ACL4

UniProt ID: Q03771
Organism: Saccharomyces cerevisiae
Review Status: COMPLETE
📝 Provide Detailed Feedback

Gene Description

ACL4 encodes the dedicated assembly chaperone for the large ribosomal subunit protein Rpl4/uL4. Acl4 binds newly synthesized Rpl4, keeps the highly basic unassembled ribosomal protein soluble, and escorts it from the cytoplasm to the nuclear pre-60S assembly site. Loss of ACL4 causes slow growth, reduced 60S subunit production, half-mer polysomes, and pre-rRNA processing defects, supporting a core role in ribosomal large subunit biogenesis rather than mitochondrial protein import.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0005741 mitochondrial outer membrane
IBA
GO_REF:0000033
REMOVE
Summary: This IBA traces to a broad PANTHER family context that UniProt labels as mitochondrial import receptor subunit TOM70, but the reviewed yeast ACL4 subfamily entry is an assembly chaperone of RPL4. UniProt and the Falcon review support cytoplasmic/nuclear localization for Acl4, not a mitochondrial outer membrane role.
Reason: The family-transfer annotation appears to have propagated TOM70-family mitochondrial localization to a divergent Acl4/Rpl4 chaperone. No primary Acl4 evidence supports mitochondrial outer membrane residence.
Supporting Evidence:
file:yeast/ACL4/ACL4-deep-research-falcon.md
Acl4 is detected in both cytoplasm and nucleus
GO:0008320 protein transmembrane transporter activity
IBA
GO_REF:0000033
REMOVE
Summary: Acl4 escorts the soluble ribosomal protein Rpl4; it is not a component of a protein transmembrane translocation channel. This IBA is inconsistent with the experimentally supported Acl4 subfamily biology.
Reason: The annotation likely reflects the TOM70-like parent family rather than Acl4. Acl4 functions as a ribosomal protein carrier chaperone, not as a transmembrane transporter or transporter subunit.
GO:0030150 protein import into mitochondrial matrix
IBA
GO_REF:0000033
REMOVE
Summary: Experimental Acl4 studies describe Rpl4 handling and nuclear pre-60S assembly, with no evidence for mitochondrial matrix protein import.
Reason: This is a family-transfer overannotation from a TOM70-like ancestor and conflicts with the specific yeast Acl4/Rpl4 literature.
GO:0030943 mitochondrion targeting sequence binding
IBA
GO_REF:0000033
REMOVE
Summary: Acl4 binds a segment of the Rpl4 long internal loop and protects unassembled Rpl4. It has no demonstrated binding to mitochondrial targeting sequences.
Reason: The supported client-binding activity is Rpl4 carrier chaperone activity. The mitochondrial targeting sequence term should not be retained for the yeast ACL4 subfamily.
Supporting Evidence:
file:yeast/ACL4/ACL4-deep-research-falcon.md
Acl4 binds newly synthesized, free Rpl4
GO:0045039 protein insertion into mitochondrial inner membrane
IBA
GO_REF:0000033
REMOVE
Summary: The experimentally supported Acl4 pathway is Rpl4 delivery to the nuclear pre-60S ribosome, not insertion of proteins into the mitochondrial inner membrane.
Reason: This IBA is not supported for ACL4 and should be removed as a TOM70-family over-transfer.
GO:0005634 nucleus
IEA
GO_REF:0000044
ACCEPT
Summary: UniProt subcellular-location mapping to nucleus is consistent with direct Acl4 localization studies and with Acl4 delivery of Rpl4 to nuclear pre-60S particles.
Reason: Acl4 is enriched in the nucleus and performs its client-delivery function at the nuclear pre-60S assembly site.
GO:0005737 cytoplasm
IEA
GO_REF:0000120
ACCEPT
Summary: Automated cytoplasm assignment is consistent with direct studies showing Acl4 in the cytoplasm, where Rpl4 is synthesized and first captured.
Reason: Cytoplasmic localization is part of the supported escort path from nascent Rpl4 capture to nuclear assembly.
GO:0042254 ribosome biogenesis
IEA
GO_REF:0000043
ACCEPT
Summary: The keyword-derived ribosome biogenesis term is broad but accurate for Acl4, which is required for efficient production of 60S ribosomal subunits.
Reason: Experimental annotations to ribosomal large subunit biogenesis provide the more specific evidence; this parent process is correct as an automated summary of Acl4 function.
GO:0005634 nucleus
IDA
PMID:25936803
Coordinated Ribosomal L4 Protein Assembly into the Pre-Ribos...
ACCEPT
Summary: Direct experimental localization supports nuclear Acl4, consistent with the Rpl4 pre-60S assembly site.
Reason: The localization matches the mechanistic model in which Acl4 delivers Rpl4 to nuclear pre-60S assembly intermediates.
Supporting Evidence:
PMID:25936803
assembly chaperone Acl4 that initially binds the universally conserved internal
GO:0005634 nucleus
IDA
PMID:26447800
The Dedicated Chaperone Acl4 Escorts Ribosomal Protein Rpl4 ...
ACCEPT
Summary: Direct microscopy in the dedicated Acl4-Rpl4 study supports nuclear localization.
Reason: Acl4 localizes to the nucleus as expected for a factor escorting Rpl4 to nuclear pre-60S assembly sites.
Supporting Evidence:
PMID:26447800
Acl4 localizes to both the cytoplasm and nucleus
GO:0005737 cytoplasm
IDA
PMID:26447800
The Dedicated Chaperone Acl4 Escorts Ribosomal Protein Rpl4 ...
ACCEPT
Summary: Direct microscopy supports cytoplasmic Acl4 localization.
Reason: Acl4 must encounter newly translated Rpl4 in the cytoplasm before nuclear delivery, so this localization is mechanistically coherent.
Supporting Evidence:
PMID:26447800
Acl4 localizes to both the cytoplasm and nucleus
GO:0042273 ribosomal large subunit biogenesis
IMP
PMID:25936803
Coordinated Ribosomal L4 Protein Assembly into the Pre-Ribos...
ACCEPT
Summary: Mutant phenotype evidence shows that ACL4 is required for normal 60S subunit production through Rpl4 assembly.
Reason: Acl4 shields Rpl4 until it can be inserted into the pre-ribosome; ACL4 loss causes large-subunit biogenesis defects, making this a core process.
Supporting Evidence:
PMID:25936803
hierarchical ribosome assembly can be achieved by eukaryotic RP extensions and
GO:0042273 ribosomal large subunit biogenesis
IMP
PMID:26447800
The Dedicated Chaperone Acl4 Escorts Ribosomal Protein Rpl4 ...
ACCEPT
Summary: The dedicated chaperone study shows that Acl4 escorts Rpl4 to its nuclear pre-60S assembly site and that loss of Acl4 compromises 60S production.
Reason: This is the central biological process for Acl4 and is supported by genetic, localization, and biochemical evidence.
Supporting Evidence:
PMID:26447800
deficiency in the production of 60S subunits
GO:0051082 unfolded protein binding
IDA
PMID:25936803
Coordinated Ribosomal L4 Protein Assembly into the Pre-Ribos...
MODIFY
Summary: Acl4 does bind and protect unassembled Rpl4, but "unfolded protein binding" is too generic and obscures the dedicated carrier-chaperone role.
Reason: The evidence supports specific ribosomal-protein carrier chaperone activity rather than generic binding to unfolded proteins.
Proposed replacements: protein carrier activity
Supporting Evidence:
file:yeast/ACL4/ACL4-deep-research-falcon.md
Acl4 is a dedicated ribosomal protein chaperone
GO:0140318 protein transporter activity
IDA
PMID:26447800
The Dedicated Chaperone Acl4 Escorts Ribosomal Protein Rpl4 ...
ACCEPT
Summary: The evidence supports Acl4 directly binding and escorting Rpl4 to the pre-60S assembly pathway, matching the current definition of protein transporter activity as binding and delivering a specific protein to a cellular location.
Reason: QuickGO places GO:0140318 under transporter activity and GO:0140597 under molecular carrier activity rather than as a parent-child pair. Retaining this SGD IDA annotation is therefore not a redundant parent annotation, and the PMID:26447800 evidence supports Acl4 escorting Rpl4 to the pre-60S assembly pathway.
Supporting Evidence:
PMID:26447800
dedicated chaperone Acl4 accompanies Rpl4
GO:0051083 'de novo' cotranslational protein folding
HGI
PMID:19325107
Comprehensive characterization of genes required for protein...
MARK AS OVER ANNOTATED
Summary: Acl4 can capture nascent Rpl4 cotranslationally, but this high-throughput genetic-interaction annotation is broad and does not define Acl4 as a general cotranslational folding factor.
Reason: The better-supported curation is the specific Rpl4 carrier-chaperone role in ribosomal large subunit biogenesis. Retaining the broad folding process as a core annotation would overstate the evidence.
GO:0005634 nucleus
HDA
PMID:14562095
Global analysis of protein localization in budding yeast.
ACCEPT
Summary: High-throughput localization to nucleus is consistent with direct Acl4 localization and its nuclear pre-60S assembly role.
Reason: Multiple independent sources support nuclear localization.
GO:0005737 cytoplasm
HDA
PMID:14562095
Global analysis of protein localization in budding yeast.
ACCEPT
Summary: High-throughput localization to cytoplasm is consistent with direct Acl4 localization and nascent Rpl4 capture.
Reason: Acl4 is distributed through cytoplasm and nucleus, matching its escort function.

