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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: Q99216
• Protein Description: RecName: Full=Pre-rRNA-processing protein PNO1; AltName: Full=Partner of NOB1; AltName: Full=Ribosomal RNA-processing protein 20;
• Gene Information: Name=PNO1; Synonyms=DIM2, RRP20; OrderedLocusNames=YOR145C; ORFNames=O3513, YOR3513C;
• Organism (full): Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
• Protein Family: Belongs to the PNO1 family. .
• Key Domains: KH-I_PNO1_first. (IPR055212); KH_dom_type_1_sf. (IPR036612); KH_PNO1_2nd. (IPR055211); KRR1-like_KH1. (IPR041174); KH_KRR1_1st (PF17903)

MANDATORY VERIFICATION STEPS:

1. Check if the gene symbol "PNO1" matches the protein description above
2. Verify the organism is correct: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
3. Check if protein family/domains align with what you find in literature
4. If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

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

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'PNO1' 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 PNO1 (gene ID: PNO1, UniProt: Q99216) 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this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.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: Q99216
• Protein Description: RecName: Full=Pre-rRNA-processing protein PNO1; AltName: Full=Partner of NOB1; AltName: Full=Ribosomal RNA-processing protein 20;
• Gene Information: Name=PNO1; Synonyms=DIM2, RRP20; OrderedLocusNames=YOR145C; ORFNames=O3513, YOR3513C;
• Organism (full): Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
• Protein Family: Belongs to the PNO1 family. .
• Key Domains: KH-I_PNO1_first. (IPR055212); KH_dom_type_1_sf. (IPR036612); KH_PNO1_2nd. (IPR055211); KRR1-like_KH1. (IPR041174); KH_KRR1_1st (PF17903)

MANDATORY VERIFICATION STEPS:

1. Check if the gene symbol "PNO1" matches the protein description above
2. Verify the organism is correct: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
3. Check if protein family/domains align with what you find in literature
4. If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

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

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'PNO1' 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 PNO1 (gene ID: PNO1, UniProt: Q99216) in yeast.

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

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

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

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

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

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

Research Report: Functional Annotation of Saccharomyces cerevisiae PNO1 (Dim2/Rrp20)

0) Target identity verification (mandatory)

The research target is PNO1 from Saccharomyces cerevisiae S288c (UniProt Q99216), also known in yeast literature as Dim2 and Rrp20 and encoded by YOR145C. A yeast primary study explicitly identifies DIM2 (ORF YOR145C) as a KH-domain ribosome biogenesis factor required for pre-rRNA processing and pre-40S export, matching the UniProt description (pre‑rRNA‑processing protein; “Partner of Nob1”) and the stated family/domain architecture (KH-type RNA-binding domains). (vanrobays2008torregulatesthe pages 1-2)

Because “PNO1” is also used for homologs in other eukaryotes (including human cancer literature), only yeast-specific sources and conserved-mechanism studies with clear organism context are used here for functional claims about Q99216/YOR145C. (vanrobays2008torregulatesthe pages 1-2, woolls2011rolesofdim2 pages 1-2)

1) Key concepts, definitions, and current understanding

1.1 Ribosome biogenesis context (SSU processome → pre-40S → mature 40S)

In yeast, small ribosomal subunit (40S) biogenesis begins cotranscriptionally on the 35S pre-rRNA within a large nucleolar precursor called the 90S/SSU processome, which is remodeled to release a pre-40S particle that is exported to the cytoplasm for final maturation. General quantitative context: yeast cells can synthesize ~2000 ribosomes/minute; eukaryotic ribosomes contain 79 ribosomal proteins; assembly requires >200 transient assembly factors. (chakermargot2018assemblyofthe pages 1-2, parker2024thekinaserio1 pages 1-2)

1.2 What Pno1/Dim2 is

Pno1/Dim2 (PNO1/DIM2/RRP20) is a conserved KH-domain-containing ribosome biogenesis factor that binds pre-rRNA and acts at multiple stages of SSU maturation—from early steps associated with the SSU processome/90S particle to late cytoplasmic pre-40S maturation. (vanrobays2008torregulatesthe pages 1-2, sturm2017interdependentactionof pages 1-2)

