TCP1 (also known as CCT1) encodes the alpha subunit of the chaperonin-containing T-complex (TRiC/CCT) in S. cerevisiae. TRiC/CCT is an essential, hetero-oligomeric, group II chaperonin composed of eight paralogous subunits (CCT1-8) arranged in two stacked rings of eight subunits each, forming a ~1 MDa complex. The complex functions as an ATP-dependent protein folding machine that assists the folding of actin, tubulin, and a small number of other substrates including WD40-repeat proteins. Each subunit contributes to the overall ATP-dependent protein folding chaperone activity of the complex; individual subunits do not independently fold substrates. TCP1/CCT1 is essential for viability and plays roles in mitotic spindle formation in yeast. The crystal structure of yeast CCT (PMID:21701561) reveals intrinsic asymmetry among the eight subunits, with each displaying unique configurations and substrate-binding properties.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0006457
protein folding
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: TCP1 is part of the TRiC/CCT complex that assists protein folding. IBA annotation is consistent with IDA evidence from PMID:16762366 demonstrating that purified yeast CCT catalyses actin folding in vitro.
Reason: Core biological process. The TRiC/CCT complex is an essential protein folding machine, and TCP1 is a required subunit. IBA is well supported by experimental data.
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
file:yeast/TCP1/TCP1-deep-research-falcon.md
TCP1/CCT1 encodes CCT1 (TCP-1; CCT-alpha), one of eight paralogous subunits that assemble into the eukaryotic cytosolic chaperonin TRiC/CCT.
|
|
GO:0005832
chaperonin-containing T-complex
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: TCP1 is the alpha subunit of the chaperonin-containing T-complex (TRiC/CCT). IBA is consistent with IDA and IPI evidence from PMID:16762366 and PMID:15704212.
Reason: Core complex membership. TCP1 is an integral, essential subunit of TRiC/CCT. Well supported by multiple experimental methods.
|
|
GO:0051082
unfolded protein binding
|
IBA
GO_REF:0000033 |
MODIFY |
Summary: GO:0051082 (unfolded protein binding) is proposed for obsoletion. TCP1, as a subunit of TRiC/CCT, does interact with unfolded substrates (actin, tubulin), but this occurs in the context of the ATP-dependent chaperonin folding cycle, not as a standalone binding function. The correct replacement is GO:0140662 (ATP-dependent protein folding chaperone), with the qualifier contributes_to since TCP1 is a subunit of the complex.
Reason: GO:0051082 is targeted for obsoletion. TCP1 binds unfolded proteins only as part of the TRiC/CCT complex's ATP-dependent folding cycle. The appropriate replacement is GO:0140662 (ATP-dependent protein folding chaperone). This IEA-level annotation via InterPro already exists for this gene.
Proposed replacements:
ATP-dependent protein folding chaperone
|
|
GO:0000166
nucleotide binding
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: TCP1 binds ATP as part of its chaperonin function. This is a parent term of ATP binding and is correct but general.
Reason: Correct. All TRiC/CCT subunits bind nucleotides (ATP/ADP). The more specific term ATP binding (GO:0005524) is also annotated. This broader IEA is acceptable.
|
|
GO:0005524
ATP binding
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: TCP1 binds ATP through its equatorial domain. Each CCT subunit has an ATP-binding site that is essential for the allosteric chaperonin cycle.
Reason: Correct and fundamental. ATP binding is essential for the TRiC/CCT folding mechanism. UniProt keywords confirm ATP-binding.
|
|
GO:0005737
cytoplasm
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: TCP1 is a cytoplasmic protein. UniProt subcellular location annotation confirms cytoplasmic localization.
Reason: Correct. TRiC/CCT is a cytoplasmic/cytosolic complex.
|
|
GO:0005832
chaperonin-containing T-complex
|
IEA
GO_REF:0000117 |
ACCEPT |
Summary: Redundant with the IBA and IDA annotations for TRiC/CCT membership. Correct ARBA-based annotation.
Reason: Correct. Redundant with experimental evidence but acceptable.
|
|
GO:0006457
protein folding
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Redundant with IBA and IDA annotations for protein folding. Correct.
Reason: Correct. Consistent with IBA and IDA evidence.
|
|
GO:0016887
ATP hydrolysis activity
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: Each TRiC/CCT subunit has ATPase activity. The crystal structure (PMID:21701561) reveals ATP-binding heterogeneity among subunits, and the complex uses a sequential ATP hydrolysis mechanism.
Reason: Correct. Each CCT subunit contributes ATPase activity to the chaperonin cycle. InterPro-based annotation is well supported.
|
|
GO:0051082
unfolded protein binding
|
IEA
GO_REF:0000120 |
MODIFY |
Summary: GO:0051082 is proposed for obsoletion. Same rationale as the IBA annotation above.
Reason: GO:0051082 is targeted for obsoletion. Should be replaced with GO:0140662 (ATP-dependent protein folding chaperone), which is already annotated via InterPro.
Proposed replacements:
ATP-dependent protein folding chaperone
|
|
GO:0140662
ATP-dependent protein folding chaperone
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: This is the correct molecular function term for TRiC/CCT subunits. InterPro-based annotation via IPR017998 (Chaperone TCP-1). TCP1 contributes to this activity as part of the hetero-oligomeric complex.
Reason: Correct and the most appropriate MF term. GO:0140662 is the proper replacement for the obsoleting GO:0051082. As a complex subunit, the qualifier should ideally be contributes_to rather than enables, but the IEA annotation is correct in substance.
|
|
GO:0005515
protein binding
|
IPI
PMID:16554755 Global landscape of protein complexes in the yeast Saccharom... |
MARK AS OVER ANNOTATED |
Summary: IPI evidence from the global landscape of protein complexes study (Krogan et al. 2006). TCP1 interacts with POP2 (P39008) and YPP1 (P46951) in TAP-MS experiments.
Reason: Protein binding is uninformative for a chaperonin subunit. Interactions detected in large-scale complex purification studies likely reflect chaperone-substrate or complex-subunit interactions already captured by the TRiC/CCT complex membership annotation. These are better described by the chaperonin complex annotation.
|
|
GO:0005515
protein binding
|
IPI
PMID:19536198 An atlas of chaperone-protein interactions in Saccharomyces ... |
MARK AS OVER ANNOTATED |
Summary: IPI evidence from the chaperone-protein interactions atlas (Gong et al. 2009). TCP1 interacts with SIT4 (P20604), POP2 (P39008), and YPP1 (P46951).
Reason: Protein binding is uninformative for a chaperonin subunit. These interactions represent chaperonin-substrate relationships that are an inherent part of TRiC/CCT function.
|
|
GO:0005515
protein binding
|
IPI
PMID:20489023 A global protein kinase and phosphatase interaction network ... |
MARK AS OVER ANNOTATED |
Summary: IPI evidence from a global protein kinase and phosphatase interaction network. TCP1 interacts with SIT4 (P20604).
Reason: Protein binding is uninformative for a chaperonin subunit.
|
|
GO:0005515
protein binding
|
IPI
PMID:21701561 The crystal structure of yeast CCT reveals intrinsic asymmet... |
MARK AS OVER ANNOTATED |
Summary: IPI evidence from the crystal structure study of yeast CCT. TCP1 interacts with ACT1 (P60010) in the CCT-actin co-crystal structure. This is a well-characterized chaperonin-substrate interaction.
Reason: Protein binding is uninformative. The TCP1-actin interaction is a direct chaperonin-substrate relationship, which is the core function of TRiC/CCT already captured by the protein folding and complex membership annotations.