Core Functions

Acl4 is a dedicated carrier chaperone for Rpl4/uL4. It binds newly synthesized Rpl4 in the cytoplasm, protects it from inappropriate interactions or aggregation, and escorts it to nuclear pre-60S particles for large ribosomal subunit assembly.

Molecular Function:
protein carrier activity
Cellular Locations:
Supporting Evidence:
  • PMID:26447800
    dedicated chaperone Acl4 accompanies Rpl4
  • file:yeast/ACL4/ACL4-deep-research-falcon.md
    Acl4 binds newly synthesized, free Rpl4

References

Annotation inferences using phylogenetic trees
Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
Combined Automated Annotation using Multiple IEA Methods
Global analysis of protein localization in budding yeast.
Comprehensive characterization of genes required for protein folding in the endoplasmic reticulum.
Coordinated Ribosomal L4 Protein Assembly into the Pre-Ribosome Is Regulated by Its Eukaryote-Specific Extension.
The Dedicated Chaperone Acl4 Escorts Ribosomal Protein Rpl4 to Its Nuclear Pre-60S Assembly Site.
file:yeast/ACL4/ACL4-deep-research-falcon.md
Falcon deep research report for ACL4

Suggested Questions for Experts

Q: Should PANTHER family PTHR46208 be split or have IBA propagation restricted so TOM70 mitochondrial import terms do not transfer to the ACL4/Rpl4 assembly chaperone subfamily?

Suggested Experiments

Experiment: Re-analyze ACL4, TOM70, and related PTHR46208 subfamilies with tree-aware GO propagation to test whether mitochondrial import annotations segregate away from the experimentally characterized Acl4/Rpl4 clade.

Hypothesis: The ACL4 subfamily lacks the mitochondrial protein import functions present in TOM70-like relatives and should not inherit those IBA terms.

Type: phylogenetic curation

📚 Additional Documentation

Deep Research Falcon

(ACL4-deep-research-falcon.md)

provider: falcon
model: Edison Scientific Literature
cached: false
start_time: '2026-05-04T10:06:12.943812'
end_time: '2026-05-04T10:19:34.189355'
duration_seconds: 801.25
template_file: templates/gene_research_go_focused.md
template_variables:
organism: yeast
gene_id: ACL4
gene_symbol: ACL4
uniprot_accession: Q03771
protein_description: 'RecName: Full=Assembly chaperone of RPL4 {ECO:0000303|PubMed:25936803};'
gene_info: Name=ACL4 {ECO:0000303|PubMed:25936803}; OrderedLocusNames=YDR161W {ECO:0000312|SGD:S000002568};
organism_full: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
protein_family: Belongs to the ACL4 family. .
protein_domains: TPR-like_helical_dom_sf. (IPR011990)
provider_config:
timeout: 600
max_retries: 3
parameters:
allowed_domains: []
temperature: 0.1
citation_count: 30


Question

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

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

Target Gene/Protein Identity (from UniProt):

  • UniProt Accession: Q03771
  • Protein Description: RecName: Full=Assembly chaperone of RPL4 {ECO:0000303|PubMed:25936803};
  • Gene Information: Name=ACL4 {ECO:0000303|PubMed:25936803}; OrderedLocusNames=YDR161W {ECO:0000312|SGD:S000002568};
  • Organism (full): Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  • Protein Family: Belongs to the ACL4 family. .
  • Key Domains: TPR-like_helical_dom_sf. (IPR011990)

MANDATORY VERIFICATION STEPS:

  1. Check if the gene symbol "ACL4" matches the protein description above
  2. Verify the organism is correct: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  3. Check if protein family/domains align with what you find in literature
  4. If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

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

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'ACL4' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information

Research Target:

Please provide a comprehensive research report on the gene ACL4 (gene ID: ACL4, UniProt: Q03771) in yeast.

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Output

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

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

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

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

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

Target Gene/Protein Identity (from UniProt):

  • UniProt Accession: Q03771
  • Protein Description: RecName: Full=Assembly chaperone of RPL4 {ECO:0000303|PubMed:25936803};
  • Gene Information: Name=ACL4 {ECO:0000303|PubMed:25936803}; OrderedLocusNames=YDR161W {ECO:0000312|SGD:S000002568};
  • Organism (full): Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  • Protein Family: Belongs to the ACL4 family. .
  • Key Domains: TPR-like_helical_dom_sf. (IPR011990)

MANDATORY VERIFICATION STEPS:

  1. Check if the gene symbol "ACL4" matches the protein description above
  2. Verify the organism is correct: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  3. Check if protein family/domains align with what you find in literature
  4. If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

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

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'ACL4' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information

Research Target:

Please provide a comprehensive research report on the gene ACL4 (gene ID: ACL4, UniProt: Q03771) 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.

