RRB1 encodes an essential nucleolar WD-repeat ribosome assembly factor that binds and chaperones ribosomal protein L3/Rpl3 during early 60S ribosomal subunit biogenesis. Rrb1 promotes soluble, assembly-competent Rpl3 delivery to preribosomal particles, supports 25S rRNA maturation, and is required for normal production of free 60S subunits. Its conserved PANTHER family (PTHR45903:SF1) includes fungal Rrb1/GRWD1-like proteins with roles in ribosome assembly, but the yeast literature supports an Rpl3-specific chaperone role rather than generic protein binding.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0005730
nucleolus
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic nucleolar localization is consistent with Rrb1's experimentally supported site of action in early 60S biogenesis.
Reason: Rrb1 is a nuclear/nucleolar WD-repeat protein and the conserved family context supports a nuclear ribosome-assembly role.
Supporting Evidence:
PMID:26112308
Rrb1, which is a mostly nucleolar protein, binds to Rpl3
file:interpro/panther/PTHR45903/PTHR45903-metadata.yaml
Some family members are implicated in ribosome biogenesis
|
|
GO:0042254
ribosome biogenesis
|
IBA
GO_REF:0000033 |
MODIFY |
Summary: The biological-process inference is correct but should be made more specific to large ribosomal subunit biogenesis.
Reason: Experimental studies show Rrb1 functions through Rpl3 in early 60S subunit assembly, not general ribosome biogenesis across both subunits.
Proposed replacements:
ribosomal large subunit biogenesis
Supporting Evidence:
PMID:11728313
Impairment of Rrb1p function results in decreased levels of free 60S ribosomal subunits.
file:yeast/RRB1/RRB1-deep-research-falcon.md
early large (60S) subunit biogenesis
|
|
GO:0005634
nucleus
|
IEA
GO_REF:0000044 |
MODIFY |
Summary: Nuclear localization is true but too broad given direct nucleolar evidence.
Reason: The functional site is best represented by nucleolus, where early preribosomal assembly occurs and where Rrb1 is enriched.
Proposed replacements:
nucleolus
Supporting Evidence:
PMID:26112308
Rrb1, which is a mostly nucleolar protein
|
|
GO:0006364
rRNA processing
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: Retain as a supported large-subunit biogenesis consequence of Rrb1 function.
Reason: Rrb1 depletion impairs 25S rRNA maturation, so rRNA processing is a valid process annotation, although the mechanistic core is Rpl3 chaperoning during 60S assembly.
Supporting Evidence:
file:yeast/RRB1/RRB1-deep-research-falcon.md
including efficient 25S rRNA maturation and production of 60S subunits
|
|
GO:0042254
ribosome biogenesis
|
IEA
GO_REF:0000043 |
MODIFY |
Summary: The UniProt keyword mapping captures the correct pathway but is less specific than the evidence warrants.
Reason: Rrb1 acts in early large ribosomal subunit biogenesis through Rpl3 rather than generic ribosome biogenesis.
Proposed replacements:
ribosomal large subunit biogenesis
Supporting Evidence:
PMID:11728313
required for proper assembly of preribosomal particles during early ribosome biogenesis, presumably by targeting L3 onto the 35S precursor rRNA
|
|
GO:0005515
protein binding
|
IPI
PMID:14759368 High-definition macromolecular composition of yeast RNA-proc... |
MARK AS OVER ANNOTATED |
Summary: Generic protein binding from a high-throughput complex study is not informative for Rrb1 function.
Reason: Rrb1's specific function is Rpl3 chaperoning during large-subunit biogenesis; a generic protein binding annotation should not be treated as a core molecular function.
Supporting Evidence:
PMID:26112308
dedicated chaperone proteins recognize the N-terminal regions of ribosomal proteins
|
|
GO:0005515
protein binding
|
IPI
PMID:16554755 Global landscape of protein complexes in the yeast Saccharom... |
MARK AS OVER ANNOTATED |
Summary: High-throughput interaction data are consistent with complex membership but too generic for molecular-function curation.
Reason: The interactions should be interpreted in the context of Rpl3 chaperoning and 60S assembly, not as a standalone protein binding function.
Supporting Evidence:
PMID:26112308
Rrb1 and Sqt1 interact with the very N-terminal residues of Rpl3 and Rpl10, respectively.
|
|
GO:0005515
protein binding
|
IPI
PMID:37968396 The social and structural architecture of the yeast protein ... |
MARK AS OVER ANNOTATED |
Summary: Interactome-derived protein binding is too broad to represent Rrb1's curated activity.
Reason: The core activity is substrate-specific ribosomal protein chaperoning; the generic term should not be accepted.
Supporting Evidence:
file:yeast/RRB1/RRB1-deep-research-falcon.md
Rrb1 is part of the broader dedicated chaperone/co-translational capture paradigm for ribosomal proteins.
|
|
GO:0051082
unfolded protein binding
|
IDA
PMID:26112308 Co-translational capturing of nascent ribosomal proteins by ... |
MODIFY |
Summary: The experiment supports chaperoning of nascent Rpl3, but unfolded protein binding is too generic.
Reason: Rrb1 captures a specific ribosomal protein client and promotes delivery to the assembly site, which is better represented as protein carrier chaperone activity.
