GO Term	Evidence	Action	Reason
GO:0006606 protein import into nucleus	IBA GO_REF:0000033	ACCEPT	Summary: The PANTHER/IBA annotation is consistent with direct yeast evidence and UniProt family context. Syo1 is a specialized import adaptor that brings Rpl5 and Rpl11 into the nucleus through Kap104. Reason: Nuclear import of the Rpl5-Rpl11 cargo pair is a core Syo1 biological process and is well supported by the experimental IGI annotation and the Falcon synthesis. Supporting Evidence: PMID:23118189 Syo1 concomitantly binds Rpl5-Rpl11 and furthermore recruits the import receptor Kap104. file:yeast/SYO1/SYO1-deep-research-falcon.md Falcon identifies Syo1 as a shuttling nuclear import adaptor for Rpl5 and Rpl11.
GO:0042273 ribosomal large subunit biogenesis	IBA GO_REF:0000033	ACCEPT	Summary: Syo1-mediated co-import of Rpl5 and Rpl11 is coupled to 5S RNP formation and 60S ribosomal large subunit assembly. The IBA annotation transfers a conserved, experimentally supported ribosome-biogenesis role. Reason: Ribosomal large subunit biogenesis is a core biological process for Syo1 and is supported by mutant ribosome-biogenesis phenotypes and mechanistic studies of 5S RNP assembly. Supporting Evidence: PMID:19806183 we associate the new genes with specific aspects of ribosomal subunit maturation, ribosomal particle association, and ribosomal subunit nuclear export file:yeast/SYO1/SYO1-deep-research-falcon.md Falcon describes Syo1 as an import adaptor and assembly chaperone that supports 5S RNP and 60S biogenesis.
GO:0051082 unfolded protein binding	IBA GO_REF:0000033	MODIFY	Summary: Syo1 does protect ribosomal-protein cargo from inappropriate interactions, but the biology is not generic unfolded-protein binding. It is a dedicated carrier chaperone/import adaptor for Rpl5 and Rpl11. Reason: GO:0051082 is too broad for Syo1. The more informative molecular-function term is protein carrier chaperone, reflecting cargo binding and escort between cytoplasm and nucleus. Proposed replacements: protein carrier chaperone Supporting Evidence: PMID:26112308 Co-translational capturing of nascent ribosomal proteins by dedicated chaperones file:yeast/SYO1/SYO1-deep-research-falcon.md Falcon frames Syo1 as a dedicated transport adaptor/chaperone rather than a general unfolded-protein binding factor.
GO:0005634 nucleus	IEA GO_REF:0000044	ACCEPT	Summary: UniProt subcellular-location mapping to nucleus is consistent with Syo1's import-adaptor role and with direct localization evidence. Reason: Syo1 acts in the nucleus after Kap104-mediated import of the Syo1-Rpl5-Rpl11 complex and is directly observed in nuclear localization datasets. Supporting Evidence: PMID:23118189 The Syo1-Rpl5-Rpl11 import complex is released from Kap104 by RanGTP
GO:0005737 cytoplasm	IEA GO_REF:0000044	ACCEPT	Summary: UniProt subcellular-location mapping to cytoplasm is consistent with Syo1 capturing newly synthesized ribosomal-protein cargo before nuclear import. Reason: Syo1 functions as a shuttling factor: it binds Rpl5/Rpl11 in the cytoplasm and carries them to the nucleus. Cytoplasm is therefore a relevant localization, although the steady-state signal can be mainly nuclear. Supporting Evidence: PMID:23118189 Syo1 can shuttle back to the cytoplasm
GO:0015031 protein transport	IEA GO_REF:0000043	MODIFY	Summary: The UniProt keyword-derived protein transport annotation captures the general concept, but Syo1's transport function is specifically nuclear import of ribosomal proteins. Reason: Replace the broad GO:0015031 term with GO:0006606 protein import into nucleus, which matches the experimentally demonstrated Syo1-Kap104 mechanism. Proposed replacements: protein import into nucleus Supporting Evidence: PMID:23118189 facilitates synchronized coimport of the two 5S-rRNA binding proteins Rpl5 and Rpl11
GO:0042254 ribosome biogenesis	IEA GO_REF:0000043	MODIFY	Summary: The broad ribosome biogenesis annotation is correct in direction, but Syo1 is specifically tied to 5S RNP/60S large subunit biogenesis. Reason: GO:0042273 ribosomal large subunit biogenesis is the better replacement because Syo1 escorts Rpl5/Rpl11 for 5S RNP formation during 60S assembly. Proposed replacements: ribosomal large subunit biogenesis Supporting Evidence: PMID:19806183 new genes with specific aspects of ribosomal subunit maturation, ribosomal particle association, and ribosomal subunit nuclear export
GO:0051082 unfolded protein binding	IDA PMID:26112308 Co-translational capturing of nascent ribosomal proteins by ...	MODIFY	Summary: The IDA evidence shows dedicated co-translational capture of ribosomal protein clients by Syo1, not general binding to unfolded proteins. Reason: Syo1 is best represented as a protein carrier chaperone: it captures and escorts a defined ribosomal-protein cargo pair rather than acting as a broad unfolded-protein binding chaperone. Proposed replacements: protein carrier chaperone Supporting Evidence: PMID:26112308 Affinity purification of four chaperones (Rrb1, Syo1, Sqt1 and Yar1) selectively enriched the mRNAs encoding their specific ribosomal protein clients file:yeast/SYO1/SYO1-deep-research-falcon.md Falcon supports replacing generic unfolded-protein binding with a dedicated carrier-chaperone interpretation.
GO:0005634 nucleus	HDA PMID:14562095 Global analysis of protein localization in budding yeast.	ACCEPT	Summary: High-throughput GFP localization placed Syo1 in the nucleus, matching its biological role in nuclear delivery and 5S RNP assembly. Reason: Nuclear localization is biologically meaningful for Syo1 and is also supported by UniProt and the mechanistic nuclear import literature. Supporting Evidence: PMID:14562095 Global analysis of protein localization in budding yeast.
GO:0005737 cytoplasm	HDA PMID:14562095 Global analysis of protein localization in budding yeast.	ACCEPT	Summary: High-throughput GFP localization also detected Syo1 in the cytoplasm, consistent with cargo capture before nuclear import and shuttling back from the nucleus. Reason: Cytoplasmic localization is part of the Syo1 transport cycle and should be retained, even though its steady-state enrichment may be nuclear. Supporting Evidence: PMID:14562095 Global analysis of protein localization in budding yeast.
GO:0006606 protein import into nucleus	IGI PMID:23118189 Synchronizing nuclear import of ribosomal proteins with ribo...	ACCEPT	Summary: The genetic interaction annotation directly reflects the Science 2012 work showing that Syo1 mediates Kap104-dependent nuclear co-import of Rpl5 and Rpl11. Reason: This is one of the central experimentally supported Syo1 annotations and captures the import component of its core function. Supporting Evidence: PMID:23118189 facilitates synchronized coimport of the two 5S-rRNA binding proteins Rpl5 and Rpl11 PMID:23118189 The Syo1-Rpl5-Rpl11 import complex is released from Kap104 by RanGTP
GO:0042273 ribosomal large subunit biogenesis	IMP PMID:19806183 Rational extension of the ribosome biogenesis pathway using ...	ACCEPT	Summary: Mutant phenotyping and the later mechanistic literature support Syo1's role in 60S large subunit biogenesis through coordinated import and assembly of the 5S RNP protein module. Reason: GO:0042273 is the appropriate specific biological-process term for the ribosome-biogenesis effect of SYO1. Supporting Evidence: PMID:19806183 confirming involvement of at least 15 new genes file:yeast/SYO1/SYO1-deep-research-falcon.md Falcon summarizes reduced free 60S, half-mer polysome, and 5S RNP assembly evidence for Syo1.