Research Report: Saccharomyces cerevisiae ACL4 (YDR161W; UniProt Q03771)

Executive summary

Acl4 is a dedicated assembly chaperone for the 60S large-subunit ribosomal protein Rpl4 (uL4) in Saccharomyces cerevisiae (strain S288c). It binds a defined segment of the Rpl4 long internal loop, keeps nascent/unassembled Rpl4 soluble, and escorts it to the nuclear pre-60S assembly site, coordinating with the importin Kap104. Loss of ACL4 causes a severe slow-growth phenotype with hallmark 60S biogenesis defects (60S shortage and half-mers). More recent work (2022–2024) extends Acl4 biology to cotranslational regulation of RPL4 mRNA abundance via NAC/Caf130/Ccr4–Not circuitry, and links Acl4-limited conditions to aggregation/quality control networks that include the E3 ligase Tom1. (pillet2015thededicatedchaperone pages 1-2, huber2017molecularbasisfor pages 1-2, pillet2015thededicatedchaperone pages 10-12, schilke2024functionalsimilaritiesand pages 1-3, pillet2022dedicatedchaperonescoordinate pages 14-16, pillet2022dedicatedchaperonescoordinate pages 20-22)


1) Identity verification and key definitions

1.1 Target identity (mandatory verification)

Primary literature explicitly identifies Acl4 as yeast YDR161W and characterizes it as the dedicated chaperone for Rpl4, matching the UniProt target Q03771 and the stated domain annotation (TPR-like helical domain superfamily). (stelter2015coordinatedribosomall4 pages 3-3, pillet2015thededicatedchaperone pages 1-2, huber2017molecularbasisfor pages 1-2)

1.2 Key concepts (current understanding)

  • Dedicated ribosomal-protein (RP) chaperone: A specialized factor that binds one (or a small set of) ribosomal protein(s) to prevent aggregation/mislocalization and to promote safe delivery to the assembly site. Acl4 is dedicated for Rpl4. (pillet2015thededicatedchaperone pages 18-20, yang2024ribosomeassemblyand pages 1-3)
  • Pre-60S assembly: Stepwise nuclear maturation of the large ribosomal subunit, involving incorporation of RPs into pre-ribosomal particles and transient binding of biogenesis factors; Acl4 acts at the stage of delivering Rpl4 to early nuclear pre-60S particles. (pillet2015thededicatedchaperone pages 18-20, pillet2015thededicatedchaperone pages 20-21)
  • Cotranslational capture: Binding of a chaperone to a nascent client during translation; Acl4 enriches RPL4 mRNA in pull-downs, consistent with cotranslational engagement. (pillet2015thededicatedchaperone pages 17-18)

2) Molecular function and mechanism

2.1 Core function: chaperoning and escort of Rpl4/uL4

Acl4 binds newly synthesized, free Rpl4, enabling soluble expression of Rpl4 and escorting it from cytoplasm to nuclear pre-60S assembly sites; Acl4 is not stably associated with mature 60S particles, consistent with a transient escort. (pillet2015thededicatedchaperone pages 1-2, pillet2015thededicatedchaperone pages 10-12)

2.2 Client-binding site on Rpl4

Mapping in yeast indicates Acl4 recognizes the C-terminal region of the long internal loop of Rpl4, with functional mapping to approximately aa 88–114 (and emphasis around ~101–114). Multiple alanine-block substitutions in this segment abolish the Acl4–Rpl4 interaction. (pillet2015thededicatedchaperone pages 14-17, pillet2015thededicatedchaperone pages 20-21)

2.3 Structural basis (TPR fold; sequestration of exposed residues)

A high-resolution structure of the Acl4–RpL4 complex shows that Acl4 adopts an α-helical TPR fold (reported as seven TPRs plus a C-terminal helix) and uses its concave surface to sequester ~70 exposed residues of the elongated RpL4 loop, providing a mechanistic basis for preventing degradation/aggregation of unassembled L4. (huber2017molecularbasisfor pages 1-2, huber2017molecularbasisfor media 4aaddfb0, huber2017molecularbasisfor media cb2e78f3)

2.4 Nuclear import and Kap104 coupling

A central mechanistic insight is that the eukaryote-specific extension of Rpl4 contains overlapping determinants for Acl4 binding and the nuclear import factor Kap104, enabling continuous protection during import. In vitro, Kap104 can form a stoichiometric Acl4–Rpl4–Kap104 trimer, and a schematic map of overlapping binding sites is provided in the structural work. (huber2017molecularbasisfor pages 1-2, pillet2015thededicatedchaperone pages 20-21, huber2017molecularbasisfor media e4ea49ee)


3) Subcellular localization and pathway placement

3.1 Localization

Fluorescent tagging and fractionation show Acl4 is present in both cytoplasm and nucleus and is recovered in soluble fractions, not as a stable component of pre-60S or mature 60S particles. This supports a “carrier/escort” rather than “structural subunit” model. (pillet2015thededicatedchaperone pages 10-12)

3.2 Pathway role in large-subunit biogenesis

Deletion of ACL4 causes a defect in 60S subunit production and characteristic half-mer polysomes, consistent with impaired assembly or supply of an essential large-subunit RP to the nucleus and pre-60S particles. (stelter2015coordinatedribosomall4 pages 3-3, pillet2015thededicatedchaperone pages 10-12)


4) Phenotypes, statistics, and quantitative evidence

4.1 Growth and ribosome biogenesis phenotypes

  • acl4Δ is viable but has severe slow growth across tested temperatures and shows a shortage of free 60S subunits, half-mer polysomes, and reduced overall polysomes. (pillet2015thededicatedchaperone pages 10-12)
  • Growth and 60S defects can be partially rescued by extra RPL4, and deletion of ACL4 impairs 60S synthesis and yields half-mers. (stelter2015coordinatedribosomall4 pages 3-3, pillet2015thededicatedchaperone pages 14-17)

4.2 Cotranslational evidence (mRNA enrichment)

Acl4 affinity purification shows strong enrichment of RPL4 mRNA (~150-fold), supporting cotranslational recognition of nascent Rpl4. (pillet2015thededicatedchaperone pages 17-18)

4.3 RPL4 mRNA regulation (Acl4 availability as a rheostat)

Recent work indicates Acl4 availability feeds back on RPL4 expression:
- RPL4 mRNA abundance is almost ~2-fold lower in Δacl4 cells versus wild type, consistent with an Acl4-dependent stabilization effect. (pillet2022dedicatedchaperonescoordinate pages 14-16)
- When Acl4 is absent/limiting, ribosome-associated Rpl4 nascent chain becomes accessible to regulatory machinery involving NAC and Caf130-associated Ccr4–Not, which promotes RPL4 mRNA degradation, limiting accumulation of aggregation-prone excess Rpl4. (pillet2022dedicatedchaperonescoordinate pages 1-4, schilke2024functionalsimilaritiesand pages 1-3)

4.4 Proteostasis/quality control linkage (Tom1)

Deregulated Rpl4 expression promotes aggregation and proteostasis defects, particularly in tom1Δ backgrounds; in such assays, wild-type proteins show nucle(ol)ar signal in <20% of Δtom1 cells, whereas deregulated variants show strong nucle(ol)ar compartment signals in most Δtom1 cells. These observations link Acl4-dependent homeostasis to ubiquitin-ligase-dependent quality control. (pillet2022dedicatedchaperonescoordinate pages 20-22)