Proposed replacements:
protein carrier chaperone
Supporting Evidence:
PMID:26112308
Rrb1, Syo1, Sqt1 and Yar1 selectively enriched the mRNAs encoding their specific ribosomal protein clients
|
|
GO:0005730
nucleolus
|
IDA
PMID:10684247 The yeast nuclear pore complex: composition, architecture, a... |
ACCEPT |
Summary: Direct nucleolar localization is consistent with Rrb1's early pre-60S assembly role.
Reason: Nucleolar enrichment matches the site of early ribosome biogenesis and is supported by independent literature synthesis.
Supporting Evidence:
file:yeast/RRB1/RRB1-deep-research-falcon.md
Rrb1 is predominantly nuclear with strong nucleolar enrichment
|
|
GO:0042254
ribosome biogenesis
|
IMP
PMID:11728313 A yeast homolog of chromatin assembly factor 1 is involved i... |
MODIFY |
Summary: The mutant phenotype supports ribosome biogenesis, but the more precise process is large subunit biogenesis.
Reason: Loss of Rrb1 specifically reduces free 60S subunits and disrupts early preribosomal assembly through Rpl3.
Proposed replacements:
ribosomal large subunit biogenesis
Supporting Evidence:
PMID:11728313
Impairment of Rrb1p function results in decreased levels of free 60S ribosomal subunits.
|
Q: What is the direct binding interface and stoichiometry of the yeast Rrb1-Rpl3 complex during co-translational capture?
Suggested experts: ribosome biogenesis experts, structural biologists
Q: Does Rrb1 hand Rpl3 directly to pre-60S particles in the nucleolus, or through an intermediate import or assembly factor?
Suggested experts: yeast ribosome assembly researchers
Experiment: Reconstitute the yeast Rrb1-Rpl3 N-terminal peptide or full-client complex and solve its structure by cryo-EM, crystallography, or crosslinking-MS to define the chaperone-client interface.
Hypothesis: Rrb1 recognizes a defined Rpl3 segment that is later buried in the 60S subunit and shields it before assembly.
Type: structural biochemistry
Experiment: Combine acute RRB1 depletion with Rpl3 pulse labeling, nuclear import assays, and pre-60S immunoprecipitation to test whether Rrb1 primarily affects Rpl3 solubility, nuclear import, or loading onto preribosomes.
Hypothesis: Rrb1 loss reduces productive Rpl3 loading onto early pre-60S particles before detectable global rRNA-processing defects.
Type: pulse-chase ribosome assembly assay
provider: falcon
model: Edison Scientific Literature
cached: false
start_time: '2026-05-04T10:04:57.090018'
end_time: '2026-05-04T10:12:10.741060'
duration_seconds: 433.65
template_file: templates/gene_research_go_focused.md
template_variables:
organism: yeast
gene_id: RRB1
gene_symbol: RRB1
uniprot_accession: Q04225
protein_description: 'RecName: Full=Ribosome assembly protein RRB1;'
gene_info: Name=RRB1; OrderedLocusNames=YMR131C; ORFNames=YM9553.07C;
organism_full: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
protein_family: Not specified in UniProt
protein_domains: Glutamate-rich_WD_repeat. (IPR051972); Histone-bd_RBBP4-like_N.
(IPR022052); WD40/YVTN_repeat-like_dom_sf. (IPR015943); WD40_repeat_CS. (IPR019775);
WD40_repeat_dom_sf. (IPR036322)
provider_config:
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citation_count: 13
BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'RRB1' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information
Please provide a comprehensive research report on the gene RRB1 (gene ID: RRB1, UniProt: Q04225) in yeast.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
Question: You are an expert researcher providing comprehensive, well-cited information.
Provide detailed information focusing on:
1. Key concepts and definitions with current understanding
2. Recent developments and latest research (prioritize 2023-2024 sources)
3. Current applications and real-world implementations
4. Expert opinions and analysis from authoritative sources
5. Relevant statistics and data from recent studies
Format as a comprehensive research report with proper citations. Include URLs and publication dates where available.
Always prioritize recent, authoritative sources and provide specific citations for all major claims.
BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'RRB1' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information
Please provide a comprehensive research report on the gene RRB1 (gene ID: RRB1, UniProt: Q04225) in yeast.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
The research target in the cited literature corresponds to S. cerevisiae RRB1/YMR131C, encoding Rrb1p, described as a nuclear/nucleolar WD-repeat protein required for large (60S) ribosomal subunit biogenesis and physically associated with ribosomal protein L3 (Rpl3/rpL3) (iouk2001rrb1payeast pages 3-4, iouk2001rrb1payeast pages 6-7). This matches the UniProt description provided (UniProt Q04225: โRibosome assembly protein RRB1โ) and the WD-repeat domain architecture implied by InterPro-like annotations (WD-repeat protein) as explicitly stated in primary literature (iouk2001rrb1payeast pages 3-4, killian2004inactivationofthe pages 1-2). No alternative non-yeast โRRB1โ targets are used for functional claims in this report.
Eukaryotic ribosome biogenesis is a compartmentalized process spanning nucleolus โ nucleoplasm โ cytoplasm, requiring coordinated rRNA processing/assembly and numerous trans-acting factors. Within this framework, a major concept relevant to Rrb1 is that some ribosomal proteins (RPs) have dedicated chaperones that bind them before their incorporation into pre-ribosomes to prevent aggregation/misfolding and to support proper nuclear delivery and assembly.
A central example is Rrb1 as a dedicated factor for Rpl3. In yeast, exponentially growing cells produce >160,000 ribosomal proteins per minute, motivating mechanisms that capture and escort newly synthesized RPs efficiently (rosado2007functionalanalysisof pages 7-8).
