TSR4

UniProt ID: P25040
Organism: Saccharomyces cerevisiae
Review Status: COMPLETE
Aliases:
YOL022C uS5 assembly chaperone
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Gene Description

TSR4 encodes a cytoplasmic, client-specific ribosomal protein carrier chaperone for Rps2/uS5. Tsr4 binds the eukaryote-specific N-terminal extension of nascent Rps2/uS5, promotes Rps2 expression and solubility, and releases the client before nuclear import and productive pre-40S assembly. Loss of Tsr4 impairs 40S ribosomal small subunit biogenesis, pre-40S export, and 20S pre-rRNA processing at site D to mature 18S rRNA.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0030490 maturation of SSU-rRNA
IBA
GO_REF:0000033
ACCEPT
Summary: IBA is consistent with Tsr4-dependent 20S pre-rRNA processing and 40S biogenesis.
Reason: SSU-rRNA maturation is a direct process-level consequence of the uS5 chaperone role.
Supporting Evidence:
PMID:19806183
YOR006C/TSR3, YOL022C/TSR4). We associate the new genes with specific aspects of...processing of 5S, 7S, 20S, 27S, and 35S rRNAs.
file:yeast/TSR4/TSR4-deep-research-falcon.md
Tsr4 enables downstream 40S assembly and pre-40S export through cytoplasmic Rps2/uS5 chaperone activity.
GO:0005737 cytoplasm
IEA
GO_REF:0000002
ACCEPT
Summary: Cytoplasmic localization is consistent with direct Tsr4 studies.
Reason: Tsr4 acts in the cytoplasm on nascent Rps2/uS5 before nuclear import.
Supporting Evidence:
PMID:31182640
Tsr4 appears to be restricted to the cytoplasm.
GO:0005829 cytosol
IEA
GO_REF:0000044
ACCEPT
Summary: Cytosol is the best location for Tsr4 carrier chaperone activity.
Reason: Direct and curated sources place Tsr4 in the cytosol/cytoplasm.
Supporting Evidence:
PMID:31062022
Tsr4 binds co-translationally to the...essential, eukaryote-specific N-terminal extension of Rps2
GO:0042254 ribosome biogenesis
IEA
GO_REF:0000043
MODIFY
Summary: Ribosome biogenesis is correct but too broad for Tsr4.
Reason: Replace with the more specific ribosomal small subunit biogenesis term.
Supporting Evidence:
PMID:31062022
Mutation of the essential Tsr4...enhance the 40S synthesis defects
GO:0005829 cytosol
IDA
PMID:31062022
Tsr4 and Nap1, two novel members of the ribosomal protein ch...
ACCEPT
Summary: Direct evidence supports cytosolic localization.
Reason: Tsr4 binds Rps2/uS5 co-translationally in the cytosol.
Supporting Evidence:
PMID:31062022
Tsr4 binds co-translationally to the...essential, eukaryote-specific N-terminal extension of Rps2
GO:0140597 protein carrier chaperone
IDA
PMID:31062022
Tsr4 and Nap1, two novel members of the ribosomal protein ch...
ACCEPT
Summary: This is the most specific molecular-function annotation for TSR4.
Reason: Tsr4 is a dedicated carrier chaperone for ribosomal protein Rps2/uS5.
Supporting Evidence:
PMID:31062022
vitro. While Tsr4 is specific for Rps2...Tsr4 binds co-translationally to the...essential, eukaryote-specific N-terminal extension of Rps2
file:yeast/TSR4/TSR4-deep-research-falcon.md
Tsr4 is a cytoplasmic, co-translational uS5 chaperone that captures the Rps2 N-terminus.
GO:0042274 ribosomal small subunit biogenesis
IMP
PMID:31062022
Tsr4 and Nap1, two novel members of the ribosomal protein ch...
ACCEPT
Summary: Tsr4 perturbation causes 40S biogenesis defects.
Reason: Rps2/uS5 chaperoning is directly tied to small subunit assembly.
Supporting Evidence:
PMID:31062022
Mutation of the essential Tsr4...enhance the 40S synthesis defects
GO:0042274 ribosomal small subunit biogenesis
IGI
PMID:31062022
Tsr4 and Nap1, two novel members of the ribosomal protein ch...
ACCEPT
Summary: Genetic evidence with RPS2 supports the 40S biogenesis annotation.
Reason: The genetic relationship supports Tsr4's role in Rps2-dependent 40S assembly.
Supporting Evidence:
PMID:31062022
identification of Nap1 and Tsr4 as direct binding partners of Rps6 and Rps2
GO:0051082 unfolded protein binding
IDA
PMID:31062022
Tsr4 and Nap1, two novel members of the ribosomal protein ch...
MODIFY
Summary: The binding evidence is specific to Rps2/uS5, not generic unfolded protein.
Reason: Replace broad unfolded protein binding with protein carrier chaperone.
Proposed replacements: protein carrier chaperone
Supporting Evidence:
PMID:31062022
Both factors promote the solubility of their r-protein clients in...vitro.
GO:0042274 ribosomal small subunit biogenesis
IMP
PMID:31182640
Tsr4 Is a Cytoplasmic Chaperone for the Ribosomal Protein Rp...
ACCEPT
Summary: Independent evidence supports the same 40S biogenesis role.
Reason: Tsr4 perturbation decreases Rps2 and phenocopies Rps2 depletion.
Supporting Evidence:
PMID:31182640
Tsr4 perturbation resulted in decreased Rps2 levels and...phenocopied Rps2 depletion.
GO:0051082 unfolded protein binding
IDA
PMID:31182640
Tsr4 Is a Cytoplasmic Chaperone for the Ribosomal Protein Rp...
MODIFY
Summary: The evidence supports specific Rps2 carrier chaperoning.
Reason: Protein carrier chaperone is the more precise molecular-function term.
Proposed replacements: protein carrier chaperone
Supporting Evidence:
PMID:31182640
Tsr4 cotranslationally associates with Rps2...cytoplasmic chaperone dedicated to Rps2.
GO:0051082 unfolded protein binding
IPI
PMID:31182640
Tsr4 Is a Cytoplasmic Chaperone for the Ribosomal Protein Rp...
MODIFY
Summary: The IPI evidence identifies a specific Rps2/uS5 client relationship.
Reason: Replace broad unfolded protein binding with protein carrier chaperone.
Proposed replacements: protein carrier chaperone
Supporting Evidence:
PMID:31182640
Rps2 harbors a...eukaryote-specific N-terminal extension that is critical for its interaction...with Tsr4.
GO:0005737 cytoplasm
IDA
PMID:31182640
Tsr4 Is a Cytoplasmic Chaperone for the Ribosomal Protein Rp...
ACCEPT
Summary: Direct microscopy and functional evidence support cytoplasmic localization.
Reason: Tsr4 acts before nuclear import and pre-ribosome assembly.
Supporting Evidence:
PMID:31182640
Despite Rps2 joining nuclear pre-40S particles, Tsr4 appears to be restricted to the cytoplasm.
GO:0005737 cytoplasm
HDA
PMID:14562095
Global analysis of protein localization in budding yeast.
ACCEPT
Summary: High-throughput cytoplasmic localization is consistent with targeted studies.
Reason: The broad cytoplasm term is correct, though cytosol is more precise.
Supporting Evidence:
PMID:31182640
Tsr4 appears to be restricted to the cytoplasm.
GO:0030490 maturation of SSU-rRNA
IMP
PMID:19806183
Rational extension of the ribosome biogenesis pathway using ...
ACCEPT
Summary: The original genetic annotation correctly identifies TSR4 in SSU rRNA maturation.
Reason: Later work explains the phenotype through defective Rps2/uS5 handling and 40S assembly.
Supporting Evidence:
PMID:19806183
YOR006C/TSR3, YOL022C/TSR4). We associate the new genes with specific aspects of...processing of 5S, 7S, 20S, 27S, and 35S rRNAs.

