PFD1 encodes the Pfd1/Gim6 beta-type subunit of the cytosolic prefoldin complex, an ATP-independent cochaperone that captures nonnative actin and tubulin folding intermediates and delivers them to CCT/TRiC, with secondary nuclear roles in transcription elongation.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0006457
protein folding
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: protein folding reviewed for PFD1: ACCEPT.
Reason: Retain as the direct biological process served by Pfd1-containing prefoldin in cytosolic actin/tubulin folding.
Supporting Evidence:
file:yeast/PFD1/PFD1-deep-research-falcon.md
as part of the prefoldin/GimC complex it **captures and stabilizes unfolded actin and tubulin intermediates** and **hands them to CCT/TRiC**
|
|
GO:0051082
unfolded protein binding
|
IBA
GO_REF:0000033 |
MODIFY |
Summary: unfolded protein binding reviewed for PFD1: MODIFY.
Reason: Unfolded protein binding is mechanistically close but too broad; Pfd1 is best represented as a prefoldin protein-folding cochaperone.
Proposed replacements:
protein folding chaperone
Supporting Evidence:
file:yeast/PFD1/PFD1-deep-research-falcon.md
prefoldin functions largely as an **ATP-independent holdase**, stabilizing folding intermediates and preventing aggregation prior to transfer to CCT/TRiC
|
|
GO:0005737
cytoplasm
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: cytoplasm reviewed for PFD1: ACCEPT.
Reason: Retain as the principal cellular compartment for the canonical prefoldin to CCT/TRiC folding pathway.
Supporting Evidence:
file:yeast/PFD1/PFD1-deep-research-falcon.md
The central pathway involving Pfd1 is the **cytosolic folding pipeline** for cytoskeletal proteins
|
|
GO:0044183
protein folding chaperone
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: protein folding chaperone reviewed for PFD1: ACCEPT.
Reason: Retain as the best molecular-function term for the ATP-independent prefoldin cochaperone role.
Supporting Evidence:
file:yeast/PFD1/PFD1-deep-research-falcon.md
Pfd1's primary function is **structural/cochaperone activity**, not catalysis
|
|
GO:0005737
cytoplasm
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: cytoplasm reviewed for PFD1: ACCEPT.
Reason: Retain as the principal cellular compartment for the canonical prefoldin to CCT/TRiC folding pathway.
Supporting Evidence:
file:yeast/PFD1/PFD1-deep-research-falcon.md
The central pathway involving Pfd1 is the **cytosolic folding pipeline** for cytoskeletal proteins
|
|
GO:0006457
protein folding
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: protein folding reviewed for PFD1: ACCEPT.
Reason: Retain as the direct biological process served by Pfd1-containing prefoldin in cytosolic actin/tubulin folding.
Supporting Evidence:
file:yeast/PFD1/PFD1-deep-research-falcon.md
as part of the prefoldin/GimC complex it **captures and stabilizes unfolded actin and tubulin intermediates** and **hands them to CCT/TRiC**
|
|
GO:0016272
prefoldin complex
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: prefoldin complex reviewed for PFD1: ACCEPT.
Reason: Retain; Pfd1/Gim6 is a component of the heterohexameric prefoldin complex.
Supporting Evidence:
file:yeast/PFD1/PFD1-deep-research-falcon.md
Canonical eukaryotic prefoldin contains **six distinct subunits (PFD1-PFD6)**, organized as **two alpha-type** and **four beta-type** subunits
|
|
GO:0051082
unfolded protein binding
|
IEA
GO_REF:0000002 |
MODIFY |
Summary: unfolded protein binding reviewed for PFD1: MODIFY.
Reason: Unfolded protein binding is mechanistically close but too broad; Pfd1 is best represented as a prefoldin protein-folding cochaperone.
Proposed replacements:
protein folding chaperone
Supporting Evidence:
file:yeast/PFD1/PFD1-deep-research-falcon.md
prefoldin functions largely as an **ATP-independent holdase**, stabilizing folding intermediates and preventing aggregation prior to transfer to CCT/TRiC
|
|
GO:0005515
protein binding
|
IPI
PMID:16429126 Proteome survey reveals modularity of the yeast cell machine... |
MARK AS OVER ANNOTATED |
Summary: protein binding reviewed for PFD1: MARK_AS_OVER_ANNOTATED.
Reason: Protein binding is too generic for curation; prefoldin complex membership and chaperone activity capture the functional interaction context.
Supporting Evidence:
file:yeast/PFD1/PFD1-deep-research-falcon.md
prefoldin binds client proteins via the distal regions ("tentacle tips") and/or the cavity of the hexamer
|
|
GO:0005515
protein binding
|
IPI
PMID:16554755 Global landscape of protein complexes in the yeast Saccharom... |
MARK AS OVER ANNOTATED |
Summary: protein binding reviewed for PFD1: MARK_AS_OVER_ANNOTATED.
Reason: Protein binding is too generic for curation; prefoldin complex membership and chaperone activity capture the functional interaction context.
Supporting Evidence:
file:yeast/PFD1/PFD1-deep-research-falcon.md
prefoldin binds client proteins via the distal regions ("tentacle tips") and/or the cavity of the hexamer
|
|
GO:0005515
protein binding
|
IPI
PMID:19536198 An atlas of chaperone-protein interactions in Saccharomyces ... |
MARK AS OVER ANNOTATED |
Summary: protein binding reviewed for PFD1: MARK_AS_OVER_ANNOTATED.
Reason: Protein binding is too generic for curation; prefoldin complex membership and chaperone activity capture the functional interaction context.
Supporting Evidence:
file:yeast/PFD1/PFD1-deep-research-falcon.md
prefoldin binds client proteins via the distal regions ("tentacle tips") and/or the cavity of the hexamer
|
|
GO:0005515
protein binding
|
IPI
PMID:37968396 The social and structural architecture of the yeast protein ... |
MARK AS OVER ANNOTATED |
Summary: protein binding reviewed for PFD1: MARK_AS_OVER_ANNOTATED.
Reason: Protein binding is too generic for curation; prefoldin complex membership and chaperone activity capture the functional interaction context.
Supporting Evidence:
file:yeast/PFD1/PFD1-deep-research-falcon.md
prefoldin binds client proteins via the distal regions ("tentacle tips") and/or the cavity of the hexamer
|
|
GO:0005515
protein binding
|
IPI
PMID:9878052 Compartmentation of protein folding in vivo: sequestration o... |
MARK AS OVER ANNOTATED |
Summary: protein binding reviewed for PFD1: MARK_AS_OVER_ANNOTATED.
Reason: Protein binding is too generic for curation; prefoldin complex membership and chaperone activity capture the functional interaction context.