Supporting Evidence:
PMID:21701561
We have solved the crystal structure of yeast CCT in complex with actin at 3.8 Å resolution, revealing the subunit organisation and the location of discrete patches of co-evolving 'signature residues' that mediate specific interactions between CCT and its substrates.
|
|
GO:0005515
protein binding
|
IPI
PMID:27107014 An inter-species protein-protein interaction network across ... |
MARK AS OVER ANNOTATED |
Summary: IPI evidence from an inter-species protein-protein interaction network. TCP1 interacts with several human proteins (cross-species interactions).
Reason: Protein binding is uninformative. Cross-species interactions in this context likely reflect conserved chaperonin-substrate relationships.
|
|
GO:0005515
protein binding
|
IPI
PMID:37968396 The social and structural architecture of the yeast protein ... |
MARK AS OVER ANNOTATED |
Summary: IPI evidence from the social and structural architecture of the yeast protein interactome. TCP1 interacts with SIT4 (P20604).
Reason: Protein binding is uninformative for a chaperonin subunit.
|
|
GO:0005515
protein binding
|
IPI
PMID:9878052 Compartmentation of protein folding in vivo: sequestration o... |
MARK AS OVER ANNOTATED |
Summary: IPI evidence from the chaperonin-GimC system study (Siegers et al. 1999). TCP1 interacts with ACT1 (P60010). This study demonstrated that TRiC and GimC form an integrated folding compartment that sequesters newly synthesized actin.
Reason: Protein binding is uninformative. The TCP1-actin interaction is a core chaperonin-substrate relationship already captured by the protein folding and complex annotations. The study supports the chaperonin function annotation.
Supporting Evidence:
PMID:9878052
We propose that TRiC and GimC form an integrated 'folding compartment' which functions in cooperation with the translation machinery.
|
|
GO:0006457
protein folding
|
IDA
PMID:16762366 Quantitative actin folding reactions using yeast CCT purifie... |
ACCEPT |
Summary: PMID:16762366 demonstrated quantitative actin folding using purified yeast CCT. The purified complex catalyses folding of both yeast ACT1p and human beta-actin with nearly identical rate constants.
Reason: Core biological process. Direct experimental demonstration of TRiC/CCT-mediated protein folding in vitro using the purified complex containing TCP1.
Supporting Evidence:
PMID:16762366
Yeast CCT catalyses the folding of yeast ACT1p and human beta-actin with nearly identical rate constants and yields.
|
|
GO:0005886
plasma membrane
|
HDA
PMID:16622836 The plasma membrane proteome of Saccharomyces cerevisiae and... |
KEEP AS NON CORE |
Summary: HDA evidence from the plasma membrane proteome study. TCP1 was detected in the plasma membrane fraction, though this may reflect co-purification rather than true membrane localization.
Reason: TCP1 was detected in the plasma membrane proteome, but TRiC/CCT is primarily a cytosolic complex. The plasma membrane association may be a minor or artifact localization. Not a core localization.
|
|
GO:0005832
chaperonin-containing T-complex
|
IPI
PMID:15704212 Physiological effects of unassembled chaperonin Cct subunits... |
ACCEPT |
Summary: PMID:15704212 studied physiological effects of unassembled Cct subunits. TCP1 was shown to be part of the complex through interaction with other subunits (with CCT6/S000002596 as supporting entity).
Reason: Core complex membership with experimental IPI 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:0005832
chaperonin-containing T-complex
|
IDA
PMID:16762366 Quantitative actin folding reactions using yeast CCT purifie... |
ACCEPT |
Summary: PMID:16762366 purified the intact yeast CCT complex, confirming TCP1 as a constituent subunit.
Reason: Core complex membership with direct experimental evidence from purified complex.
|
|
GO:0051082
unfolded protein binding
|
IDA
PMID:16762366 Quantitative actin folding reactions using yeast CCT purifie... |
MODIFY |
Summary: GO:0051082 is proposed for obsoletion. PMID:16762366 demonstrated that the purified CCT complex binds actin folding intermediates (Ac(I)) and processes them to native actin in an ATP-dependent manner. This is chaperonin-mediated folding, not passive unfolded protein binding.
Reason: GO:0051082 is targeted for obsoletion. The experimental evidence from PMID:16762366 actually demonstrates ATP-dependent protein folding chaperone activity. The CCT complex binds actin intermediates in a pre-equilibrium step followed by ATP-driven processing to native actin. This is GO:0140662 (ATP-dependent protein folding chaperone).
Proposed replacements:
ATP-dependent protein folding chaperone
Supporting Evidence:
PMID:16762366
The results from this controlled CCT-actin folding assay are consistent with a model where CCT and Ac(I) are in a binding pre-equilibrium with a rate-limiting binding step, followed by a faster ATP-driven processing to native actin.
|
Q: Which yeast TRiC/CCT substrates require CCT1-specific apical or chamber-facing contacts rather than generic complex-level chaperonin activity?
Q: Should the emerging nuclear TRiC/CCT RNA polymerase II role be curated for TCP1 after peer-reviewed confirmation, or treated as a non-core complex phenotype?
Experiment: Combine CCT1 apical/chamber-surface mutants with purified yeast TRiC folding assays and in vivo client abundance/activity readouts for ACT1, tubulins, Cdh1, and Cdc20.
Hypothesis: CCT1 contributes substrate-specific contacts that are required for efficient folding of selected actin, tubulin, or WD40-repeat clients.
Type: client-specific folding assay
Experiment: Validate nuclear TRiC occupancy and RNAPII/RNA phenotypes using independently tagged CCT subunits, acute degron or anchor-away perturbations, and rescue with cytoplasm-restricted versus nucleus-permissive CCT1 variants.
Hypothesis: The nuclear RNA polymerase II phenotype of cct1-2 reflects assembled TRiC/CCT function rather than indirect cytoplasmic proteostasis stress.
Type: nuclear TRiC validation
provider: falcon
model: Edison Scientific Literature
cached: false
start_time: '2026-05-04T12:06:03.709954'
end_time: '2026-05-04T12:17:33.901999'
duration_seconds: 690.19
template_file: templates/gene_research_go_focused.md
template_variables:
organism: yeast
gene_id: TCP1
gene_symbol: TCP1
uniprot_accession: P12612
protein_description: 'RecName: Full=T-complex protein 1 subunit alpha; Short=TCP-1-alpha;
AltName: Full=CCT-alpha;'
gene_info: Name=TCP1; Synonyms=CCT1; OrderedLocusNames=YDR212W; ORFNames=YD8142.13,
YD8142B.04;
organism_full: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
protein_family: Belongs to the TCP-1 chaperonin family. .
protein_domains: Chap_CCT_alpha. (IPR012715); Chaperone_TCP-1. (IPR017998); Chaperonin_TCP-1_CS.
(IPR002194); Cpn60/GroEL/TCP-1. (IPR002423); GroEL-like_apical_dom_sf. (IPR027409)
provider_config:
timeout: 600
max_retries: 3
parameters:
allowed_domains: []
temperature: 0.1
citation_count: 31
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.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'TCP1' 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
Please provide a comprehensive research report on the gene TCP1 (gene ID: TCP1, UniProt: P12612) 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.
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.
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.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'TCP1' 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
Please provide a comprehensive research report on the gene TCP1 (gene ID: TCP1, UniProt: P12612) 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.