Across multiple experimental lines, yeast Rrb1p is best defined as an early 60S assembly factor / Rpl3-handling protein that forms a complex with Rpl3 and supports efficient large-subunit production, including proper 25S rRNA maturation and 60S subunit accumulation (iouk2001rrb1payeast pages 6-7, schaper2001ayeasthomolog pages 4-5, iouk2001rrb1payeast pages 10-11).
Iouk et al. (2001) identified a ~40 kDa polypeptide that co-purified with Rrb1-HA from nuclear extracts and peptide-microsequenced it as ribosomal protein L3 (rpL3/Rpl3), supporting a specific physical association (iouk2001rrb1payeast pages 3-4, iouk2001rrb1payeast pages 6-7). The authors further interpreted this specificity as consistent with Rrb1 binding free rpL3 prior to its stable incorporation into the 60S particle (iouk2001rrb1payeast pages 10-11).
Schaper et al. (2001) proposed that Rrb1p forms a direct complex with L3 and functions โas a chaperone for assembly of ribosomal protein L3 onto the precursor rRNA transcript,โ placing the interaction very early in 60S assembly (schaper2001ayeasthomolog pages 4-5).
Upon Rrb1 depletion, yeast exhibits a large-subunit-specific defect: reduced 60S subunits and appearance of half-mer polysomes (indicative of limiting 60S joining), along with impaired production/delayed maturation of 25S rRNA (with 18S comparatively less affected) (iouk2001rrb1payeast pages 6-7, iouk2001rrb1payeast pages 9-10).
These phenotypes support a model where Rrb1 is required for efficient early LSU biogenesis, plausibly through ensuring timely and correct Rpl3 availability/loading, which is known to be an early-assembling LSU protein.
Overproduction of Rrb1 increases cellular rpL3 abundance and can drive nuclear accumulation of rpL3-GFP, with specificity relative to other tested ribosomal protein GFP fusions (iouk2001rrb1payeast pages 6-7, iouk2001rrb1payeast pages 1-2). This is consistent with Rrb1 binding/sequestering rpL3 and/or stabilizing it in a nuclear/nucleolar pool.
Killian et al. (2004) placed RRB1 within a conserved ribosome-biogenesis-associated pathway involving Yph1 (pescadillo homolog) and associated factors (including ERB1 and ORC6), reporting physical/functional connections among RRB1, RPL3, and the Yph1 complex (killian2004inactivationofthe pages 1-2). Critically, RPL3 overexpression rescued a temperature-sensitive rrb1-1 phenotype, strengthening the functional coupling between Rrb1 and Rpl3 biology (killian2004inactivationofthe pages 1-2).
Rrb1 is predominantly nuclear with strong nucleolar enrichment based on immunofluorescence and colocalization with the nucleolar marker Nop1, supported by nuclear fractionation/Western analysis (iouk2001rrb1payeast media 3c21063c). This localization matches its role in early steps of 60S biogenesis that occur in the nucleolus.
RRB1 is essential for viability. Iouk et al. (2001) provided genetic evidence from disruption/depletion strategies (including GAL1-regulated expression) showing growth dependence on RRB1 expression (iouk2001rrb1payeast pages 3-4).
Key quantitative/diagnostic phenotypes upon depletion include:
- Reduced free 60S subunits and half-mers in polysome gradients (iouk2001rrb1payeast media 3c21063c).
- Delayed processing/formation of mature 25S rRNA, assessed by pulse-chase labeling of rRNA precursors (iouk2001rrb1payeast pages 6-7, iouk2001rrb1payeast media b700a353).
Killian et al. (2004) reported that partial inactivation of RRB1 (rrb1-1) caused chromosomal instability and mitotic defects, including arrest at a metaphase/anaphase transition with G2 arrest by flow cytometry, linking impaired ribosome biogenesis modules to genome stability phenotypes in yeast (killian2004inactivationofthe pages 1-2). While these are likely downstream consequences of ribosome biogenesis disruption, they are experimentally documented.
Within the retrieved corpus, direct 2023โ2024 primary research specifically centered on yeast Rrb1 (YMR131C/Q04225) was limited; the mechanistic foundation remains dominated by 2001โ2015 primary studies that established Rrb1โs localization, essentiality, Rpl3 binding, and 60S assembly function (iouk2001rrb1payeast pages 3-4, schaper2001ayeasthomolog pages 4-5, rosado2007functionalanalysisof pages 7-8).
The most relevant โrecentโ conceptual framework supporting Rrb1โs role is the dedicated-chaperone/co-translational capture model formalized for multiple ribosomal proteins, where Rrb1 is one of the exemplar dedicated factors for Rpl3 (rosado2007functionalanalysisof pages 7-8). Although the key Nature Communications paper is 2015, it remains highly influential for the current mechanistic understanding of how proteins like Rrb1 prevent harmful accumulation/aggregation of basic ribosomal proteins and align their production with assembly demands.
A 2024 preprint in Arabidopsis (AtRRB1) references the conserved function of RRB1 homologs in 60S assembly (non-yeast system; not used here for yeast-specific claims), supporting that RRB1-like proteins are still under active study in 2024 in broader eukaryotic contexts (see paper metadata in tool output; no yeast-specific claims are drawn from it).