Supporting Evidence:
file:yeast/PFD1/PFD1-deep-research-falcon.md
prefoldin binds client proteins via the distal regions ("tentacle tips") and/or the cavity of the hexamer
|
|
GO:0006457
protein folding
|
NAS
PMID:9463374 A novel protein complex promoting formation of functional al... |
ACCEPT |
Summary: protein folding reviewed for PFD1: ACCEPT.
Reason: Retain as the direct biological process served by Pfd1-containing prefoldin in cytosolic actin/tubulin folding.
Supporting Evidence:
file:yeast/PFD1/PFD1-deep-research-falcon.md
Yeast prefoldin/GimC physically interacts with TRiC/CCT in vivo and in vitro
|
|
GO:0032968
positive regulation of transcription elongation by RNA polymerase II
|
IMP
PMID:24068951 The prefoldin complex regulates chromatin dynamics during tr... |
KEEP AS NON CORE |
Summary: positive regulation of transcription elongation by RNA polymerase II reviewed for PFD1: KEEP_AS_NON_CORE.
Reason: Keep as an evidence-supported secondary nuclear/chromatin role, but do not treat it as the core evolved role of Pfd1.
Supporting Evidence:
file:yeast/PFD1/PFD1-deep-research-falcon.md
PFD1 deletion reduces RNAPII occupancy across gene bodies
|
|
GO:0032968
positive regulation of transcription elongation by RNA polymerase II
|
IGI
PMID:24068951 The prefoldin complex regulates chromatin dynamics during tr... |
KEEP AS NON CORE |
Summary: positive regulation of transcription elongation by RNA polymerase II reviewed for PFD1: KEEP_AS_NON_CORE.
Reason: Keep as an evidence-supported secondary nuclear/chromatin role, but do not treat it as the core evolved role of Pfd1.
Supporting Evidence:
file:yeast/PFD1/PFD1-deep-research-falcon.md
PFD1 deletion reduces RNAPII occupancy across gene bodies
|
|
GO:0006457
protein folding
|
IMP
PMID:9630229 Prefoldin, a chaperone that delivers unfolded proteins to cy... |
ACCEPT |
Summary: protein folding reviewed for PFD1: ACCEPT.
Reason: Retain as the direct biological process served by Pfd1-containing prefoldin in cytosolic actin/tubulin folding.
Supporting Evidence:
file:yeast/PFD1/PFD1-deep-research-falcon.md
actin folding by TRiC is slowed ~5-fold compared with wild type
|
|
GO:0007010
cytoskeleton organization
|
IMP
PMID:9630229 Prefoldin, a chaperone that delivers unfolded proteins to cy... |
KEEP AS NON CORE |
Summary: cytoskeleton organization reviewed for PFD1: KEEP_AS_NON_CORE.
Reason: Keep as a downstream consequence of actin/tubulin folding defects rather than the direct molecular role.
Supporting Evidence:
file:yeast/PFD1/PFD1-deep-research-falcon.md
gim deletion mutants exhibit actin and tubulin phenotypes resembling TRiC mutants
|
|
GO:0016272
prefoldin complex
|
IMP
PMID:9630229 Prefoldin, a chaperone that delivers unfolded proteins to cy... |
ACCEPT |
Summary: prefoldin complex reviewed for PFD1: ACCEPT.
Reason: Retain; Pfd1/Gim6 is a component of the heterohexameric prefoldin complex.
Supporting Evidence:
file:yeast/PFD1/PFD1-deep-research-falcon.md
Canonical eukaryotic prefoldin contains **six distinct subunits (PFD1-PFD6)**, organized as **two alpha-type** and **four beta-type** subunits
|
|
GO:0051082
unfolded protein binding
|
IMP
PMID:9630229 Prefoldin, a chaperone that delivers unfolded proteins to cy... |
MODIFY |
Summary: unfolded protein binding reviewed for PFD1: MODIFY.
Reason: Unfolded protein binding is mechanistically close but too broad; Pfd1 is best represented as a prefoldin protein-folding cochaperone.
Proposed replacements:
protein folding chaperone
Supporting Evidence:
file:yeast/PFD1/PFD1-deep-research-falcon.md
prefoldin functions largely as an **ATP-independent holdase**, stabilizing folding intermediates and preventing aggregation prior to transfer to CCT/TRiC
|
Q: Which Pfd1-containing prefoldin surfaces distinguish cytoskeletal client capture from the secondary nuclear transcription role?
Q: Does Pfd1 have subunit-specific client preferences within yeast prefoldin beyond the canonical actin and tubulin pathway?
Experiment: Generate Pfd1 separation-of-function mutants at endogenous expression levels and compare actin/tubulin folding, prefoldin complex integrity, chromatin occupancy, and RNA polymerase II elongation phenotypes.
Hypothesis: Pfd1 has separable surfaces for canonical actin/tubulin cochaperone function and non-core transcription-associated function.
Type: separation-of-function mutagenesis
provider: falcon
model: Edison Scientific Literature
cached: false
start_time: '2026-05-04T11:07:42.209301'
end_time: '2026-05-04T11:20:10.413564'
duration_seconds: 748.2
template_file: templates/gene_research_go_focused.md
template_variables:
organism: yeast
gene_id: PFD1
gene_symbol: PFD1
uniprot_accession: P46988
protein_description: 'RecName: Full=Prefoldin subunit 1; AltName: Full=Genes involved
in microtubule biogenesis protein 6; AltName: Full=Gim complex subunit 6; Short=GimC
subunit 6;'
gene_info: Name=PFD1; Synonyms=GIM6; OrderedLocusNames=YJL179W; ORFNames=J0488;
organism_full: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
protein_family: Belongs to the prefoldin subunit beta family.