📚 Additional Documentation

Deep Research Falcon

(SYO1-deep-research-falcon.md)

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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: Q07395
Protein Description: RecName: Full=Synchronized import protein 1; AltName: Full=Symportin 1;
Gene Information: Name=SYO1; OrderedLocusNames=YDL063C;
Organism (full): Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Protein Family: Belongs to the nuclear import and ribosome assembly adapter
Key Domains: ARM-like. (IPR011989); ARM-type_fold. (IPR016024); SYO1-like. (IPR052616); TPR_SYO1. (IPR057990); TPR_SYO1 (PF25567)

MANDATORY VERIFICATION STEPS:

Check if the gene symbol "SYO1" matches the protein description above
Verify the organism is correct: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Check if protein family/domains align with what you find in literature
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 'SYO1' 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 SYO1 (gene ID: SYO1, UniProt: Q07395) 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: Q07395
Protein Description: RecName: Full=Synchronized import protein 1; AltName: Full=Symportin 1;
Gene Information: Name=SYO1; OrderedLocusNames=YDL063C;
Organism (full): Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Protein Family: Belongs to the nuclear import and ribosome assembly adapter
Key Domains: ARM-like. (IPR011989); ARM-type_fold. (IPR016024); SYO1-like. (IPR052616); TPR_SYO1. (IPR057990); TPR_SYO1 (PF25567)

MANDATORY VERIFICATION STEPS:

Check if the gene symbol "SYO1" matches the protein description above
Verify the organism is correct: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Check if protein family/domains align with what you find in literature
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:

Research Target:

Please provide a comprehensive research report on the gene SYO1 (gene ID: SYO1, UniProt: Q07395) 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.

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.

Research report: SYO1 (UniProt Q07395; YDL063C; “Synchronized import protein 1” / Symportin 1) in Saccharomyces cerevisiae S288c

1) Key concepts, definitions, and current understanding

1.1 Gene/protein identity verification (critical disambiguation)

SYO1 in budding yeast (Saccharomyces cerevisiae S288c) corresponds to ORF YDL063C and is named Syo1 (for “synchronized import” / “symportin”). It is described in the primary literature as a conserved, all-α α‑solenoid protein composed of ARM repeats followed by HEAT repeats, functioning as a specialized nuclear import adaptor/chaperone for ribosome biogenesis cargo. These properties match the provided UniProt Q07395 identity and domain/family expectations. (kressler2012synchronizingnuclearimport pages 2-3)

1.2 What SYO1 is (and is not)

Syo1 is not an enzyme and does not catalyze a chemical reaction; its “substrate specificity” is best described as cargo specificity for ribosomal proteins and their assembly intermediates. Its established primary function is to bind and co-transport two ribosomal proteins (Rpl5/uL18 and Rpl11/uL5) into the nucleus, and to couple this import to early steps of 5S ribonucleoprotein (5S RNP) assembly that feed into 60S large ribosomal subunit biogenesis. (kressler2012synchronizingnuclearimport pages 1-2, kressler2012synchronizingnuclearimport pages 6-6, calvino2015symportin1chaperones pages 1-2)

1.3 The biological module Syo1 serves: 5S RNP and central protuberance assembly

The 5S RNP is a conserved ribosomal assembly module consisting of 5S rRNA + Rpl5 (uL18) + Rpl11 (uL5). In assembling pre-60S particles, a key docking interaction relies on Rpl11 binding to helix 84 (H84) of 25S rRNA. Syo1 helps prepare/escort these components so that correct stoichiometry and geometry are achieved prior to docking into pre-60S particles. (calvino2015symportin1chaperones pages 1-2, kressler2012synchronizingnuclearimport pages 1-2)

2) Molecular function, mechanism, binding partners, and localization (best-supported core annotation)

2.1 Core binding partners/cargo

The best-supported direct partners/cargo of yeast Syo1 are:
- Rpl5 (uL18)
- Rpl11 (uL5)
- 5S rRNA (binds the Syo1–Rpl5–Rpl11 complex to form an early Syo1-containing 5S RNP intermediate)
- The import receptor Kap104 (karyopherin/importin β family)
Downstream assembly factors Rpf2–Rrs1 are implicated in the handoff/maturation of this module toward pre-60S incorporation. (kressler2012synchronizingnuclearimport pages 1-2, kressler2012synchronizingnuclearimport pages 6-6, estrada2023structureofnascent pages 11-12)

2.2 Nuclear import mechanism: “synchronized” co-import via Kap104 and RanGTP

Kressler et al. established that Syo1 forms a heterotrimeric Syo1–Rpl5–Rpl11 complex and recruits the import receptor Kap104, yielding an import-competent complex that is released by RanGTP in the nucleus; the cargo can then be directly transferred onto 5S rRNA. (kressler2012synchronizingnuclearimport pages 1-2, kressler2012synchronizingnuclearimport pages 6-6)

Mechanistically, Syo1 contains an N‑terminal PY/bPY nuclear localization signal (PY-NLS/bPY-NLS) that is required and sufficient for Kap104 binding (described in follow-up mechanistic work). (bange2013newtwistto pages 7-8, bange2013newtwistto pages 5-7)

2.3 Subcellular localization and trafficking

Syo1 is a shuttling factor that supports cytoplasm-to-nucleus transport of its ribosomal cargo and can return to the cytoplasm via interaction with phenylalanine–glycine (FG) nucleoporins, consistent with a transport-adaptor role. (kressler2012synchronizingnuclearimport pages 1-2, bange2013newtwistto pages 5-7, kressler2012synchronizingnuclearimport pages 4-6)

A curated expert review classifies Syo1’s steady-state localization as “mainly nuclear.” (pillet2017holdonto pages 2-3)

3) Structural basis for function (domain architecture, interaction surfaces, and assembly logic)

3.1 Domain architecture

Syo1 is an elongated α‑solenoid comprising four complete ARM repeats (residues ~65–260) followed by six HEAT repeats (residues ~274–675) in the structurally characterized homolog used for crystallography, and is described as an “unusual chimera” of these repeat types. (kressler2012synchronizingnuclearimport pages 2-3, kressler2012synchronizingnuclearimport pages 4-6)

3.2 Rpl5 recognition: linear N-terminus captured in a groove

A central mechanistic point is that Syo1 recognizes the Rpl5 N‑terminus as a linear motif; the N‑terminal 41 amino acids of Rpl5 are necessary and sufficient for robust Syo1 interaction, and residues 2–20 are accommodated in the Syo1 groove. This region of Rpl5 is normally involved in 5S rRNA binding, implying Syo1 can shield RNA-binding surfaces until correct assembly. (kressler2012synchronizingnuclearimport pages 2-3, kressler2012synchronizingnuclearimport pages 4-6)

Structural statistics from the Science 2012 study include:
- ctSyo1 crystal structure at 2.1 Å
- ctSyo1–ctL5-N complex at 2.95 Å
- A reported binding interface of ~980 Å² (for the L5-N interaction). (kressler2012synchronizingnuclearimport pages 2-3)

3.3 Rpl11 recognition and prevention of premature rRNA docking

A 2015 Nature Communications study determined the crystal structure of a ternary Syo1–RpL5-N–RpL11 complex and proposed a direct assembly logic: Syo1 guards the 25S rRNA-binding surface on RpL11 and thereby competes with helix 84 (H84) of 25S rRNA. In biochemical pull-down experiments, H84 can release RpL11 from the ternary complex unless 5S RNA is present, supporting a model in which 5S rRNA incorporation stabilizes productive assembly intermediates. (calvino2015symportin1chaperones pages 1-2)

The same study provides detailed crystallographic implementation parameters (construct boundaries, crystal system and unit cell), and identifies disordered loops that may be functionally important:
- Syo1 construct: residues 26–674; RpL5-N 2–30; RpL11 15–167
- Disordered Syo1 acidic loop 328–384 and RpL11 basic loop 135–154
- Crystal form P212121 with unit cell a=60.1, b=106.0, c=147.2 Å, one complex per ASU, Matthews coefficient 2.1 Å²/Da, solvent content ~41%. (calvino2015symportin1chaperones pages 1-2)

4) Functional evidence in vivo: phenotypes and genetic interactions

4.1 Essentiality and growth phenotypes

SYO1 is nonessential (deletion viable), but functionally important: syo1Δ cells display reduced growth, particularly at low temperature, and show ribosome biogenesis defects including reduced free 60S relative to 40S and half-mer polysomes—a classic hallmark of 60S subunit limitation during translation initiation. (kressler2012synchronizingnuclearimport pages 2-3)