While RRB1 is not an โapplication geneโ in an industrial sense, its well-defined role makes it a useful experimental handle for:
- Studying early 60S assembly and interpreting polysome profiles/half-mers as a functional readout of 60S biogenesis defects (iouk2001rrb1payeast media 3c21063c).
- Dissecting co-translational chaperoning pathways for ribosomal proteins, where Rrb1 serves as a model dedicated chaperone for Rpl3 (rosado2007functionalanalysisof pages 7-8).
Disruption of ribosome biogenesis is widely leveraged as a perturbation to probe cell cycle checkpoints and proteostasis constraints. RRB1 perturbation provides a genetically tractable way to connect ribosome assembly defects to downstream phenotypes such as genome instability (killian2004inactivationofthe pages 1-2).
A key authoritative synthesis is the Annual Review by de la Cruz, Karbstein, and Woolford (2015), which frames ribosomal proteins and their accessory factors as active participants in assembly and references factors like Rrb1 in the context of Rpl3 biology and early LSU assembly (rosado2007functionalanalysisof pages 7-8). This expert review perspective supports interpreting Rrb1 not as a generic scaffold but as a specialized factor in the assembly pathway.
The following table provides a compact evidence map of the main claims, experimental approaches, and primary sources.
| Claim | Evidence type | Key experimental readout | Source (authors year journal) | URL/DOI | Notes/limitations |
|---|---|---|---|---|---|
| Rrb1 localizes to the nucleus with strong nucleolar enrichment | Cell biology | HA immunofluorescence and GFP-tagged Rrb1 colocalization with nucleolar marker Nop1; nuclear fractionation/Western blot | Iouk et al. 2001, Molecular and Cellular Biology (iouk2001rrb1payeast pages 3-4, iouk2001rrb1payeast media 3c21063c) | https://doi.org/10.1128/MCB.21.4.1260-1271.2001 | Foundational localization evidence; mainly steady-state imaging/fractionation rather than live trafficking measurements |
| RRB1 is essential for viability/growth | Genetics | Gene disruption analysis and GAL1-regulated depletion strains showing growth dependence on RRB1 expression | Iouk et al. 2001, Molecular and Cellular Biology (iouk2001rrb1payeast pages 3-4) | https://doi.org/10.1128/MCB.21.4.1260-1271.2001 | Essentiality is strong, but depletion systems can have indirect secondary effects on ribosome biogenesis |
| Rrb1 physically interacts with ribosomal protein Rpl3/rpL3 | Biochemical | Co-immunoprecipitation/copurification from nuclear extracts; 40-kDa copurifying band peptide-microsequenced as rpL3 | Iouk et al. 2001, Molecular and Cellular Biology (iouk2001rrb1payeast pages 3-4, iouk2001rrb1payeast pages 6-7, iouk2001rrb1payeast pages 10-11) | https://doi.org/10.1128/MCB.21.4.1260-1271.2001 | Supports a specific Rrb1โRpl3 association; does not by itself prove exact binding interface or stoichiometry |
| Rrb1 functions as an early Rpl3 assembly factor/chaperone-like factor for 60S biogenesis | Biochemical, genetics | Early preribosomal association model; low-molecular-weight Rrb1โL3 complexes; mutant Rrb1-TAP enriches early assembly intermediates; genetic interactions with rpl3 alleles | Schaper et al. 2001, Current Biology; Rosado et al. 2007, Nucleic Acids Research (schaper2001ayeasthomolog pages 4-5, rosado2007functionalanalysisof pages 7-8) | https://doi.org/10.1016/S0960-9822(01)00584-X ; https://doi.org/10.1093/nar/gkm388 | โChaperoneโ is a mechanistic model inferred from early-complex capture and genetics; evidence is persuasive but not a full reconstitution |
| Rrb1 is part of the broader dedicated chaperone/co-translational capture paradigm for ribosomal proteins; exponentially growing yeast make >160,000 ribosomal proteins per minute | Biochemical, conceptual synthesis | Affinity purification of dedicated chaperones enriched client mRNAs; Rrb1 selectively enriched RPL3 mRNA, supporting co-translational capture of nascent Rpl3 | Pausch et al. 2015, Nature Communications (rosado2007functionalanalysisof pages 7-8) | https://doi.org/10.1038/ncomms8494 | Statistic and co-translational model come from the dedicated-chaperone study; this extends the 2001 Rrb1 findings into a mechanistic framework rather than replacing them |
| Rrb1 depletion impairs 25S rRNA maturation and causes a 60S deficit with half-mer polysomes | Cell biology, biochemical | Polysome profiling showing reduced 60S and half-mers; pulse-chase rRNA labeling showing delayed 25S maturation with comparatively unaffected 18S production | Iouk et al. 2001, Molecular and Cellular Biology (iouk2001rrb1payeast pages 6-7, iouk2001rrb1payeast pages 9-10, iouk2001rrb1payeast media 3c21063c) | https://doi.org/10.1128/MCB.21.4.1260-1271.2001 | Strong functional evidence for a large-subunit-specific defect; depletion phenotypes may reflect both direct and downstream consequences |