protein_domains: PFD_beta-like. (IPR002777); Prefoldin. (IPR009053); Prefoldin_2
(PF01920)
provider_config:
timeout: 600
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citation_count: 38
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 'PFD1' 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 PFD1 (gene ID: PFD1, UniProt: P46988) 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 'PFD1' 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 PFD1 (gene ID: PFD1, UniProt: P46988) 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 literature retrieved here is consistent that S. cerevisiae PFD1 is the prefoldin subunit also called Gim6 (Genes Involved in Microtubule biogenesis), encoded by YJL179W, and corresponds to the canonical eukaryotic prefoldin subunit often denoted PFDN1 in cross-species nomenclature. This matches the UniProt-provided description (Prefoldin subunit 1; Gim complex subunit 6; prefoldin β-family member), and no conflicting “PFD1” identity from another organism was used for functional claims in this report. (millanzambrano2014nuclearfunctionsof pages 2-3, tahmaz2023prefoldin2contributes pages 1-2)
Eukaryotic prefoldin (also termed GimC in yeast) is a heterohexameric cochaperone whose best-characterized role is to bind non-native nascent polypeptides—especially actin and tubulins—and deliver them to the cytosolic group II chaperonin CCT/TRiC for ATP-dependent folding. Prefoldin functions largely as an ATP-independent holdase, stabilizing folding intermediates and preventing aggregation prior to transfer to CCT/TRiC. (simons2004selectivecontributionof pages 1-2, millanzambrano2014nuclearfunctionsof pages 2-3, tahmaz2023prefoldin2contributes pages 1-2)
Canonical eukaryotic prefoldin contains six distinct subunits (PFD1–PFD6), organized as two α-type and four β-type subunits. In budding yeast, the complex is described as containing α subunits Pac10/Pfd3 and Gim5/Pfd5, and β subunits Pfd1 (Gim6), Gim4/Pfd2, Gim3/Pfd4, and Yke2/Pfd6. (tahmaz2023prefoldin2contributes pages 1-2, millanzambrano2014nuclearfunctionsof pages 2-3)
Structural syntheses place PFD1 (with PFD5 and PFD6) on one side of the “jellyfish-like” prefoldin hexamer, opposite PFD2/PFD3/PFD4. This arrangement rationalizes how different subunits contribute to distinct client-binding surfaces while preserving a shared central cavity. (arranz2018structureandfunction pages 1-3, simons2004selectivecontributionof pages 7-8)
Pfd1’s primary function is structural/cochaperone activity, not catalysis: as part of the prefoldin/GimC complex it captures and stabilizes unfolded actin and tubulin intermediates and hands them to CCT/TRiC for final folding, enabling cytoskeleton assembly. (simons2004selectivecontributionof pages 1-2, millanzambrano2014nuclearfunctionsof pages 2-3, tahmaz2023prefoldin2contributes pages 1-2)
Yeast prefoldin/GimC physically interacts with TRiC/CCT in vivo and in vitro, and gim deletion mutants exhibit actin and tubulin phenotypes resembling TRiC mutants, supporting a shared folding pathway. Importantly, in strains deleted for one or more GIM genes, actin folding by TRiC is slowed ~5-fold compared with wild type, consistent with prefoldin increasing folding efficiency by facilitating productive substrate handling/release. (leroux1999mtgimcanovel pages 1-2)
Biochemical reconstitution and binding assays support that prefoldin binds client proteins via the distal regions (“tentacle tips”) and/or the cavity of the hexamer. The tentacle tips are required for stable binary complexes with actin and tubulin, and different but overlapping sets of subunits contribute to actin vs tubulin binding, implying subunit-specific client-recognition contributions within the shared complex. (simons2004selectivecontributionof pages 8-8, simons2004selectivecontributionof pages 1-2)
The central pathway involving Pfd1 is the cytosolic folding pipeline for cytoskeletal proteins: prefoldin binds nascent/non-native actin/tubulin and transfers them to CCT/TRiC for folding into assembly-competent monomers that form actin filaments and microtubules. This functional axis explains why prefoldin mutants show cytoskeletal abnormalities. (millanzambrano2014nuclearfunctionsof pages 2-3, leroux1999mtgimcanovel pages 1-2)
Beyond cytoskeletal folding, yeast prefoldin has a well-supported nuclear function: it is present in the nucleus, and a subset of prefoldin subunits is recruited to chromatin in a transcription-dependent manner. Functionally, prefoldin influences RNA polymerase II elongation rate, with pronounced effects on long genes and TATA-containing promoters, and is linked to histone dynamics after nucleosome remodeling (cotranscriptional histone eviction). (millanzambrano2013theprefoldincomplex pages 1-2)
For Pfd1 specifically, a prefoldin-focused review summarizes evidence that PFD1 deletion reduces RNAPII occupancy across gene bodies, consistent with an elongation/chromatin role for Pfd1-containing prefoldin in yeast. (tahmaz2022prefoldinfunctionin pages 3-5)
The canonical prefoldin role implies predominant cytosolic localization (client binding and transfer to cytosolic CCT/TRiC), but multiple sources support that prefoldin subunits can also localize to the nucleus and associate with chromatin under transcriptional engagement and/or stress conditions. (millanzambrano2014nuclearfunctionsof pages 2-3, millanzambrano2013theprefoldincomplex pages 1-2, tahmaz2022prefoldinfunctionin pages 3-5)
A 2023 study in BMC Biology extended yeast prefoldin biology beyond cytoskeleton folding by showing that loss of Pfd2/Gim4 affects mitochondrial morphology, respiratory growth, and abundance of some respiratory chain complexes, and that Pfd2 interacts with the mitochondrial import receptor Tom70. While this is not Pfd1-specific, it supports the emerging view that prefoldin supports broader cytosolic proteostasis relevant to organellar protein biogenesis and stress tolerance (consistent with prefoldin’s ATP-independent holdase activity). (tahmaz2023prefoldin2contributes pages 1-2)
Publication date/URL: Sep 2023, https://doi.org/10.1186/s12915-023-01695-y (tahmaz2023prefoldin2contributes pages 1-2)
A 2024 bioRxiv preprint reported a non-canonical role for yeast Pfd5 in 26S proteasome assembly, specifically affecting formation of the Rpt AAA+ ATPase ring (19S base). Only PFD5 deletion among single prefoldin subunit deletions reduced 26S activity in their assays, arguing for subunit-specific contributions to proteostasis machinery beyond canonical actin/tubulin delivery. This provides a contemporary example of prefoldin subunits acquiring additional functions, and contextualizes Pfd1’s established nuclear and cytoskeletal roles in a broader proteostasis network. (ghahe2024identificationofa pages 1-5, ghahe2024identificationofa pages 12-15)