4.5 System-level scale statistics (context for why Acl4 matters)

  • In an exponentially growing yeast cell, there are ~200,000 ribosomes, requiring synthesis of >2,000 ribosomes/minute (≈160,000 ribosomal proteins per minute) to maintain growth—illustrating why tight control of RP supply (including Acl4-mediated handling of Rpl4) is crucial. (pillet2022dedicatedchaperonescoordinate pages 1-4)
  • Across eukaryotes, ribosome assembly requires several hundred ribosome biogenesis factors (RBFs), compared with ~50 in bacteria, reflecting increased complexity and the need for specialized factors such as dedicated RP chaperones. (dorner2023ribosomebiogenesisfactors—from pages 1-2)
  • Yeast ribosomes contain 79 ribosomal proteins, while humans have ~80; the 60S contains 46 RPs in yeast and 47 in humans. (dorner2023ribosomebiogenesisfactors—from pages 1-2, yang2024ribosomeassemblyand pages 1-3)
  • Ribosome production is extremely resource-intensive (yeast allocation estimates include ~60% of transcription and ~50% of translation events, among others), motivating quality-control and repair/assembly-control systems. (yang2024ribosomeassemblyand pages 1-3)

5) Recent developments (prioritizing 2023–2024)

5.1 2024: Integration of Acl4 into cotranslational regulatory networks

A 2024 study of NAC subunits in S. cerevisiae explicitly frames Acl4 as the specialized chaperone for Rpl4, noting that without Acl4 Rpl4 is aggregation-prone and cells grow very slowly. It further places Acl4-limited states into a regulatory pathway where Rpl4 mRNA is targeted for degradation via the CCR4–Not complex, and highlights quantitative NAC subunit abundance differences (Nacβ2 is ~20–100× less abundant than the major NAC subunits). (schilke2024functionalsimilaritiesand pages 1-3)

5.2 2023: Expert synthesis on why mechanistic annotation matters

A high-citation 2023 EMBO Journal review argues that assigning detailed molecular functions to ribosome biogenesis factors is essential for understanding and treating diseases linked to disturbed ribosome assembly, including ribosomopathies and cancers. While Acl4 is not the focus, this review provides field-level justification for precise mechanistic annotation of factors like Acl4. (dorner2023ribosomebiogenesisfactors—from pages 1-2)

5.3 2024: Assembly and repair framework (expert view)

A 2024 Annual Review article frames dedicated chaperones as part of the cellular strategy to manage small, basic, aggregation-prone RPs and maintain ribosome integrity through quality control and repair, with dedicated RP chaperones known for at least ~13 RPs. This strengthens the conceptual placement of Acl4 as a dedicated RP chaperone integrating assembly and proteostasis. (yang2024ribosomeassemblyand pages 1-3)


6) Current applications and real-world implementations

6.1 Yeast Acl4 as a model for conserved principles

Acl4 exemplifies how eukaryotes solve the “RP handling problem” created by (i) cytoplasmic synthesis but nuclear assembly and (ii) aggregation propensity of basic RPs. Structural definition of the Acl4–L4 interface provides a mechanistic template for understanding analogous dedicated-chaperone systems and their coupling to nuclear import pathways (e.g., overlapping chaperone/importin binding sites). (huber2017molecularbasisfor pages 1-2, huber2017molecularbasisfor media e4ea49ee)

6.2 Disease relevance via ribosome biogenesis concepts

Although Acl4 itself is a yeast protein, authoritative reviews stress that detailed knowledge of ribosome assembly factors is key for understanding disease states (ribosomopathies, cancers) linked to perturbed ribosome assembly and quality control, supporting the broader translational relevance of dissecting dedicated-chaperone mechanisms in model organisms. (dorner2023ribosomebiogenesisfactors—from pages 1-2, yang2024ribosomeassemblyand pages 1-3)


7) Visual evidence (structure and import coupling)

Figures from the Acl4–RpL4 structural study show (i) the overall complex architecture, (ii) the interaction interface/hotspots, and (iii) a schematic of overlapping Acl4 and Kap104 binding sites on RpL4 (supporting the escort/import model). (huber2017molecularbasisfor media 4aaddfb0, huber2017molecularbasisfor media cb2e78f3, huber2017molecularbasisfor media e4ea49ee)