| RRB1 overexpression increases RPL3 transcript/protein and causes nuclear/nucleolar accumulation of free Rpl3 | Biochemical, cell biology | Increased steady-state RPL3 mRNA/protein upon RRB1 overexpression; rpL3-GFP accumulates in nucleus/nucleolus when Rrb1 is overproduced | Iouk et al. 2001, Molecular and Cellular Biology (iouk2001rrb1payeast pages 6-7, iouk2001rrb1payeast pages 1-2, iouk2001rrb1payeast pages 9-10) | https://doi.org/10.1128/MCB.21.4.1260-1271.2001 | Overexpression can create nonphysiologic pools; nevertheless, the selective effect on RPL3 is notable and mechanistically informative |
| Rrb1 interacts functionally with the Yph1/Pescadillo pathway and RPL3 overexpression rescues the rrb1-1 temperature-sensitive defect | Genetics, pathway analysis | Physical/functional linkage to Yph1 complex members (including YPH1, RPL3, ERB1, ORC6); suppression of rrb1-1 by RPL3 overexpression | Killian et al. 2004, Oncogene (killian2004inactivationofthe pages 1-2) | https://doi.org/10.1038/sj.onc.1207845 | Connects Rrb1 to a conserved ribosome-biogenesis module; rescue supports close functional coupling but not necessarily direct replacement of Rrb1 activity |
| Partial loss of Rrb1 causes chromosomal instability and mitotic/G2-M arrest phenotypes | Genetics, cell biology | Temperature-sensitive rrb1-1 mutants show sectoring/CIN, G2 arrest by flow cytometry, and mitotic morphologies with short spindles | Killian et al. 2004, Oncogene; Rosado et al. 2007, Nucleic Acids Research (killian2004inactivationofthe pages 1-2, rosado2007functionalanalysisof pages 7-8) | https://doi.org/10.1038/sj.onc.1207845 ; https://doi.org/10.1093/nar/gkm388 | Likely secondary to disruption of early 60S assembly/ribosome homeostasis, but the phenotype is experimentally documented |
| Current consensus annotation: Rrb1 is an early nucleolar large-subunit assembly factor that binds/handles Rpl3 before or during its loading onto pre-60S particles | Review synthesis from primary data | Integration of localization, Rpl3-binding, 25S maturation defects, and early-assembly phenotypes into LSU biogenesis models | Iouk et al. 2001; Schaper et al. 2001; de la Cruz et al. 2015 review (iouk2001rrb1payeast pages 1-2, schaper2001ayeasthomolog pages 4-5, iouk2001rrb1payeast pages 10-11) | https://doi.org/10.1128/MCB.21.4.1260-1271.2001 ; https://doi.org/10.1016/S0960-9822(01)00584-X ; https://doi.org/10.1146/annurev-biochem-060614-033917 | Strongly supported overall, but direct structural visualization of the yeast Rrb1โRpl3 complex was not provided in the cited primary studies |
Table: This table summarizes the main experimentally supported claims about yeast RRB1/YMR131C, including localization, essentiality, interaction with Rpl3, effects on 60S biogenesis, and genetically linked phenotypes. It is useful as a compact evidence map for constructing the full research report.
Figure panels from Iouk et al. (2001) directly support two central claims:
- Nucleolar enrichment of Rrb1 (immunofluorescence colocalization with nucleolar marker) (iouk2001rrb1payeast media 3c21063c).
- Half-mer polysomes / 60S deficit and delayed 25S rRNA maturation upon Rrb1 depletion (polysome profiles and pulse-chase rRNA processing) (iouk2001rrb1payeast media b700a353).
RRB1 (YMR131C; UniProt Q04225) encodes an essential, nuclear/nucleolar WD-repeat protein (Rrb1p) that binds ribosomal protein L3 (Rpl3) and is required for early large (60S) subunit biogenesis, including efficient 25S rRNA maturation and production of 60S subunits. Disruption causes characteristic 60S biogenesis signatures (half-mers) and can produce downstream genome instability/mitotic phenotypes in partial-loss mutants (iouk2001rrb1payeast pages 6-7, killian2004inactivationofthe pages 1-2, iouk2001rrb1payeast media 3c21063c).
References
(iouk2001rrb1payeast pages 3-4): Tatiana L. Iouk, John D. Aitchison, Shawna Maguire, and Richard W. Wozniak. Rrb1p, a yeast nuclear wd-repeat protein involved in the regulation of ribosome biosynthesis. Molecular and Cellular Biology, 21:1260-1271, Feb 2001. URL: https://doi.org/10.1128/mcb.21.4.1260-1271.2001, doi:10.1128/mcb.21.4.1260-1271.2001. This article has 97 citations and is from a domain leading peer-reviewed journal.
(iouk2001rrb1payeast pages 6-7): Tatiana L. Iouk, John D. Aitchison, Shawna Maguire, and Richard W. Wozniak. Rrb1p, a yeast nuclear wd-repeat protein involved in the regulation of ribosome biosynthesis. Molecular and Cellular Biology, 21:1260-1271, Feb 2001. URL: https://doi.org/10.1128/mcb.21.4.1260-1271.2001, doi:10.1128/mcb.21.4.1260-1271.2001. This article has 97 citations and is from a domain leading peer-reviewed journal.
(killian2004inactivationofthe pages 1-2): Audrey Killian, Nathalie Le Meur, Richard Sesboรผรฉ, Jeannette Bourguignon, Gaรซlle Bougeard, Julien Gautherot, Christian Bastard, Thierry Frรฉbourg, and Jean-Michel Flaman. Inactivation of the rrb1-pescadillo pathway involved in ribosome biogenesis induces chromosomal instability. Oncogene, 23:8597-8602, Nov 2004. URL: https://doi.org/10.1038/sj.onc.1207845, doi:10.1038/sj.onc.1207845. This article has 88 citations and is from a domain leading peer-reviewed journal.