The UniProt entry provided (P12612) describes T-complex protein 1 subunit alpha (also called TCP-1-alpha, CCT-alpha) encoded by TCP1 (synonym CCT1) in Saccharomyces cerevisiae S288c. The literature gathered here consistently uses TCP1/CCT1 to refer to the CCT/TRiC cytosolic group II chaperonin subunit (not unrelated “TCP1” symbols in other organisms), including yeast genetics that explicitly uses a cct1-2 temperature-sensitive allele to perturb TRiC/CCT function. (gvozdenov2024triccctchaperoningoverns pages 30-33, narayanan2021sorbitolandpkc1 pages 1-3)
Limitation: within the retrieved full-text corpus, I did not find an explicit string mapping (e.g., “UniProt P12612” or “YDR212W”) inside the papers; thus, the identifier-level mapping to P12612/YDR212W is taken from the user-provided UniProt record, while mechanistic/functional claims are supported by peer-reviewed literature on yeast CCT1/TCP1. (gvozdenov2024triccctchaperoningoverns pages 30-33, narayanan2021sorbitolandpkc1 pages 1-3)
TCP1/CCT1 encodes CCT1 (TCP-1; CCT-alpha), one of eight paralogous subunits that assemble into the eukaryotic cytosolic chaperonin TRiC/CCT. TRiC/CCT is a ~1 MDa ATP-dependent double-ring machine, with eight distinct subunits per ring (CCT1–CCT8), and each subunit has apical/intermediate/equatorial domains; the equatorial domain binds ATP and supports ring assembly, while apical surfaces mediate substrate recognition and the built-in lid. (gestaut2019theatppoweredgymnastics pages 1-2, que2024theroleof pages 2-4, willison2018thesubstratespecificity pages 1-2)
TRiC/CCT’s primary biological function is ATP-coupled folding (and in some cases assembly/biogenesis) of a select set of cytosolic proteins, especially those that are topologically complex and aggregation-prone. Substrates bind TRiC in non-native conformations; ATP binding/hydrolysis drives conformational changes that close the chamber and promote productive folding. (gestaut2019theatppoweredgymnastics pages 1-2, gestaut2019theatppoweredgymnastics pages 4-5)
Quantitatively, TRiC/CCT is commonly estimated to engage on the order of ~10% of cytosolic proteins (review-level estimate), reflecting a substantial but selective role in proteostasis. (que2024theroleof pages 2-4, gestaut2019theatppoweredgymnastics pages 4-5)
TRiC/CCT subunits are not redundant: subunit diversification creates asymmetry in ATP binding/allostery and in substrate-recognition surfaces. A key mechanistic concept is a hierarchy of ATP affinities across subunits; in one model, the “high-affinity hemisphere” includes CCT5, CCT4, CCT1, and CCT2, which initiates ATP-driven conformational transitions. (gestaut2019theatppoweredgymnastics pages 4-5)
In budding yeast and across eukaryotes, the most established obligate clients of TRiC/CCT are actin and tubulin, which require TRiC/CCT to reach native, functional states. (willison2018thesubstratespecificity pages 1-2, gestaut2019theatppoweredgymnastics pages 4-5)
A major additional client class is WD40-repeat β-propeller proteins. In yeast, TRiC/CCT is reported as the only known folding pathway producing functional, active Cdh1p and Cdc20p (APC/C coactivators that are WD40 propellers), linking TRiC directly to cell-cycle control via APC/C regulation. (willison2018thesubstratespecificity pages 6-6, willison2018thesubstratespecificity pages 1-2)
In a targeted analysis of yeast 7-bladed WD40 proteins (plus one 8-bladed WD40 protein), many showed some binding to CCT, but only a subset were strong interactors (including Cdh1p and Cdc20p), consistent with a restricted substrate spectrum rather than generic folding of all WD40 proteins. (willison2018thesubstratespecificity pages 5-6)
Substrate specificity is driven largely by apical domain surfaces that differ among subunits, enabling polyvalent, subunit-selective binding. Review synthesis emphasizes that TRiC tends to fold proteins enriched in β-structure/topological complexity and that it can act as a folding machine and/or a regulated holding/assembly platform for some propellers. (gestaut2019theatppoweredgymnastics pages 4-5, willison2018thesubstratespecificity pages 5-6, monkemeyer2019structuralandfunctional pages 29-31)
TRiC/CCT is classically a cytosolic chaperonin, functioning co- and post-translationally in general proteostasis and in cytoskeletal protein biogenesis (actin/tubulin). (que2024theroleof pages 2-4, willison2018thesubstratespecificity pages 1-2)
Recent work in budding yeast reports an assembled TRiC/CCT pool in the nucleus (supported by GFP-tagged subunits and biochemical fractionation/SEC consistent with a ~1 MDa holo-complex in nuclear fractions), and uses the cct1-2 allele to show nuclear TRiC/CCT modulates RNA polymerase II activity and RNA homeostasis. (gvozdenov2024triccctchaperoningoverns pages 6-9, gvozdenov2024triccctchaperoningoverns pages 13-17)
CCT/TRiC is discussed as a major ribosome-associated chaperone within the CLIPS (Chaperones Linked to Protein Synthesis) network, connecting TCP1/CCT1 function to translation elongation and nascent-chain maturation. (que2024theroleof pages 2-4)
By folding the WD40 propeller proteins Cdh1p and Cdc20p, TRiC/CCT contributes directly to APC/C function and thus cell-cycle progression. (willison2018thesubstratespecificity pages 6-6, willison2018thesubstratespecificity pages 1-2)
A yeast cct1-2 mutant shows sensitivity to cell-wall stress agents (SDS, congo red), and its temperature sensitivity is suppressed by 1 M sorbitol or PKC1 overexpression (PKC1 is a key regulator of the yeast cell wall integrity pathway). This supports a functional link between TRiC/CCT proteostasis and maintenance of cell wall integrity, likely via folding/biogenesis of proteins required for cell wall homeostasis. (narayanan2021sorbitolandpkc1 pages 1-3)
In the 2024 preprint, TRiC/CCT inactivation using cct1-2 causes widespread transcriptional/RNA anomalies, including extensive accumulation of cryptic/noncoding RNAs and increased intergenic transcription. The authors propose TRiC acts as an RNAPII “rheostat” linking proteostasis state to transcriptional output. (gvozdenov2024triccctchaperoningoverns pages 6-9, gvozdenov2024triccctchaperoningoverns pages 13-17)
High-resolution cryo-EM and crosslinking mass spectrometry has advanced mechanistic understanding of how TRiC cooperates with cochaperones (e.g., prefoldin and phosducin-like proteins). In particular, 2024 structural work shows an ATP-driven cycle in which PhLP2A binds open TRiC via subunit-selective contacts and rearranges upon chamber closure; in substrate-containing complexes, inner-surface contacts involve a subset of subunits including CCT1. (junsun2024astructuralvista pages 1-2)
The 2024 Nature Communications study reports that actin and/or PhLP2A engage positively charged chamber-facing residues from CCT1/CCT3/CCT6/CCT8, and crosslinks can place cochaperone helices proximal to CCT1 cavity-facing residues, supporting direct involvement of CCT1 surfaces in substrate/cochaperone positioning inside the folding chamber. (junsun2024astructuralvista pages 1-2)