Evidence summary table

Topic Key findings Key source(s) with year and DOI URL
Identity ACL4 in this report refers to Saccharomyces cerevisiae YDR161W, encoding Acl4, the dedicated assembly chaperone/escort for large-subunit ribosomal protein Rpl4/uL4; this matches UniProt Q03771. (stelter2015coordinatedribosomall4 pages 3-3, pillet2015thededicatedchaperone pages 1-2) Pillet et al., 2015, PLOS Genet. https://doi.org/10.1371/journal.pgen.1005565; Stelter et al., 2015, Mol Cell. https://doi.org/10.1016/j.molcel.2015.03.029
Molecular function Acl4 is a dedicated ribosomal protein chaperone that binds newly made, free Rpl4, promotes its soluble expression, protects exposed basic regions from inappropriate interactions/aggregation, and escorts it toward its nuclear pre-60S assembly site. (pillet2015thededicatedchaperone pages 18-20, huber2017molecularbasisfor pages 1-2, pillet2015thededicatedchaperone pages 17-18) Pillet et al., 2015, PLOS Genet. https://doi.org/10.1371/journal.pgen.1005565; Huber & Hoelz, 2017, Nat Commun. https://doi.org/10.1038/ncomms14354
Client protein The specific client is Rpl4 (large-subunit protein uL4/eL4 family naming context), and affinity purification/pulse-chase evidence supports cotranslational capture of nascent Rpl4 by Acl4. (stelter2015coordinatedribosomall4 pages 3-3, pillet2015thededicatedchaperone pages 17-18) Stelter et al., 2015, Mol Cell. https://doi.org/10.1016/j.molcel.2015.03.029; Pillet et al., 2015, PLOS Genet. https://doi.org/10.1371/journal.pgen.1005565
Binding region Acl4 binds the C-terminal part of Rpl4’s long internal loop, with mapping to roughly aa 88–114 and especially residues around 101–114; multiple alanine-block substitutions disrupt binding. (pillet2015thededicatedchaperone pages 14-17, pillet2015thededicatedchaperone pages 20-21) Pillet et al., 2015, PLOS Genet. https://doi.org/10.1371/journal.pgen.1005565
Structural fold/domain Structural work shows Acl4 is an α-helical TPR-family chaperone with about 6.5–7 TPR repeats plus a C-terminal helix, using its concave surface to sequester about 70 exposed residues of the RpL4 loop. This agrees with the UniProt/IPR annotation of a TPR-like helical domain. (huber2017molecularbasisfor pages 1-2, pillet2015thededicatedchaperone pages 17-18, huber2017molecularbasisfor media 4aaddfb0) Huber & Hoelz, 2017, Nat Commun. https://doi.org/10.1038/ncomms14354; Pillet et al., 2015, PLOS Genet. https://doi.org/10.1371/journal.pgen.1005565
Localization Acl4 is detected in both cytoplasm and nucleus and is found in soluble fractions rather than stably bound to mature 60S or persistent pre-60S particles, fitting a transient escort function. (pillet2015thededicatedchaperone pages 1-2, pillet2015thededicatedchaperone pages 10-12) Pillet et al., 2015, PLOS Genet. https://doi.org/10.1371/journal.pgen.1005565
Nuclear import mechanism Acl4 lacks a predicted NLS, so the favored model is co-import with Rpl4. The Rpl4 C-terminal eukaryote-specific extension contains overlapping NLS/importin-binding determinants; Kap104 can form a stoichiometric Acl4–Rpl4–Kap104 trimer, and Ran-GTP is proposed to trigger release before assembly. (pillet2015thededicatedchaperone pages 18-20, huber2017molecularbasisfor pages 1-2, pillet2015thededicatedchaperone pages 20-21, huber2017molecularbasisfor media e4ea49ee) Pillet et al., 2015, PLOS Genet. https://doi.org/10.1371/journal.pgen.1005565; Huber & Hoelz, 2017, Nat Commun. https://doi.org/10.1038/ncomms14354
Role in pre-60S assembly Acl4 delivers Rpl4 to the early nuclear pre-60S assembly site. It associates only very transiently with early pre-60S particles, and release is coupled to proper Rpl4 insertion, including contacts involving Rpl4’s eukaryote-specific extension and neighboring 60S components such as Rpl18/Rpl7/ES7L. (pillet2015thededicatedchaperone pages 18-20, pillet2015thededicatedchaperone pages 20-21) Pillet et al., 2015, PLOS Genet. https://doi.org/10.1371/journal.pgen.1005565
Phenotypes acl4Δ cells are viable but show severe slow growth at multiple temperatures, 60S deficiency, half-mer polysomes, reduced overall polysomes, and pre-rRNA processing defects (reduced 27SB and 7S). Extra RPL4 can partially suppress the defect; combined loss with RPL4A worsens growth. (stelter2015coordinatedribosomall4 pages 3-3, pillet2015thededicatedchaperone pages 14-17, pillet2015thededicatedchaperone pages 10-12) Stelter et al., 2015, Mol Cell. https://doi.org/10.1016/j.molcel.2015.03.029; Pillet et al., 2015, PLOS Genet. https://doi.org/10.1371/journal.pgen.1005565
Quality control / proteostasis link Acl4 protects unassembled Rpl4 from Tom1-linked degradation/quality control and from aggregation. When Acl4 is limiting or Rpl4 expression is deregulated, RPL4 mRNA can be downregulated through NAC–Caf130–Ccr4-Not circuitry, while excess Rpl4 becomes aggregation-prone, especially in tom1Δ cells. (huber2017molecularbasisfor pages 1-2, schilke2024functionalsimilaritiesand pages 1-3, pillet2022dedicatedchaperonescoordinate pages 1-4, pillet2022dedicatedchaperonescoordinate pages 14-16, pillet2022dedicatedchaperonescoordinate pages 20-22) Huber & Hoelz, 2017, Nat Commun. https://doi.org/10.1038/ncomms14354; Pillet et al., 2022, bioRxiv. https://doi.org/10.1101/2021.10.05.463164; Schilke et al., 2024, Cell Stress Chaperones. https://doi.org/10.1016/j.cstres.2024.10.004
Recent developments (2022–2024) Recent work extends Acl4 biology beyond escort alone: cotranslational Acl4 binding helps stabilize RPL4 mRNA, whereas limited Acl4 exposes nascent Rpl4 to CCR4–Not-dependent mRNA decay and proteostasis stress; 2024 analysis of NAC subunits further supports this regulatory network. Broader 2023–2024 reviews frame dedicated RP chaperones like Acl4 as central nodes in ribosome biogenesis and quality control. (schilke2024functionalsimilaritiesand pages 1-3, pillet2022dedicatedchaperonescoordinate pages 1-4, pillet2022dedicatedchaperonescoordinate pages 14-16) Pillet et al., 2022, bioRxiv. https://doi.org/10.1101/2021.10.05.463164; Schilke et al., 2024, Cell Stress Chaperones. https://doi.org/10.1016/j.cstres.2024.10.004

Table: This table summarizes the core functional-annotation evidence for Saccharomyces cerevisiae Acl4/YDR161W, including identity verification, mechanism, localization, pre-60S role, and recent regulatory insights. It is useful as a compact evidence-backed reference for gene/protein annotation.


Key references (with URLs and publication dates)

  • Pillet B. et al. The Dedicated Chaperone Acl4 Escorts Ribosomal Protein Rpl4 to Its Nuclear Pre-60S Assembly Site. PLOS Genetics (Oct 2015). https://doi.org/10.1371/journal.pgen.1005565 (pillet2015thededicatedchaperone pages 1-2, pillet2015thededicatedchaperone pages 10-12)
  • Stelter P. et al. Coordinated Ribosomal L4 Protein Assembly into the Pre-Ribosome Is Regulated by Its Eukaryote-Specific Extension. Molecular Cell (Jun 2015). https://doi.org/10.1016/j.molcel.2015.03.029 (stelter2015coordinatedribosomall4 pages 3-3)
  • Huber F.M., Hoelz A. Molecular basis for protection of ribosomal protein L4 from cellular degradation. Nature Communications (Feb 2017). https://doi.org/10.1038/ncomms14354 (huber2017molecularbasisfor pages 1-2)
  • Pillet B. et al. Dedicated chaperones coordinate co-translational regulation of ribosomal protein production with ribosome assembly to preserve proteostasis. bioRxiv (posted Oct 2022). https://doi.org/10.1101/2021.10.05.463164 (pillet2022dedicatedchaperonescoordinate pages 1-4, pillet2022dedicatedchaperonescoordinate pages 14-16)
  • Dörner K. et al. Ribosome biogenesis factors—from names to functions. The EMBO Journal (Feb 2023). https://doi.org/10.15252/embj.2022112699 (dorner2023ribosomebiogenesisfactors—from pages 1-2)
  • Schilke B.A. et al. Functional similarities and differences among subunits of the NAC of Saccharomyces cerevisiae. Cell Stress and Chaperones (Dec 2024). https://doi.org/10.1016/j.cstres.2024.10.004 (schilke2024functionalsimilaritiesand pages 1-3)
  • Yang Y.-M., Karbstein K. Ribosome Assembly and Repair. Annual Review of Cell and Developmental Biology (Oct 2024). https://doi.org/10.1146/annurev-cellbio-111822-113326 (yang2024ribosomeassemblyand pages 1-3)

References

  1. (pillet2015thededicatedchaperone pages 1-2): Benjamin Pillet, Juan J. García-Gómez, Patrick Pausch, Laurent Falquet, Gert Bange, Jesús de la Cruz, and Dieter Kressler. The dedicated chaperone acl4 escorts ribosomal protein rpl4 to its nuclear pre-60s assembly site. PLOS Genetics, 11:e1005565, Oct 2015. URL: https://doi.org/10.1371/journal.pgen.1005565, doi:10.1371/journal.pgen.1005565. This article has 84 citations and is from a domain leading peer-reviewed journal.

  2. (huber2017molecularbasisfor pages 1-2): Ferdinand M. Huber and André Hoelz. Molecular basis for protection of ribosomal protein l4 from cellular degradation. Nature Communications, Feb 2017. URL: https://doi.org/10.1038/ncomms14354, doi:10.1038/ncomms14354. This article has 37 citations and is from a highest quality peer-reviewed journal.