(rosado2007functionalanalysisof pages 7-8): I. V. Rosado, D. Kressler, and J. de la Cruz. Functional analysis of saccharomyces cerevisiae ribosomal protein rpl3p in ribosome synthesis. Nucleic Acids Research, 35:4203-4213, Jun 2007. URL: https://doi.org/10.1093/nar/gkm388, doi:10.1093/nar/gkm388. This article has 77 citations and is from a highest quality peer-reviewed journal.
(schaper2001ayeasthomolog pages 4-5): Sigrid Schaper, Micheline Fromont-Racine, Patrick Linder, Jesรบs de la Cruz, Abdelkader Namane, and Moshe Yaniv. A yeast homolog of chromatin assembly factor 1 is involved in early ribosome assembly. Current Biology, 11:1885-1890, Nov 2001. URL: https://doi.org/10.1016/s0960-9822(01)00584-x, doi:10.1016/s0960-9822(01)00584-x. This article has 57 citations and is from a highest quality peer-reviewed journal.
(iouk2001rrb1payeast pages 10-11): Tatiana L. Iouk, John D. Aitchison, Shawna Maguire, and Richard W. Wozniak. Rrb1p, a yeast nuclear wd-repeat protein involved in the regulation of ribosome biosynthesis. Molecular and Cellular Biology, 21:1260-1271, Feb 2001. URL: https://doi.org/10.1128/mcb.21.4.1260-1271.2001, doi:10.1128/mcb.21.4.1260-1271.2001. This article has 97 citations and is from a domain leading peer-reviewed journal.
(iouk2001rrb1payeast pages 9-10): Tatiana L. Iouk, John D. Aitchison, Shawna Maguire, and Richard W. Wozniak. Rrb1p, a yeast nuclear wd-repeat protein involved in the regulation of ribosome biosynthesis. Molecular and Cellular Biology, 21:1260-1271, Feb 2001. URL: https://doi.org/10.1128/mcb.21.4.1260-1271.2001, doi:10.1128/mcb.21.4.1260-1271.2001. This article has 97 citations and is from a domain leading peer-reviewed journal.
(iouk2001rrb1payeast pages 1-2): Tatiana L. Iouk, John D. Aitchison, Shawna Maguire, and Richard W. Wozniak. Rrb1p, a yeast nuclear wd-repeat protein involved in the regulation of ribosome biosynthesis. Molecular and Cellular Biology, 21:1260-1271, Feb 2001. URL: https://doi.org/10.1128/mcb.21.4.1260-1271.2001, doi:10.1128/mcb.21.4.1260-1271.2001. This article has 97 citations and is from a domain leading peer-reviewed journal.
(iouk2001rrb1payeast media 3c21063c): Tatiana L. Iouk, John D. Aitchison, Shawna Maguire, and Richard W. Wozniak. Rrb1p, a yeast nuclear wd-repeat protein involved in the regulation of ribosome biosynthesis. Molecular and Cellular Biology, 21:1260-1271, Feb 2001. URL: https://doi.org/10.1128/mcb.21.4.1260-1271.2001, doi:10.1128/mcb.21.4.1260-1271.2001. This article has 97 citations and is from a domain leading peer-reviewed journal.
(iouk2001rrb1payeast media b700a353): Tatiana L. Iouk, John D. Aitchison, Shawna Maguire, and Richard W. Wozniak. Rrb1p, a yeast nuclear wd-repeat protein involved in the regulation of ribosome biosynthesis. Molecular and Cellular Biology, 21:1260-1271, Feb 2001. URL: https://doi.org/10.1128/mcb.21.4.1260-1271.2001, doi:10.1128/mcb.21.4.1260-1271.2001. This article has 97 citations and is from a domain leading peer-reviewed journal.
id: Q04225
gene_symbol: RRB1
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:559292
label: Saccharomyces cerevisiae
description: >-
RRB1 encodes an essential nucleolar WD-repeat ribosome assembly factor that
binds and chaperones ribosomal protein L3/Rpl3 during early 60S ribosomal
subunit biogenesis. Rrb1 promotes soluble, assembly-competent Rpl3 delivery to
preribosomal particles, supports 25S rRNA maturation, and is required for
normal production of free 60S subunits. Its conserved PANTHER family
(PTHR45903:SF1) includes fungal Rrb1/GRWD1-like proteins with roles in
ribosome assembly, but the yeast literature supports an Rpl3-specific
chaperone role rather than generic protein binding.
references:
- id: GO_REF:0000033
title: Annotation inferences using phylogenetic trees
findings: []
- id: GO_REF:0000043
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
findings: []
- id: GO_REF:0000044
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
findings: []
- id: PMID:10684247
title: 'The yeast nuclear pore complex: composition, architecture, and transport mechanism.'
findings:
- statement: >-
The GOA nucleolus IDA annotation traces to the Rout et al. 2000 nuclear
pore complex proteomics paper; RRB1 appears to have been identified in
nuclear/nucleolar fractions co-purifying with NPC preparations.
supporting_text: The GOA annotation uses this PMID as direct evidence for nucleolar localization.
- id: PMID:11728313
title: A yeast homolog of chromatin assembly factor 1 is involved in early ribosome assembly.
findings:
- statement: Rrb1 is associated with Rpl3 and required for proper early ribosome assembly.
supporting_text: "Rrb1p is associated with ribosomal protein L3. A fraction of Rrb1p is also found in a protein-precursor rRNA complex."