A 2023 yeast kinetic analysis of a disease-linked CCT2 double mutation shows that slowing ADP off-rate can stabilize the closed state and that TRiC ATPase activity is stimulated by a non-folded substrate. Although this work is on CCT2, it strengthens the mechanistic framework for how the TRiC ATPase cycle (in which CCT1 is part of the high-affinity hemisphere) couples nucleotide exchange to folding output. (roy2023reducedadpoffrate pages 1-2, gestaut2019theatppoweredgymnastics pages 4-5)
A 2023 cryo-EM ensemble of substrate-engaged TRiC states (human endogenous TRiC with tubulin) provides a modern reference trajectory for how substrates move and stabilize during ring closure across the ATPase cycle. While not yeast-specific, the mechanism supports functional inference for yeast TCP1/CCT1 as part of the conserved folding machine for tubulin-class substrates. (liu2023pathwayandmechanism pages 1-2)
CCT/TRiC is commonly estimated to assist folding/maturation of ~10% of cytoplasmic proteins (review synthesis). (que2024theroleof pages 2-4, gestaut2019theatppoweredgymnastics pages 4-5)
A quantitative figure caption in an authoritative substrate-specificity review reports yeast mRNA copy-number estimates: TCP1 ~1.81 mRNA copies/cell, with similar magnitudes for other CCT subunits, and much higher values for abundant clients such as ACT1 ~28.97 and TUB2 ~5.94. (willison2018thesubstratespecificity media 549e9c0a, willison2018thesubstratespecificity media 4a831a29)
In the cct1-2 mutant background, the preprint reports strong genome-wide RNA effects. Examples include: intergenic coverage increasing dramatically, and a substantial fraction of the genome exhibiting strong nascent-RNA increases (e.g., ~22.8% of the genome meeting a ≥4-fold threshold for increased nascent RNAs in one analysis), plus measurable readthrough/termination defects at subsets of snoRNA loci. (gvozdenov2024triccctchaperoningoverns pages 6-9, gvozdenov2024triccctchaperoningoverns pages 13-17)
Temperature-sensitive yeast TRiC mutants (including cct1-2) are used as tractable tools for genetic suppression screens and pathway probing, as demonstrated by suppression of cct phenotypes via osmotic stabilization or PKC1 overexpression. This is a concrete real-world implementation of TCP1/CCT1 genetics for dissecting cellular proteostasis and stress pathways. (narayanan2021sorbitolandpkc1 pages 1-3)
Modern structural studies of TRiC with clients/cochaperones are explicitly discussed as informing design of agents targeting TRiC–substrate interactions (e.g., in tubulin folding contexts). While this is largely developed in mammalian systems, it represents translationally oriented use of TRiC mechanistic knowledge enabled by conserved chaperonin architecture that includes CCT1/CCT-alpha. (liu2023pathwayandmechanism pages 1-2)
A consistent expert view is that TRiC/CCT is a specialist folding machine (not a generalist chaperone), focusing on a restricted client set enriched for difficult-to-fold, aggregation-prone, β-structure-rich proteins, and that subunit diversification (including CCT1) is central to this specialization via asymmetric ATP allostery and subunit-specific binding surfaces. (gestaut2019theatppoweredgymnastics pages 4-5, willison2018thesubstratespecificity pages 7-8, monkemeyer2019structuralandfunctional pages 29-31)
The following table lists the most relevant recent and foundational sources used for this annotation, emphasizing 2023–2024 where available.
| Year | Citation (short) | Publication type | Key contribution for TCP1/CCT1 functional annotation | Organism/system | URL/DOI |
|---|---|---|---|---|---|
| 2024 | Gvozdenov et al. 2024 | Preprint | Uses the yeast cct1-2 allele to show TRiC/CCT has an assembled nuclear pool and directly modulates RNA polymerase II activity and RNA homeostasis; expands TCP1/CCT1 annotation beyond canonical cytosolic folding to nuclear transcriptional control in budding yeast (gvozdenov2024triccctchaperoningoverns pages 6-9, gvozdenov2024triccctchaperoningoverns pages 13-17, gvozdenov2024triccctchaperoningoverns pages 30-33) | Saccharomyces cerevisiae | https://doi.org/10.1101/2024.09.26.615188 |
| 2024 | Park et al. 2024 | Primary research | Cryo-EM/XL-MS defines ATP-driven cooperation between PhLP2A and TRiC; identifies chamber-facing contacts involving CCT1/CCT3/CCT6/CCT8, supporting a subunit-specific inner-surface role for CCT1/TCP1 in substrate/cochaperone positioning during folding (junsun2024astructuralvista pages 1-2) | Mammalian TRiC with general eukaryotic relevance | https://doi.org/10.1038/s41467-024-45242-x |
| 2024 | Que et al. 2024 | Review | Summarizes CCT/TRiC as a 1-MDa ATP-dependent 16-subunit complex and major ribosome-associated chaperone in the CLIPS network, assisting folding of roughly 10% of cytoplasmic proteins; useful for defining TCP1/CCT1 core function in translation-linked proteostasis (que2024theroleof pages 2-4) | General eukaryotes, includes yeast context | https://doi.org/10.1016/j.heliyon.2024.e29029 |
| 2023 | Roy et al. 2023 | Primary research | Yeast kinetic study of disease-linked CCT2 mutation shows altered ADP off-rate and stabilization of the closed state, clarifying TRiC mechanochemistry relevant to interpreting how ATP-driven cycling supports functions of all subunits including TCP1/CCT1 (roy2023reducedadpoffrate pages 1-2) | Saccharomyces cerevisiae | https://doi.org/10.1038/s42003-023-05261-8 |
| 2023 | Liu et al. 2023 | Primary research | Cryo-EM captures the tubulin folding pathway through the TRiC ATPase cycle, showing staged substrate translocation and stabilization in the chamber; provides current mechanistic framework for annotating TCP1/CCT1 as part of the ATP-driven folding machine (liu2023pathwayandmechanism pages 1-2) | Human endogenous TRiC; mechanism relevant to eukaryotes including yeast | https://doi.org/10.1038/s42003-023-04915-x |
| 2019 | Gestaut et al. 2019 | Review | Authoritative review of asymmetric ATP-driven allostery in TRiC/CCT; places CCT1 in the higher-ATP-affinity hemisphere with CCT5/4/2 and explains how subunit diversification underlies specialized substrate contacts and folding dynamics (gestaut2019theatppoweredgymnastics pages 4-5) | General eukaryotes with yeast emphasis | https://doi.org/10.1016/j.sbi.2019.03.002 |
| 2018 | Willison 2018 | Review | Landmark substrate-specificity review: defines CCT/TRiC clients as actin, tubulin, and selected WD40 proteins; notes that yeast TCP1 is a core subunit and gives useful yeast quantitative context, including TCP1 mRNA copy number ~1.81/cell and strong links to Cdh1/Cdc20 folding (willison2018thesubstratespecificity pages 6-6, willison2018thesubstratespecificity pages 7-8, willison2018thesubstratespecificity pages 1-2, willison2018thesubstratespecificity pages 5-6, willison2018thesubstratespecificity media 549e9c0a) | Saccharomyces cerevisiae and comparative eukaryotes | https://doi.org/10.1098/rstb.2017.0192 |
Table: This table summarizes the most relevant recent and foundational sources for annotating yeast TCP1/CCT1 as a TRiC/CCT subunit. It highlights what each paper contributes to understanding molecular function, subunit-specific roles, and cellular pathways.
A yeast-focused evidence map of TCP1/CCT1 functional annotation categories is provided here.