  3. (pillet2015thededicatedchaperone pages 10-12): Benjamin Pillet, Juan J. García-Gómez, Patrick Pausch, Laurent Falquet, Gert Bange, Jesús de la Cruz, and Dieter Kressler. The dedicated chaperone acl4 escorts ribosomal protein rpl4 to its nuclear pre-60s assembly site. PLOS Genetics, 11:e1005565, Oct 2015. URL: https://doi.org/10.1371/journal.pgen.1005565, doi:10.1371/journal.pgen.1005565. This article has 84 citations and is from a domain leading peer-reviewed journal.

  4. (schilke2024functionalsimilaritiesand pages 1-3): Brenda A. Schilke, Thomas Ziegelhoffer, Przemyslaw Domanski, Jaroslaw Marszalek, Bartlomiej Tomiczek, and Elizabeth A. Craig. Functional similarities and differences among subunits of the nascent polypeptide-associated complex (nac) of saccharomyces cerevisiae. Cell Stress and Chaperones, 29:721-734, Dec 2024. URL: https://doi.org/10.1016/j.cstres.2024.10.004, doi:10.1016/j.cstres.2024.10.004. This article has 1 citations and is from a peer-reviewed journal.

  5. (pillet2022dedicatedchaperonescoordinate pages 14-16): Benjamin Pillet, Alfonso Méndez-Godoy, Guillaume Murat, Sébastien Favre, Michael Stumpe, Laurent Falquet, and Dieter Kressler. Dedicated chaperones coordinate co-translational regulation of ribosomal protein production with ribosome assembly to preserve proteostasis. BioRxiv, Oct 2022. URL: https://doi.org/10.1101/2021.10.05.463164, doi:10.1101/2021.10.05.463164. This article has 30 citations.

  6. (pillet2022dedicatedchaperonescoordinate pages 20-22): Benjamin Pillet, Alfonso Méndez-Godoy, Guillaume Murat, Sébastien Favre, Michael Stumpe, Laurent Falquet, and Dieter Kressler. Dedicated chaperones coordinate co-translational regulation of ribosomal protein production with ribosome assembly to preserve proteostasis. BioRxiv, Oct 2022. URL: https://doi.org/10.1101/2021.10.05.463164, doi:10.1101/2021.10.05.463164. This article has 30 citations.

  7. (stelter2015coordinatedribosomall4 pages 3-3): Philipp Stelter, Ferdinand M. Huber, Ruth Kunze, Dirk Flemming, André Hoelz, and Ed Hurt. Coordinated ribosomal l4 protein assembly into the pre-ribosome is regulated by its eukaryote-specific extension. Molecular cell, 58 5:854-62, Jun 2015. URL: https://doi.org/10.1016/j.molcel.2015.03.029, doi:10.1016/j.molcel.2015.03.029. This article has 78 citations and is from a highest quality peer-reviewed journal.

  8. (pillet2015thededicatedchaperone pages 18-20): Benjamin Pillet, Juan J. García-Gómez, Patrick Pausch, Laurent Falquet, Gert Bange, Jesús de la Cruz, and Dieter Kressler. The dedicated chaperone acl4 escorts ribosomal protein rpl4 to its nuclear pre-60s assembly site. PLOS Genetics, 11:e1005565, Oct 2015. URL: https://doi.org/10.1371/journal.pgen.1005565, doi:10.1371/journal.pgen.1005565. This article has 84 citations and is from a domain leading peer-reviewed journal.

  9. (yang2024ribosomeassemblyand pages 1-3): Yoon-Mo Yang and Katrin Karbstein. Ribosome assembly and repair. Annual Review of Cell and Developmental Biology, 40:241-264, Oct 2024. URL: https://doi.org/10.1146/annurev-cellbio-111822-113326, doi:10.1146/annurev-cellbio-111822-113326. This article has 18 citations and is from a domain leading peer-reviewed journal.

  10. (pillet2015thededicatedchaperone pages 20-21): Benjamin Pillet, Juan J. García-Gómez, Patrick Pausch, Laurent Falquet, Gert Bange, Jesús de la Cruz, and Dieter Kressler. The dedicated chaperone acl4 escorts ribosomal protein rpl4 to its nuclear pre-60s assembly site. PLOS Genetics, 11:e1005565, Oct 2015. URL: https://doi.org/10.1371/journal.pgen.1005565, doi:10.1371/journal.pgen.1005565. This article has 84 citations and is from a domain leading peer-reviewed journal.

  11. (pillet2015thededicatedchaperone pages 17-18): Benjamin Pillet, Juan J. García-Gómez, Patrick Pausch, Laurent Falquet, Gert Bange, Jesús de la Cruz, and Dieter Kressler. The dedicated chaperone acl4 escorts ribosomal protein rpl4 to its nuclear pre-60s assembly site. PLOS Genetics, 11:e1005565, Oct 2015. URL: https://doi.org/10.1371/journal.pgen.1005565, doi:10.1371/journal.pgen.1005565. This article has 84 citations and is from a domain leading peer-reviewed journal.

  12. (pillet2015thededicatedchaperone pages 14-17): Benjamin Pillet, Juan J. García-Gómez, Patrick Pausch, Laurent Falquet, Gert Bange, Jesús de la Cruz, and Dieter Kressler. The dedicated chaperone acl4 escorts ribosomal protein rpl4 to its nuclear pre-60s assembly site. PLOS Genetics, 11:e1005565, Oct 2015. URL: https://doi.org/10.1371/journal.pgen.1005565, doi:10.1371/journal.pgen.1005565. This article has 84 citations and is from a domain leading peer-reviewed journal.

  13. (huber2017molecularbasisfor media 4aaddfb0): Ferdinand M. Huber and André Hoelz. Molecular basis for protection of ribosomal protein l4 from cellular degradation. Nature Communications, Feb 2017. URL: https://doi.org/10.1038/ncomms14354, doi:10.1038/ncomms14354. This article has 37 citations and is from a highest quality peer-reviewed journal.

  14. (huber2017molecularbasisfor media cb2e78f3): Ferdinand M. Huber and André Hoelz. Molecular basis for protection of ribosomal protein l4 from cellular degradation. Nature Communications, Feb 2017. URL: https://doi.org/10.1038/ncomms14354, doi:10.1038/ncomms14354. This article has 37 citations and is from a highest quality peer-reviewed journal.

  15. (huber2017molecularbasisfor media e4ea49ee): Ferdinand M. Huber and André Hoelz. Molecular basis for protection of ribosomal protein l4 from cellular degradation. Nature Communications, Feb 2017. URL: https://doi.org/10.1038/ncomms14354, doi:10.1038/ncomms14354. This article has 37 citations and is from a highest quality peer-reviewed journal.

  16. (pillet2022dedicatedchaperonescoordinate pages 1-4): Benjamin Pillet, Alfonso Méndez-Godoy, Guillaume Murat, Sébastien Favre, Michael Stumpe, Laurent Falquet, and Dieter Kressler. Dedicated chaperones coordinate co-translational regulation of ribosomal protein production with ribosome assembly to preserve proteostasis. BioRxiv, Oct 2022. URL: https://doi.org/10.1101/2021.10.05.463164, doi:10.1101/2021.10.05.463164. This article has 30 citations.