Core Functions

Cytoplasmic protein carrier chaperone for ribosomal protein Rps2/uS5. Tsr4 binds nascent Rps2/uS5 and maintains the client in a soluble assembly-competent state before nuclear import and incorporation into pre-40S particles.

Supporting Evidence:
  • PMID:31062022
    identification of Nap1 and Tsr4 as direct binding partners of Rps6 and Rps2...Both factors promote the solubility of their r-protein clients
  • PMID:31182640
    Tsr4 perturbation resulted in decreased Rps2 levels and...phenocopied Rps2 depletion.
  • file:yeast/TSR4/TSR4-deep-research-falcon.md
    Tsr4 is a cytoplasmic, co-translational uS5 chaperone that captures the Rps2 N-terminus.

References

Gene Ontology annotation through association of InterPro records with GO terms
Annotation inferences using phylogenetic trees
Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping
Global analysis of protein localization in budding yeast.
Rational extension of the ribosome biogenesis pathway using network-guided genetics.
  • TSR4 was identified as a ribosome biogenesis factor
    "Network-guided genetics associated YOL022C/TSR4 with ribosome biogenesis and pre-rRNA processing."
Tsr4 and Nap1, two novel members of the ribosomal protein chaperOME.
  • Tsr4 is a direct Rps2/uS5 carrier chaperone
    "Tsr4 is specific for Rps2, binds co-translationally to its N-terminal extension, and promotes solubility."
Tsr4 Is a Cytoplasmic Chaperone for the Ribosomal Protein Rps2 in Saccharomyces cerevisiae.
  • Tsr4 is a cytoplasmic chaperone dedicated to Rps2
    "Tsr4 cotranslationally associates with Rps2; perturbation decreases Rps2 levels."
file:yeast/TSR4/TSR4-deep-research-falcon.md
Falcon deep research report for TSR4
  • TSR4 is a cytoplasmic uS5/Rps2 carrier chaperone
    "The report synthesizes evidence that Tsr4 captures nascent Rps2/uS5 and enables downstream 40S assembly."

Suggested Questions for Experts

Q: Should older GO:0051082 annotations for Tsr4 be replaced by GO:0140597 protein carrier chaperone where evidence is specific Rps2/uS5 chaperoning?

📚 Additional Documentation

Deep Research Falcon

(TSR4-deep-research-falcon.md)

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Full=20S rRNA accumulation protein 4;'
gene_info: Name=TSR4; OrderedLocusNames=YOL022C;
organism_full: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
protein_family: Belongs to the TSR4 family. .
protein_domains: PDCD2_C. (IPR007320); PDCD2_C (PF04194)
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Question

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

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

Target Gene/Protein Identity (from UniProt):

  • UniProt Accession: P25040
  • Protein Description: RecName: Full=uS5 assembly chaperone {ECO:0000305}; AltName: Full=20S rRNA accumulation protein 4;
  • Gene Information: Name=TSR4; OrderedLocusNames=YOL022C;
  • Organism (full): Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  • Protein Family: Belongs to the TSR4 family. .
  • Key Domains: PDCD2_C. (IPR007320); PDCD2_C (PF04194)

MANDATORY VERIFICATION STEPS:

  1. Check if the gene symbol "TSR4" 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 'TSR4' 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 TSR4 (gene ID: TSR4, UniProt: P25040) 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: P25040
  • Protein Description: RecName: Full=uS5 assembly chaperone {ECO:0000305}; AltName: Full=20S rRNA accumulation protein 4;
  • Gene Information: Name=TSR4; OrderedLocusNames=YOL022C;
  • Organism (full): Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  • Protein Family: Belongs to the TSR4 family. .
  • Key Domains: PDCD2_C. (IPR007320); PDCD2_C (PF04194)

MANDATORY VERIFICATION STEPS:

  1. Check if the gene symbol "TSR4" 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 'TSR4' 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 TSR4 (gene ID: TSR4, UniProt: P25040) 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 TSR4 (UniProt P25040; YOL022C)

0) Target verification (gene/protein identity)

The yeast gene TSR4 (ordered locus YOL022C; UniProt P25040) corresponds to the ribosome biogenesis factor historically described as “20S rRNA accumulation protein 4” and is now experimentally established as a uS5 (Rps2) assembly chaperone. Primary yeast studies that biochemically and genetically characterize Tsr4 (the protein product of TSR4) identify its client as the small-subunit ribosomal protein Rps2/uS5 and show a cytoplasmic chaperone role (black2019tsr4isa pages 1-3, black2019tsr4isa pages 15-17).

Domain/family verification matches the UniProt context: a comparative genomics analysis reports that yeast TSR4 is annotated in Pfam as containing a C-terminal PDCD2_C domain and unifies TSR4 with eukaryotic homologs PDCD2/PDCD2L (and related proteins) into a larger duplicated-repeat superfamily termed TYPP, proposed to mediate protein–protein interactions consistent with chaperone-like function (burroughs2014analysisoftwo pages 3-5, burroughs2014analysisoftwo pages 5-7).

1) Key concepts and current understanding

1.1 Dedicated ribosomal-protein chaperones (concept)

Eukaryotic ribosome biogenesis requires safe handling of newly synthesized ribosomal proteins (RPs), many of which are highly basic and/or contain intrinsically disordered, eukaryote-specific extensions that are aggregation-prone. Dedicated RP chaperones are specialized factors that bind specific RPs to promote solubility, prevent nonproductive interactions, and enable correct delivery/assembly (rossler2019tsr4andnap1 pages 1-2, black2019tsr4isa pages 1-3).

TSR4/Tsr4 is a canonical example of this class: it is described as a dedicated chaperone that binds Rps2/uS5 and promotes its solubility and productive assembly into 40S subunits (rossler2019tsr4andnap1 pages 14-15, black2019tsr4isa pages 15-17).

1.2 What TSR4 does at a molecular level

Molecular function (best-supported): Tsr4 binds nascent Rps2/uS5 co-translationally in the cytoplasm and acts as a client-specific chaperone to stabilize Rps2 and support 40S biogenesis (black2019tsr4isa pages 1-3, rossler2019tsr4andnap1 pages 12-13).

Client recognition: Multiple experiments map Tsr4 recognition primarily to the eukaryote-specific N-terminal extension of Rps2, with the first ~42 amino acids sufficient/required for robust interaction (rossler2019tsr4andnap1 pages 12-13). This binding is consistent with the general principle that dedicated chaperones often recognize eukaryote-specific RP extensions (rossler2019tsr4andnap1 pages 1-2).

Chaperone effect on solubility: Rps2 expressed alone is aggregation-prone, while co-expression with Tsr4 keeps Rps2 soluble and supports complex formation in vitro and in vivo (rossler2019tsr4andnap1 pages 14-15).