| Category | Key points | Best supporting evidence | Notes/limitations |
|---|---|---|---|
| molecular function | TCP1/CCT1 is the alpha subunit of the essential eukaryotic cytosolic chaperonin TRiC/CCT, a ~1 MDa ATP-dependent double-ring complex with eight distinct subunits per ring. Its primary function is not catalysis of a small-molecule reaction but ATP-coupled assistance of protein folding by binding non-native polypeptides and promoting their productive folding inside the chamber. CCT1 is part of the higher-ATP-affinity hemisphere that helps drive allosteric ring closure and substrate handling. | Willison 2018; Gestaut 2019; Que 2024 (willison2018thesubstratespecificity pages 1-2, gestaut2019theatppoweredgymnastics pages 4-5, que2024theroleof pages 2-4) | Most mechanistic detail is for the whole TRiC/CCT complex rather than TCP1 alone; direct yeast CCT1 biochemical dissection is limited in the retrieved literature. |
| clients | Best-supported obligate/major client classes are actin and tubulin, plus a restricted subset of WD40/β-propeller proteins including APC/C regulators Cdh1p and Cdc20p. CCT recognizes topologically complex, aggregation-prone substrates and can serve as an assembly/holding platform for some propeller proteins rather than simply releasing a fully folded monomer. | Willison 2018; Gestaut 2019; Que 2024 (willison2018thesubstratespecificity pages 1-2, willison2018thesubstratespecificity pages 5-6, willison2018thesubstratespecificity pages 7-8, gestaut2019theatppoweredgymnastics pages 4-5, que2024theroleof pages 2-4) | Many client assignments are to the CCT complex as a whole; subunit-specific client preference for yeast CCT1 is inferred from chamber asymmetry and apical-domain specialization. |
| localization | Canonically cytosolic, where it acts co- and post-translationally in proteostasis and cytoskeletal protein biogenesis. Recent yeast work also supports an assembled nuclear TRiC/CCT pool, with cct1-2 perturbation affecting nuclear RNA metabolism and RNA polymerase II output. | Gvozdenov 2024; Willison 2018 (gvozdenov2024triccctchaperoningoverns pages 6-9, gvozdenov2024triccctchaperoningoverns pages 13-17, gvozdenov2024triccctchaperoningoverns pages 30-33, willison2018thesubstratespecificity pages 7-8) | Nuclear role comes from a 2024 preprint and should be treated as emerging rather than fully settled. |
| pathways | Strongest pathway links are proteostasis, cytoskeleton biogenesis, cell-cycle control, translation-linked folding (CLIPS network), and assembly/function of WD40-containing regulators. Emerging evidence adds transcription/RNA homeostasis via RNAP II regulation in yeast nuclei. Cell-wall integrity phenotypes indicate indirect coupling to PKC1-dependent stress pathways. | Willison 2018; Que 2024; Gvozdenov 2024; Narayanan 2021 (willison2018thesubstratespecificity pages 7-8, que2024theroleof pages 2-4, gvozdenov2024triccctchaperoningoverns pages 13-17, narayanan2021sorbitolandpkc1 pages 1-3) | Some pathway links are direct client-folding effects; others are downstream consequences of proteostasis failure. |
| subunit-specific evidence for CCT1 | CCT1 contributes specialized chamber/apical surfaces for substrate or cochaperone contacts and participates in the high-affinity ATPase hemisphere. Structural data show actin/PhLP2A interactions involving chamber-facing residues from CCT1 together with CCT3/6/8, supporting a direct role in substrate/cochaperone positioning during the folding cycle. | Park 2024; Gestaut 2019 (junsun2024astructuralvista pages 1-2, gestaut2019theatppoweredgymnastics pages 4-5) | Structural evidence is from mammalian TRiC, but the subunit architecture and mechanism are highly conserved and routinely used to interpret yeast CCT1/TCP1. |
| phenotypes | Yeast cct1-2 is temperature-sensitive, with growth at 30°C and severe defects at higher temperature; mutants are also sensitive to SDS and congo red, implicating cell-wall integrity defects. Sorbitol and PKC1 overexpression suppress temperature sensitivity, whereas HSP82 overexpression does not. In a newer nuclear context, cct1-2 causes strong accumulation of cryptic/noncoding RNAs and altered transcriptional outputs. | Narayanan 2021; Gvozdenov 2024 (narayanan2021sorbitolandpkc1 pages 1-3, gvozdenov2024triccctchaperoningoverns pages 6-9, gvozdenov2024triccctchaperoningoverns pages 13-17, gvozdenov2024triccctchaperoningoverns pages 30-33) | Phenotypes reflect loss of complex function, not necessarily a unique moonlighting activity of TCP1 alone. |
| quantitative data | CCT is estimated to assist folding/maturation of about 10% of cytoplasmic proteins. Yeast TCP1 mRNA copy number is reported at ~1.81 per cell, alongside similar low-copy expression of other CCT subunits; ACT1 and TUB2 are much higher (~28.97 and ~5.94). In yeast cct1-2, nascent RNAs increased broadly (~22.8% of genome ≥4-fold), and intergenic transcription rose strongly; ~30 of 68 snoRNAs showed readthrough defects in the 2024 preprint. | Que 2024; Willison 2018; Gvozdenov 2024 (que2024theroleof pages 2-4, willison2018thesubstratespecificity pages 7-8, willison2018thesubstratespecificity media 549e9c0a, gvozdenov2024triccctchaperoningoverns pages 6-9, gvozdenov2024triccctchaperoningoverns pages 13-17) | Some values are review-derived or preprint-derived; copy-number figures are mRNA estimates, not protein stoichiometry. |
Table: This table summarizes the most relevant functional annotation points for yeast TCP1/CCT1, organized by molecular role, clients, localization, pathways, phenotypes, and quantitative evidence. It is designed as a compact evidence map for building the final research report.
References
(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.
(narayanan2021sorbitolandpkc1 pages 1-3): Aswathy Narayanan and M. Anaul Kabir. Sorbitol and pkc1 overexpression alleviate temperature sensitivity in chaperonin mutants of saccharomyces cerevisiae. microPublication Biology, Aug 2021. URL: https://doi.org/10.17912/micropub.biology.000440, doi:10.17912/micropub.biology.000440. This article has 1 citations.
(gestaut2019theatppoweredgymnastics pages 1-2): Daniel Gestaut, Antonio Limatola, Lukasz Joachimiak, and Judith Frydman. The atp-powered gymnastics of tric/cct: an asymmetric protein folding machine with a symmetric origin story. Current opinion in structural biology, 55:50-58, Apr 2019. URL: https://doi.org/10.1016/j.sbi.2019.03.002, doi:10.1016/j.sbi.2019.03.002. This article has 106 citations and is from a peer-reviewed journal.
(que2024theroleof pages 2-4): 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.
(willison2018thesubstratespecificity pages 1-2): Keith R. Willison. The substrate specificity of eukaryotic cytosolic chaperonin cct. Philosophical Transactions of the Royal Society B: Biological Sciences, 373:20170192, Jun 2018. URL: https://doi.org/10.1098/rstb.2017.0192, doi:10.1098/rstb.2017.0192. This article has 75 citations and is from a domain leading peer-reviewed journal.
(gestaut2019theatppoweredgymnastics pages 4-5): Daniel Gestaut, Antonio Limatola, Lukasz Joachimiak, and Judith Frydman. The atp-powered gymnastics of tric/cct: an asymmetric protein folding machine with a symmetric origin story. Current opinion in structural biology, 55:50-58, Apr 2019. URL: https://doi.org/10.1016/j.sbi.2019.03.002, doi:10.1016/j.sbi.2019.03.002. This article has 106 citations and is from a peer-reviewed journal.
(willison2018thesubstratespecificity pages 6-6): Keith R. Willison. The substrate specificity of eukaryotic cytosolic chaperonin cct. Philosophical Transactions of the Royal Society B: Biological Sciences, 373:20170192, Jun 2018. URL: https://doi.org/10.1098/rstb.2017.0192, doi:10.1098/rstb.2017.0192. This article has 75 citations and is from a domain leading peer-reviewed journal.
(willison2018thesubstratespecificity pages 5-6): Keith R. Willison. The substrate specificity of eukaryotic cytosolic chaperonin cct. Philosophical Transactions of the Royal Society B: Biological Sciences, 373:20170192, Jun 2018. URL: https://doi.org/10.1098/rstb.2017.0192, doi:10.1098/rstb.2017.0192. This article has 75 citations and is from a domain leading peer-reviewed journal.
(monkemeyer2019structuralandfunctional pages 29-31): Leonie Mönkemeyer. Structural and functional studies on the eukaryotic chaperonin tric/cct and its cooperating chaperone hgh1. Dissertation, Jan 2019. URL: https://doi.org/10.5282/edoc.23750, doi:10.5282/edoc.23750. This article has 0 citations.