Publication date/URL: Apr 2024, https://doi.org/10.1101/2024.04.22.590501 (ghahe2024identificationofa pages 1-5)
Within the retrieved 2023–2024 corpus, no new Pfd1/Gim6-specific biochemical activity beyond the established canonical prefoldin role (actin/tubulin handoff to CCT) and prior-described nuclear/transcription functions was identified. This likely reflects either genuine research sparsity on Pfd1-specific mechanisms in that period or retrieval limitations. (tahmaz2023prefoldin2contributes pages 1-2, ghahe2024identificationofa pages 1-5)
Recent pathway-level work (in fungal systems) supports the concept that disrupting GimC/prefoldin-dependent processes yields characteristic phenotypes (e.g., nuclear positioning and actin/cell wall defects) and can be exploited as a mechanistic probe for cytoskeleton-linked vulnerabilities. While not a Pfd1-specific application, this highlights prefoldin biology as actionable for functional dissection of cytoskeletal biogenesis pathways and antifungal target discovery approaches at the pathway level. (tahmaz2023prefoldin2contributes pages 1-2)
Because prefoldin subunits are non-essential in yeast yet yield informative phenotypes in cytoskeleton and transcription, prefoldin mutants (including pfd1/gim6 perturbations) are useful for dissecting: (i) chaperone-assisted cytoskeletal biogenesis, (ii) coupling of proteostasis to transcription/chromatin dynamics, and (iii) stress responses that may involve nuclear relocalization of chaperone components. (millanzambrano2014nuclearfunctionsof pages 2-3, millanzambrano2013theprefoldincomplex pages 1-2, tahmaz2022prefoldinfunctionin pages 3-5)
Authoritative reviews emphasize that prefoldin’s canonical function—delivery of actin/tubulin to CCT/TRiC—is well established, but accumulating evidence supports broader roles in protein homeostasis, transcription regulation, and protein turnover, sometimes involving subunit-specific behavior and alternative assemblies. In yeast, this aligns with findings that prefoldin is present in the nucleus/chromatin and affects transcription elongation, and with more recent yeast studies demonstrating non-canonical subunit roles (e.g., Pfd5 in proteasome assembly; Pfd2 in mitochondrial-related phenotypes). (millanzambrano2014nuclearfunctionsof pages 2-3, tahmaz2023prefoldin2contributes pages 1-2, ghahe2024identificationofa pages 1-5)
Given the strongest direct evidence, Pfd1/Gim6 should be annotated primarily as a β-type canonical prefoldin subunit required for efficient actin/tubulin biogenesis via CCT/TRiC. A secondary, evidence-supported annotation is involvement in nuclear gene expression control, especially transcription elongation and chromatin/histone dynamics, likely reflecting either (i) nuclear localization of the prefoldin complex/subunits or (ii) a bridging role connecting proteostasis and transcriptional machinery under basal and stress conditions. (leroux1999mtgimcanovel pages 1-2, millanzambrano2013theprefoldincomplex pages 1-2, tahmaz2022prefoldinfunctionin pages 3-5)
A representative structural schematic/model of the prefoldin hexamer showing the proposed arrangement of subunits (including PFD1) is available from Simons et al. (JBC 2004). (simons2004selectivecontributionof media b05b75fc)
The following table consolidates identity, function, localization, pathways, and quantitative evidence for yeast PFD1/GIM6.
| Aspect | Summary | Evidence (with citation IDs) | Source URL + publication date |
|---|---|---|---|
| Gene/protein identity | PFD1 in Saccharomyces cerevisiae corresponds to Gim6/YJL179W and is the yeast ortholog of PFDN1; it matches UniProt P46988 and is part of the canonical prefoldin/GimC system rather than an unrelated PFD1 symbol from another organism. | (millanzambrano2014nuclearfunctionsof pages 2-3, arranz2018structureandfunction pages 1-3, tahmaz2023prefoldin2contributes pages 1-2) | https://doi.org/10.1098/rsob.140085 (2014-07); https://doi.org/10.1007/978-3-030-00737-9_9 (2018-01); https://doi.org/10.1186/s12915-023-01695-y (2023-09) |
| Subunit type | Pfd1/Gim6 is a β-type prefoldin subunit. Canonical eukaryotic prefoldin contains 2 α-type + 4 β-type subunits; the β set is Pfd1, Pfd2/Gim4, Pfd4/Gim3, Pfd6/Yke2. | (tahmaz2023prefoldin2contributes pages 1-2, millanzambrano2014nuclearfunctionsof pages 2-3) | https://doi.org/10.1186/s12915-023-01695-y (2023-09); https://doi.org/10.1098/rsob.140085 (2014-07); https://doi.org/10.1186/s12915-023-01695-y (2023-09) |
| Complex membership | Pfd1 is a component of the canonical heterohexameric prefoldin complex (GimC/PFD), a jellyfish-like cochaperone made of six distinct subunits (PFD1–PFD6). Structural models place PFD1/PFD5/PFD6 on one side of the hexamer, opposite PFD2/PFD3/PFD4. | (arranz2018structureandfunction pages 1-3, simons2004selectivecontributionof pages 7-8, simons2004selectivecontributionof media b05b75fc) | https://doi.org/10.1007/978-3-030-00737-9_9 (2018-01); https://doi.org/10.1007/978-3-030-00737-9_9 (2018-01); https://doi.org/10.1074/jbc.m306053200 (2004-02) |
| Primary molecular function | Pfd1’s primary role is as part of an ATP-independent holdase/cochaperone that captures non-native or nascent actin and tubulin and delivers them to the cytosolic group II chaperonin CCT/TRiC for productive folding and cytoskeletal biogenesis. It is not an enzyme or transporter. | (simons2004selectivecontributionof pages 1-2, millanzambrano2014nuclearfunctionsof pages 2-3, liang2020thefunctionsand pages 1-2, tahmaz2023prefoldin2contributes pages 1-2) | https://doi.org/10.1074/jbc.m306053200 (2004-02); https://doi.org/10.1098/rsob.140085 (2014-07); https://doi.org/10.1186/s13578-020-00446-8 (2020-07); https://doi.org/10.1186/s12915-023-01695-y (2023-09) |
| Substrate specificity / clients | The best-established native clients are cytoskeletal proteins, especially actin and α/β-tubulin. Eukaryotic prefoldin uses tentacle/cavity regions to bind these folding intermediates before handoff to CCT. | (simons2004selectivecontributionof pages 1-2, simons2004selectivecontributionof pages 8-8, yang2024prefoldinsubunitsand pages 2-4, herranzmontoya2021acomprehensiveanalysis pages 5-7) | https://doi.org/10.1074/jbc.m306053200 (2004-02); https://doi.org/10.1074/jbc.m306053200 (2004-02); https://doi.org/10.3390/plants13040556 (2024-02); https://doi.org/10.1016/j.isci.2021.103273 (2021-11) |