1.3 Cellular process and pathway context

TSR4 acts within small (40S) ribosomal subunit biogenesis, specifically by enabling accumulation and assembly of Rps2/uS5 into pre-40S particles. Loss of TSR4 phenocopies reduced uS5 availability, producing severe 40S defects and pre-40S export problems (black2019tsr4isa pages 15-17, rossler2019tsr4andnap1 pages 15-16).

A 2023 review synthesizing cross-species evidence frames TSR4/PDCD2 as an evolutionarily conserved uS5 chaperone module that monitors uS5 availability/folding and supports pre-rRNA maturation outcomes consistent with 40S assembly (e.g., accumulation of 20S/21S pre-rRNAs and reduced uS5 incorporation when the module is perturbed) (landryvoyer2023ribosomalproteinus5 pages 6-8, landryvoyer2023ribosomalproteinus5 pages 8-10).

2) Experimentally supported biology of yeast TSR4/Tsr4

2.1 Binding partners and mechanism

Primary binding partner: Rps2/uS5.

Co-translational association: Tsr4 purifications enrich RPS2 mRNA, consistent with binding to nascent chains during translation; interaction mapping supports specificity for the Rps2 N-terminus (rossler2019tsr4andnap1 pages 12-13). Black et al. likewise report co-translational association and dependence on the eukaryote-specific Rps2 N-terminal extension (black2019tsr4isa pages 1-3).

Key mechanistic inference: Tsr4 appears to act upstream of nuclear pre-40S assembly, stabilizing Rps2 before (or during) handoff to nuclear import/assembly pathways, rather than being a stable component of nuclear pre-ribosomes (black2019tsr4isa pages 17-20, black2019tsr4isa pages 15-17).

2.2 Subcellular localization (where it acts)

Multiple lines of evidence support that yeast Tsr4 is predominantly cytoplasmic and does not undergo obvious Crm1-dependent shuttling:

  • Black et al. performed a Crm1 inhibition assay (leptomycin B in a Crm1-sensitized strain) where the Crm1 cargo control Nmd3 relocalizes to the nucleus, but Tsr4 remains cytoplasmic, arguing against Crm1-dependent nucleocytoplasmic shuttling (black2019tsr4isa media 141d3d19).
  • Functional mutation of a predicted NLS in Tsr4 still complements loss of Tsr4, consistent with the idea that nuclear entry is not required for its essential function (black2019tsr4isa pages 15-17).

2.3 Consequences of TSR4 loss: phenotypes and readouts

Ribosome biogenesis output (polysome profiling): Loss of Tsr4 produces a dramatic small subunit defect described as a missing 40S peak, increased free 60S, and reduced 80S/polysomes (rossler2019tsr4andnap1 pages 15-16).

Pre-40S export / nuclear accumulation: Repression of TSR4 (or RPS2) causes nuclear accumulation of ITS1, interpreted as a block in pre-40S export (black2019tsr4isa pages 15-17).

Rps2 abundance: Perturbation of Tsr4 reduces Rps2 levels and phenocopies Rps2 depletion, consistent with a stabilizing chaperone function (black2019tsr4isa pages 1-3).

Genetic suppression: Increasing RPS2 dosage can partially bypass TSR4 loss (viability rescue), supporting a direct client-chaperone relationship; however, the rescued strains have impaired growth (growth defects at 25–30°C; inviability at 37°C), consistent with incomplete restoration of robust biogenesis (rossler2019tsr4andnap1 pages 15-16).

Quantitative notes:
* Estimated abundance: ~1,500 Tsr4 molecules/cell (black2019tsr4isa pages 6-8).
* Rps2-GFP steady-state localization: in wild-type, ~72% of cells show nuclear exclusion of Rps2-GFP; in the absence of Tsr4, Rps2 reporters show nuclear signal/accumulation (rossler2019tsr4andnap1 pages 15-16, rossler2019tsr4andnap1 pages 16-16).

3) Recent developments and latest research (2023–2024 prioritized)

3.1 2023: Nuclear import of Rps2/uS5 is Tsr4-independent

A focused mechanistic study (Steiner et al., July 2023) dissected nuclear import signals of yeast Rps2/uS5. Key findings:

  • An internal region Rps2(76–145) is sufficient for nuclear targeting and contains a critical basic cluster R95/R97/K99; mutation of these residues strongly disrupts nuclear localization (steiner2023dissectingthenuclear pages 6-9, steiner2023dissectingthenuclear pages 1-2).
  • A second nuclear targeting element lies in the N-terminal region (~10–28) (RG-rich/basic), which overlaps the Tsr4-binding region (steiner2023dissectingthenuclear pages 1-2, steiner2023dissectingthenuclear pages 15-18).
  • Importin Pse1 (Kap121) interacts with and contributes to import of the internal NLS, but import is not exclusively Pse1-dependent, consistent with redundancy among importins (steiner2023dissectingthenuclear pages 2-4, steiner2023dissectingthenuclear pages 15-18).
  • Critically, nuclear import via either the internal or N-terminal element does not require Tsr4, supporting a model where Tsr4’s essential function is chaperoning/assembly competence rather than serving as the import adaptor (steiner2023dissectingthenuclear pages 2-4, steiner2023dissectingthenuclear pages 13-15).

This resolves an important mechanistic ambiguity noted in reviews: because Tsr4 binds near an NLS, it was plausible that Tsr4 was required for import; instead, import can occur without it, while assembly remains defective (steiner2023dissectingthenuclear pages 2-4, rossler2019tsr4andnap1 pages 16-16).

3.2 2023: Consolidation of the conserved uS5 interactome

A 2023 review (Landry-Voyer et al., May 2023) synthesizes evidence that PDCD2 and its homologs (including yeast Tsr4) are dedicated uS5 chaperones that recognize nascent uS5 co-translationally and whose perturbation phenocopies uS5 deficiency (landryvoyer2023ribosomalproteinus5 pages 6-8, landryvoyer2023ribosomalproteinus5 pages 8-10). The review also highlights unanswered questions, including how the chaperone–uS5 complex is disassembled and coordinated with import/assembly (landryvoyer2023ribosomalproteinus5 pages 8-10).

3.3 2024: Framing Tsr4 in modern “chaperome” and coordination questions

A 2024 Biomolecules editorial (Pertschy & Zierler, Dec 2024) highlights the open question created by overlap of Tsr4 binding and an N-terminal uS5 NLS: how are chaperoning and import coordinated in space and time? (pertschy2024ribosomalproteinsin pages 1-2).

A 2024 Annual Review (Yang & Karbstein, Oct 2024) places dedicated RP chaperones (including the Tsr4/Nap1 chaperome work) into a broader conceptual framework where specialized chaperones can contribute to assembly and potentially to maintenance/repair processes (yang2024ribosomeassemblyand pages 20-21, yang2024ribosomeassemblyand pages 11-13).

3.4 2023: Ribosome repair after oxidative damage—Tsr4 does not extract Rps2

Yang et al. (Molecular Cell, May 2023) demonstrated chaperone-mediated extraction of oxidized Rps26 by Tsr2 during oxidative stress, but explicitly report that neither Rps2 nor Rps3 were released by their chaperones (Tsr4 and Yar1) in their in vitro extraction assays (yang2023chaperonedirectedribosomerepair pages 3-5, yang2023chaperonedirectedribosomerepair pages 5-7). This suggests that, unlike Tsr2–Rps26, the Tsr4–Rps2 pair is not (or is not readily) deployed for extraction-based repair under those experimental conditions.