(gvozdenov2024triccctchaperoningoverns pages 6-9): 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.
(gvozdenov2024triccctchaperoningoverns pages 13-17): 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.
(junsun2024astructuralvista pages 1-2): Junsun Park, Hyunmin Kim, Daniel Gestaut, Seyeon Lim, Kwadwo A. Opoku-Nsiah, Alexander Leitner, Judith Frydman, and Soung-Hun Roh. A structural vista of phosducin-like phlp2a-chaperonin tric cooperation during the atp-driven folding cycle. Nature Communications, Feb 2024. URL: https://doi.org/10.1038/s41467-024-45242-x, doi:10.1038/s41467-024-45242-x. This article has 16 citations and is from a highest quality peer-reviewed journal.
(roy2023reducedadpoffrate pages 1-2): Mousam Roy, Rachel C. Fleisher, Alexander I. Alexandrov, and Amnon Horovitz. Reduced adp off-rate by the yeast cct2 double mutation t394p/r510h which causes leber congenital amaurosis in humans. Communications Biology, Aug 2023. URL: https://doi.org/10.1038/s42003-023-05261-8, doi:10.1038/s42003-023-05261-8. This article has 9 citations and is from a peer-reviewed journal.
(liu2023pathwayandmechanism pages 1-2): Caixuan Liu, Mingliang Jin, Shutian Wang, Wenyu Han, Qiaoyu Zhao, Yifan Wang, Cong Xu, Lei Diao, Yue Yin, Chao Peng, Lan Bao, Yanxing Wang, and Yao Cong. Pathway and mechanism of tubulin folding mediated by tric/cct along its atpase cycle revealed using cryo-em. Communications Biology, May 2023. URL: https://doi.org/10.1038/s42003-023-04915-x, doi:10.1038/s42003-023-04915-x. This article has 28 citations and is from a peer-reviewed journal.
(willison2018thesubstratespecificity media 549e9c0a): Keith R. Willison. The substrate specificity of eukaryotic cytosolic chaperonin cct. Philosophical Transactions of the Royal Society B: Biological Sciences, 373:20170192, Jun 2018. URL: https://doi.org/10.1098/rstb.2017.0192, doi:10.1098/rstb.2017.0192. This article has 75 citations and is from a domain leading peer-reviewed journal.
(willison2018thesubstratespecificity media 4a831a29): Keith R. Willison. The substrate specificity of eukaryotic cytosolic chaperonin cct. Philosophical Transactions of the Royal Society B: Biological Sciences, 373:20170192, Jun 2018. URL: https://doi.org/10.1098/rstb.2017.0192, doi:10.1098/rstb.2017.0192. This article has 75 citations and is from a domain leading peer-reviewed journal.
(willison2018thesubstratespecificity pages 7-8): Keith R. Willison. The substrate specificity of eukaryotic cytosolic chaperonin cct. Philosophical Transactions of the Royal Society B: Biological Sciences, 373:20170192, Jun 2018. URL: https://doi.org/10.1098/rstb.2017.0192, doi:10.1098/rstb.2017.0192. This article has 75 citations and is from a domain leading peer-reviewed journal.
id: P12612
gene_symbol: TCP1
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:559292
label: Saccharomyces cerevisiae
description: >-
TCP1 (also known as CCT1) encodes the alpha subunit of the chaperonin-containing T-complex
(TRiC/CCT) in S. cerevisiae. TRiC/CCT is an essential, hetero-oligomeric, group II chaperonin
composed of eight paralogous subunits (CCT1-8) arranged in two stacked rings of eight subunits
each, forming a ~1 MDa complex. The complex functions as an ATP-dependent protein folding
machine that assists the folding of actin, tubulin, and a small number of other substrates
including WD40-repeat proteins. Each subunit contributes to the overall ATP-dependent protein
folding chaperone activity of the complex; individual subunits do not independently fold
substrates. TCP1/CCT1 is essential for viability and plays roles in mitotic spindle formation
in yeast. The crystal structure of yeast CCT (PMID:21701561) reveals intrinsic asymmetry
among the eight subunits, with each displaying unique configurations and substrate-binding
properties.
existing_annotations:
# ============================================================
# IBA ANNOTATIONS (phylogenetically inferred)
# ============================================================
- term:
id: GO:0006457
label: protein folding
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
TCP1 is part of the TRiC/CCT complex that assists protein folding. IBA annotation
is consistent with IDA evidence from PMID:16762366 demonstrating that purified yeast
CCT catalyses actin folding in vitro.
action: ACCEPT
reason: >-
Core biological process. The TRiC/CCT complex is an essential protein folding machine,
and TCP1 is a required subunit. IBA is well supported by experimental data.
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_id: file:yeast/TCP1/TCP1-deep-research-falcon.md
supporting_text: >-
TCP1/CCT1 encodes CCT1 (TCP-1; CCT-alpha), one of eight paralogous
subunits that assemble into the eukaryotic cytosolic chaperonin
TRiC/CCT.
- term:
id: GO:0005832
label: chaperonin-containing T-complex
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
TCP1 is the alpha subunit of the chaperonin-containing T-complex (TRiC/CCT). IBA is
consistent with IDA and IPI evidence from PMID:16762366 and PMID:15704212.
action: ACCEPT
reason: >-
Core complex membership. TCP1 is an integral, essential subunit of TRiC/CCT.
Well supported by multiple experimental methods.
- term:
id: GO:0051082
label: unfolded protein binding
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
GO:0051082 (unfolded protein binding) is proposed for obsoletion. TCP1, as a subunit
of TRiC/CCT, does interact with unfolded substrates (actin, tubulin), but this occurs
in the context of the ATP-dependent chaperonin folding cycle, not as a standalone
binding function. The correct replacement is GO:0140662 (ATP-dependent protein folding
chaperone), with the qualifier contributes_to since TCP1 is a subunit of the complex.
action: MODIFY
reason: >-
GO:0051082 is targeted for obsoletion. TCP1 binds unfolded proteins only as part of
the TRiC/CCT complex's ATP-dependent folding cycle. The appropriate replacement is
GO:0140662 (ATP-dependent protein folding chaperone). This IEA-level annotation via
InterPro already exists for this gene.
proposed_replacement_terms:
- id: GO:0140662
label: ATP-dependent protein folding chaperone
# ============================================================
# IEA ANNOTATIONS (computationally inferred)
# ============================================================
- term:
id: GO:0000166
label: nucleotide binding
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
TCP1 binds ATP as part of its chaperonin function. This is a parent term of ATP binding
and is correct but general.
action: ACCEPT
reason: >-
Correct. All TRiC/CCT subunits bind nucleotides (ATP/ADP). The more specific term
ATP binding (GO:0005524) is also annotated. This broader IEA is acceptable.
- term:
id: GO:0005524
label: ATP binding
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
TCP1 binds ATP through its equatorial domain. Each CCT subunit has an ATP-binding
site that is essential for the allosteric chaperonin cycle.
action: ACCEPT
reason: >-
Correct and fundamental. ATP binding is essential for the TRiC/CCT folding mechanism.
UniProt keywords confirm ATP-binding.
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IEA
original_reference_id: GO_REF:0000044
review:
summary: >-
TCP1 is a cytoplasmic protein. UniProt subcellular location annotation confirms
cytoplasmic localization.
action: ACCEPT
reason: >-
Correct. TRiC/CCT is a cytoplasmic/cytosolic complex.
- term:
id: GO:0005832
label: chaperonin-containing T-complex
evidence_type: IEA
original_reference_id: GO_REF:0000117
review:
summary: >-
Redundant with the IBA and IDA annotations for TRiC/CCT membership. Correct ARBA-based
annotation.
action: ACCEPT
reason: >-
Correct. Redundant with experimental evidence but acceptable.