An expert review similarly summarizes the null phenotype as “slow growth at low temperature.” (pillet2017holdonto pages 2-3)

4.2 Genetic linkage to Rpl5 function

Genetic analyses support a tight functional coupling between SYO1 and RPL5:
- Synthetic lethality between syo1Δ and certain rpl5 alleles
- High-copy RPL5 suppresses the cold-sensitive syo1Δ phenotype
- Syo1 overexpression can rescue slow-growth or lethal phenotypes of specific Rpl5 mutant alleles (example noted: rpl5L104S). (kressler2012synchronizingnuclearimport pages 2-3)

5) Recent developments (2023–2024 prioritized): updated mechanistic/structural understanding

5.1 2023 cryo-EM: Syo1 is part of a conserved hexameric nascent 5S RNP

A major 2023 advance used biochemical reconstitution and cryo-EM to show that Syo1 can persist as a component of a conserved hexameric 5S RNP precursor containing Syo1, Rpf2, Rrs1, uL18 (Rpl5), uL5 (Rpl11), and 5S rRNA, clarifying how nascent 5S rRNA associates with the initial import complex and then transitions toward pre-60S incorporation. (estrada2023structureofnascent pages 1-2, estrada2023structureofnascent pages 2-4)

This work also mapped direct Syo1:5S rRNA contacts and tested them genetically:
- Two contacts (‘A’ and ‘B’) in the Syo1 N-terminus touch 5S rRNA loop D in helix IV.
- A third contact (‘C’) involves a Syo1 C-terminal helix (residues 650–671) contacting the 5S rRNA middle region.
- Single mutants syo1-A (R118E) and syo1-B (K74E,K76E) had no obvious growth defect alone, but the combined syo1-AB caused complete loss of Syo1 function, resembling syo1Δ.
- syo1-AB is synthetically lethal with uL18 (Rpl5) G169S, and biochemical purification showed strongly reduced 5S rRNA co-precipitation in this sensitized background.
These data sharpen the functional definition of Syo1 from “import adaptor” to import adaptor + assembly factor that directly engages 5S rRNA. (estrada2023structureofnascent pages 6-7)

5.2 2023 reconstitution assays: docking to early pre-60S particles

The same 2023 study implemented an in vitro system to test whether hexameric 5S RNP is a precursor that assembles into pre-ribosomes. Using early pre-60S particles depleted of 5S RNP (generated by repressing 5S RNP components, including GAL-regulated depletion), the authors reconstituted 5S RNP binding with high specificity and visualized recruitment by negative-stain EM using a uL18–3×GFP tag (extra density at the central protuberance region). They also used an electrophoretic mobility shift assay (EMSA) to show robust binding/shift for an RNA corresponding to 25S rRNA H81–H87, supporting the idea that this region serves as an initial docking site. (estrada2023structureofnascent pages 6-7)

5.3 2024 review context (homology/biomedicine)

A 2024 review on ribosome biogenesis in cancer references the conserved chaperone concept in which Syo1/HEATR3 enables nuclear import/assembly of 5S RNP components; while human-focused, it reinforces the conserved mechanistic framing relevant to interpreting yeast Syo1 as a foundational model. (estrada2023structureofnascent pages 1-2)

6) Current applications and real-world implementations

Because SYO1 is a non-enzymatic adaptor/chaperone, “applications” are primarily experimental and biotechnology/biomedicine enabling uses:

Reconstituted nuclear import/assembly systems: Reconstitution of a Kap104–Syo1–Rpl5–Rpl11 import complex with defined stoichiometry and RanGTP-triggered release provides a tractable system for mechanistic dissection of nuclear import coupling to RNP assembly. This includes gel filtration, static light scattering, and in vitro transcribed 5S rRNA binding readouts. (kressler2012synchronizingnuclearimport pages 6-6)
Structural-guided functional mutagenesis: Structural mapping of Syo1 interfaces (Rpl5-binding groove; 5S rRNA contact sites) enables rational mutation (e.g., K74E/K76E/R118E; R118E) to probe assembly steps and synthetic interactions. (estrada2023structureofnascent pages 6-7)
Ribosome biogenesis assay toolkit (in yeast systems broadly used to study factors like SYO1): Polysome profiling and affinity-purification approaches are standard readouts to quantify large subunit deficiencies and map co-translational capture or assembly intermediates; detailed gradient parameters for these assays are described in related ribosome-chaperone work and are directly applicable to SYO1-centric experiments. (pillet2015thededicatedchaperone pages 24-25)

7) Expert opinion and analysis (authoritative synthesis)

An authoritative chaperone-focused review places Syo1 among a small set of dedicated ribosomal protein chaperones in yeast, emphasizing that r-proteins are aggregation-prone and that dedicated chaperones (including Syo1) protect and deliver specific r-proteins to the nucleus/nucleolus; for Syo1, the review summarizes key clients (Rpl5/Rpl11), its mainly nuclear steady-state localization, and the mapped Rpl5 N-terminus (2–20) binding region. (pillet2017holdonto pages 2-3)

Primary mechanistic studies frame Syo1 as a solution to a logistics/stoichiometry problem: ensuring that two functionally paired 5S rRNA-binding proteins (Rpl5 and Rpl11) are co-imported and poised for productive 5S RNP formation and pre-60S assembly, rather than arriving separately and risking misfolding or inappropriate interactions. (kressler2012synchronizingnuclearimport pages 1-2, calvino2015symportin1chaperones pages 1-2)

8) Key statistics and data points (recent and classic)

Stoichiometry
Syo1:Rpl5:Rpl11 1:1:1 in reconstituted heterotrimer (Science 2012). (kressler2012synchronizingnuclearimport pages 1-2)
Kap104:Syo1:Rpl5:Rpl11 1:1:1:1 in reconstituted import complex; RanGTP releases cargo (Science 2012). (kressler2012synchronizingnuclearimport pages 6-6)
Structural resolutions and interfaces
ctSyo1 crystal structure 2.1 Å; ctSyo1–ctL5-N 2.95 Å; Rpl5-binding interface ~980 Å² (Science 2012). (kressler2012synchronizingnuclearimport pages 2-3)
Ternary complex construct boundaries and crystallographic parameters (Nat Commun 2015): Syo1 26–674, RpL5-N 2–30, RpL11 15–167; disordered loops Syo1 328–384 and RpL11 135–154; unit cell 60.1 × 106.0 × 147.2 Å, solvent content ~41%. (calvino2015symportin1chaperones pages 1-2)
In vivo phenotypes
syo1Δ viable but cold-sensitive, with reduced free 60S, half-mer polysomes (Science 2012). (kressler2012synchronizingnuclearimport pages 2-3)
2023 residue-level functional mapping
Syo1–5S rRNA contact helix at Syo1 residues 650–671; loss-of-function combination K74E/K76E/R118E; synthetic lethality with uL18 G169S (Nat Struct Mol Biol 2023). (estrada2023structureofnascent pages 6-7)

9) Suggested concise functional annotation (evidence-weighted)

SYO1 encodes a shuttling nuclear import adaptor and assembly chaperone that binds ribosomal proteins Rpl5 (uL18) and Rpl11 (uL5) in the cytoplasm, recruits Kap104 through an N-terminal PY/bPY-NLS, and mediates their co-import into the nucleus. After RanGTP-driven release, Syo1 supports early 5S RNP assembly by coordinating transfer to 5S rRNA and shielding rRNA-binding surfaces (notably on Rpl11) until appropriate docking and maturation steps during 60S ribosomal subunit biogenesis. (kressler2012synchronizingnuclearimport pages 1-2, kressler2012synchronizingnuclearimport pages 6-6, calvino2015symportin1chaperones pages 1-2, estrada2023structureofnascent pages 6-7)