  17. (dorner2023ribosomebiogenesisfactors—from pages 1-2): Kerstin Dörner, Chiara Ruggeri, Ivo Zemp, and Ulrike Kutay. Ribosome biogenesis factors—from names to functions. The EMBO Journal, Feb 2023. URL: https://doi.org/10.15252/embj.2022112699, doi:10.15252/embj.2022112699. This article has 201 citations.

Citations

  1. pillet2015thededicatedchaperone pages 17-18
  2. pillet2015thededicatedchaperone pages 10-12
  3. pillet2022dedicatedchaperonescoordinate pages 14-16
  4. pillet2022dedicatedchaperonescoordinate pages 20-22
  5. pillet2022dedicatedchaperonescoordinate pages 1-4
  6. yang2024ribosomeassemblyand pages 1-3
  7. schilke2024functionalsimilaritiesand pages 1-3
  8. huber2017molecularbasisfor pages 1-2
  9. pillet2015thededicatedchaperone pages 1-2
  10. pillet2015thededicatedchaperone pages 18-20
  11. pillet2015thededicatedchaperone pages 20-21
  12. pillet2015thededicatedchaperone pages 14-17
  13. https://doi.org/10.1371/journal.pgen.1005565;
  14. https://doi.org/10.1016/j.molcel.2015.03.029
  15. https://doi.org/10.1038/ncomms14354
  16. https://doi.org/10.1016/j.molcel.2015.03.029;
  17. https://doi.org/10.1371/journal.pgen.1005565
  18. https://doi.org/10.1038/ncomms14354;
  19. https://doi.org/10.1101/2021.10.05.463164;
  20. https://doi.org/10.1016/j.cstres.2024.10.004
  21. https://doi.org/10.1101/2021.10.05.463164
  22. https://doi.org/10.15252/embj.2022112699
  23. https://doi.org/10.1146/annurev-cellbio-111822-113326
  24. https://doi.org/10.1371/journal.pgen.1005565,
  25. https://doi.org/10.1038/ncomms14354,
  26. https://doi.org/10.1016/j.cstres.2024.10.004,
  27. https://doi.org/10.1101/2021.10.05.463164,
  28. https://doi.org/10.1016/j.molcel.2015.03.029,
  29. https://doi.org/10.1146/annurev-cellbio-111822-113326,
  30. https://doi.org/10.15252/embj.2022112699,