4) Applications and real-world implementations

4.1 TSR4 as an experimental handle for uS5 handling and 40S biogenesis

In yeast, TSR4 is used as a mechanistic probe to study co-translational RP capture, client stabilization, and the pathway linking RP availability to pre-40S export. The strong, diagnostic phenotypes (missing 40S peak; nuclear ITS1 accumulation) provide clear, implementation-ready assays for perturbations in the uS5 supply chain (rossler2019tsr4andnap1 pages 15-16, black2019tsr4isa pages 15-17).

4.2 Translational relevance via conserved homologs (PDCD2/PDCD2L)

While the present target is yeast TSR4, the TSR4–PDCD2/PDCD2L homology provides direct translational relevance: PDCD2 is described as a conserved uS5 chaperone that underlies essential roles in proliferation and development, and has reported associations with human disease contexts (as summarized in the 2023 uS5 review) (landryvoyer2023ribosomalproteinus5 pages 6-8, landryvoyer2023ribosomalproteinus5 pages 8-10). PDCD2L is discussed as a candidate late-acting uS5 interactor and potential pre-40S export adaptor (XPO1/CRM1-associated via an NES), supporting a conserved “uS5 handling network” spanning chaperoning and nucleocytoplasmic trafficking (landryvoyer2023ribosomalproteinus5 pages 8-10, landryvoyer2023ribosomalproteinus5 pages 10-12).

5) Expert synthesis and open questions

Collectively, the best-supported model is that Tsr4 is a cytoplasmic, co-translational uS5 chaperone that captures the eukaryote-specific N-terminus of Rps2, promotes soluble/assembly-competent Rps2 accumulation, and enables downstream 40S assembly and pre-40S export. Nuclear import of Rps2 proceeds via at least two NLS elements and importin-β pathways that do not require Tsr4, implying a handoff step from Tsr4-bound uS5 to importins and/or other factors remains to be mechanistically defined (black2019tsr4isa pages 17-20, steiner2023dissectingthenuclear pages 2-4).

Key unresolved areas highlighted across primary studies and recent reviews include (i) how the limited pool of Tsr4 efficiently targets nascent Rps2 (possible mRNA targeting), (ii) what triggers Tsr4 release from Rps2, and (iii) how binding overlaps with N-terminal targeting signals without blocking productive import/assembly (black2019tsr4isa pages 17-20, landryvoyer2023ribosomalproteinus5 pages 8-10, pertschy2024ribosomalproteinsin pages 1-2).

Evidence summary table

The following table consolidates major conclusions, assays, and quantitative notes.

Finding Molecular function Binding partner(s) Evidence type / assay Subcellular localization Ribosome biogenesis role Quantitative notes Supporting citations
Core identity Dedicated uS5/Rps2 assembly chaperone; matches yeast TSR4/P25040 annotation Rps2 (uS5) AP-MS/TAP purification, co-IP, genetic analysis Predominantly cytoplasmic Required for efficient 40S assembly TSR4 is essential in tested yeast backgrounds (black2019tsr4isa pages 1-3, rossler2019tsr4andnap1 pages 2-2)
Client recognition mechanism Co-translational capture of nascent Rps2 via eukaryote-specific N-terminus Rps2 N-terminal extension (aa 1–42; strongest determinants distributed across first 42 aa) Cycloheximide-linked mRNA co-purification, Y2H mapping, truncation/mutational analysis Cytoplasmic encounter with nascent client Prevents misfolding/inefficient maturation of newly synthesized uS5 First 42 aa sufficient for interaction; first 22 aa alone weak; Tsr4 ΔN40 loses binding (rossler2019tsr4andnap1 pages 12-13)
Chaperone activity Promotes solubility/stability of Rps2 Rps2 In vitro co-expression/solubility assays; co-purification in vitro and in vivo Cytoplasm Supplies assembly-competent uS5 for pre-40S incorporation Rps2 aggregates when expressed alone but is solubilized by Tsr4 (rossler2019tsr4andnap1 pages 14-15)
Localization of Tsr4 Cytoplasmic chaperone, not a Crm1-shuttling nucleo-cytoplasmic factor Fluorescence microscopy, LMB/Crm1 shuttling assay, NLS mutagenesis Cytoplasmic; no Crm1-dependent nuclear accumulation Acts before or during handoff to import/assembly pathway rather than as an export cargo Tsr4-mCherry stayed cytoplasmic after LMB while Nmd3-GFP accumulated in nucleus (black2019tsr4isa pages 15-17, black2019tsr4isa pages 17-20, black2019tsr4isa media 141d3d19)
Effect on Rps2 localization Needed mainly for productive assembly, not strictly for nuclear entry Rps2; importins indirectly Rps2-GFP localization in tsr4 mutants Loss of Tsr4 causes nuclear accumulation of Rps2 reporters Indicates imported uS5 is not efficiently assembled into pre-ribosomes without Tsr4 ~72% of WT cells show nuclear exclusion of Rps2-GFP; ~82% of tsr4 cells show nuclear signal in one study (rossler2019tsr4andnap1 pages 16-16, rossler2019tsr4andnap1 pages 15-16)
Role in 40S biogenesis/export Required for small-subunit production and pre-40S export Pre-40S particles indirectly via Rps2 supply Polysome profiling, ITS1 FISH, depletion/repression experiments Functional consequence seen as nuclear ITS1 accumulation Loss phenocopies RPS2 depletion, blocking late 40S maturation/export Missing or strongly reduced 40S peak, increased 60S, reduced 80S/polysomes; ITS1 accumulates in nucleus after TSR4 repression (black2019tsr4isa pages 34-37, black2019tsr4isa pages 15-17, rossler2019tsr4andnap1 pages 15-16)
Genetic suppression Increased client dosage can partially bypass chaperone loss RPS2 Plasmid shuffle, dosage suppression, growth assays Supports chaperone-client relationship Extra RPS2 restores viability but suppressed tsr4 strains grow poorly at 25–30°C and are inviable at 37°C (black2019tsr4isa pages 15-17, rossler2019tsr4andnap1 pages 15-16)
Abundance / limiting factor Modestly expressed, consistent with titration by excess N-terminal Rps2 fragments Rps2 fragments can sequester Tsr4 Quantitative Western/blot comparison; dominant-negative fragment assays Cytoplasm Limiting chaperone pool may constrain uS5 maturation ~1,500 Tsr4 molecules/cell; high-copy TSR4 fully suppresses one dominant-negative Rps2 N-fragment and partially suppresses another (black2019tsr4isa pages 17-20, black2019tsr4isa pages 6-8)
Relation to nuclear import Not required for either identified Rps2 NLS-driven import route Rps2; Pse1/Kap121, Kap123/Kap104 contribute Reporter import assays, mutagenesis, pse1 mutant analysis, TurboID/Y2H Tsr4 overlaps N-terminal NLS region but is dispensable for import itself Distinguishes chaperoning from import; Tsr4 functions upstream of productive assembly Internal NLS at aa 76–145; key residues R95/R97/K99; second N-terminal NLS at aa 10–28 (steiner2023dissectingthenuclear pages 6-9, steiner2023dissectingthenuclear pages 2-4, steiner2023dissectingthenuclear pages 15-18, steiner2023dissectingthenuclear pages 13-15)
Family/domain context Yeast TSR4 is the fungal homolog within PDCD2/PDCD2L-related TYPP/PDCD2_C superfamily PDCD2/PDCD2L homologous family; uS5 pathway conserved Comparative domain/evolution analysis; cross-species functional comparison Yeast Tsr4 mainly cytoplasmic; metazoan PDCD2 can accompany uS5 into nucleus Conserved dedicated uS5 chaperone module across eukaryotes C-terminal PDCD2_C annotation; broader TYPP repeat architecture proposed (burroughs2014analysisoftwo pages 5-7, burroughs2014analysisoftwo pages 3-5, landryvoyer2023ribosomalproteinus5 pages 6-8, landryvoyer2020pdcd2functionsas pages 13-14)

Table: This table condenses the main experimentally supported findings for Saccharomyces cerevisiae TSR4 (UniProt P25040), including its chaperone function, binding to Rps2/uS5, localization, and role in 40S ribosome biogenesis. It also highlights useful quantitative observations and cites the supporting evidence by context ID.