Evidence summary table

Aspect	Evidence-based summary for SYO1 / YDL063C / Symportin 1 in Saccharomyces cerevisiae	Key data	Top citations (year + URL)
Verified identity	Literature matches the requested target: yeast Syo1/Ydl063c, called symportin 1, a conserved ARM/HEAT-repeat α-solenoid factor functioning in ribosomal protein import and 5S RNP/60S assembly. This aligns with UniProt Q07395 domain/family expectations. (kressler2012synchronizingnuclearimport pages 1-2, kressler2012synchronizingnuclearimport pages 2-3)	Syo1 architecture reported as 4 ARM repeats + 6 HEAT repeats; ctSyo1 residues 65–260 (ARM) and 274–675 (HEAT). (kressler2012synchronizingnuclearimport pages 4-6, kressler2012synchronizingnuclearimport pages 2-3)	Kressler et al., 2012, https://doi.org/10.1126/science.1226960; Calviño et al., 2015, https://doi.org/10.1038/ncomms7510
Primary molecular function	Dedicated transport adaptor/chaperone that synchronizes nuclear co-import of the two 5S rRNA-binding ribosomal proteins Rpl5/uL18 and Rpl11/uL5, protects cargo surfaces important for RNA binding/assembly, and helps generate an early 5S RNP assembly intermediate. (kressler2012synchronizingnuclearimport pages 1-2, bange2013newtwistto pages 5-7, calvino2015symportin1chaperones pages 1-2)	Heterotrimeric Syo1–Rpl5–Rpl11 complex with 1:1:1 stoichiometry. (kressler2012synchronizingnuclearimport pages 1-2)	Kressler et al., 2012, https://doi.org/10.1126/science.1226960; Calviño et al., 2015, https://doi.org/10.1038/ncomms7510
Key binding partners / cargo	Direct cargo/partners are Rpl5 (uL18) and Rpl11 (uL5); after import, the complex can bind 5S rRNA to form a transient Syo1-containing pre-5S/5S RNP intermediate. Downstream factors Rpf2–Rrs1 promote progression toward assembly-competent 5S RNP and pre-60S incorporation. (kressler2012synchronizingnuclearimport pages 1-2, kressler2012synchronizingnuclearimport pages 6-6, estrada2023structureofnascent pages 11-12, estrada2023structureofnascent pages 2-4, calvino2015symportin1chaperones pages 1-2)	Rpl5 N-terminus is the major mapped Syo1-binding region; Rpl11 binds a distinct site including a β-sheet/basic-loop region. (bange2013newtwistto pages 7-8, pillet2017holdonto pages 2-3, calvino2015symportin1chaperones pages 1-2)	Kressler et al., 2012, https://doi.org/10.1126/science.1226960; Calviño et al., 2015, https://doi.org/10.1038/ncomms7510; de Estrada et al., 2023, https://doi.org/10.1038/s41594-023-01006-7
Import receptor and transport signals	Syo1 contains an N-terminal PY/bPY-NLS that is required and sufficient for interaction with the import receptor Kap104 (yeast Kapβ2 homolog). The Syo1–Rpl5–Rpl11 complex is a preferred Kap104 cargo; RanGTP releases the trimer from Kap104 after import. (bange2013newtwistto pages 7-8, bange2013newtwistto pages 5-7, kressler2012synchronizingnuclearimport pages 6-6, estrada2023structureofnascent pages 11-12)	Stable import complex measured as 1:1:1:1 Syo1:Rpl5:Rpl11:Kap104. (kressler2012synchronizingnuclearimport pages 6-6) Recent work notes flexible Syo1 N-terminus including the PY-NLS in 5S RNP intermediates. (estrada2023structureofnascent pages 1-2)	Kressler et al., 2012, https://doi.org/10.1126/science.1226960; Bange et al., 2013, https://doi.org/10.4161/cib.24792; de Estrada et al., 2023, https://doi.org/10.1038/s41594-023-01006-7
Role in 5S RNP and 60S biogenesis	Syo1 links import to assembly: it escorts Rpl5/Rpl11 into the nucleus, then supports loading of 5S rRNA to form an early Syo1-bound 5S RNP. Syo1 also occupies/shields an essential rRNA-binding surface on Rpl11 and competes with 25S rRNA helix H84 until 5S RNP maturation and docking into pre-60S particles. (kressler2012synchronizingnuclearimport pages 6-6, estrada2023structureofnascent pages 11-12, calvino2015symportin1chaperones pages 1-2)	2023 cryo-EM work resolved a conserved hexameric 5S RNP precursor containing Syo1, Rpf2, Rrs1, uL18, uL5, and 5S rRNA, showing Syo1 persists deeper into early assembly than previously appreciated. (estrada2023structureofnascent pages 1-2, estrada2023structureofnascent pages 2-4, estrada2023structureofnascent pages 6-7)	Calviño et al., 2015, https://doi.org/10.1038/ncomms7510; de Estrada et al., 2023, https://doi.org/10.1038/s41594-023-01006-7
Subcellular localization / shuttling	Syo1 is mainly nuclear at steady state but is a shuttling factor: it captures cargo produced in the cytoplasm, mediates import into the nucleus/nucle(ol)us, and can return to the cytoplasm through affinity for FG-repeat nucleoporins (facilitated diffusion). (kressler2012synchronizingnuclearimport pages 1-2, bange2013newtwistto pages 5-7, kressler2012synchronizingnuclearimport pages 4-6, pillet2017holdonto pages 2-3)	Nuclear accumulation is Kap104-dependent; Syo1-GFP fails to accumulate in nuclei of kap104-16 cells in the cited import assay system. (kressler2012synchronizingnuclearimport pages 4-6)	Kressler et al., 2012, https://doi.org/10.1126/science.1226960; Pillet et al., 2017, https://doi.org/10.1002/bies.201600153
Structural organization	Syo1 is an elongated α-solenoid. The HEAT-repeat concave surface binds the Rpl5 N-terminus, while an opposing site accommodates Rpl11; the ARM repeats are not the main cargo-binding surface in the ternary complex structure. (bange2013newtwistto pages 7-8, calvino2015symportin1chaperones pages 1-2, calvino2015symportin1chaperones media 33ad6edf)	Standalone ctSyo1 crystal structure at 2.1 Å; ctSyo1–ctL5-N complex at 2.95 Å. Ternary Syo1–RpL5-N–RpL11 structure used Syo1 residues 26–674, RpL5 residues 2–30, RpL11 residues 15–167. (kressler2012synchronizingnuclearimport pages 2-3, calvino2015symportin1chaperones pages 1-2)	Kressler et al., 2012, https://doi.org/10.1126/science.1226960; Calviño et al., 2015, https://doi.org/10.1038/ncomms7510
Mapped interaction regions	The N-terminal 41 aa of Rpl5 are necessary and sufficient for robust Syo1 interaction; more precisely, Rpl5 aa 2–20 dock into an extended Syo1 groove. Rpl11 binding is more complex; one summary maps it to aa 16–131, and the crystal study notes a disordered basic loop aa 135–154. Syo1 also contains a disordered acidic loop aa 328–384. (bange2013newtwistto pages 7-8, pillet2017holdonto pages 2-3, calvino2015symportin1chaperones pages 1-2, kressler2012synchronizingnuclearimport pages 2-3)	Rpl5-binding interface buries about 980 Å². (kressler2012synchronizingnuclearimport pages 2-3)	Kressler et al., 2012, https://doi.org/10.1126/science.1226960; Calviño et al., 2015, https://doi.org/10.1038/ncomms7510; Pillet et al., 2017, https://doi.org/10.1002/bies.201600153
Mutational/functional evidence	syo1Δ cells are viable but show cold-sensitive/slow-growth phenotypes, decreased free 60S relative to 40S, and half-mer polysomes, indicating impaired large-subunit biogenesis. Genetic interactions tie SYO1 tightly to RPL5 function; RPL5 high-copy suppresses syo1Δ cold sensitivity, and Syo1 overexpression can rescue dysfunctional Rpl5 variants. (bange2013newtwistto pages 8-9, pillet2017holdonto pages 2-3, kressler2012synchronizingnuclearimport pages 2-3)	2023 structure-guided mutants: syo1-A R118E and syo1-B K74E,K76E impair function; combined syo1-AB causes complete loss of function and is synthetically lethal with uL18 G169S. (estrada2023structureofnascent pages 6-7)	Kressler et al., 2012, https://doi.org/10.1126/science.1226960; Bange et al., 2013, https://doi.org/10.4161/cib.24792; de Estrada et al., 2023, https://doi.org/10.1038/s41594-023-01006-7
2023–2024 developments	Recent work extends Syo1 from a simple import adaptor to a structural component of nascent hexameric 5S RNP intermediates, with direct contacts to 5S rRNA and a role in docking to early pre-60S particles. This supports a broader model in which Syo1/HEATR3-like proteins couple import, pre-5S RNP maturation, and checkpoint-linked ribosome biogenesis. (estrada2023structureofnascent pages 1-2, estrada2023structureofnascent pages 2-4, estrada2023structureofnascent pages 6-7)	In the 2023 hexameric 5S RNP study, contacts A/B in the Syo1 N-terminus contact 5S rRNA helix IV loop D, and contact C involves a C-terminal helix aa 650–671; a human Mdm2–5S RNP cryo-EM structure was solved at 4.1 Å, illustrating conserved pathway branching under nucleolar stress. (estrada2023structureofnascent pages 8-10, estrada2023structureofnascent pages 6-7)	de Estrada et al., 2023, https://doi.org/10.1038/s41594-023-01006-7; Hwang & Denicourt, 2024, https://doi.org/10.1093/narcan/zcae017
Best concise functional annotation	Syo1 is a nonessential but important nuclear import and ribosome-assembly adaptor/chaperone that co-transports Rpl5 and Rpl11 via Kap104, promotes formation of early 5S RNP intermediates with 5S rRNA, and thereby supports correct 60S ribosomal subunit biogenesis in budding yeast. (kressler2012synchronizingnuclearimport pages 1-2, kressler2012synchronizingnuclearimport pages 6-6, kressler2012synchronizingnuclearimport pages 2-3, estrada2023structureofnascent pages 11-12)	Not an enzyme or membrane transporter; substrate/cargo specificity is primarily Rpl5/uL18 + Rpl11/uL5, with subsequent functional engagement of 5S rRNA. (kressler2012synchronizingnuclearimport pages 1-2, calvino2015symportin1chaperones pages 1-2)	Kressler et al., 2012, https://doi.org/10.1126/science.1226960; Calviño et al., 2015, https://doi.org/10.1038/ncomms7510; de Estrada et al., 2023, https://doi.org/10.1038/s41594-023-01006-7