- id: PMID:14759368
title: High-definition macromolecular composition of yeast RNA-processing complexes.
findings:
- statement: High-throughput interaction data place Rrb1 in RNA-processing/ribosome-biogenesis complexes but do not define a specific molecular function beyond generic binding.
supporting_text: "Some of the pre-rRNA-processing complexes that were obtained are discrete complexes required for proper processing of the ITS2 region of the ribosomal RNA."
- id: PMID:16554755
title: Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
findings:
- statement: High-throughput complex data support physical associations but not a curatable generic protein binding core function.
supporting_text: "Global landscape of protein complexes in the yeast Saccharomyces cerevisiae."
- id: PMID:26112308
title: Co-translational capturing of nascent ribosomal proteins by their dedicated chaperones.
findings:
- statement: Rrb1 selectively captures nascent Rpl3 and functions as a dedicated ribosomal protein chaperone.
supporting_text: "Affinity purification of four chaperones (Rrb1, Syo1, Sqt1 and Yar1) selectively enriched the mRNAs encoding their specific ribosomal protein clients."
- id: PMID:37968396
title: The social and structural architecture of the yeast protein interactome.
findings:
- statement: Interactome data provide broad physical-interaction support but are too generic for accepting protein binding as the functional annotation.
supporting_text: "The social and structural architecture of the yeast protein interactome."
- id: file:yeast/RRB1/RRB1-deep-research-falcon.md
title: Falcon deep research report on RRB1
findings:
- statement: Falcon synthesis identifies Rrb1 as a nuclear/nucleolar Rpl3-handling factor required for early large-subunit biogenesis.
supporting_text: "RRB1 encodes an essential, nuclear/nucleolar WD-repeat protein (Rrb1p) that binds ribosomal protein L3 (Rpl3) and is required for early large (60S) subunit biogenesis."
- id: file:interpro/panther/PTHR45903/PTHR45903-metadata.yaml
title: PANTHER family PTHR45903 metadata
findings:
- statement: RRB1 is in the glutamate-rich WD-repeat PANTHER family, with yeast RRB1 in subfamily PTHR45903:SF1.
supporting_text: "Some family members are implicated in ribosome biogenesis, specifically in the early assembly of the 60S ribosomal subunit, by targeting ribosomal protein L3 onto precursor rRNA."
existing_annotations:
- term:
id: GO:0005730
label: nucleolus
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: Phylogenetic nucleolar localization is consistent with Rrb1's experimentally supported site of action in early 60S biogenesis.
action: ACCEPT
reason: Rrb1 is a nuclear/nucleolar WD-repeat protein and the conserved family context supports a nuclear ribosome-assembly role.
supported_by:
- reference_id: PMID:26112308
supporting_text: "Rrb1, which is a mostly nucleolar protein, binds to Rpl3"
- reference_id: file:interpro/panther/PTHR45903/PTHR45903-metadata.yaml
supporting_text: "Some family members are implicated in ribosome biogenesis"
- term:
id: GO:0042254
label: ribosome biogenesis
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: The biological-process inference is correct but should be made more specific to large ribosomal subunit biogenesis.
action: MODIFY
reason: Experimental studies show Rrb1 functions through Rpl3 in early 60S subunit assembly, not general ribosome biogenesis across both subunits.
proposed_replacement_terms:
- id: GO:0042273
label: ribosomal large subunit biogenesis
supported_by:
- reference_id: PMID:11728313
supporting_text: "Impairment of Rrb1p function results in decreased levels of free 60S ribosomal subunits."
- reference_id: file:yeast/RRB1/RRB1-deep-research-falcon.md
supporting_text: "early large (60S) subunit biogenesis"
- term:
id: GO:0005634
label: nucleus
evidence_type: IEA
original_reference_id: GO_REF:0000044
review:
summary: Nuclear localization is true but too broad given direct nucleolar evidence.
action: MODIFY
reason: The functional site is best represented by nucleolus, where early preribosomal assembly occurs and where Rrb1 is enriched.
proposed_replacement_terms:
- id: GO:0005730
label: nucleolus
supported_by:
- reference_id: PMID:26112308
supporting_text: "Rrb1, which is a mostly nucleolar protein"
- term:
id: GO:0006364
label: rRNA processing
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: Retain as a supported large-subunit biogenesis consequence of Rrb1 function.
action: ACCEPT
reason: Rrb1 depletion impairs 25S rRNA maturation, so rRNA processing is a valid process annotation, although the mechanistic core is Rpl3 chaperoning during 60S assembly.
supported_by:
- reference_id: file:yeast/RRB1/RRB1-deep-research-falcon.md
supporting_text: "including efficient 25S rRNA maturation and production of 60S subunits"
- term:
id: GO:0042254
label: ribosome biogenesis
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: The UniProt keyword mapping captures the correct pathway but is less specific than the evidence warrants.
action: MODIFY
reason: Rrb1 acts in early large ribosomal subunit biogenesis through Rpl3 rather than generic ribosome biogenesis.
proposed_replacement_terms:
- id: GO:0042273
label: ribosomal large subunit biogenesis
supported_by:
- reference_id: PMID:11728313
supporting_text: "required for proper assembly of preribosomal particles during early ribosome biogenesis, presumably by targeting L3 onto the 35S precursor rRNA"
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:14759368
review:
summary: Generic protein binding from a high-throughput complex study is not informative for Rrb1 function.