Key definitional points:
- KH domain: an RNA-binding fold; in yeast Pno1/Dim2 the KH motif is critical for pre-rRNA association, with residues in the KH region (including the conserved G207) required for binding and proper processing. (vanrobays2008torregulatesthe pages 1-2, knox2010regulationofthea pages 57-61)
- ITS1 (internal transcribed spacer 1): Pno1/Dim2 binds the 5′ end of ITS1 (often discussed as the D–A2 region in yeast processing maps), positioning it at the SSU/ITS1 junction relevant for small-subunit processing and later cleavage events. (vanrobays2008torregulatesthe pages 1-2)

1.3 Primary molecular function (what Pno1/Dim2 “does”)

PNO1 is not an enzyme catalyzing a chemical reaction; rather, it is an RNA-binding assembly factor and checkpoint/regulatory factor.

The best-supported primary function is that Pno1/Dim2:
1) binds pre-rRNA (ITS1 region) via its KH domain to promote proper SSU assembly/processing, and
2) partners with and regulates the endonuclease Nob1 during the essential final step of 18S rRNA 3′-end formation (D-site cleavage of 20S pre-rRNA → mature 18S), including controlling access/positioning and coupling cleavage to downstream release/quality control. (woolls2011rolesofdim2 pages 1-2, scaiola2018structureofa pages 1-2)

Mechanistic evidence in yeast indicates Dim2 physically interacts with Nob1; this interaction increases Nob1’s RNA affinity and is required for efficient D-site cleavage. Disrupting the Dim2–Nob1 interaction causes accumulation of pre-ribosomes containing Nob1 and 20S pre-rRNA, consistent with a block in final 18S maturation. (woolls2011rolesofdim2 pages 1-2)

2) Molecular mechanism and pathway placement

2.1 Early nucleolar/cotranscriptional roles: SSU processome/90S

A yeast study characterizes DIM2 as required for cotranscriptional ribosome assembly and early nucleolar pre-rRNA processing; Dim2 binds pre-rRNAs at the 5′ end of ITS1 via its KH domain. A single KH-motif point mutation G207A inhibits pre-rRNA processing similarly to DIM2 depletion, demonstrating that RNA binding through the KH domain is functionally important. (vanrobays2008torregulatesthe pages 1-2)

A structural/mechanistic study further places Dim2/Pno1 in two successive stages of SSU biogenesis: it acts first on the 90S particle and then relocates to the pre-40S platform after remodeling events (including U3 snoRNP removal) during the 90S→pre‑40S transition. (sturm2017interdependentactionof pages 1-2)

2.2 Nuclear export and growth-control coupling (TOR)

Dim2/Pno1 is a nucleocytoplasmic shuttling factor with a conserved nuclear export sequence (NES) required for efficient pre-40S export. Export can be uncoupled experimentally from some early processing phenotypes using dominant-negative constructs.

Key yeast findings:
- Dim2 and the export factor Rrp12 become nucleolar-sequestered under stress conditions, and this relocalization is TOR-dependent; rapamycin triggers nucleolar entrapment. (vanrobays2008torregulatesthe pages 1-2, vanrobays2008torregulatesthe pages 5-7)
- A DNES construct causes a strong pre-40S export defect and can phenocopy depletion for growth and A1–A2 processing defects, while conservative leucine substitutions did not disrupt export in tested assays—supporting that export depends on the NES architecture rather than any single leucine. (vanrobays2008torregulatesthe pages 5-7)

These observations connect Pno1/Dim2 function to nutrient-responsive regulation of ribosome production through TOR signaling. (vanrobays2008torregulatesthe pages 1-2, vanrobays2008torregulatesthe pages 7-8)

2.3 Late cytoplasmic maturation: structural “placeholder” and Nob1 regulation

Cryo-EM structures of cytoplasmic yeast pre-40S place Pno1 on the SSU platform near the mRNA binding channel, and show that it occupies the binding site for the ribosomal protein Rps26/eS26, thereby preventing premature Rps26 incorporation. This is consistent with Pno1 serving as a late-stage placeholder/checkpoint factor and provides a structural rationale for why Pno1 must be remodeled or released for final maturation. (scaiola2018structureofa media 392eda28, scaiola2018structureofa pages 1-2)

Biochemically, Dim2’s KH-like domain can be “repurposed” as a protein–protein interaction surface: the Dim2–Nob1 interaction maps to the canonical KH-like RNA-binding surface of Dim2, and disrupting it blocks maturation at the 20S→18S step. (woolls2011rolesofdim2 pages 1-2)

2.4 Rio1-mediated licensing checkpoint (current model)

A central modern concept is that Rio1, together with Nob1 and Pno1, establishes a quality-control checkpoint preventing immature/misprocessed 40S subunits from entering the translating pool.