- term:
id: GO:0006457
label: protein folding
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
Redundant with IBA and IDA annotations for protein folding. Correct.
action: ACCEPT
reason: >-
Correct. Consistent with IBA and IDA evidence.
- term:
id: GO:0016887
label: ATP hydrolysis activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
Each TRiC/CCT subunit has ATPase activity. The crystal structure (PMID:21701561)
reveals ATP-binding heterogeneity among subunits, and the complex uses a sequential
ATP hydrolysis mechanism.
action: ACCEPT
reason: >-
Correct. Each CCT subunit contributes ATPase activity to the chaperonin cycle.
InterPro-based annotation is well supported.
- term:
id: GO:0051082
label: unfolded protein binding
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
GO:0051082 is proposed for obsoletion. Same rationale as the IBA annotation above.
action: MODIFY
reason: >-
GO:0051082 is targeted for obsoletion. Should be replaced with GO:0140662
(ATP-dependent protein folding chaperone), which is already annotated via InterPro.
proposed_replacement_terms:
- id: GO:0140662
label: ATP-dependent protein folding chaperone
- term:
id: GO:0140662
label: ATP-dependent protein folding chaperone
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
This is the correct molecular function term for TRiC/CCT subunits. InterPro-based
annotation via IPR017998 (Chaperone TCP-1). TCP1 contributes to this activity as
part of the hetero-oligomeric complex.
action: ACCEPT
reason: >-
Correct and the most appropriate MF term. GO:0140662 is the proper replacement for
the obsoleting GO:0051082. As a complex subunit, the qualifier should ideally be
contributes_to rather than enables, but the IEA annotation is correct in substance.
# ============================================================
# IPI ANNOTATIONS (protein binding)
# ============================================================
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:16554755
review:
summary: >-
IPI evidence from the global landscape of protein complexes study (Krogan et al. 2006).
TCP1 interacts with POP2 (P39008) and YPP1 (P46951) in TAP-MS experiments.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Protein binding is uninformative for a chaperonin subunit. Interactions detected in
large-scale complex purification studies likely reflect chaperone-substrate or
complex-subunit interactions already captured by the TRiC/CCT complex membership
annotation. These are better described by the chaperonin complex annotation.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:19536198
review:
summary: >-
IPI evidence from the chaperone-protein interactions atlas (Gong et al. 2009).
TCP1 interacts with SIT4 (P20604), POP2 (P39008), and YPP1 (P46951).
action: MARK_AS_OVER_ANNOTATED
reason: >-
Protein binding is uninformative for a chaperonin subunit. These interactions
represent chaperonin-substrate relationships that are an inherent part of TRiC/CCT
function.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:20489023
review:
summary: >-
IPI evidence from a global protein kinase and phosphatase interaction network.
TCP1 interacts with SIT4 (P20604).
action: MARK_AS_OVER_ANNOTATED
reason: >-
Protein binding is uninformative for a chaperonin subunit.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:21701561
review:
summary: >-
IPI evidence from the crystal structure study of yeast CCT. TCP1 interacts with
ACT1 (P60010) in the CCT-actin co-crystal structure. This is a well-characterized
chaperonin-substrate interaction.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Protein binding is uninformative. The TCP1-actin interaction is a direct
chaperonin-substrate relationship, which is the core function of TRiC/CCT
already captured by the protein folding and complex membership annotations.
supported_by:
- reference_id: PMID:21701561
supporting_text: "We have solved the crystal structure of yeast CCT in complex with actin at 3.8 Å resolution, revealing the subunit organisation and the location of discrete patches of co-evolving 'signature residues' that mediate specific interactions between CCT and its substrates."
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:27107014
review:
summary: >-
IPI evidence from an inter-species protein-protein interaction network. TCP1 interacts
with several human proteins (cross-species interactions).
action: MARK_AS_OVER_ANNOTATED
reason: >-
Protein binding is uninformative. Cross-species interactions in this context
likely reflect conserved chaperonin-substrate relationships.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:37968396
review:
summary: >-
IPI evidence from the social and structural architecture of the yeast protein
interactome. TCP1 interacts with SIT4 (P20604).
action: MARK_AS_OVER_ANNOTATED
reason: >-
Protein binding is uninformative for a chaperonin subunit.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:9878052
review:
summary: >-
IPI evidence from the chaperonin-GimC system study (Siegers et al. 1999). TCP1
interacts with ACT1 (P60010). This study demonstrated that TRiC and GimC form an
integrated folding compartment that sequesters newly synthesized actin.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Protein binding is uninformative. The TCP1-actin interaction is a core
chaperonin-substrate relationship already captured by the protein folding and
complex annotations. The study supports the chaperonin function annotation.
supported_by:
- reference_id: PMID:9878052
supporting_text: "We propose that TRiC and GimC form an integrated 'folding compartment' which functions in cooperation with the translation machinery."
# ============================================================
# IDA ANNOTATIONS (direct experimental evidence)
# ============================================================
- term:
id: GO:0006457
label: protein folding
evidence_type: IDA
original_reference_id: PMID:16762366
review:
summary: >-
PMID:16762366 demonstrated quantitative actin folding using purified yeast CCT.
The purified complex catalyses folding of both yeast ACT1p and human beta-actin
with nearly identical rate constants.
action: ACCEPT
reason: >-
Core biological process. Direct experimental demonstration of TRiC/CCT-mediated
protein folding in vitro using the purified complex containing TCP1.
supported_by:
- reference_id: PMID:16762366
supporting_text: "Yeast CCT catalyses the folding of yeast ACT1p and human beta-actin with nearly identical rate constants and yields."
- term:
id: GO:0005886
label: plasma membrane
evidence_type: HDA
original_reference_id: PMID:16622836
review:
summary: >-
HDA evidence from the plasma membrane proteome study. TCP1 was detected in the
plasma membrane fraction, though this may reflect co-purification rather than
true membrane localization.
action: KEEP_AS_NON_CORE
reason: >-
TCP1 was detected in the plasma membrane proteome, but TRiC/CCT is primarily
a cytosolic complex. The plasma membrane association may be a minor or
artifact localization. Not a core localization.
- term:
id: GO:0005832
label: chaperonin-containing T-complex
evidence_type: IPI
original_reference_id: PMID:15704212
review:
summary: >-
PMID:15704212 studied physiological effects of unassembled Cct subunits. TCP1
was shown to be part of the complex through interaction with other subunits
(with CCT6/S000002596 as supporting entity).
action: ACCEPT
reason: >-
Core complex membership with experimental IPI 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"
- term:
id: GO:0005832
label: chaperonin-containing T-complex
evidence_type: IDA
original_reference_id: PMID:16762366
review:
summary: >-
PMID:16762366 purified the intact yeast CCT complex, confirming TCP1 as a
constituent subunit.
action: ACCEPT
reason: >-
Core complex membership with direct experimental evidence from purified complex.
- term:
id: GO:0051082
label: unfolded protein binding
evidence_type: IDA
original_reference_id: PMID:16762366
review:
summary: >-
GO:0051082 is proposed for obsoletion. PMID:16762366 demonstrated that the purified
CCT complex binds actin folding intermediates (Ac(I)) and processes them to native
actin in an ATP-dependent manner. This is chaperonin-mediated folding, not passive
unfolded protein binding.
action: MODIFY
reason: >-
GO:0051082 is targeted for obsoletion. The experimental evidence from PMID:16762366
actually demonstrates ATP-dependent protein folding chaperone activity. The CCT complex
binds actin intermediates in a pre-equilibrium step followed by ATP-driven processing
to native actin. This is GO:0140662 (ATP-dependent protein folding chaperone).
proposed_replacement_terms:
- id: GO:0140662
label: ATP-dependent protein folding chaperone
supported_by:
- reference_id: PMID:16762366
supporting_text: "The results from this controlled CCT-actin folding assay are consistent with a model where CCT and Ac(I) are in a binding pre-equilibrium with a rate-limiting binding step, followed by a faster ATP-driven processing to native actin."
