complexes, are assembled into two rings, each of which is composed
        of a stoichiometric array of eight different subunits
      reference_section_type: ABSTRACT
- term:
    id: GO:0051082
    label: unfolded protein binding
  qualifier: enables
  evidence_type: IDA
  original_reference_id: PMID:16762366
  review:
    summary: >-
      unfolded protein binding reflects substrate engagement by TRiC/CCT, but it is less informative than
      the ATP-dependent folding chaperone function of the complex.
    action: MODIFY
    reason: >-
      Replace generic substrate-binding language with the specific chaperonin activity supported by yeast
      CCT actin-folding assays and domain evidence.
    proposed_replacement_terms:
    - id: GO:0140662
      label: ATP-dependent protein folding chaperone
    supported_by:
    - reference_id: PMID:16762366
      supporting_text: >-
        The eukaryotic cytosolic chaperonin CCT is an essential ATP-dependent protein folding machine
        whose action is required for folding the cytoskeletal proteins actin and tubulin
      reference_section_type: ABSTRACT
core_functions:
- description: >-
    CCT3 is the gamma subunit of the cytosolic TRiC/CCT chaperonin. The subunit contributes ATPase and
    substrate-contact surfaces to the hetero-oligomeric double-ring complex, whose ATP-dependent conformational
    cycle folds actin, tubulin, and other cytosolic client proteins. The synthesized function is modeled
    as subunit ATP hydrolysis contributing to the complex-level ATP-dependent protein folding chaperone
    activity.
  molecular_function:
    id: GO:0016887
    label: ATP hydrolysis activity
  contributes_to_molecular_function:
    id: GO:0140662
    label: ATP-dependent protein folding chaperone
  directly_involved_in:
  - id: GO:0006457
    label: protein folding
  locations:
  - id: GO:0005737
    label: cytoplasm
  in_complex:
    id: GO:0005832
    label: chaperonin-containing T-complex
  supported_by:
  - reference_id: PMID:16762366
    supporting_text: >-
      The eukaryotic cytosolic chaperonin CCT is an essential ATP-dependent protein folding machine whose
      action is required for folding the cytoskeletal proteins actin and tubulin
    reference_section_type: ABSTRACT
  - reference_id: PMID:15704212
    supporting_text: >-
      Eukaryotic chaperonins, the Cct complexes, are assembled into two rings, each of which is composed
      of a stoichiometric array of eight different subunits
    reference_section_type: ABSTRACT
suggested_questions:
- question: >-
    Which yeast client proteins depend specifically on Cct3 apical-domain contacts rather than on generic
    TRiC/CCT chamber activity?
suggested_experiments:
- hypothesis: Cct3 contributes subunit-specific contacts for a subset of aggregation-prone or Q/N-rich
    clients.
  description: >-
    Profile client aggregation, solubility, and folding reporter behavior in conditional CCT3 mutants
    under permissive and restrictive conditions, with actin and tubulin reporters as controls.
  experiment_type: conditional mutant proteostasis profiling