Mechanistic model from recent yeast work:
- Pre-40S containing 20S pre-rRNA is bound by Nob1 and Pno1; Pno1 helps stabilize Nob1 and the pair blocks mRNA recruitment and Rps26 binding, preventing translation initiation. (parker2024thekinaserio1 pages 1-2)
- Nob1 cleaves the 3′ end of 18S rRNA (D-site cleavage) to convert 20S to mature 18S.
- Rio1 then removes both Nob1 and Pno1, licensing the nascent 40S for translation and enabling Rps26 binding. (parker2024thekinaserio1 pages 1-2)

A key “precision” statistic from this framework is that retention of as few as 3 precursor nucleotides at the 18S 3′ end is incompatible with yeast viability, emphasizing stringent QC at this step. (parker2024thekinaserio1 pages 1-2)

3) Recent developments (prioritizing 2023–2024)

3.1 2023: Quality control synthesis (authoritative review)

A 2023 review synthesizes evidence that a Rio1-dependent QC mechanism ensures only ribosomes with precise 18S rRNA cleavage are licensed to translate, and that Pno1 (Dim2) and Nob1 are central to this checkpoint. The review notes that weakening Pno1 binding can bypass the checkpoint, allowing ribosomes with uncleaved 20S pre-rRNA or miscleaved 18S rRNA to enter translation, where they cause translation defects (e.g., collisions/errors). (parker2023qualitycontrolensures pages 10-12)

Citation:
- Parker MD, Karbstein K. Quality control ensures fidelity in ribosome assembly and cellular health. J Cell Biol. Feb 2023. https://doi.org/10.1083/jcb.202209115 (parker2023qualitycontrolensures pages 10-12)

3.2 2024: Quantitative miscleavage and collision-dependent decay (primary study)

A 2024 yeast study directly quantifies how bypassing the Rio1/Pno1 checkpoint changes the abundance of miscleaved 18S rRNA:
- WT: 1.9% miscleaved 18S
- Pno1-KKKF checkpoint-bypass allele: 2.5% miscleaved 18S

The study further reports deep sequencing metrics (~2.8–4.5 million reads/sample, with 96–99% mapping to the 3′ end region analyzed) and multiple biological replicates for key assays. Miscleaved ribosomes that enter translation are slowed and induce ribosome collisions, leading to decay pathways that remove these altered ribosomes. (parker2024thekinaserio1 pages 15-17)

Citation:
- Parker MD et al. The kinase Rio1 and a ribosome collision-dependent decay pathway survey the integrity of 18S rRNA cleavage. PLOS Biology. Apr 2024. https://doi.org/10.1371/journal.pbio.3001767 (parker2024thekinaserio1 pages 15-17)

3.3 2023: Structural checkpointing via ribosomal protein cluster assembly

A 2023 cryo-EM study examined SSU precursors from yeast mutants affecting the S0-cluster (rpS0/rpS2/rpS21) and concluded that S0-cluster formation enables initial recruitment of Nob1 and promotes hierarchical rRNA folding events, including central pseudoknot maturation. The work discusses that factors such as Pno1 are retained in these precursor states, helping place Pno1 into an updated, structure-based maturation trajectory for cytoplasmic checkpoints. (poll2023impactofthe pages 1-5)

Citation:
- Pöll G et al. Impact of the yeast S0/uS2-cluster ribosomal protein rpS21/eS21 on rRNA folding and the architecture of small ribosomal subunit precursors. Jan 2023 (bioRxiv/PLOS ONE record as retrieved). https://doi.org/10.1101/2023.01.18.524556 (poll2023impactofthe pages 1-5)