Table: This table summarizes the most established and recent evidence for Saccharomyces cerevisiae SYO1/Q07395, including verified identity, cargo specificity, import mechanism, role in 5S RNP and 60S biogenesis, localization, structural details, and key citations.

Key primary figures (visual evidence)

Calviño et al. provide the crystal structure of the Syo1–RpL5-N–RpL11 ternary complex and a schematic model for 5S RNP assembly steps involving Syo1 (calvino2015symportin1chaperones media 33ad6edf, calvino2015symportin1chaperones media a6c13487).

References with URLs and publication dates (most central)

Kressler D. et al. “Synchronizing nuclear import of ribosomal proteins with ribosome assembly.” Science (2 Nov 2012). https://doi.org/10.1126/science.1226960 (kressler2012synchronizingnuclearimport pages 1-2, kressler2012synchronizingnuclearimport pages 2-3)
Calviño F.R. et al. “Symportin 1 chaperones 5S RNP assembly during ribosome biogenesis by occupying an essential rRNA-binding site.” Nature Communications (7 Apr 2015). https://doi.org/10.1038/ncomms7510 (calvino2015symportin1chaperones pages 1-2)
Duque de Estrada N.M.C. et al. “Structure of nascent 5S RNPs at the crossroad between ribosome assembly and MDM2–p53 pathways.” Nature Structural & Molecular Biology (Jun 2023; vol. 30, Aug issue). https://doi.org/10.1038/s41594-023-01006-7 (estrada2023structureofnascent pages 1-2, estrada2023structureofnascent pages 6-7)
Pillet B. et al. “Hold on to your friends: Dedicated chaperones of ribosomal proteins.” BioEssays (Jan 2017). https://doi.org/10.1002/bies.201600153 (pillet2017holdonto pages 2-3)
Bange G. et al. “New twist to nuclear import: when two travel together.” Communicative & Integrative Biology (Jul 2013). https://doi.org/10.4161/cib.24792 (bange2013newtwistto pages 7-8, bange2013newtwistto pages 5-7)