Visual evidence

A key localization control supporting cytoplasmic restriction of Tsr4 is shown in Black et al. 2019 Figure 8B: in a leptomycin B Crm1 export-blocking assay, the Crm1 cargo control Nmd3 accumulates in the nucleus while Tsr4 remains cytoplasmic (black2019tsr4isa media 141d3d19).


Key references (with URLs and publication dates)

  • Black JJ, Musalgaonkar S, Johnson AW. Tsr4 Is a Cytoplasmic Chaperone for the Ribosomal Protein Rps2 in Saccharomyces cerevisiae. Molecular and Cellular Biology. Sep 2019. https://doi.org/10.1128/mcb.00094-19 (black2019tsr4isa pages 1-3)
  • Rössler I et al. Tsr4 and Nap1, two novel members of the ribosomal protein chaperOME. Nucleic Acids Research. May 2019. https://doi.org/10.1093/nar/gkz317 (rossler2019tsr4andnap1 pages 1-2)
  • Steiner A et al. Dissecting the Nuclear Import of the Ribosomal Protein Rps2 (uS5). Biomolecules. Jul 2023. https://doi.org/10.3390/biom13071127 (steiner2023dissectingthenuclear pages 1-2)
  • Landry-Voyer A-M et al. Ribosomal Protein uS5 and Friends: Protein–Protein Interactions Involved in Ribosome Assembly and Beyond. Biomolecules. May 2023. https://doi.org/10.3390/biom13050853 (landryvoyer2023ribosomalproteinus5 pages 6-8)
  • Yang Y-M et al. Chaperone-directed ribosome repair after oxidative damage. Molecular Cell. May 2023. https://doi.org/10.1016/j.molcel.2023.03.030 (yang2023chaperonedirectedribosomerepair pages 3-5)
  • 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)
  • Pertschy B, Zierler I. Ribosomal Proteins in Ribosome Assembly. Biomolecules. Dec 2024. https://doi.org/10.3390/biom15010013 (pertschy2024ribosomalproteinsin pages 1-2)

References

  1. (black2019tsr4isa pages 1-3): Joshua J. Black, Sharmishtha Musalgaonkar, and Arlen W. Johnson. Tsr4 is a cytoplasmic chaperone for the ribosomal protein rps2 in saccharomyces cerevisiae. Molecular and Cellular Biology, Sep 2019. URL: https://doi.org/10.1128/mcb.00094-19, doi:10.1128/mcb.00094-19. This article has 28 citations and is from a domain leading peer-reviewed journal.

  2. (black2019tsr4isa pages 15-17): Joshua J. Black, Sharmishtha Musalgaonkar, and Arlen W. Johnson. Tsr4 is a cytoplasmic chaperone for the ribosomal protein rps2 in saccharomyces cerevisiae. Molecular and Cellular Biology, Sep 2019. URL: https://doi.org/10.1128/mcb.00094-19, doi:10.1128/mcb.00094-19. This article has 28 citations and is from a domain leading peer-reviewed journal.

  3. (burroughs2014analysisoftwo pages 3-5): A. M. Burroughs, L. Aravind, and R. Emes. Analysis of two domains with novel rna-processing activities throws light on the complex evolution of ribosomal rna biogenesis. Frontiers in Genetics, Dec 2014. URL: https://doi.org/10.3389/fgene.2014.00424, doi:10.3389/fgene.2014.00424. This article has 26 citations and is from a peer-reviewed journal.

  4. (burroughs2014analysisoftwo pages 5-7): A. M. Burroughs, L. Aravind, and R. Emes. Analysis of two domains with novel rna-processing activities throws light on the complex evolution of ribosomal rna biogenesis. Frontiers in Genetics, Dec 2014. URL: https://doi.org/10.3389/fgene.2014.00424, doi:10.3389/fgene.2014.00424. This article has 26 citations and is from a peer-reviewed journal.

  5. (rossler2019tsr4andnap1 pages 1-2): Ingrid Rössler, Julia Embacher, Benjamin Pillet, Guillaume Murat, Laura Liesinger, Jutta Hafner, Julia Judith Unterluggauer, Ruth Birner-Gruenberger, Dieter Kressler, and Brigitte Pertschy. Tsr4 and nap1, two novel members of the ribosomal protein chaperome. Nucleic Acids Research, 47:6984-7002, May 2019. URL: https://doi.org/10.1093/nar/gkz317, doi:10.1093/nar/gkz317. This article has 38 citations and is from a highest quality peer-reviewed journal.

  6. (rossler2019tsr4andnap1 pages 14-15): Ingrid Rössler, Julia Embacher, Benjamin Pillet, Guillaume Murat, Laura Liesinger, Jutta Hafner, Julia Judith Unterluggauer, Ruth Birner-Gruenberger, Dieter Kressler, and Brigitte Pertschy. Tsr4 and nap1, two novel members of the ribosomal protein chaperome. Nucleic Acids Research, 47:6984-7002, May 2019. URL: https://doi.org/10.1093/nar/gkz317, doi:10.1093/nar/gkz317. This article has 38 citations and is from a highest quality peer-reviewed journal.

  7. (rossler2019tsr4andnap1 pages 12-13): Ingrid Rössler, Julia Embacher, Benjamin Pillet, Guillaume Murat, Laura Liesinger, Jutta Hafner, Julia Judith Unterluggauer, Ruth Birner-Gruenberger, Dieter Kressler, and Brigitte Pertschy. Tsr4 and nap1, two novel members of the ribosomal protein chaperome. Nucleic Acids Research, 47:6984-7002, May 2019. URL: https://doi.org/10.1093/nar/gkz317, doi:10.1093/nar/gkz317. This article has 38 citations and is from a highest quality peer-reviewed journal.

  8. (rossler2019tsr4andnap1 pages 15-16): Ingrid Rössler, Julia Embacher, Benjamin Pillet, Guillaume Murat, Laura Liesinger, Jutta Hafner, Julia Judith Unterluggauer, Ruth Birner-Gruenberger, Dieter Kressler, and Brigitte Pertschy. Tsr4 and nap1, two novel members of the ribosomal protein chaperome. Nucleic Acids Research, 47:6984-7002, May 2019. URL: https://doi.org/10.1093/nar/gkz317, doi:10.1093/nar/gkz317. This article has 38 citations and is from a highest quality peer-reviewed journal.