4) Cellular localization and where Pno1/Dim2 acts

4.1 Compartmentalization across the maturation pathway

Yeast Dim2/Pno1 acts in both:
- the nucleolus/nucleus (early SSU processome/cotranscriptional assembly; stress/TOR-dependent sequestration), and
- the cytoplasm (pre‑40S late maturation; regulation of Nob1 cleavage; Rio1-controlled release). (vanrobays2008torregulatesthe pages 1-2, parker2024thekinaserio1 pages 1-2)

4.2 TOR-regulated redistribution

Dim2 and Rrp12 relocalize to the nucleolus under stress and with rapamycin in a TOR-dependent manner, supporting a model in which nutrient signaling modulates the subcellular trafficking and/or availability of pre-40S export/maturation factors. (vanrobays2008torregulatesthe pages 5-7, vanrobays2008torregulatesthe pages 8-10)

4.3 Export signal requirement

Dim2 contains a C-terminal NES required for efficient pre-40S export; deletion/obliteration can cause severe export phenotypes (including dominant-negative effects), underscoring that its spatial trafficking is integral to function. (vanrobays2008torregulatesthe pages 5-7)

5) Interaction partners and complexes

Key interactors supported by yeast literature:
- Nob1: direct binding partner; interaction promotes/controls Nob1 activity and affects 20S→18S maturation. (woolls2011rolesofdim2 pages 1-2)
- Rio2: implicated in early cytoplasmic complexes with Pno1/Nob1 immediately after export (model supported by in vitro interactions and pathway logic). (turowski2014rio1mediatesatpdependent pages 7-8)
- Rio1: binds late pre-40S particles shortly before cleavage and removes Pno1/Nob1 to license translation; Rio1 inactivity impairs release of Pno1/Nob1 from late intermediates. (cerezo2019maturationofpre‐40s pages 4-5, parker2024thekinaserio1 pages 1-2)
- Rrp12: linked to export and shares TOR-regulated nucleolar sequestration with Dim2. (vanrobays2008torregulatesthe pages 5-7)

6) Real-world applications and implementations

Although PNO1 is not a classical “biotech target” in yeast, it is widely used in real experimental implementations as a node to interrogate ribosome assembly, export, and quality control:

1) Conditional essential gene perturbation: Dim2 is essential; strains with regulated DIM2 expression (e.g., galactose-inducible or tet-off designs) are used to create controlled blocks in SSU maturation and to map consequences on rRNA processing/export. (woolls2011rolesofdim2 pages 4-5, vanrobays2008torregulatesthe pages 1-2)

2) Readouts for rRNA processing pathway diagnostics:
- Early processing defects: KH-domain perturbation (e.g., G207A) can block A1/A2 cleavages and yield accumulation of 22S pre-rRNA. (vanrobays2008torregulatesthe pages 8-10)
- Late maturation defects: Dim2–Nob1 interaction mutants accumulate 20S (and other intermediates such as 21S/23S) and stall final 18S 3′ end formation. (woolls2011rolesofdim2 pages 1-2, woolls2011rolesofdim2 pages 4-5)

3) Nuclear export assays and signaling integration:
- Export defects induced by NES deletion constructs (DNES) provide a tool to isolate nuclear export contributions from early processing contributions. (vanrobays2008torregulatesthe pages 5-7)
- TOR/rapamycin-induced nucleolar entrapment provides a practical linkage between nutrient signaling and ribosome biogenesis factor distribution. (vanrobays2008torregulatesthe pages 5-7)

4) Ribosome QC and translation fidelity research (2023–2024 focus):
- Pno1 checkpoint-bypass alleles allow controlled release of misprocessed ribosomes into translation, enabling direct study of collision-dependent decay and the cellular consequences of ribosome heterogeneity. (parker2024thekinaserio1 pages 15-17, parker2023qualitycontrolensures pages 10-12)

7) Relevant statistics and data (recent and/or authoritative)

7.1 System-level ribosome biogenesis numbers

• ~2000 ribosomes/min synthesized in rapidly growing yeast. (chakermargot2018assemblyofthe pages 1-2)
• Eukaryotic ribosome contains 4 rRNAs and 79 proteins; assembly uses >200 transient assembly factors. (chakermargot2018assemblyofthe pages 1-2, parker2024thekinaserio1 pages 1-2)
• An estimate from proteomics-based reviews: ~200 proteins in the small subunit assembly machinery, comprising ~20% of essential yeast proteins. (karbstein2011insidethe40s pages 1-2)