References

(kressler2012synchronizingnuclearimport pages 2-3): Dieter Kressler, Gert Bange, Yutaka Ogawa, Goran Stjepanovic, Bettina Bradatsch, Dagmar Pratte, Stefan Amlacher, Daniela Strauß, Yoshihiro Yoneda, Jun Katahira, Irmgard Sinning, and Ed Hurt. Synchronizing nuclear import of ribosomal proteins with ribosome assembly. Science, 338:666-671, Nov 2012. URL: https://doi.org/10.1126/science.1226960, doi:10.1126/science.1226960. This article has 142 citations and is from a highest quality peer-reviewed journal.
(kressler2012synchronizingnuclearimport pages 1-2): Dieter Kressler, Gert Bange, Yutaka Ogawa, Goran Stjepanovic, Bettina Bradatsch, Dagmar Pratte, Stefan Amlacher, Daniela Strauß, Yoshihiro Yoneda, Jun Katahira, Irmgard Sinning, and Ed Hurt. Synchronizing nuclear import of ribosomal proteins with ribosome assembly. Science, 338:666-671, Nov 2012. URL: https://doi.org/10.1126/science.1226960, doi:10.1126/science.1226960. This article has 142 citations and is from a highest quality peer-reviewed journal.
(kressler2012synchronizingnuclearimport pages 6-6): Dieter Kressler, Gert Bange, Yutaka Ogawa, Goran Stjepanovic, Bettina Bradatsch, Dagmar Pratte, Stefan Amlacher, Daniela Strauß, Yoshihiro Yoneda, Jun Katahira, Irmgard Sinning, and Ed Hurt. Synchronizing nuclear import of ribosomal proteins with ribosome assembly. Science, 338:666-671, Nov 2012. URL: https://doi.org/10.1126/science.1226960, doi:10.1126/science.1226960. This article has 142 citations and is from a highest quality peer-reviewed journal.
(calvino2015symportin1chaperones pages 1-2): Fabiola R. Calviño, Satyavati Kharde, Alessandro Ori, Astrid Hendricks, Klemens Wild, Dieter Kressler, Gert Bange, Ed Hurt, Martin Beck, and Irmgard Sinning. Symportin 1 chaperones 5s rnp assembly during ribosome biogenesis by occupying an essential rrna-binding site. Nature Communications, Apr 2015. URL: https://doi.org/10.1038/ncomms7510, doi:10.1038/ncomms7510. This article has 82 citations and is from a highest quality peer-reviewed journal.
(estrada2023structureofnascent pages 11-12): Nestor Miguel Castillo Duque de Estrada, Matthias Thoms, Dirk Flemming, Henrik M. Hammaren, Robert Buschauer, Michael Ameismeier, Jochen Baßler, Martin Beck, Roland Beckmann, and Ed Hurt. Structure of nascent 5s rnps at the crossroad between ribosome assembly and mdm2–p53 pathways. Nature Structural & Molecular Biology, 30:1119-1131, Jun 2023. URL: https://doi.org/10.1038/s41594-023-01006-7, doi:10.1038/s41594-023-01006-7. This article has 35 citations and is from a highest quality peer-reviewed journal.
(bange2013newtwistto pages 7-8): Gert Bange, Guillaume Murat, Irmgard Sinning, Ed Hurt, and Dieter Kressler. New twist to nuclear import: when two travel together. Communicative & Integrative Biology, 6:e24792, Jul 2013. URL: https://doi.org/10.4161/cib.24792, doi:10.4161/cib.24792. This article has 42 citations and is from a peer-reviewed journal.
(bange2013newtwistto pages 5-7): Gert Bange, Guillaume Murat, Irmgard Sinning, Ed Hurt, and Dieter Kressler. New twist to nuclear import: when two travel together. Communicative & Integrative Biology, 6:e24792, Jul 2013. URL: https://doi.org/10.4161/cib.24792, doi:10.4161/cib.24792. This article has 42 citations and is from a peer-reviewed journal.
(kressler2012synchronizingnuclearimport pages 4-6): Dieter Kressler, Gert Bange, Yutaka Ogawa, Goran Stjepanovic, Bettina Bradatsch, Dagmar Pratte, Stefan Amlacher, Daniela Strauß, Yoshihiro Yoneda, Jun Katahira, Irmgard Sinning, and Ed Hurt. Synchronizing nuclear import of ribosomal proteins with ribosome assembly. Science, 338:666-671, Nov 2012. URL: https://doi.org/10.1126/science.1226960, doi:10.1126/science.1226960. This article has 142 citations and is from a highest quality peer-reviewed journal.
(pillet2017holdonto pages 2-3): Benjamin Pillet, Valentin Mitterer, Dieter Kressler, and Brigitte Pertschy. Hold on to your friends: dedicated chaperones of ribosomal proteins. BioEssays, 39:1-12, Jan 2017. URL: https://doi.org/10.1002/bies.201600153, doi:10.1002/bies.201600153. This article has 93 citations and is from a peer-reviewed journal.
(estrada2023structureofnascent pages 1-2): Nestor Miguel Castillo Duque de Estrada, Matthias Thoms, Dirk Flemming, Henrik M. Hammaren, Robert Buschauer, Michael Ameismeier, Jochen Baßler, Martin Beck, Roland Beckmann, and Ed Hurt. Structure of nascent 5s rnps at the crossroad between ribosome assembly and mdm2–p53 pathways. Nature Structural & Molecular Biology, 30:1119-1131, Jun 2023. URL: https://doi.org/10.1038/s41594-023-01006-7, doi:10.1038/s41594-023-01006-7. This article has 35 citations and is from a highest quality peer-reviewed journal.
(estrada2023structureofnascent pages 2-4): Nestor Miguel Castillo Duque de Estrada, Matthias Thoms, Dirk Flemming, Henrik M. Hammaren, Robert Buschauer, Michael Ameismeier, Jochen Baßler, Martin Beck, Roland Beckmann, and Ed Hurt. Structure of nascent 5s rnps at the crossroad between ribosome assembly and mdm2–p53 pathways. Nature Structural & Molecular Biology, 30:1119-1131, Jun 2023. URL: https://doi.org/10.1038/s41594-023-01006-7, doi:10.1038/s41594-023-01006-7. This article has 35 citations and is from a highest quality peer-reviewed journal.
(estrada2023structureofnascent pages 6-7): Nestor Miguel Castillo Duque de Estrada, Matthias Thoms, Dirk Flemming, Henrik M. Hammaren, Robert Buschauer, Michael Ameismeier, Jochen Baßler, Martin Beck, Roland Beckmann, and Ed Hurt. Structure of nascent 5s rnps at the crossroad between ribosome assembly and mdm2–p53 pathways. Nature Structural & Molecular Biology, 30:1119-1131, Jun 2023. URL: https://doi.org/10.1038/s41594-023-01006-7, doi:10.1038/s41594-023-01006-7. This article has 35 citations and is from a highest quality peer-reviewed journal.
(pillet2015thededicatedchaperone pages 24-25): 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.
(calvino2015symportin1chaperones media 33ad6edf): Fabiola R. Calviño, Satyavati Kharde, Alessandro Ori, Astrid Hendricks, Klemens Wild, Dieter Kressler, Gert Bange, Ed Hurt, Martin Beck, and Irmgard Sinning. Symportin 1 chaperones 5s rnp assembly during ribosome biogenesis by occupying an essential rrna-binding site. Nature Communications, Apr 2015. URL: https://doi.org/10.1038/ncomms7510, doi:10.1038/ncomms7510. This article has 82 citations and is from a highest quality peer-reviewed journal.
(bange2013newtwistto pages 8-9): Gert Bange, Guillaume Murat, Irmgard Sinning, Ed Hurt, and Dieter Kressler. New twist to nuclear import: when two travel together. Communicative & Integrative Biology, 6:e24792, Jul 2013. URL: https://doi.org/10.4161/cib.24792, doi:10.4161/cib.24792. This article has 42 citations and is from a peer-reviewed journal.
(estrada2023structureofnascent pages 8-10): Nestor Miguel Castillo Duque de Estrada, Matthias Thoms, Dirk Flemming, Henrik M. Hammaren, Robert Buschauer, Michael Ameismeier, Jochen Baßler, Martin Beck, Roland Beckmann, and Ed Hurt. Structure of nascent 5s rnps at the crossroad between ribosome assembly and mdm2–p53 pathways. Nature Structural & Molecular Biology, 30:1119-1131, Jun 2023. URL: https://doi.org/10.1038/s41594-023-01006-7, doi:10.1038/s41594-023-01006-7. This article has 35 citations and is from a highest quality peer-reviewed journal.
(calvino2015symportin1chaperones media a6c13487): Fabiola R. Calviño, Satyavati Kharde, Alessandro Ori, Astrid Hendricks, Klemens Wild, Dieter Kressler, Gert Bange, Ed Hurt, Martin Beck, and Irmgard Sinning. Symportin 1 chaperones 5s rnp assembly during ribosome biogenesis by occupying an essential rrna-binding site. Nature Communications, Apr 2015. URL: https://doi.org/10.1038/ncomms7510, doi:10.1038/ncomms7510. This article has 82 citations and is from a highest quality peer-reviewed journal.

Citations

kressler2012synchronizingnuclearimport pages 2-3
pillet2017holdonto pages 2-3
estrada2023structureofnascent pages 6-7
estrada2023structureofnascent pages 1-2
kressler2012synchronizingnuclearimport pages 6-6
pillet2015thededicatedchaperone pages 24-25
kressler2012synchronizingnuclearimport pages 1-2
kressler2012synchronizingnuclearimport pages 4-6
estrada2023structureofnascent pages 11-12
bange2013newtwistto pages 7-8
bange2013newtwistto pages 5-7
estrada2023structureofnascent pages 2-4
bange2013newtwistto pages 8-9
estrada2023structureofnascent pages 8-10
https://doi.org/10.1126/science.1226960;
https://doi.org/10.1038/ncomms7510
https://doi.org/10.1038/ncomms7510;
https://doi.org/10.1038/s41594-023-01006-7
https://doi.org/10.4161/cib.24792;
https://doi.org/10.1002/bies.201600153
https://doi.org/10.1038/s41594-023-01006-7;
https://doi.org/10.1093/narcan/zcae017
https://doi.org/10.1126/science.1226960
https://doi.org/10.4161/cib.24792
https://doi.org/10.1126/science.1226960,
https://doi.org/10.1038/ncomms7510,
https://doi.org/10.1038/s41594-023-01006-7,
https://doi.org/10.4161/cib.24792,
https://doi.org/10.1002/bies.201600153,
https://doi.org/10.1371/journal.pgen.1005565,