| Mechanistic pathway | Pfd1 functions in the prefoldin → CCT/TRiC pathway for cytoskeletal protein biogenesis. Yeast GimC physically interacts with TRiC/CCT in vivo and in vitro, consistent with direct substrate transfer rather than an indirect effect. | (leroux1999mtgimcanovel pages 1-2, herranzmontoya2021acomprehensiveanalysis pages 5-7, tahmaz2023prefoldin2contributes pages 1-2) | https://doi.org/10.1093/emboj/18.23.6730 (1999-12); https://doi.org/10.1016/j.isci.2021.103273 (2021-11); https://doi.org/10.1186/s12915-023-01695-y (2023-09) |
| Quantitative evidence for canonical role | In yeast, loss of Gim/prefoldin function slows actin folding by ~5-fold and prefoldin increases cytoskeletal protein folding efficiency by about 5-fold; defects are linked to slower actin release from TRiC and leakage of non-native polypeptides. | (leroux1999mtgimcanovel pages 1-2, herranzmontoya2021acomprehensiveanalysis pages 5-7, liang2020thefunctionsand pages 1-2) | https://doi.org/10.1093/emboj/18.23.6730 (1999-12); https://doi.org/10.1016/j.isci.2021.103273 (2021-11); https://doi.org/10.1186/s13578-020-00446-8 (2020-07) |
| Cytoskeletal phenotypes on loss | Deletion/mutation of yeast prefoldin subunits causes actin and tubulin cytoskeletal defects, including impaired microtubule-related functions; these phenotypes resemble TRiC/CCT mutant phenotypes, supporting a shared folding pathway. | (millanzambrano2014nuclearfunctionsof pages 2-3, simons2004selectivecontributionof pages 1-2, leroux1999mtgimcanovel pages 1-2, blancotourinan2021ageneticapproach pages 1-2) | https://doi.org/10.1098/rsob.140085 (2014-07); https://doi.org/10.1074/jbc.m306053200 (2004-02); https://doi.org/10.1093/emboj/18.23.6730 (1999-12); https://doi.org/10.1093/plphys/kiab348 (2021-07) |
| Localization | The main canonical site of action is the cytosol, where prefoldin captures nascent clients and hands them to CCT/TRiC. However, prefoldin subunits are also detected in the nucleus, and some are recruited to chromatin in a transcription-dependent manner. | (millanzambrano2014nuclearfunctionsof pages 2-3, millanzambrano2013theprefoldincomplex pages 1-2) | https://doi.org/10.1098/rsob.140085 (2014-07); https://doi.org/10.1371/journal.pgen.1003776 (2013-09); https://doi.org/10.1371/journal.pgen.1003776 (2013-09) |
| Non-canonical/nuclear role | Beyond cytoskeletal folding, yeast prefoldin contributes to transcription elongation and chromatin dynamics. In particular, PFD1 deletion reduces RNA polymerase II occupancy across gene bodies, implicating Pfd1 in elongation and histone removal/remodeling-linked processes. | (millanzambrano2013theprefoldincomplex pages 1-2, tahmaz2022prefoldinfunctionin pages 3-5) | https://doi.org/10.1371/journal.pgen.1003776 (2013-09); https://doi.org/10.3389/fcell.2021.816214 (2022-01) |
| Stress-linked nuclear function | Prefoldin subunits including Pfd1 can relocalize to the nucleus under stress to support transcription of stress-response genes, reinforcing that at least part of Pfd1 function is condition-dependent and nuclear. | (tahmaz2022prefoldinfunctionin pages 3-5, millanzambrano2014nuclearfunctionsof pages 2-3) | https://doi.org/10.3389/fcell.2021.816214 (2022-01); https://doi.org/10.1098/rsob.140085 (2014-07) |
| Essentiality and annotation confidence | PFD1 is non-essential for yeast viability, but this does not imply dispensability: loss of a single prefoldin subunit can destabilize the hexamer and produce clear cytoskeletal, transcriptional, and proteostasis defects. | (millanzambrano2014nuclearfunctionsof pages 2-3, herranzmontoya2021acomprehensiveanalysis pages 5-7, tahmaz2023prefoldin2contributes pages 1-2) | https://doi.org/10.1098/rsob.140085 (2014-07); https://doi.org/10.1016/j.isci.2021.103273 (2021-11); https://doi.org/10.1186/s12915-023-01695-y (2023-09) |
| Recent developments (2023–2024) | Recent yeast work broadens prefoldin biology beyond actin/tubulin folding: Pfd2 was linked to mitochondrial morphology/respiratory growth (2023), and Pfd5 to 26S proteasome assembly (2024 preprint). These findings support a broader proteostasis network role for prefoldin, although they do not yet provide a new Pfd1-specific biochemical function beyond its established canonical and nuclear roles. | (tahmaz2023prefoldin2contributes pages 1-2, ghahe2024identificationofa pages 1-5, ghahe2024identificationofa pages 12-15) | https://doi.org/10.1186/s12915-023-01695-y (2023-09); https://doi.org/10.1101/2024.04.22.590501 (2024-04); https://doi.org/10.1101/2024.04.22.590501 (2024-04) |
Table: This table summarizes the best-supported functional annotation points for yeast PFD1/GIM6/YJL179W, including its identity, canonical prefoldin role, localization, nuclear functions, and representative quantitative evidence. It is useful as a compact evidence map for interpreting UniProt P46988 in the context of yeast proteostasis and gene expression.
References
(millanzambrano2014nuclearfunctionsof pages 2-3): Gonzalo Millán-Zambrano and Sebastián Chávez. Nuclear functions of prefoldin. Open Biology, 4:140085, Jul 2014. URL: https://doi.org/10.1098/rsob.140085, doi:10.1098/rsob.140085. This article has 91 citations and is from a peer-reviewed journal.
(tahmaz2023prefoldin2contributes pages 1-2): Ismail Tahmaz, Somayeh Shahmoradi Ghahe, Monika Stasiak, Kamila P. Liput, Katarzyna Jonak, and Ulrike Topf. Prefoldin 2 contributes to mitochondrial morphology and function. BMC Biology, Sep 2023. URL: https://doi.org/10.1186/s12915-023-01695-y, doi:10.1186/s12915-023-01695-y. This article has 13 citations and is from a domain leading peer-reviewed journal.
(simons2004selectivecontributionof pages 1-2): C. Torrey Simons, An Staes, Heidi Rommelaere, Christophe Ampe, Sally A. Lewis, and Nicholas J. Cowan. Selective contribution of eukaryotic prefoldin subunits to actin and tubulin binding*. Journal of Biological Chemistry, 279:4196-4203, Feb 2004. URL: https://doi.org/10.1074/jbc.m306053200, doi:10.1074/jbc.m306053200. This article has 75 citations and is from a domain leading peer-reviewed journal.
(arranz2018structureandfunction pages 1-3): Rocío Arranz, Jaime Martín-Benito, and José M. Valpuesta. Structure and function of the cochaperone prefoldin. Advances in experimental medicine and biology, 1106:119-131, Jan 2018. URL: https://doi.org/10.1007/978-3-030-00737-9_9, doi:10.1007/978-3-030-00737-9_9. This article has 32 citations and is from a peer-reviewed journal.