7.2 Pno1/Rio1 QC quantitative outcomes (2024)

• Miscleaved 18S rRNA fraction increases from 1.9% (WT) to 2.5% (Pno1-KKKF) when QC is bypassed. (parker2024thekinaserio1 pages 15-17)
• Sequencing depth in those assays: ~2.8–4.5 million reads/sample, with 96–99% mapping to the analyzed 18S 3′-end region. (parker2024thekinaserio1 pages 15-17)

7.3 Mutational/phenotype quantitation (export/processing)

• A single KH-motif mutation G207A can cause a severe growth impact (~3.5-fold growth impact as reported) and inhibits pre-rRNA processing similarly to DIM2 depletion. (vanrobays2008torregulatesthe pages 1-2)
• NES deletion constructs can induce rapid and strong export defects within ~1 hour in the referenced assay context. (vanrobays2008torregulatesthe pages 7-8)

8) Expert opinions and analysis (authoritative synthesis)

Two themes emerge from authoritative sources and recent primary data:

1) PNO1/DIM2 integrates structural assembly with enzymatic timing. Structural placement of Pno1 near the mRNA channel and at the Rps26 site, and biochemical evidence that it modulates Nob1’s substrate interactions, support a model in which Pno1 prevents premature translation engagement and coordinates the final rRNA processing step with acquisition of translation competence. (scaiola2018structureofa media 392eda28, woolls2011rolesofdim2 pages 1-2)

2) The late 40S assembly checkpoint is a fidelity gate with measurable error rates. The 2024 quantification of miscleavage, and the observation that altered ribosomes can enter translation but trigger collisions/decay, supports a modern view in which assembly QC is not purely binary but tunes the probability of defective ribosomes entering the translating pool, with Rio1/Pno1 as key determinants of that stringency. (parker2024thekinaserio1 pages 15-17, parker2023qualitycontrolensures pages 10-12)

9) Visual evidence from structural work (figure-based)

Cryo-EM evidence places Pno1 on the cytoplasmic pre-40S platform near the mRNA channel and supports its role as an Rps26-site placeholder and Nob1 regulator. (scaiola2018structureofa media 392eda28, scaiola2018structureofa media 37cb333c)

10) Summary of functional annotation (yeast PNO1 / UniProt Q99216)

• Molecular function: KH-domain RNA-binding ribosome assembly factor; regulates and partners with Nob1 for final 18S 3′-end maturation; acts as a late-stage placeholder that blocks Rps26 incorporation and translation entry until licensing by Rio1. (woolls2011rolesofdim2 pages 1-2, scaiola2018structureofa media 392eda28, parker2024thekinaserio1 pages 1-2)
• Biological process: SSU processome maturation; 90S→pre-40S transition; pre-40S export; cytoplasmic 20S→18S processing; quality-control gating for translation competence. (sturm2017interdependentactionof pages 1-2, vanrobays2008torregulatesthe pages 5-7, parker2024thekinaserio1 pages 15-17)
• Cellular localization: Nucleolus/nucleus and cytoplasm; shuttling factor with TOR-regulated redistribution and NES-dependent export functionality. (vanrobays2008torregulatesthe pages 5-7, vanrobays2008torregulatesthe pages 1-2)

Structured summary table

Table: This table summarizes the experimentally supported functions, mechanisms, complexes, localization, and quality-control roles of Saccharomyces cerevisiae PNO1/Dim2/Rrp20. It integrates core yeast studies and recent QC-focused work, including structural placement and quantitative miscleavage data.