📄 View Raw YAML

id: Q07395
gene_symbol: SYO1
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:559292
  label: Saccharomyces cerevisiae
description: >-
  SYO1 encodes Syo1/symportin 1, a conserved ARM/HEAT-repeat nuclear import
  adaptor and dedicated ribosomal-protein carrier chaperone. Syo1 binds the
  5S-rRNA-associated ribosomal proteins Rpl5/uL18 and Rpl11/uL5, recruits the
  import receptor Kap104, and coordinates their cytoplasm-to-nucleus co-import.
  After RanGTP-dependent release from Kap104, the Syo1-Rpl5-Rpl11 cargo complex
  can be handed to 5S rRNA, linking ribosomal-protein import with early 5S RNP
  assembly and 60S ribosomal large subunit biogenesis. Recent structural work
  places Syo1 in a conserved hexameric nascent 5S RNP precursor with 5S rRNA,
  Rpl5/uL18, Rpl11/uL5, Rpf2 and Rrs1 (PMID:37291423). Syo1 is therefore best
  curated as a specific protein carrier chaperone/import adaptor, not as a
  generic unfolded-protein binding factor.
existing_annotations:
- term:
    id: GO:0006606
    label: protein import into nucleus
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      The PANTHER/IBA annotation is consistent with direct yeast evidence and
      UniProt family context. Syo1 is a specialized import adaptor that brings
      Rpl5 and Rpl11 into the nucleus through Kap104.
    action: ACCEPT
    reason: >-
      Nuclear import of the Rpl5-Rpl11 cargo pair is a core Syo1 biological
      process and is well supported by the experimental IGI annotation and the
      Falcon synthesis.
    supported_by:
    - reference_id: PMID:23118189
      supporting_text: "Syo1 concomitantly binds Rpl5-Rpl11 and furthermore recruits the import receptor Kap104."
    - reference_id: file:yeast/SYO1/SYO1-deep-research-falcon.md
      supporting_text: Falcon identifies Syo1 as a shuttling nuclear import adaptor for Rpl5 and Rpl11.
- term:
    id: GO:0042273
    label: ribosomal large subunit biogenesis
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      Syo1-mediated co-import of Rpl5 and Rpl11 is coupled to 5S RNP formation
      and 60S ribosomal large subunit assembly. The IBA annotation transfers a
      conserved, experimentally supported ribosome-biogenesis role.
    action: ACCEPT
    reason: >-
      Ribosomal large subunit biogenesis is a core biological process for Syo1
      and is supported by mutant ribosome-biogenesis phenotypes and mechanistic
      studies of 5S RNP assembly.
    supported_by:
    - reference_id: PMID:19806183
      supporting_text: "we associate the new genes with specific aspects of ribosomal subunit maturation, ribosomal particle association, and ribosomal subunit nuclear export"
    - reference_id: file:yeast/SYO1/SYO1-deep-research-falcon.md
      supporting_text: Falcon describes Syo1 as an import adaptor and assembly chaperone that supports 5S RNP and 60S biogenesis.
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      Syo1 does protect ribosomal-protein cargo from inappropriate interactions,
      but the biology is not generic unfolded-protein binding. It is a dedicated
      carrier chaperone/import adaptor for Rpl5 and Rpl11.
    action: MODIFY
    reason: >-
      GO:0051082 is too broad for Syo1. The more informative molecular-function
      term is protein carrier chaperone, reflecting cargo binding and escort
      between cytoplasm and nucleus.
    proposed_replacement_terms:
    - id: GO:0140597
      label: protein carrier chaperone
    supported_by:
    - reference_id: PMID:26112308
      supporting_text: "Co-translational capturing of nascent ribosomal proteins by dedicated chaperones"
    - reference_id: file:yeast/SYO1/SYO1-deep-research-falcon.md
      supporting_text: Falcon frames Syo1 as a dedicated transport adaptor/chaperone rather than a general unfolded-protein binding factor.
- 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 Syo1's
      import-adaptor role and with direct localization evidence.
    action: ACCEPT
    reason: >-
      Syo1 acts in the nucleus after Kap104-mediated import of the
      Syo1-Rpl5-Rpl11 complex and is directly observed in nuclear localization
      datasets.
    supported_by:
    - reference_id: PMID:23118189
      supporting_text: "The Syo1-Rpl5-Rpl11 import complex is released from Kap104 by RanGTP"
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: >-
      UniProt subcellular-location mapping to cytoplasm is consistent with Syo1
      capturing newly synthesized ribosomal-protein cargo before nuclear import.
    action: ACCEPT
    reason: >-
      Syo1 functions as a shuttling factor: it binds Rpl5/Rpl11 in the cytoplasm
      and carries them to the nucleus. Cytoplasm is therefore a relevant
      localization, although the steady-state signal can be mainly nuclear.
    supported_by:
    - reference_id: PMID:23118189
      supporting_text: "Syo1 can shuttle back to the cytoplasm"
- term:
    id: GO:0015031
    label: protein transport
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      The UniProt keyword-derived protein transport annotation captures the
      general concept, but Syo1's transport function is specifically nuclear
      import of ribosomal proteins.
    action: MODIFY
    reason: >-
      Replace the broad GO:0015031 term with GO:0006606 protein import into
      nucleus, which matches the experimentally demonstrated Syo1-Kap104
      mechanism.
    proposed_replacement_terms:
    - id: GO:0006606
      label: protein import into nucleus
    supported_by:
    - reference_id: PMID:23118189
      supporting_text: "facilitates synchronized coimport of the two 5S-rRNA binding proteins Rpl5 and Rpl11"
- term:
    id: GO:0042254
    label: ribosome biogenesis
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      The broad ribosome biogenesis annotation is correct in direction, but
      Syo1 is specifically tied to 5S RNP/60S large subunit biogenesis.
    action: MODIFY
    reason: >-
      GO:0042273 ribosomal large subunit biogenesis is the better replacement
      because Syo1 escorts Rpl5/Rpl11 for 5S RNP formation during 60S assembly.
    proposed_replacement_terms:
    - id: GO:0042273
      label: ribosomal large subunit biogenesis
    supported_by:
    - reference_id: PMID:19806183
      supporting_text: "new genes with specific aspects of ribosomal subunit maturation, ribosomal particle association, and ribosomal subunit nuclear export"
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IDA
  original_reference_id: PMID:26112308
  review:
    summary: >-
      The IDA evidence shows dedicated co-translational capture of ribosomal
      protein clients by Syo1, not general binding to unfolded proteins.
    action: MODIFY
    reason: >-
      Syo1 is best represented as a protein carrier chaperone: it captures and
      escorts a defined ribosomal-protein cargo pair rather than acting as a
      broad unfolded-protein binding chaperone.
    proposed_replacement_terms:
    - id: GO:0140597
      label: protein carrier chaperone
    supported_by:
    - reference_id: PMID:26112308
      supporting_text: "Affinity purification of four chaperones (Rrb1, Syo1, Sqt1 and Yar1) selectively enriched the mRNAs encoding their specific ribosomal protein clients"
    - reference_id: file:yeast/SYO1/SYO1-deep-research-falcon.md
      supporting_text: Falcon supports replacing generic unfolded-protein binding with a dedicated carrier-chaperone interpretation.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: HDA
  original_reference_id: PMID:14562095
  review:
    summary: >-
      High-throughput GFP localization placed Syo1 in the nucleus, matching its
      biological role in nuclear delivery and 5S RNP assembly.
    action: ACCEPT
    reason: >-
      Nuclear localization is biologically meaningful for Syo1 and is also
      supported by UniProt and the mechanistic nuclear import literature.
    supported_by:
    - reference_id: PMID:14562095
      supporting_text: "Global analysis of protein localization in budding yeast."
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: HDA
  original_reference_id: PMID:14562095
  review:
    summary: >-
      High-throughput GFP localization also detected Syo1 in the cytoplasm,
      consistent with cargo capture before nuclear import and shuttling back
      from the nucleus.
    action: ACCEPT
    reason: >-
      Cytoplasmic localization is part of the Syo1 transport cycle and should
      be retained, even though its steady-state enrichment may be nuclear.
    supported_by:
    - reference_id: PMID:14562095
      supporting_text: "Global analysis of protein localization in budding yeast."
- term:
    id: GO:0006606
    label: protein import into nucleus
  evidence_type: IGI
  original_reference_id: PMID:23118189
  review:
    summary: >-
      The genetic interaction annotation directly reflects the Science 2012
      work showing that Syo1 mediates Kap104-dependent nuclear co-import of
      Rpl5 and Rpl11.
    action: ACCEPT
    reason: >-
      This is one of the central experimentally supported Syo1 annotations and
      captures the import component of its core function.
    supported_by:
    - reference_id: PMID:23118189
      supporting_text: "facilitates synchronized coimport of the two 5S-rRNA binding proteins Rpl5 and Rpl11"
    - reference_id: PMID:23118189
      supporting_text: "The Syo1-Rpl5-Rpl11 import complex is released from Kap104 by RanGTP"
- term:
    id: GO:0042273
    label: ribosomal large subunit biogenesis
  evidence_type: IMP
  original_reference_id: PMID:19806183
  review:
    summary: >-
      Mutant phenotyping and the later mechanistic literature support Syo1's
      role in 60S large subunit biogenesis through coordinated import and
      assembly of the 5S RNP protein module.
    action: ACCEPT
    reason: >-
      GO:0042273 is the appropriate specific biological-process term for the
      ribosome-biogenesis effect of SYO1.
    supported_by:
    - reference_id: PMID:19806183
      supporting_text: "confirming involvement of at least 15 new genes"
    - reference_id: file:yeast/SYO1/SYO1-deep-research-falcon.md
      supporting_text: Falcon summarizes reduced free 60S, half-mer polysome, and 5S RNP assembly evidence for Syo1.
references:
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings:
  - statement: >-
      PANTHER phylogenetic propagation transfers the conserved Syo1
      symportin/r-protein-carrier functions (protein import into nucleus,
      ribosomal large subunit biogenesis, unfolded protein binding)
      across SYO1 orthologues consistent with the experimental yeast data.
- id: GO_REF:0000043
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
  findings:
  - statement: >-
      UniProtKB keywords KW-0653 (Protein transport) and KW-0690 (Ribosome
      biogenesis) on SYO1 are mapped to protein transport (GO:0015031) and
      ribosome biogenesis (GO:0042254) respectively.
- 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:
  - statement: >-
      UniProtKB Subcellular Location annotation for Syo1 (Cytoplasm; Nucleus,
      transported by Kap104) is mapped to nucleus (GO:0005634) and cytoplasm
      (GO:0005737).
- id: PMID:14562095
  title: Global analysis of protein localization in budding yeast.
  findings:
  - statement: High-throughput GFP localization reported nuclear and cytoplasmic localization for Syo1.
    supporting_text: "Global analysis of protein localization in budding yeast."
- id: PMID:19806183
  title: Rational extension of the ribosome biogenesis pathway using network-guided genetics.
  findings:
  - statement: SYO1 was included among genes whose mutants support roles in ribosome biogenesis.
    supporting_text: "confirming involvement of at least 15 new genes"
  - statement: The study associated newly confirmed genes with specific ribosomal subunit maturation and trafficking steps.
    supporting_text: "new genes with specific aspects of ribosomal subunit maturation, ribosomal particle association, and ribosomal subunit nuclear export"
- id: PMID:23118189
  title: Synchronizing nuclear import of ribosomal proteins with ribosome assembly.
  findings:
  - statement: Syo1 mediates synchronized nuclear co-import of Rpl5 and Rpl11.
    supporting_text: "facilitates synchronized coimport of the two 5S-rRNA binding proteins Rpl5 and Rpl11"
  - statement: Syo1 binds Rpl5-Rpl11 and recruits Kap104.
    supporting_text: "Syo1 concomitantly binds Rpl5-Rpl11 and furthermore recruits the import receptor Kap104"
  - statement: The import complex is released by RanGTP and can be transferred to 5S rRNA.
    supporting_text: "The Syo1-Rpl5-Rpl11 import complex is released from Kap104 by RanGTP"
- id: PMID:37291423
  title: Structure of nascent 5S RNPs at the crossroad between ribosome assembly
    and MDM2-p53 pathways.
  findings:
  - statement: >-
      Structural reconstitution places Syo1 in the conserved hexameric nascent
      5S RNP precursor with 5S rRNA, uL18/Rpl5, uL5/Rpl11, Rpf2 and Rrs1.
    supporting_text: >-
      This reveals how the nascent 5S rRNA associates with the initial
      nuclear import complex Syo1-uL18-uL5 and, upon further recruitment of
      the nucleolar factors Rpf2 and Rrs1, develops into the 5S RNP precursor
      that can assemble into the pre-ribosome.
    reference_section_type: ABSTRACT
- id: PMID:26112308
  title: Co-translational capturing of nascent ribosomal proteins by their dedicated chaperones.
  findings:
  - statement: Syo1 is one of the dedicated ribosomal-protein chaperones that co-translationally captures specific clients.
    supporting_text: "Affinity purification of four chaperones (Rrb1, Syo1, Sqt1 and Yar1) selectively enriched the mRNAs encoding their specific ribosomal protein clients"
  - statement: Dedicated chaperones prevent inappropriate interactions and aggregation of ribosomal proteins before assembly.
    supporting_text: "Co-translational capturing of nascent ribosomal proteins by dedicated chaperones"
- id: file:yeast/SYO1/SYO1-deep-research-falcon.md
  title: Falcon deep research report on SYO1
  findings:
  - statement: Falcon synthesis identifies Syo1 as a shuttling nuclear import adaptor and assembly chaperone for Rpl5/Rpl11 and early 5S RNP/60S biogenesis.
core_functions:
- description: >-
    Syo1 functions as a dedicated ribosomal-protein carrier chaperone and nuclear
    import adaptor. It captures Rpl5/uL18 and Rpl11/uL5, recruits Kap104 for
    synchronized cytoplasm-to-nucleus import, and supports transfer of the cargo
    pair into early 5S RNP intermediates during 60S ribosomal large subunit
    biogenesis.
  molecular_function:
    id: GO:0140597
    label: protein carrier chaperone
  directly_involved_in:
  - id: GO:0006606
    label: protein import into nucleus
  - id: GO:0042273
    label: ribosomal large subunit biogenesis
  locations:
  - id: GO:0005737
    label: cytoplasm
  - id: GO:0005634
    label: nucleus
  supported_by:
  - reference_id: PMID:23118189
    supporting_text: "facilitates synchronized coimport of the two 5S-rRNA binding proteins Rpl5 and Rpl11"
  - reference_id: PMID:26112308
    supporting_text: "Affinity purification of four chaperones (Rrb1, Syo1, Sqt1 and Yar1) selectively enriched the mRNAs encoding their specific ribosomal protein clients"
  - reference_id: file:yeast/SYO1/SYO1-deep-research-falcon.md
    supporting_text: Falcon synthesis supports Syo1 as a dedicated carrier chaperone/import adaptor coupling Rpl5/Rpl11 import to 5S RNP and 60S assembly.
proposed_new_terms: []
suggested_questions:
- question: >-
    Should Syo1 receive a direct curated GO:0140597 protein carrier chaperone
    annotation, replacing the older unfolded protein binding annotations?
  experts:
  - Kressler D
  - Hurt E
  - Bange G
suggested_experiments:
- hypothesis: >-
    Syo1's carrier-chaperone function depends on separable cargo-binding,
    Kap104-binding, and 5S-rRNA-contact surfaces.
  description: >-
    Combine structure-guided SYO1 interface mutants with Rpl5/Rpl11 co-import
    assays, 5S RNP co-purification, and polysome profiling to distinguish defects
    in cargo capture, nuclear import, and downstream 60S assembly.
  experiment_type: structure-guided ribosome biogenesis assay