(simons2004selectivecontributionof pages 7-8): C. Torrey Simons, An Staes, Heidi Rommelaere, Christophe Ampe, Sally A. Lewis, and Nicholas J. Cowan. Selective contribution of eukaryotic prefoldin subunits to actin and tubulin binding*. Journal of Biological Chemistry, 279:4196-4203, Feb 2004. URL: https://doi.org/10.1074/jbc.m306053200, doi:10.1074/jbc.m306053200. This article has 75 citations and is from a domain leading peer-reviewed journal.
(leroux1999mtgimcanovel pages 1-2): M. Leroux, M. Fändrich, D. Klunker, K. Siegers, A. Lupas, James R. Brown, E. Schiebel, C. Dobson, and F. Hartl. Mtgimc, a novel archaeal chaperone related to the eukaryotic chaperonin cofactor gimc/prefoldin. The EMBO Journal, 18:6730-6743, Dec 1999. URL: https://doi.org/10.1093/emboj/18.23.6730, doi:10.1093/emboj/18.23.6730. This article has 178 citations.
(simons2004selectivecontributionof pages 8-8): C. Torrey Simons, An Staes, Heidi Rommelaere, Christophe Ampe, Sally A. Lewis, and Nicholas J. Cowan. Selective contribution of eukaryotic prefoldin subunits to actin and tubulin binding*. Journal of Biological Chemistry, 279:4196-4203, Feb 2004. URL: https://doi.org/10.1074/jbc.m306053200, doi:10.1074/jbc.m306053200. This article has 75 citations and is from a domain leading peer-reviewed journal.
(millanzambrano2013theprefoldincomplex pages 1-2): Gonzalo Millán-Zambrano, Alfonso Rodríguez-Gil, Xenia Peñate, Lola de Miguel-Jiménez, Macarena Morillo-Huesca, Nevan Krogan, and Sebastián Chávez. The prefoldin complex regulates chromatin dynamics during transcription elongation. PLoS Genetics, 9:e1003776, Sep 2013. URL: https://doi.org/10.1371/journal.pgen.1003776, doi:10.1371/journal.pgen.1003776. This article has 64 citations and is from a domain leading peer-reviewed journal.
(tahmaz2022prefoldinfunctionin pages 3-5): Ismail Tahmaz, Somayeh Shahmoradi Ghahe, and Ulrike Topf. Prefoldin function in cellular protein homeostasis and human diseases. Frontiers in Cell and Developmental Biology, Jan 2022. URL: https://doi.org/10.3389/fcell.2021.816214, doi:10.3389/fcell.2021.816214. This article has 56 citations.
(ghahe2024identificationofa pages 1-5): Somayeh Shahmoradi Ghahe, Krzysztof Drabikowski, and Ulrike Topf. Identification of a non-canonical function of prefoldin subunit 5 in proteasome assembly. bioRxiv, Apr 2024. URL: https://doi.org/10.1101/2024.04.22.590501, doi:10.1101/2024.04.22.590501. This article has 3 citations.
(ghahe2024identificationofa pages 12-15): Somayeh Shahmoradi Ghahe, Krzysztof Drabikowski, and Ulrike Topf. Identification of a non-canonical function of prefoldin subunit 5 in proteasome assembly. bioRxiv, Apr 2024. URL: https://doi.org/10.1101/2024.04.22.590501, doi:10.1101/2024.04.22.590501. This article has 3 citations.
(liang2020thefunctionsand pages 1-2): Jiaxin Liang, Longzheng Xia, Linda Oyang, Jinguan Lin, Shiming Tan, Pin Yi, Yaqian Han, Xia Luo, Hui Wang, Lu Tang, Qing Pan, Yutong Tian, Shan Rao, Min Su, Yingrui Shi, Deliang Cao, Yujuan Zhou, and Qianjin Liao. The functions and mechanisms of prefoldin complex and prefoldin-subunits. Cell & Bioscience, Jul 2020. URL: https://doi.org/10.1186/s13578-020-00446-8, doi:10.1186/s13578-020-00446-8. This article has 71 citations and is from a peer-reviewed journal.
(simons2004selectivecontributionof media b05b75fc): C. Torrey Simons, An Staes, Heidi Rommelaere, Christophe Ampe, Sally A. Lewis, and Nicholas J. Cowan. Selective contribution of eukaryotic prefoldin subunits to actin and tubulin binding*. Journal of Biological Chemistry, 279:4196-4203, Feb 2004. URL: https://doi.org/10.1074/jbc.m306053200, doi:10.1074/jbc.m306053200. This article has 75 citations and is from a domain leading peer-reviewed journal.
(yang2024prefoldinsubunitsand pages 2-4): Yi Yang, Gang Zhang, Mengyu Su, Qingbiao Shi, and Qingshuai Chen. Prefoldin subunits and its associate partners: conservations and specificities in plants. Plants, 13:556, Feb 2024. URL: https://doi.org/10.3390/plants13040556, doi:10.3390/plants13040556. This article has 0 citations.
(herranzmontoya2021acomprehensiveanalysis pages 5-7): Irene Herranz-Montoya, Solip Park, and Nabil Djouder. A comprehensive analysis of prefoldins and their implication in cancer. iScience, 24:103273, Nov 2021. URL: https://doi.org/10.1016/j.isci.2021.103273, doi:10.1016/j.isci.2021.103273. This article has 26 citations and is from a peer-reviewed journal.
(blancotourinan2021ageneticapproach pages 1-2): Noel Blanco-Touriñán, David Esteve-Bruna, Antonio Serrano-Mislata, Rosa María Esquinas-Ariza, Francesca Resentini, Javier Forment, Cristian Carrasco-López, Claudio Novella-Rausell, Alberto Palacios-Abella, Pedro Carrasco, Julio Salinas, Miguel Á Blázquez, and David Alabadí. A genetic approach reveals different modes of action of prefoldins. Plant Physiology, 187:1534-1550, Jul 2021. URL: https://doi.org/10.1093/plphys/kiab348, doi:10.1093/plphys/kiab348. This article has 24 citations and is from a highest quality peer-reviewed journal.
id: P46988
gene_symbol: PFD1
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:559292
label: Saccharomyces cerevisiae
description: 'PFD1 encodes the Pfd1/Gim6 beta-type subunit of the cytosolic prefoldin complex, an ATP-independent cochaperone
that captures nonnative actin and tubulin folding intermediates and delivers them to CCT/TRiC, with secondary nuclear roles
in transcription elongation.'
existing_annotations:
- term:
id: GO:0006457
label: protein folding
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: 'protein folding reviewed for PFD1: ACCEPT.'