  9. (landryvoyer2023ribosomalproteinus5 pages 6-8): Anne-Marie Landry-Voyer, Zabih Mir Hassani, Mariano Avino, and François Bachand. Ribosomal protein us5 and friends: protein–protein interactions involved in ribosome assembly and beyond. Biomolecules, 13:853, May 2023. URL: https://doi.org/10.3390/biom13050853, doi:10.3390/biom13050853. This article has 20 citations.

  10. (landryvoyer2023ribosomalproteinus5 pages 8-10): Anne-Marie Landry-Voyer, Zabih Mir Hassani, Mariano Avino, and François Bachand. Ribosomal protein us5 and friends: protein–protein interactions involved in ribosome assembly and beyond. Biomolecules, 13:853, May 2023. URL: https://doi.org/10.3390/biom13050853, doi:10.3390/biom13050853. This article has 20 citations.

  11. (black2019tsr4isa pages 17-20): Joshua J. Black, Sharmishtha Musalgaonkar, and Arlen W. Johnson. Tsr4 is a cytoplasmic chaperone for the ribosomal protein rps2 in saccharomyces cerevisiae. Molecular and Cellular Biology, Sep 2019. URL: https://doi.org/10.1128/mcb.00094-19, doi:10.1128/mcb.00094-19. This article has 28 citations and is from a domain leading peer-reviewed journal.

  12. (black2019tsr4isa media 141d3d19): Joshua J. Black, Sharmishtha Musalgaonkar, and Arlen W. Johnson. Tsr4 is a cytoplasmic chaperone for the ribosomal protein rps2 in saccharomyces cerevisiae. Molecular and Cellular Biology, Sep 2019. URL: https://doi.org/10.1128/mcb.00094-19, doi:10.1128/mcb.00094-19. This article has 28 citations and is from a domain leading peer-reviewed journal.

  13. (black2019tsr4isa pages 6-8): Joshua J. Black, Sharmishtha Musalgaonkar, and Arlen W. Johnson. Tsr4 is a cytoplasmic chaperone for the ribosomal protein rps2 in saccharomyces cerevisiae. Molecular and Cellular Biology, Sep 2019. URL: https://doi.org/10.1128/mcb.00094-19, doi:10.1128/mcb.00094-19. This article has 28 citations and is from a domain leading peer-reviewed journal.

  14. (rossler2019tsr4andnap1 pages 16-16): Ingrid Rössler, Julia Embacher, Benjamin Pillet, Guillaume Murat, Laura Liesinger, Jutta Hafner, Julia Judith Unterluggauer, Ruth Birner-Gruenberger, Dieter Kressler, and Brigitte Pertschy. Tsr4 and nap1, two novel members of the ribosomal protein chaperome. Nucleic Acids Research, 47:6984-7002, May 2019. URL: https://doi.org/10.1093/nar/gkz317, doi:10.1093/nar/gkz317. This article has 38 citations and is from a highest quality peer-reviewed journal.

  15. (steiner2023dissectingthenuclear pages 6-9): Andreas Steiner, Sébastien Favre, Maximilian Mack, Annika Hausharter, Benjamin Pillet, Jutta Hafner, Valentin Mitterer, Dieter Kressler, Brigitte Pertschy, and Ingrid Zierler. Dissecting the nuclear import of the ribosomal protein rps2 (us5). Biomolecules, 13:1127, Jul 2023. URL: https://doi.org/10.3390/biom13071127, doi:10.3390/biom13071127. This article has 7 citations.

  16. (steiner2023dissectingthenuclear pages 1-2): Andreas Steiner, Sébastien Favre, Maximilian Mack, Annika Hausharter, Benjamin Pillet, Jutta Hafner, Valentin Mitterer, Dieter Kressler, Brigitte Pertschy, and Ingrid Zierler. Dissecting the nuclear import of the ribosomal protein rps2 (us5). Biomolecules, 13:1127, Jul 2023. URL: https://doi.org/10.3390/biom13071127, doi:10.3390/biom13071127. This article has 7 citations.

  17. (steiner2023dissectingthenuclear pages 15-18): Andreas Steiner, Sébastien Favre, Maximilian Mack, Annika Hausharter, Benjamin Pillet, Jutta Hafner, Valentin Mitterer, Dieter Kressler, Brigitte Pertschy, and Ingrid Zierler. Dissecting the nuclear import of the ribosomal protein rps2 (us5). Biomolecules, 13:1127, Jul 2023. URL: https://doi.org/10.3390/biom13071127, doi:10.3390/biom13071127. This article has 7 citations.

  18. (steiner2023dissectingthenuclear pages 2-4): Andreas Steiner, Sébastien Favre, Maximilian Mack, Annika Hausharter, Benjamin Pillet, Jutta Hafner, Valentin Mitterer, Dieter Kressler, Brigitte Pertschy, and Ingrid Zierler. Dissecting the nuclear import of the ribosomal protein rps2 (us5). Biomolecules, 13:1127, Jul 2023. URL: https://doi.org/10.3390/biom13071127, doi:10.3390/biom13071127. This article has 7 citations.

  19. (steiner2023dissectingthenuclear pages 13-15): Andreas Steiner, Sébastien Favre, Maximilian Mack, Annika Hausharter, Benjamin Pillet, Jutta Hafner, Valentin Mitterer, Dieter Kressler, Brigitte Pertschy, and Ingrid Zierler. Dissecting the nuclear import of the ribosomal protein rps2 (us5). Biomolecules, 13:1127, Jul 2023. URL: https://doi.org/10.3390/biom13071127, doi:10.3390/biom13071127. This article has 7 citations.

  20. (pertschy2024ribosomalproteinsin pages 1-2): Brigitte Pertschy and Ingrid Zierler. Ribosomal proteins in ribosome assembly. Biomolecules, 15:13, Dec 2024. URL: https://doi.org/10.3390/biom15010013, doi:10.3390/biom15010013. This article has 4 citations.

  21. (yang2024ribosomeassemblyand pages 20-21): 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.

  22. (yang2024ribosomeassemblyand pages 11-13): 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.

  23. (yang2023chaperonedirectedribosomerepair pages 3-5): Yoon-Mo Yang, Youngeun Jung, Daniel Abegg, Alexander Adibekian, Kate S. Carroll, and Katrin Karbstein. Chaperone-directed ribosome repair after oxidative damage. Molecular Cell, 83:1527-1537.e5, May 2023. URL: https://doi.org/10.1016/j.molcel.2023.03.030, doi:10.1016/j.molcel.2023.03.030. This article has 70 citations and is from a highest quality peer-reviewed journal.

  24. (yang2023chaperonedirectedribosomerepair pages 5-7): Yoon-Mo Yang, Youngeun Jung, Daniel Abegg, Alexander Adibekian, Kate S. Carroll, and Katrin Karbstein. Chaperone-directed ribosome repair after oxidative damage. Molecular Cell, 83:1527-1537.e5, May 2023. URL: https://doi.org/10.1016/j.molcel.2023.03.030, doi:10.1016/j.molcel.2023.03.030. This article has 70 citations and is from a highest quality peer-reviewed journal.

  25. (landryvoyer2023ribosomalproteinus5 pages 10-12): Anne-Marie Landry-Voyer, Zabih Mir Hassani, Mariano Avino, and François Bachand. Ribosomal protein us5 and friends: protein–protein interactions involved in ribosome assembly and beyond. Biomolecules, 13:853, May 2023. URL: https://doi.org/10.3390/biom13050853, doi:10.3390/biom13050853. This article has 20 citations.