Key references (publication date and URL)

• Vanrobays E, et al. Oct 2008. TOR regulates the subcellular distribution of DIM2… RNA. https://doi.org/10.1261/rna.1176708 (vanrobays2008torregulatesthe pages 1-2)
• Woolls HA, Lamanna AC, Karbstein K. Jan 2011. Roles of Dim2 in Ribosome Assembly. J Biol Chem. https://doi.org/10.1074/jbc.m110.191494 (woolls2011rolesofdim2 pages 1-2)
• Sturm M, et al. Dec 2017. Interdependent action of KH domain proteins Krr1 and Dim2… Nat Commun. https://doi.org/10.1038/s41467-017-02199-4 (sturm2017interdependentactionof pages 1-2)
• Scaiola A, et al. Apr 2018. Structure of a eukaryotic cytoplasmic pre-40S ribosomal subunit. EMBO J. https://doi.org/10.15252/embj.201798499 (scaiola2018structureofa pages 1-2)
• Chaker-Margot M. Apr 2018. Assembly of the small ribosomal subunit in yeast: mechanism and regulation. RNA. https://doi.org/10.1261/rna.066985.118 (chakermargot2018assemblyofthe pages 1-2)
• Parker MD, Karbstein K. Feb 2023. Quality control ensures fidelity in ribosome assembly and cellular health. J Cell Biol. https://doi.org/10.1083/jcb.202209115 (parker2023qualitycontrolensures pages 10-12)
• Pöll G, et al. Jan 2023. Impact of the yeast S0/uS2-cluster… (record retrieved). https://doi.org/10.1101/2023.01.18.524556 (poll2023impactofthe pages 1-5)
• Parker MD, et al. Apr 2024. The kinase Rio1 and a ribosome collision-dependent decay pathway survey the integrity of 18S rRNA cleavage. PLOS Biology. https://doi.org/10.1371/journal.pbio.3001767 (parker2024thekinaserio1 pages 15-17)

References

1. (vanrobays2008torregulatesthe pages 1-2): Emmanuel Vanrobays, Alexis Leplus, Yvonne N. Osheim, Ann L. Beyer, Ludivine Wacheul, and Denis L.J. Lafontaine. Tor regulates the subcellular distribution of dim2, a kh domain protein required for cotranscriptional ribosome assembly and pre-40s ribosome export. RNA, 14 10:2061-73, Oct 2008. URL: https://doi.org/10.1261/rna.1176708, doi:10.1261/rna.1176708. This article has 69 citations and is from a domain leading peer-reviewed journal.

2. (woolls2011rolesofdim2 pages 1-2): Heather A. Woolls, Allison C. Lamanna, and Katrin Karbstein. Roles of dim2 in ribosome assembly. Journal of Biological Chemistry, 286:2578-2586, Jan 2011. URL: https://doi.org/10.1074/jbc.m110.191494, doi:10.1074/jbc.m110.191494. This article has 58 citations and is from a domain leading peer-reviewed journal.

3. (chakermargot2018assemblyofthe pages 1-2): Malik Chaker-Margot. Assembly of the small ribosomal subunit in yeast: mechanism and regulation. RNA, 24:881-891, Apr 2018. URL: https://doi.org/10.1261/rna.066985.118, doi:10.1261/rna.066985.118. This article has 34 citations and is from a domain leading peer-reviewed journal.

4. (parker2024thekinaserio1 pages 1-2): Melissa D. Parker, Elise S. Brunk, Adam J. Getzler, and Katrin Karbstein. The kinase rio1 and a ribosome collision-dependent decay pathway survey the integrity of 18s rrna cleavage. PLOS Biology, 22:e3001767, Apr 2024. URL: https://doi.org/10.1371/journal.pbio.3001767, doi:10.1371/journal.pbio.3001767. This article has 14 citations and is from a highest quality peer-reviewed journal.

5. (sturm2017interdependentactionof pages 1-2): Miriam Sturm, Jingdong Cheng, Jochen Baßler, Roland Beckmann, and Ed Hurt. Interdependent action of kh domain proteins krr1 and dim2 drive the 40s platform assembly. Nature Communications, Dec 2017. URL: https://doi.org/10.1038/s41467-017-02199-4, doi:10.1038/s41467-017-02199-4. This article has 45 citations and is from a highest quality peer-reviewed journal.

6. (knox2010regulationofthea pages 57-61): AA Knox. Regulation of the u3 small subunit processome and associated rna-binding proteins. Unknown journal, 2010.

7. (scaiola2018structureofa pages 1-2): Alain Scaiola, Cohue Peña, Melanie Weisser, Daniel Böhringer, Marc Leibundgut, Purnima Klingauf‐Nerurkar, Stefan Gerhardy, Vikram Govind Panse, and Nenad Ban. Structure of a eukaryotic cytoplasmic pre‐40s ribosomal subunit. The EMBO Journal, Apr 2018. URL: https://doi.org/10.15252/embj.201798499, doi:10.15252/embj.201798499. This article has 110 citations.