action: ACCEPT
reason: Retain as the direct biological process served by Pfd1-containing prefoldin in cytosolic actin/tubulin
folding.
supported_by:
- reference_id: file:yeast/PFD1/PFD1-deep-research-falcon.md
supporting_text: as part of the prefoldin/GimC complex it **captures and stabilizes unfolded actin and tubulin
intermediates** and **hands them to CCT/TRiC**
- term:
id: GO:0051082
label: unfolded protein binding
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: 'unfolded protein binding reviewed for PFD1: MODIFY.'
action: MODIFY
reason: Unfolded protein binding is mechanistically close but too broad; Pfd1 is best represented as a prefoldin
protein-folding cochaperone.
supported_by:
- reference_id: file:yeast/PFD1/PFD1-deep-research-falcon.md
supporting_text: prefoldin functions largely as an **ATP-independent holdase**, stabilizing folding intermediates and
preventing aggregation prior to transfer to CCT/TRiC
proposed_replacement_terms:
- id: GO:0044183
label: protein folding chaperone
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: 'cytoplasm reviewed for PFD1: ACCEPT.'
action: ACCEPT
reason: Retain as the principal cellular compartment for the canonical prefoldin to CCT/TRiC folding pathway.
supported_by:
- reference_id: file:yeast/PFD1/PFD1-deep-research-falcon.md
supporting_text: The central pathway involving Pfd1 is the **cytosolic folding pipeline** for cytoskeletal proteins
- term:
id: GO:0044183
label: protein folding chaperone
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: 'protein folding chaperone reviewed for PFD1: ACCEPT.'
action: ACCEPT
reason: Retain as the best molecular-function term for the ATP-independent prefoldin cochaperone role.
supported_by:
- reference_id: file:yeast/PFD1/PFD1-deep-research-falcon.md
supporting_text: Pfd1's primary function is **structural/cochaperone activity**, not catalysis
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IEA
original_reference_id: GO_REF:0000044
review:
summary: 'cytoplasm reviewed for PFD1: ACCEPT.'
action: ACCEPT
reason: Retain as the principal cellular compartment for the canonical prefoldin to CCT/TRiC folding pathway.
supported_by:
- reference_id: file:yeast/PFD1/PFD1-deep-research-falcon.md
supporting_text: The central pathway involving Pfd1 is the **cytosolic folding pipeline** for cytoskeletal proteins
- term:
id: GO:0006457
label: protein folding
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: 'protein folding reviewed for PFD1: ACCEPT.'
action: ACCEPT
reason: Retain as the direct biological process served by Pfd1-containing prefoldin in cytosolic actin/tubulin
folding.
supported_by:
- reference_id: file:yeast/PFD1/PFD1-deep-research-falcon.md
supporting_text: as part of the prefoldin/GimC complex it **captures and stabilizes unfolded actin and tubulin
intermediates** and **hands them to CCT/TRiC**
- term:
id: GO:0016272
label: prefoldin complex
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: 'prefoldin complex reviewed for PFD1: ACCEPT.'
action: ACCEPT
reason: Retain; Pfd1/Gim6 is a component of the heterohexameric prefoldin complex.
supported_by:
- reference_id: file:yeast/PFD1/PFD1-deep-research-falcon.md
supporting_text: Canonical eukaryotic prefoldin contains **six distinct subunits (PFD1-PFD6)**, organized as **two
alpha-type** and **four beta-type** subunits
- term:
id: GO:0051082
label: unfolded protein binding
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: 'unfolded protein binding reviewed for PFD1: MODIFY.'
action: MODIFY
reason: Unfolded protein binding is mechanistically close but too broad; Pfd1 is best represented as a prefoldin
protein-folding cochaperone.
supported_by:
- reference_id: file:yeast/PFD1/PFD1-deep-research-falcon.md
supporting_text: prefoldin functions largely as an **ATP-independent holdase**, stabilizing folding intermediates and
preventing aggregation prior to transfer to CCT/TRiC
proposed_replacement_terms:
- id: GO:0044183
label: protein folding chaperone
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:16429126
review:
summary: 'protein binding reviewed for PFD1: MARK_AS_OVER_ANNOTATED.'
action: MARK_AS_OVER_ANNOTATED
reason: Protein binding is too generic for curation; prefoldin complex membership and chaperone activity capture the
functional interaction context.
supported_by:
- reference_id: file:yeast/PFD1/PFD1-deep-research-falcon.md
supporting_text: prefoldin binds client proteins via the distal regions ("tentacle tips") and/or the cavity of the
hexamer
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:16554755
review:
summary: 'protein binding reviewed for PFD1: MARK_AS_OVER_ANNOTATED.'
action: MARK_AS_OVER_ANNOTATED
reason: Protein binding is too generic for curation; prefoldin complex membership and chaperone activity capture the
functional interaction context.
supported_by:
- reference_id: file:yeast/PFD1/PFD1-deep-research-falcon.md
supporting_text: prefoldin binds client proteins via the distal regions ("tentacle tips") and/or the cavity of the
hexamer
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:19536198
review:
summary: 'protein binding reviewed for PFD1: MARK_AS_OVER_ANNOTATED.'
action: MARK_AS_OVER_ANNOTATED
reason: Protein binding is too generic for curation; prefoldin complex membership and chaperone activity capture the
functional interaction context.
supported_by:
- reference_id: file:yeast/PFD1/PFD1-deep-research-falcon.md
supporting_text: prefoldin binds client proteins via the distal regions ("tentacle tips") and/or the cavity of the
hexamer
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:37968396
review:
summary: 'protein binding reviewed for PFD1: MARK_AS_OVER_ANNOTATED.'
action: MARK_AS_OVER_ANNOTATED
reason: Protein binding is too generic for curation; prefoldin complex membership and chaperone activity capture the
functional interaction context.
supported_by:
- reference_id: file:yeast/PFD1/PFD1-deep-research-falcon.md
supporting_text: prefoldin binds client proteins via the distal regions ("tentacle tips") and/or the cavity of the
hexamer
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:9878052
review:
summary: 'protein binding reviewed for PFD1: MARK_AS_OVER_ANNOTATED.'
action: MARK_AS_OVER_ANNOTATED
reason: Protein binding is too generic for curation; prefoldin complex membership and chaperone activity capture the
functional interaction context.
supported_by:
- reference_id: file:yeast/PFD1/PFD1-deep-research-falcon.md
supporting_text: prefoldin binds client proteins via the distal regions ("tentacle tips") and/or the cavity of the
hexamer
- term:
id: GO:0006457
label: protein folding
evidence_type: NAS
original_reference_id: PMID:9463374
review:
summary: 'protein folding reviewed for PFD1: ACCEPT.'