  26. (rossler2019tsr4andnap1 pages 2-2): Ingrid Rössler, Julia Embacher, Benjamin Pillet, Guillaume Murat, Laura Liesinger, Jutta Hafner, Julia Judith Unterluggauer, Ruth Birner-Gruenberger, Dieter Kressler, and Brigitte Pertschy. Tsr4 and nap1, two novel members of the ribosomal protein chaperome. Nucleic Acids Research, 47:6984-7002, May 2019. URL: https://doi.org/10.1093/nar/gkz317, doi:10.1093/nar/gkz317. This article has 38 citations and is from a highest quality peer-reviewed journal.

  27. (black2019tsr4isa pages 34-37): Joshua J. Black, Sharmishtha Musalgaonkar, and Arlen W. Johnson. Tsr4 is a cytoplasmic chaperone for the ribosomal protein rps2 in saccharomyces cerevisiae. Molecular and Cellular Biology, Sep 2019. URL: https://doi.org/10.1128/mcb.00094-19, doi:10.1128/mcb.00094-19. This article has 28 citations and is from a domain leading peer-reviewed journal.

  28. (landryvoyer2020pdcd2functionsas pages 13-14): Anne-Marie Landry-Voyer, Danny Bergeron, Carlo Yague-Sanz, Breac Baker, and Francois Bachand. Pdcd2 functions as an evolutionarily conserved chaperone dedicated for the 40s ribosomal protein us5 (rps2). Nucleic Acids Research, 48:12900-12916, Nov 2020. URL: https://doi.org/10.1093/nar/gkaa1108, doi:10.1093/nar/gkaa1108. This article has 26 citations and is from a highest quality peer-reviewed journal.

  29. (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.

Citations

  1. pertschy2024ribosomalproteinsin pages 1-2
  2. steiner2023dissectingthenuclear pages 1-2
  3. yang2023chaperonedirectedribosomerepair pages 3-5
  4. yang2024ribosomeassemblyand pages 1-3
  5. burroughs2014analysisoftwo pages 3-5
  6. burroughs2014analysisoftwo pages 5-7
  7. steiner2023dissectingthenuclear pages 6-9
  8. steiner2023dissectingthenuclear pages 15-18
  9. steiner2023dissectingthenuclear pages 2-4
  10. steiner2023dissectingthenuclear pages 13-15
  11. yang2024ribosomeassemblyand pages 20-21
  12. yang2024ribosomeassemblyand pages 11-13
  13. yang2023chaperonedirectedribosomerepair pages 5-7
  14. https://doi.org/10.1128/mcb.00094-19
  15. https://doi.org/10.1093/nar/gkz317
  16. https://doi.org/10.3390/biom13071127
  17. https://doi.org/10.3390/biom13050853
  18. https://doi.org/10.1016/j.molcel.2023.03.030
  19. https://doi.org/10.1146/annurev-cellbio-111822-113326
  20. https://doi.org/10.3390/biom15010013
  21. https://doi.org/10.1128/mcb.00094-19,
  22. https://doi.org/10.3389/fgene.2014.00424,
  23. https://doi.org/10.1093/nar/gkz317,
  24. https://doi.org/10.3390/biom13050853,
  25. https://doi.org/10.3390/biom13071127,
  26. https://doi.org/10.3390/biom15010013,
  27. https://doi.org/10.1146/annurev-cellbio-111822-113326,
  28. https://doi.org/10.1016/j.molcel.2023.03.030,
  29. https://doi.org/10.1093/nar/gkaa1108,