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: Studied physiological effects of overexpressing individual CCT subunits
supporting_text: "Overexpression of a single CCT gene in Saccharomyces cerevisiae causes an increase of the corresponding Cct subunit, but not of the Cct complex."
- statement: Showed that CCT subunits form a stoichiometric array of eight different subunits in two rings
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:16554755
title: Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
findings: []
- id: PMID:16622836
title: The plasma membrane proteome of Saccharomyces cerevisiae and its response
to the antifungal calcofluor.
findings: []
- id: PMID:16762366
title: Quantitative actin folding reactions using yeast CCT purified via an internal
tag in the CCT3/gamma subunit.
findings:
- statement: Developed efficient purification protocol for yeast CCT
supporting_text: "An efficient purification protocol for CCT from Saccharomyces cerevisiae has been developed."
- statement: Demonstrated quantitative actin folding by purified yeast CCT in vitro
supporting_text: "Yeast CCT catalyses the folding of yeast ACT1p and human beta-actin with nearly identical rate constants and yields."
- statement: CCT catalyses folding via a binding pre-equilibrium followed by ATP-driven processing
supporting_text: "The results from this controlled CCT-actin folding assay are consistent with a model where CCT and Ac(I) are in a binding pre-equilibrium with a rate-limiting binding step, followed by a faster ATP-driven processing to native actin."
- id: PMID:19536198
title: 'An atlas of chaperone-protein interactions in Saccharomyces cerevisiae:
implications to protein folding pathways in the cell.'
findings: []
- id: PMID:20489023
title: A global protein kinase and phosphatase interaction network in yeast.
findings: []
- id: PMID:21701561
title: The crystal structure of yeast CCT reveals intrinsic asymmetry of eukaryotic
cytosolic chaperonins.
findings:
- statement: Solved crystal structure of yeast CCT in complex with actin at 3.8 Å
supporting_text: "We have solved the crystal structure of yeast CCT in complex with actin at 3.8 Å resolution, revealing the subunit organisation and the location of discrete patches of co-evolving 'signature residues' that mediate specific interactions between CCT and its substrates."
- statement: Revealed intrinsic asymmetry and subunit individuality in the complex
supporting_text: "The intrinsic asymmetry is revealed by the structural individuality of the CCT subunits, which display unique configurations, substrate binding properties, ATP-binding heterogeneity and subunit-subunit interactions."
- statement: CCT uses a sequential rather than concerted ATP hydrolysis mechanism
supporting_text: "the mechanism by which CCT assists folding is distinct from other chaperonins, with no hydrophobic wall lining a potential Anfinsen cage, and a sequential rather than concerted ATP hydrolysis mechanism."
- id: PMID:27107014
title: An inter-species protein-protein interaction network across vast evolutionary
distance.
findings: []
- id: PMID:37968396
title: The social and structural architecture of the yeast protein interactome.
findings: []
- id: PMID:9878052
title: 'Compartmentation of protein folding in vivo: sequestration of non-native
polypeptide by the chaperonin-GimC system.'
findings:
- statement: TRiC and GimC form an integrated folding compartment for newly synthesized actin
supporting_text: "We propose that TRiC and GimC form an integrated 'folding compartment' which functions in cooperation with the translation machinery."
- statement: GimC accelerates actin folding on TRiC at least 5-fold
supporting_text: "GimC accelerates actin folding at least 5-fold and prevents the premature release of non-native protein from TRiC."
- id: UniProt:P12612
title: UniProtKB entry for Saccharomyces cerevisiae TCP1/CCT1
findings:
- statement: TCP1 encodes CCT-alpha, a member of the TCP-1 chaperonin family.
supporting_text: "RecName: Full=T-complex protein 1 subunit alpha; Short=TCP-1-alpha; AltName: Full=CCT-alpha;"
- id: file:yeast/TCP1/TCP1-deep-research-falcon.md
title: Falcon deep research report for yeast TCP1/CCT1
findings:
- statement: TCP1/CCT1 is a TRiC/CCT subunit in the cytosolic ATP-dependent chaperonin complex.
supporting_text: >-
TCP1/CCT1 encodes CCT1 (TCP-1; CCT-alpha), one of eight paralogous
subunits that assemble into the eukaryotic cytosolic chaperonin
TRiC/CCT.
- id: file:interpro/panther/PTHR11353/PTHR11353-metadata.yaml
title: PANTHER family PTHR11353 chaperonin metadata
findings:
- statement: PTHR11353 supports TCP1 as part of the conserved chaperonin family.
supporting_text: PANTHER family PTHR11353 is named CHAPERONIN and integrates InterPro IPR017998.
core_functions:
- 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
description: >-
TCP1 is the alpha subunit of the TRiC/CCT chaperonin complex. It contributes to the
complex-level ATP-dependent protein folding chaperone activity (GO:0140662) that folds
actin, tubulin, and other substrates. Individual subunits do not independently fold
substrates; the activity emerges from the assembled hetero-oligomeric complex. The
crystal structure (PMID:21701561) reveals that each subunit has unique configurations
and substrate-binding properties, suggesting specialized roles within the complex.
TCP1 binds ATP and contributes ATPase activity to the sequential ATP hydrolysis
mechanism that drives the chaperonin cycle.
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_id: PMID:21701561
supporting_text: "The cytosolic chaperonin CCT is a 1-MDa protein-folding machine essential for eukaryotic life."
- reference_id: file:yeast/TCP1/TCP1-deep-research-falcon.md
supporting_text: >-
TCP1/CCT1 encodes CCT1 (TCP-1; CCT-alpha), one of eight paralogous
subunits that assemble into the eukaryotic cytosolic chaperonin
TRiC/CCT. TRiC/CCT is a ~1 MDa ATP-dependent double-ring machine,
with eight distinct subunits per ring.
- reference_id: file:interpro/panther/PTHR11353/PTHR11353-metadata.yaml
supporting_text: PANTHER family PTHR11353 is named CHAPERONIN and supports TCP1/CCT1 membership in the conserved chaperonin family.
proposed_new_terms: []
suggested_questions:
- question: >-
Which yeast TRiC/CCT substrates require CCT1-specific apical or
chamber-facing contacts rather than generic complex-level chaperonin
activity?
- question: >-
Should the emerging nuclear TRiC/CCT RNA polymerase II role be curated for
TCP1 after peer-reviewed confirmation, or treated as a non-core complex
phenotype?
suggested_experiments:
- experiment_type: client-specific folding assay
hypothesis: >-
CCT1 contributes substrate-specific contacts that are required for
efficient folding of selected actin, tubulin, or WD40-repeat clients.
description: >-
Combine CCT1 apical/chamber-surface mutants with purified yeast TRiC
folding assays and in vivo client abundance/activity readouts for ACT1,
tubulins, Cdh1, and Cdc20.
- experiment_type: nuclear TRiC validation
hypothesis: >-
The nuclear RNA polymerase II phenotype of cct1-2 reflects assembled
TRiC/CCT function rather than indirect cytoplasmic proteostasis stress.
description: >-
Validate nuclear TRiC occupancy and RNAPII/RNA phenotypes using
independently tagged CCT subunits, acute degron or anchor-away
perturbations, and rescue with cytoplasm-restricted versus
nucleus-permissive CCT1 variants.