8. (vanrobays2008torregulatesthe pages 5-7): Emmanuel Vanrobays, Alexis Leplus, Yvonne N. Osheim, Ann L. Beyer, Ludivine Wacheul, and Denis L.J. Lafontaine. Tor regulates the subcellular distribution of dim2, a kh domain protein required for cotranscriptional ribosome assembly and pre-40s ribosome export. RNA, 14 10:2061-73, Oct 2008. URL: https://doi.org/10.1261/rna.1176708, doi:10.1261/rna.1176708. This article has 69 citations and is from a domain leading peer-reviewed journal.

9. (vanrobays2008torregulatesthe pages 7-8): Emmanuel Vanrobays, Alexis Leplus, Yvonne N. Osheim, Ann L. Beyer, Ludivine Wacheul, and Denis L.J. Lafontaine. Tor regulates the subcellular distribution of dim2, a kh domain protein required for cotranscriptional ribosome assembly and pre-40s ribosome export. RNA, 14 10:2061-73, Oct 2008. URL: https://doi.org/10.1261/rna.1176708, doi:10.1261/rna.1176708. This article has 69 citations and is from a domain leading peer-reviewed journal.

10. (scaiola2018structureofa media 392eda28): Alain Scaiola, Cohue Peña, Melanie Weisser, Daniel Böhringer, Marc Leibundgut, Purnima Klingauf‐Nerurkar, Stefan Gerhardy, Vikram Govind Panse, and Nenad Ban. Structure of a eukaryotic cytoplasmic pre‐40s ribosomal subunit. The EMBO Journal, Apr 2018. URL: https://doi.org/10.15252/embj.201798499, doi:10.15252/embj.201798499. This article has 110 citations.

11. (parker2023qualitycontrolensures pages 10-12): Melissa D. Parker and Katrin Karbstein. Quality control ensures fidelity in ribosome assembly and cellular health. The Journal of Cell Biology, Feb 2023. URL: https://doi.org/10.1083/jcb.202209115, doi:10.1083/jcb.202209115. This article has 29 citations.

12. (parker2024thekinaserio1 pages 15-17): Melissa D. Parker, Elise S. Brunk, Adam J. Getzler, and Katrin Karbstein. The kinase rio1 and a ribosome collision-dependent decay pathway survey the integrity of 18s rrna cleavage. PLOS Biology, 22:e3001767, Apr 2024. URL: https://doi.org/10.1371/journal.pbio.3001767, doi:10.1371/journal.pbio.3001767. This article has 14 citations and is from a highest quality peer-reviewed journal.

13. (poll2023impactofthe pages 1-5): Gisela Pöll, Joachim Griesenbeck, Herbert Tschochner, and Philipp Milkereit. Impact of the yeast s0/us2-cluster ribosomal protein rps21/es21 on rrna folding and the architecture of small ribosomal subunit precursors. PLOS ONE, Jan 2023. URL: https://doi.org/10.1101/2023.01.18.524556, doi:10.1101/2023.01.18.524556. This article has 3 citations and is from a peer-reviewed journal.

14. (vanrobays2008torregulatesthe pages 8-10): Emmanuel Vanrobays, Alexis Leplus, Yvonne N. Osheim, Ann L. Beyer, Ludivine Wacheul, and Denis L.J. Lafontaine. Tor regulates the subcellular distribution of dim2, a kh domain protein required for cotranscriptional ribosome assembly and pre-40s ribosome export. RNA, 14 10:2061-73, Oct 2008. URL: https://doi.org/10.1261/rna.1176708, doi:10.1261/rna.1176708. This article has 69 citations and is from a domain leading peer-reviewed journal.

15. (turowski2014rio1mediatesatpdependent pages 7-8): Tomasz W. Turowski, Simon Lebaron, Elodie Zhang, Lauri Peil, Tatiana Dudnakova, Elisabeth Petfalski, Sander Granneman, Juri Rappsilber, and David Tollervey. Rio1 mediates atp-dependent final maturation of 40s ribosomal subunits. Nucleic Acids Research, 42:12189-12199, Oct 2014. URL: https://doi.org/10.1093/nar/gku878, doi:10.1093/nar/gku878. This article has 114 citations and is from a highest quality peer-reviewed journal.