📄 View Raw YAML

id: Q03771
gene_symbol: ACL4
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:559292
  label: Saccharomyces cerevisiae
description: >-
  ACL4 encodes the dedicated assembly chaperone for the large ribosomal subunit
  protein Rpl4/uL4. Acl4 binds newly synthesized Rpl4, keeps the highly basic
  unassembled ribosomal protein soluble, and escorts it from the cytoplasm to
  the nuclear pre-60S assembly site. Loss of ACL4 causes slow growth, reduced
  60S subunit production, half-mer polysomes, and pre-rRNA processing defects,
  supporting a core role in ribosomal large subunit biogenesis rather than
  mitochondrial protein import.
existing_annotations:
- term:
    id: GO:0005741
    label: mitochondrial outer membrane
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      This IBA traces to a broad PANTHER family context that UniProt labels as
      mitochondrial import receptor subunit TOM70, but the reviewed yeast ACL4
      subfamily entry is an assembly chaperone of RPL4. UniProt and the Falcon
      review support cytoplasmic/nuclear localization for Acl4, not a
      mitochondrial outer membrane role.
    action: REMOVE
    reason: >-
      The family-transfer annotation appears to have propagated TOM70-family
      mitochondrial localization to a divergent Acl4/Rpl4 chaperone. No primary
      Acl4 evidence supports mitochondrial outer membrane residence.
    supported_by:
    - reference_id: file:yeast/ACL4/ACL4-deep-research-falcon.md
      supporting_text: "Acl4 is detected in both cytoplasm and nucleus"
- term:
    id: GO:0008320
    label: protein transmembrane transporter activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: contributes_to
  review:
    summary: >-
      Acl4 escorts the soluble ribosomal protein Rpl4; it is not a component of
      a protein transmembrane translocation channel. This IBA is inconsistent
      with the experimentally supported Acl4 subfamily biology.
    action: REMOVE
    reason: >-
      The annotation likely reflects the TOM70-like parent family rather than
      Acl4. Acl4 functions as a ribosomal protein carrier chaperone, not as a
      transmembrane transporter or transporter subunit.
- term:
    id: GO:0030150
    label: protein import into mitochondrial matrix
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      Experimental Acl4 studies describe Rpl4 handling and nuclear pre-60S
      assembly, with no evidence for mitochondrial matrix protein import.
    action: REMOVE
    reason: >-
      This is a family-transfer overannotation from a TOM70-like ancestor and
      conflicts with the specific yeast Acl4/Rpl4 literature.
- term:
    id: GO:0030943
    label: mitochondrion targeting sequence binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      Acl4 binds a segment of the Rpl4 long internal loop and protects
      unassembled Rpl4. It has no demonstrated binding to mitochondrial targeting
      sequences.
    action: REMOVE
    reason: >-
      The supported client-binding activity is Rpl4 carrier chaperone activity.
      The mitochondrial targeting sequence term should not be retained for the
      yeast ACL4 subfamily.
    supported_by:
    - reference_id: file:yeast/ACL4/ACL4-deep-research-falcon.md
      supporting_text: "Acl4 binds newly synthesized, free Rpl4"
- term:
    id: GO:0045039
    label: protein insertion into mitochondrial inner membrane
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      The experimentally supported Acl4 pathway is Rpl4 delivery to the nuclear
      pre-60S ribosome, not insertion of proteins into the mitochondrial inner
      membrane.
    action: REMOVE
    reason: >-
      This IBA is not supported for ACL4 and should be removed as a TOM70-family
      over-transfer.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: >-
      UniProt subcellular-location mapping to nucleus is consistent with direct
      Acl4 localization studies and with Acl4 delivery of Rpl4 to nuclear
      pre-60S particles.
    action: ACCEPT
    reason: >-
      Acl4 is enriched in the nucleus and performs its client-delivery function
      at the nuclear pre-60S assembly site.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      Automated cytoplasm assignment is consistent with direct studies showing
      Acl4 in the cytoplasm, where Rpl4 is synthesized and first captured.
    action: ACCEPT
    reason: >-
      Cytoplasmic localization is part of the supported escort path from
      nascent Rpl4 capture to nuclear assembly.
- term:
    id: GO:0042254
    label: ribosome biogenesis
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      The keyword-derived ribosome biogenesis term is broad but accurate for
      Acl4, which is required for efficient production of 60S ribosomal subunits.
    action: ACCEPT
    reason: >-
      Experimental annotations to ribosomal large subunit biogenesis provide the
      more specific evidence; this parent process is correct as an automated
      summary of Acl4 function.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IDA
  original_reference_id: PMID:25936803
  review:
    summary: >-
      Direct experimental localization supports nuclear Acl4, consistent with
      the Rpl4 pre-60S assembly site.
    action: ACCEPT
    reason: >-
      The localization matches the mechanistic model in which Acl4 delivers
      Rpl4 to nuclear pre-60S assembly intermediates.
    supported_by:
    - reference_id: PMID:25936803
      supporting_text: "assembly chaperone Acl4 that initially binds the universally conserved internal"
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IDA
  original_reference_id: PMID:26447800
  review:
    summary: >-
      Direct microscopy in the dedicated Acl4-Rpl4 study supports nuclear
      localization.
    action: ACCEPT
    reason: >-
      Acl4 localizes to the nucleus as expected for a factor escorting Rpl4 to
      nuclear pre-60S assembly sites.
    supported_by:
    - reference_id: PMID:26447800
      supporting_text: "Acl4 localizes to both the cytoplasm and nucleus"
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IDA
  original_reference_id: PMID:26447800
  review:
    summary: >-
      Direct microscopy supports cytoplasmic Acl4 localization.
    action: ACCEPT
    reason: >-
      Acl4 must encounter newly translated Rpl4 in the cytoplasm before nuclear
      delivery, so this localization is mechanistically coherent.
    supported_by:
    - reference_id: PMID:26447800
      supporting_text: "Acl4 localizes to both the cytoplasm and nucleus"
- term:
    id: GO:0042273
    label: ribosomal large subunit biogenesis
  evidence_type: IMP
  original_reference_id: PMID:25936803
  review:
    summary: >-
      Mutant phenotype evidence shows that ACL4 is required for normal 60S
      subunit production through Rpl4 assembly.
    action: ACCEPT
    reason: >-
      Acl4 shields Rpl4 until it can be inserted into the pre-ribosome; ACL4
      loss causes large-subunit biogenesis defects, making this a core process.
    supported_by:
    - reference_id: PMID:25936803
      supporting_text: "hierarchical ribosome assembly can be achieved by eukaryotic RP extensions and"
- term:
    id: GO:0042273
    label: ribosomal large subunit biogenesis
  evidence_type: IMP
  original_reference_id: PMID:26447800
  review:
    summary: >-
      The dedicated chaperone study shows that Acl4 escorts Rpl4 to its nuclear
      pre-60S assembly site and that loss of Acl4 compromises 60S production.
    action: ACCEPT
    reason: >-
      This is the central biological process for Acl4 and is supported by
      genetic, localization, and biochemical evidence.
    supported_by:
    - reference_id: PMID:26447800
      supporting_text: "deficiency in the production of 60S subunits"
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IDA
  original_reference_id: PMID:25936803
  review:
    summary: >-
      Acl4 does bind and protect unassembled Rpl4, but "unfolded protein
      binding" is too generic and obscures the dedicated carrier-chaperone role.
    action: MODIFY
    reason: >-
      The evidence supports specific ribosomal-protein carrier chaperone
      activity rather than generic binding to unfolded proteins.
    proposed_replacement_terms:
    - id: GO:0140597
      label: protein carrier activity
    supported_by:
    - reference_id: file:yeast/ACL4/ACL4-deep-research-falcon.md
      supporting_text: "Acl4 is a dedicated ribosomal protein chaperone"
- term:
    id: GO:0140318
    label: protein transporter activity
  evidence_type: IDA
  original_reference_id: PMID:26447800
  review:
    summary: >-
      The evidence supports Acl4 directly binding and escorting Rpl4 to the
      pre-60S assembly pathway, matching the current definition of protein
      transporter activity as binding and delivering a specific protein to a
      cellular location.
    action: ACCEPT
    reason: >-
      QuickGO places GO:0140318 under transporter activity and GO:0140597 under
      molecular carrier activity rather than as a parent-child pair. Retaining
      this SGD IDA annotation is therefore not a redundant parent annotation,
      and the PMID:26447800 evidence supports Acl4 escorting Rpl4 to the
      pre-60S assembly pathway.
    supported_by:
    - reference_id: PMID:26447800
      supporting_text: "dedicated chaperone Acl4 accompanies Rpl4"
- term:
    id: GO:0051083
    label: "'de novo' cotranslational protein folding"
  evidence_type: HGI
  original_reference_id: PMID:19325107
  review:
    summary: >-
      Acl4 can capture nascent Rpl4 cotranslationally, but this high-throughput
      genetic-interaction annotation is broad and does not define Acl4 as a
      general cotranslational folding factor.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The better-supported curation is the specific Rpl4 carrier-chaperone role
      in ribosomal large subunit biogenesis. Retaining the broad folding process
      as a core annotation would overstate the evidence.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: HDA
  original_reference_id: PMID:14562095
  review:
    summary: >-
      High-throughput localization to nucleus is consistent with direct Acl4
      localization and its nuclear pre-60S assembly role.
    action: ACCEPT
    reason: >-
      Multiple independent sources support nuclear localization.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: HDA
  original_reference_id: PMID:14562095
  review:
    summary: >-
      High-throughput localization to cytoplasm is consistent with direct Acl4
      localization and nascent Rpl4 capture.
    action: ACCEPT
    reason: >-
      Acl4 is distributed through cytoplasm and nucleus, matching its escort
      function.
core_functions:
- molecular_function:
    id: GO:0140597
    label: protein carrier activity
  directly_involved_in:
  - id: GO:0042273
    label: ribosomal large subunit biogenesis
  locations:
  - id: GO:0005737
    label: cytoplasm
  - id: GO:0005634
    label: nucleus
  description: >-
    Acl4 is a dedicated carrier chaperone for Rpl4/uL4. It binds newly
    synthesized Rpl4 in the cytoplasm, protects it from inappropriate
    interactions or aggregation, and escorts it to nuclear pre-60S particles for
    large ribosomal subunit assembly.
  supported_by:
  - reference_id: PMID:26447800
    supporting_text: "dedicated chaperone Acl4 accompanies Rpl4"
  - reference_id: file:yeast/ACL4/ACL4-deep-research-falcon.md
    supporting_text: "Acl4 binds newly synthesized, free Rpl4"
proposed_new_terms: []
suggested_questions:
- question: >-
    Should PANTHER family PTHR46208 be split or have IBA propagation restricted
    so TOM70 mitochondrial import terms do not transfer to the ACL4/Rpl4
    assembly chaperone subfamily?
suggested_experiments:
- description: >-
    Re-analyze ACL4, TOM70, and related PTHR46208 subfamilies with tree-aware
    GO propagation to test whether mitochondrial import annotations segregate
    away from the experimentally characterized Acl4/Rpl4 clade.
  experiment_type: phylogenetic curation
  hypothesis: >-
    The ACL4 subfamily lacks the mitochondrial protein import functions present
    in TOM70-like relatives and should not inherit those IBA terms.
references:
- 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:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:14562095
  title: Global analysis of protein localization in budding yeast.
  findings: []
- id: PMID:19325107
  title: Comprehensive characterization of genes required for protein folding in the endoplasmic reticulum.
  findings: []
- id: PMID:25936803
  title: Coordinated Ribosomal L4 Protein Assembly into the Pre-Ribosome Is Regulated by Its Eukaryote-Specific Extension.
  findings: []
- id: PMID:26447800
  title: The Dedicated Chaperone Acl4 Escorts Ribosomal Protein Rpl4 to Its Nuclear Pre-60S Assembly Site.
  findings: []
- id: file:yeast/ACL4/ACL4-deep-research-falcon.md
  title: Falcon deep research report for ACL4
  findings: []