action: MARK_AS_OVER_ANNOTATED
reason: Rrb1's specific function is Rpl3 chaperoning during large-subunit biogenesis; a generic protein binding annotation should not be treated as a core molecular function.
supported_by:
- reference_id: PMID:26112308
supporting_text: "dedicated chaperone proteins recognize the N-terminal regions of ribosomal proteins"
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:16554755
review:
summary: High-throughput interaction data are consistent with complex membership but too generic for molecular-function curation.
action: MARK_AS_OVER_ANNOTATED
reason: The interactions should be interpreted in the context of Rpl3 chaperoning and 60S assembly, not as a standalone protein binding function.
supported_by:
- reference_id: PMID:26112308
supporting_text: "Rrb1 and Sqt1 interact with the very N-terminal residues of Rpl3 and Rpl10, respectively."
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:37968396
review:
summary: Interactome-derived protein binding is too broad to represent Rrb1's curated activity.
action: MARK_AS_OVER_ANNOTATED
reason: The core activity is substrate-specific ribosomal protein chaperoning; the generic term should not be accepted.
supported_by:
- reference_id: file:yeast/RRB1/RRB1-deep-research-falcon.md
supporting_text: "Rrb1 is part of the broader dedicated chaperone/co-translational capture paradigm for ribosomal proteins."
- term:
id: GO:0051082
label: unfolded protein binding
evidence_type: IDA
original_reference_id: PMID:26112308
review:
summary: The experiment supports chaperoning of nascent Rpl3, but unfolded protein binding is too generic.
action: MODIFY
reason: Rrb1 captures a specific ribosomal protein client and promotes delivery to the assembly site, which is better represented as protein carrier chaperone activity.
proposed_replacement_terms:
- id: GO:0140597
label: protein carrier chaperone
supported_by:
- reference_id: PMID:26112308
supporting_text: "Rrb1, Syo1, Sqt1 and Yar1 selectively enriched the mRNAs encoding their specific ribosomal protein clients"
- term:
id: GO:0005730
label: nucleolus
evidence_type: IDA
original_reference_id: PMID:10684247
review:
summary: Direct nucleolar localization is consistent with Rrb1's early pre-60S assembly role.
action: ACCEPT
reason: Nucleolar enrichment matches the site of early ribosome biogenesis and is supported by independent literature synthesis.
supported_by:
- reference_id: file:yeast/RRB1/RRB1-deep-research-falcon.md
supporting_text: "Rrb1 is predominantly nuclear with strong nucleolar enrichment"
- term:
id: GO:0042254
label: ribosome biogenesis
evidence_type: IMP
original_reference_id: PMID:11728313
review:
summary: The mutant phenotype supports ribosome biogenesis, but the more precise process is large subunit biogenesis.
action: MODIFY
reason: Loss of Rrb1 specifically reduces free 60S subunits and disrupts early preribosomal assembly through Rpl3.
proposed_replacement_terms:
- id: GO:0042273
label: ribosomal large subunit biogenesis
supported_by:
- reference_id: PMID:11728313
supporting_text: "Impairment of Rrb1p function results in decreased levels of free 60S ribosomal subunits."
core_functions:
- description: >-
Rrb1 is a dedicated protein carrier chaperone for ribosomal protein L3/Rpl3.
It captures or stabilizes Rpl3 before incorporation into early pre-60S
particles, thereby supporting 25S rRNA maturation and large ribosomal subunit
biogenesis in the nucleolus.
molecular_function:
id: GO:0140597
label: protein carrier chaperone
directly_involved_in:
- id: GO:0042273
label: ribosomal large subunit biogenesis
- id: GO:0006364
label: rRNA processing
locations:
- id: GO:0005730
label: nucleolus
supported_by:
- reference_id: PMID:11728313
supporting_text: "Rrb1p is associated with ribosomal protein L3."
- reference_id: PMID:26112308
supporting_text: "Rrb1 and Sqt1 recognize the N termini of Rpl3 and Rpl10"
- reference_id: file:yeast/RRB1/RRB1-deep-research-falcon.md
supporting_text: "essential, nuclear/nucleolar WD-repeat protein (Rrb1p) that binds ribosomal protein L3"
proposed_new_terms: []
suggested_questions:
- question: What is the direct binding interface and stoichiometry of the yeast Rrb1-Rpl3 complex during co-translational capture?
experts:
- ribosome biogenesis experts
- structural biologists
- question: Does Rrb1 hand Rpl3 directly to pre-60S particles in the nucleolus, or through an intermediate import or assembly factor?
experts:
- yeast ribosome assembly researchers
suggested_experiments:
- experiment_type: structural biochemistry
description: Reconstitute the yeast Rrb1-Rpl3 N-terminal peptide or full-client complex and solve its structure by cryo-EM, crystallography, or crosslinking-MS to define the chaperone-client interface.
hypothesis: Rrb1 recognizes a defined Rpl3 segment that is later buried in the 60S subunit and shields it before assembly.
- experiment_type: pulse-chase ribosome assembly assay
description: Combine acute RRB1 depletion with Rpl3 pulse labeling, nuclear import assays, and pre-60S immunoprecipitation to test whether Rrb1 primarily affects Rpl3 solubility, nuclear import, or loading onto preribosomes.
hypothesis: Rrb1 loss reduces productive Rpl3 loading onto early pre-60S particles before detectable global rRNA-processing defects.