📄 View Raw YAML

id: P25040
gene_symbol: TSR4
product_type: PROTEIN
status: COMPLETE
aliases:
- YOL022C
- uS5 assembly chaperone
taxon:
  id: NCBITaxon:559292
  label: Saccharomyces cerevisiae
description: >-
  TSR4 encodes a cytoplasmic, client-specific ribosomal protein carrier
  chaperone for Rps2/uS5. Tsr4 binds the eukaryote-specific N-terminal extension
  of nascent Rps2/uS5, promotes Rps2 expression and solubility, and releases the
  client before nuclear import and productive pre-40S assembly. Loss of Tsr4
  impairs 40S ribosomal small subunit biogenesis, pre-40S export, and 20S
  pre-rRNA processing at site D to mature 18S rRNA.
existing_annotations:
- term:
    id: GO:0030490
    label: maturation of SSU-rRNA
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: IBA is consistent with Tsr4-dependent 20S pre-rRNA processing and 40S biogenesis.
    action: ACCEPT
    reason: SSU-rRNA maturation is a direct process-level consequence of the uS5 chaperone role.
    supported_by:
    - reference_id: PMID:19806183
      supporting_text: YOR006C/TSR3, YOL022C/TSR4). We associate the new genes with specific aspects of...processing of 5S, 7S, 20S, 27S, and 35S rRNAs.
    - reference_id: file:yeast/TSR4/TSR4-deep-research-falcon.md
      supporting_text: Tsr4 enables downstream 40S assembly and pre-40S export through cytoplasmic Rps2/uS5 chaperone activity.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: Cytoplasmic localization is consistent with direct Tsr4 studies.
    action: ACCEPT
    reason: Tsr4 acts in the cytoplasm on nascent Rps2/uS5 before nuclear import.
    supported_by:
    - reference_id: PMID:31182640
      supporting_text: Tsr4 appears to be restricted to the cytoplasm.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: Cytosol is the best location for Tsr4 carrier chaperone activity.
    action: ACCEPT
    reason: Direct and curated sources place Tsr4 in the cytosol/cytoplasm.
    supported_by:
    - reference_id: PMID:31062022
      supporting_text: Tsr4 binds co-translationally to the...essential, eukaryote-specific N-terminal extension of Rps2
- term:
    id: GO:0042254
    label: ribosome biogenesis
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: Ribosome biogenesis is correct but too broad for Tsr4.
    action: MODIFY
    reason: Replace with the more specific ribosomal small subunit biogenesis term.
    proposed_replacement_terms:
    - id: GO:0042274
      label: ribosomal small subunit biogenesis
    supported_by:
    - reference_id: PMID:31062022
      supporting_text: Mutation of the essential Tsr4...enhance the 40S synthesis defects
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IDA
  original_reference_id: PMID:31062022
  review:
    summary: Direct evidence supports cytosolic localization.
    action: ACCEPT
    reason: Tsr4 binds Rps2/uS5 co-translationally in the cytosol.
    supported_by:
    - reference_id: PMID:31062022
      supporting_text: Tsr4 binds co-translationally to the...essential, eukaryote-specific N-terminal extension of Rps2
- term:
    id: GO:0140597
    label: protein carrier chaperone
  evidence_type: IDA
  original_reference_id: PMID:31062022
  review:
    summary: This is the most specific molecular-function annotation for TSR4.
    action: ACCEPT
    reason: Tsr4 is a dedicated carrier chaperone for ribosomal protein Rps2/uS5.
    supported_by:
    - reference_id: PMID:31062022
      supporting_text: vitro. While Tsr4 is specific for Rps2...Tsr4 binds co-translationally to the...essential, eukaryote-specific N-terminal extension of Rps2
    - reference_id: file:yeast/TSR4/TSR4-deep-research-falcon.md
      supporting_text: Tsr4 is a cytoplasmic, co-translational uS5 chaperone that captures the Rps2 N-terminus.
- term:
    id: GO:0042274
    label: ribosomal small subunit biogenesis
  evidence_type: IMP
  original_reference_id: PMID:31062022
  review:
    summary: Tsr4 perturbation causes 40S biogenesis defects.
    action: ACCEPT
    reason: Rps2/uS5 chaperoning is directly tied to small subunit assembly.
    supported_by:
    - reference_id: PMID:31062022
      supporting_text: Mutation of the essential Tsr4...enhance the 40S synthesis defects
- term:
    id: GO:0042274
    label: ribosomal small subunit biogenesis
  evidence_type: IGI
  original_reference_id: PMID:31062022
  review:
    summary: Genetic evidence with RPS2 supports the 40S biogenesis annotation.
    action: ACCEPT
    reason: The genetic relationship supports Tsr4's role in Rps2-dependent 40S assembly.
    supported_by:
    - reference_id: PMID:31062022
      supporting_text: identification of Nap1 and Tsr4 as direct binding partners of Rps6 and Rps2
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IDA
  original_reference_id: PMID:31062022
  review:
    summary: The binding evidence is specific to Rps2/uS5, not generic unfolded protein.
    action: MODIFY
    reason: Replace broad unfolded protein binding with protein carrier chaperone.
    proposed_replacement_terms:
    - id: GO:0140597
      label: protein carrier chaperone
    supported_by:
    - reference_id: PMID:31062022
      supporting_text: Both factors promote the solubility of their r-protein clients in...vitro.
- term:
    id: GO:0042274
    label: ribosomal small subunit biogenesis
  evidence_type: IMP
  original_reference_id: PMID:31182640
  review:
    summary: Independent evidence supports the same 40S biogenesis role.
    action: ACCEPT
    reason: Tsr4 perturbation decreases Rps2 and phenocopies Rps2 depletion.
    supported_by:
    - reference_id: PMID:31182640
      supporting_text: Tsr4 perturbation resulted in decreased Rps2 levels and...phenocopied Rps2 depletion.
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IDA
  original_reference_id: PMID:31182640
  review:
    summary: The evidence supports specific Rps2 carrier chaperoning.
    action: MODIFY
    reason: Protein carrier chaperone is the more precise molecular-function term.
    proposed_replacement_terms:
    - id: GO:0140597
      label: protein carrier chaperone
    supported_by:
    - reference_id: PMID:31182640
      supporting_text: Tsr4 cotranslationally associates with Rps2...cytoplasmic chaperone dedicated to Rps2.
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IPI
  original_reference_id: PMID:31182640
  review:
    summary: The IPI evidence identifies a specific Rps2/uS5 client relationship.
    action: MODIFY
    reason: Replace broad unfolded protein binding with protein carrier chaperone.
    proposed_replacement_terms:
    - id: GO:0140597
      label: protein carrier chaperone
    supported_by:
    - reference_id: PMID:31182640
      supporting_text: Rps2 harbors a...eukaryote-specific N-terminal extension that is critical for its interaction...with Tsr4.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IDA
  original_reference_id: PMID:31182640
  review:
    summary: Direct microscopy and functional evidence support cytoplasmic localization.
    action: ACCEPT
    reason: Tsr4 acts before nuclear import and pre-ribosome assembly.
    supported_by:
    - reference_id: PMID:31182640
      supporting_text: Despite Rps2 joining nuclear pre-40S particles, Tsr4 appears to be restricted to the cytoplasm.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: HDA
  original_reference_id: PMID:14562095
  review:
    summary: High-throughput cytoplasmic localization is consistent with targeted studies.
    action: ACCEPT
    reason: The broad cytoplasm term is correct, though cytosol is more precise.
    supported_by:
    - reference_id: PMID:31182640
      supporting_text: Tsr4 appears to be restricted to the cytoplasm.
- term:
    id: GO:0030490
    label: maturation of SSU-rRNA
  evidence_type: IMP
  original_reference_id: PMID:19806183
  review:
    summary: The original genetic annotation correctly identifies TSR4 in SSU rRNA maturation.
    action: ACCEPT
    reason: Later work explains the phenotype through defective Rps2/uS5 handling and 40S assembly.
    supported_by:
    - reference_id: PMID:19806183
      supporting_text: YOR006C/TSR3, YOL022C/TSR4). We associate the new genes with specific aspects of...processing of 5S, 7S, 20S, 27S, and 35S rRNAs.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000043
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping
  findings: []
- id: PMID:14562095
  title: Global analysis of protein localization in budding yeast.
  findings: []
- id: PMID:19806183
  title: Rational extension of the ribosome biogenesis pathway using network-guided genetics.
  findings:
  - statement: TSR4 was identified as a ribosome biogenesis factor
    supporting_text: Network-guided genetics associated YOL022C/TSR4 with ribosome biogenesis and pre-rRNA processing.
- id: PMID:31062022
  title: Tsr4 and Nap1, two novel members of the ribosomal protein chaperOME.
  findings:
  - statement: Tsr4 is a direct Rps2/uS5 carrier chaperone
    supporting_text: Tsr4 is specific for Rps2, binds co-translationally to its N-terminal extension, and promotes solubility.
- id: PMID:31182640
  title: Tsr4 Is a Cytoplasmic Chaperone for the Ribosomal Protein Rps2 in Saccharomyces cerevisiae.
  findings:
  - statement: Tsr4 is a cytoplasmic chaperone dedicated to Rps2
    supporting_text: Tsr4 cotranslationally associates with Rps2; perturbation decreases Rps2 levels.
- id: file:yeast/TSR4/TSR4-deep-research-falcon.md
  title: Falcon deep research report for TSR4
  findings:
  - statement: TSR4 is a cytoplasmic uS5/Rps2 carrier chaperone
    supporting_text: The report synthesizes evidence that Tsr4 captures nascent Rps2/uS5 and enables downstream 40S assembly.
core_functions:
- description: >-
    Cytoplasmic protein carrier chaperone for ribosomal protein Rps2/uS5. Tsr4
    binds nascent Rps2/uS5 and maintains the client in a soluble
    assembly-competent state before nuclear import and incorporation into
    pre-40S particles.
  molecular_function:
    id: GO:0140597
    label: protein carrier chaperone
  directly_involved_in:
  - id: GO:0042274
    label: ribosomal small subunit biogenesis
  - id: GO:0030490
    label: maturation of SSU-rRNA
  locations:
  - id: GO:0005829
    label: cytosol
  - id: GO:0005737
    label: cytoplasm
  supported_by:
  - reference_id: PMID:31062022
    supporting_text: identification of Nap1 and Tsr4 as direct binding partners of Rps6 and Rps2...Both factors promote the solubility of their r-protein clients
  - reference_id: PMID:31182640
    supporting_text: Tsr4 perturbation resulted in decreased Rps2 levels and...phenocopied Rps2 depletion.
  - reference_id: file:yeast/TSR4/TSR4-deep-research-falcon.md
    supporting_text: Tsr4 is a cytoplasmic, co-translational uS5 chaperone that captures the Rps2 N-terminus.
proposed_new_terms: []
suggested_questions:
- question: Should older GO:0051082 annotations for Tsr4 be replaced by GO:0140597 protein carrier chaperone where evidence is specific Rps2/uS5 chaperoning?
suggested_experiments: []