16. (cerezo2019maturationofpre‐40s pages 4-5): Emilie Cerezo, Célia Plisson‐Chastang, Anthony K. Henras, Simon Lebaron, Pierre‐Emmanuel Gleizes, Marie‐Françoise O'Donohue, Yves Romeo, and Yves Henry. Maturation of pre‐40s particles in yeast and humans. Wiley Interdisciplinary Reviews: RNA, Nov 2019. URL: https://doi.org/10.1002/wrna.1516, doi:10.1002/wrna.1516. This article has 56 citations.

17. (woolls2011rolesofdim2 pages 4-5): Heather A. Woolls, Allison C. Lamanna, and Katrin Karbstein. Roles of dim2 in ribosome assembly. Journal of Biological Chemistry, 286:2578-2586, Jan 2011. URL: https://doi.org/10.1074/jbc.m110.191494, doi:10.1074/jbc.m110.191494. This article has 58 citations and is from a domain leading peer-reviewed journal.

18. (karbstein2011insidethe40s pages 1-2): Katrin Karbstein. Inside the 40s ribosome assembly machinery. Current opinion in chemical biology, 15 5:657-63, Oct 2011. URL: https://doi.org/10.1016/j.cbpa.2011.07.023, doi:10.1016/j.cbpa.2011.07.023. This article has 76 citations and is from a peer-reviewed journal.

19. (scaiola2018structureofa media 37cb333c): Alain Scaiola, Cohue Peña, Melanie Weisser, Daniel Böhringer, Marc Leibundgut, Purnima Klingauf‐Nerurkar, Stefan Gerhardy, Vikram Govind Panse, and Nenad Ban. Structure of a eukaryotic cytoplasmic pre‐40s ribosomal subunit. The EMBO Journal, Apr 2018. URL: https://doi.org/10.15252/embj.201798499, doi:10.15252/embj.201798499. This article has 110 citations.

20. (knox2010regulationoftheb pages 57-61): AA Knox. Regulation of the u3 small subunit processome and associated rna-binding proteins. Unknown journal, 2010.

Citations

1. vanrobays2008torregulatesthe pages 1-2
2. sturm2017interdependentactionof pages 1-2
3. vanrobays2008torregulatesthe pages 5-7
4. parker2023qualitycontrolensures pages 10-12
5. poll2023impactofthe pages 1-5
6. vanrobays2008torregulatesthe pages 8-10
7. chakermargot2018assemblyofthe pages 1-2
8. vanrobays2008torregulatesthe pages 7-8
9. scaiola2018structureofa pages 1-2
10. knox2010regulationofthea pages 57-61
11. knox2010regulationoftheb pages 57-61
12. https://doi.org/10.1083/jcb.202209115
13. https://doi.org/10.1371/journal.pbio.3001767
14. https://doi.org/10.1101/2023.01.18.524556
15. https://doi.org/10.1261/rna.1176708;
16. https://doi.org/10.1074/jbc.m110.191494
17. https://doi.org/10.1261/rna.1176708
18. https://doi.org/10.1038/s41467-017-02199-4
19. https://doi.org/10.1093/nar/gku878
20. https://doi.org/10.15252/embj.201798499
21. https://doi.org/10.1002/wrna.1516
22. https://doi.org/10.1083/jcb.202209115;
23. https://doi.org/10.1261/rna.066985.118
24. https://doi.org/10.1261/rna.1176708,
25. https://doi.org/10.1074/jbc.m110.191494,
26. https://doi.org/10.1261/rna.066985.118,
27. https://doi.org/10.1371/journal.pbio.3001767,
28. https://doi.org/10.1038/s41467-017-02199-4,
29. https://doi.org/10.15252/embj.201798499,
30. https://doi.org/10.1083/jcb.202209115,
31. https://doi.org/10.1101/2023.01.18.524556,
32. https://doi.org/10.1093/nar/gku878,
33. https://doi.org/10.1002/wrna.1516,
34. https://doi.org/10.1016/j.cbpa.2011.07.023,