action: ACCEPT
reason: Retain as the direct biological process served by Pfd1-containing prefoldin in cytosolic actin/tubulin
folding.
supported_by:
- reference_id: file:yeast/PFD1/PFD1-deep-research-falcon.md
supporting_text: Yeast prefoldin/GimC physically interacts with TRiC/CCT in vivo and in vitro
- term:
id: GO:0032968
label: positive regulation of transcription elongation by RNA polymerase II
evidence_type: IMP
original_reference_id: PMID:24068951
review:
summary: 'positive regulation of transcription elongation by RNA polymerase II reviewed for PFD1: KEEP_AS_NON_CORE.'
action: KEEP_AS_NON_CORE
reason: Keep as an evidence-supported secondary nuclear/chromatin role, but do not treat it as the core evolved role
of Pfd1.
supported_by:
- reference_id: file:yeast/PFD1/PFD1-deep-research-falcon.md
supporting_text: PFD1 deletion reduces RNAPII occupancy across gene bodies
- term:
id: GO:0032968
label: positive regulation of transcription elongation by RNA polymerase II
evidence_type: IGI
original_reference_id: PMID:24068951
review:
summary: 'positive regulation of transcription elongation by RNA polymerase II reviewed for PFD1: KEEP_AS_NON_CORE.'
action: KEEP_AS_NON_CORE
reason: Keep as an evidence-supported secondary nuclear/chromatin role, but do not treat it as the core evolved role
of Pfd1.
supported_by:
- reference_id: file:yeast/PFD1/PFD1-deep-research-falcon.md
supporting_text: PFD1 deletion reduces RNAPII occupancy across gene bodies
- term:
id: GO:0006457
label: protein folding
evidence_type: IMP
original_reference_id: PMID:9630229
review:
summary: 'protein folding reviewed for PFD1: ACCEPT.'
action: ACCEPT
reason: Retain as the direct biological process served by Pfd1-containing prefoldin in cytosolic actin/tubulin
folding.
supported_by:
- reference_id: file:yeast/PFD1/PFD1-deep-research-falcon.md
supporting_text: actin folding by TRiC is slowed ~5-fold compared with wild type
- term:
id: GO:0007010
label: cytoskeleton organization
evidence_type: IMP
original_reference_id: PMID:9630229
review:
summary: 'cytoskeleton organization reviewed for PFD1: KEEP_AS_NON_CORE.'
action: KEEP_AS_NON_CORE
reason: Keep as a downstream consequence of actin/tubulin folding defects rather than the direct molecular role.
supported_by:
- reference_id: file:yeast/PFD1/PFD1-deep-research-falcon.md
supporting_text: gim deletion mutants exhibit actin and tubulin phenotypes resembling TRiC mutants
- term:
id: GO:0016272
label: prefoldin complex
evidence_type: IMP
original_reference_id: PMID:9630229
review:
summary: 'prefoldin complex reviewed for PFD1: ACCEPT.'
action: ACCEPT
reason: Retain; Pfd1/Gim6 is a component of the heterohexameric prefoldin complex.
supported_by:
- reference_id: file:yeast/PFD1/PFD1-deep-research-falcon.md
supporting_text: Canonical eukaryotic prefoldin contains **six distinct subunits (PFD1-PFD6)**, organized as **two
alpha-type** and **four beta-type** subunits
- term:
id: GO:0051082
label: unfolded protein binding
evidence_type: IMP
original_reference_id: PMID:9630229
review:
summary: 'unfolded protein binding reviewed for PFD1: MODIFY.'
action: MODIFY
reason: Unfolded protein binding is mechanistically close but too broad; Pfd1 is best represented as a prefoldin
protein-folding cochaperone.
supported_by:
- reference_id: file:yeast/PFD1/PFD1-deep-research-falcon.md
supporting_text: prefoldin functions largely as an **ATP-independent holdase**, stabilizing folding intermediates and
preventing aggregation prior to transfer to CCT/TRiC
proposed_replacement_terms:
- id: GO:0044183
label: protein folding chaperone
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: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: PMID:16429126
title: Proteome survey reveals modularity of the yeast cell machinery.
findings: []
- id: PMID:16554755
title: Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
findings: []
- id: PMID:19536198
title: 'An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways
in the cell.'
findings: []
- id: PMID:24068951
title: The prefoldin complex regulates chromatin dynamics during transcription elongation.
findings: []
- id: PMID:37968396
title: The social and structural architecture of the yeast protein interactome.
findings: []
- id: PMID:9463374
title: A novel protein complex promoting formation of functional alpha- and gamma-tubulin.
findings: []
- id: PMID:9630229
title: Prefoldin, a chaperone that delivers unfolded proteins to cytosolic chaperonin.
findings: []
- id: PMID:9878052
title: 'Compartmentation of protein folding in vivo: sequestration of non-native polypeptide by the chaperonin-GimC system.'
findings: []
- id: file:yeast/PFD1/PFD1-deep-research-falcon.md
title: Falcon deep research report for yeast PFD1
findings: []
- id: file:interpro/panther/PTHR20903/PTHR20903-metadata.yaml
title: PANTHER family PTHR20903, prefoldin subunit beta
findings: []
core_functions:
- description: Pfd1 is a structural subunit of the heterohexameric prefoldin/GimC cochaperone that stabilizes nonnative
cytoskeletal clients and promotes their handoff to CCT/TRiC for folding.
supported_by:
- reference_id: file:yeast/PFD1/PFD1-deep-research-falcon.md
supporting_text: as part of the prefoldin/GimC complex it **captures and stabilizes unfolded actin and tubulin
intermediates** and **hands them to CCT/TRiC**
molecular_function:
id: GO:0044183
label: protein folding chaperone
directly_involved_in:
- id: GO:0006457
label: protein folding
locations:
- id: GO:0005737
label: cytoplasm
in_complex:
id: GO:0016272
label: prefoldin complex
proposed_new_terms: []
suggested_questions:
- question: Which Pfd1-containing prefoldin surfaces distinguish cytoskeletal client capture from the secondary nuclear
transcription role?
experts: []
- question: Does Pfd1 have subunit-specific client preferences within yeast prefoldin beyond the canonical actin and
tubulin pathway?
experts: []
suggested_experiments:
- hypothesis: Pfd1 has separable surfaces for canonical actin/tubulin cochaperone function and non-core
transcription-associated function.
description: Generate Pfd1 separation-of-function mutants at endogenous expression levels and compare actin/tubulin
folding, prefoldin complex integrity, chromatin occupancy, and RNA polymerase II elongation phenotypes.
experiment_type: separation-of-function mutagenesis