SYO1

Gene Description

Existing Annotations Review

Core Functions

References

Suggested Questions for Experts

Suggested Experiments

📚 Additional Documentation

Deep Research Falcon

Question

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

Target Gene/Protein Identity (from UniProt):

MANDATORY VERIFICATION STEPS:

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

Research Target:

Output

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

Target Gene/Protein Identity (from UniProt):

MANDATORY VERIFICATION STEPS:

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

Research Target:

Research report: SYO1 (UniProt Q07395; YDL063C; “Synchronized import protein 1” / Symportin 1) in Saccharomyces cerevisiae S288c

1) Key concepts, definitions, and current understanding

1.1 Gene/protein identity verification (critical disambiguation)

1.2 What SYO1 is (and is not)

1.3 The biological module Syo1 serves: 5S RNP and central protuberance assembly

2) Molecular function, mechanism, binding partners, and localization (best-supported core annotation)

2.1 Core binding partners/cargo

2.2 Nuclear import mechanism: “synchronized” co-import via Kap104 and RanGTP

2.3 Subcellular localization and trafficking

3) Structural basis for function (domain architecture, interaction surfaces, and assembly logic)

3.1 Domain architecture

3.2 Rpl5 recognition: linear N-terminus captured in a groove

3.3 Rpl11 recognition and prevention of premature rRNA docking

4) Functional evidence in vivo: phenotypes and genetic interactions

4.1 Essentiality and growth phenotypes

4.2 Genetic linkage to Rpl5 function

5) Recent developments (2023–2024 prioritized): updated mechanistic/structural understanding

5.1 2023 cryo-EM: Syo1 is part of a conserved hexameric nascent 5S RNP

5.2 2023 reconstitution assays: docking to early pre-60S particles

5.3 2024 review context (homology/biomedicine)

6) Current applications and real-world implementations

7) Expert opinion and analysis (authoritative synthesis)

8) Key statistics and data points (recent and classic)

9) Suggested concise functional annotation (evidence-weighted)

Evidence summary table

Key primary figures (visual evidence)

References with URLs and publication dates (most central)

Citations

📄 View Raw YAML