GO:0043023 ribosomal large subunit binding: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0043023 (ribosomal large subunit binding) is a molecular function defined as binding to a large ribosomal subunit.
• It is central to ribosome biogenesis, translation initiation, and quality control of the 60S subunit in eukaryotes and the 50S subunit in bacteria.
• Key proteins include Gcn2, UFM1 E3 ligase components (UFL1, UFBP1, UFM1), NPM1, and bacterial initiation factor IF3.
• Dysregulation of large subunit binding is linked to ribosomopathies, cancer, and neurodegenerative stress responses.
• CRISPR knockout, point mutation, knock-in, and overexpression models enable causal dissection of large subunit binding factors.
• EDITGENE provides end-to-end CRISPR services to study GO:0043023-related genes in disease and translation research.
Description
GO:0043023, ribosomal large subunit binding, is a molecular function that describes the physical interaction of a protein or complex with the large ribosomal subunit. This function is essential for ribosome assembly, translation initiation, and the recycling of ribosomal subunits from the endoplasmic reticulum (ER). Researchers study this term to understand how cells regulate protein synthesis under stress, how ribosome quality control operates, and how mutations in binding factors contribute to human disease. The large ribosomal subunit, known as the 60S in eukaryotes and the 50S in bacteria, is a massive ribonucleoprotein complex that catalyzes peptide bond formation. Proteins that bind this subunit often act as chaperones, assembly factors, or regulatory kinases that monitor ribosome status. Because ribosomal large subunit binding is a hub for cellular stress signaling and ribosome homeostasis, it is a high-value target for functional genomics and drug discovery.
ribosomal large subunit binding At A Glance
| GO ID | GO:0043023 |
|---|---|
| GO term | ribosomal large subunit binding |
| Ontology | molecular_function |
| Synonym | none |
| Major function | Binding to the large ribosomal subunit (60S in eukaryotes, 50S in bacteria) |
| Related processes | Ribosome biogenesis, translation initiation, ribosome recycling, stress response |
| Example proteins | Gcn2, UFL1, UFBP1, UFM1, NPM1, IF3 |
| Disease relevance | Ribosomopathies, cancer, neurodegeneration, ER stress |
| Research methods | CRISPR KO/KI, Ribo-seq, proteomics, cryo-EM, imaging |
What Is GO:0043023?
According to the Gene Ontology, GO:0043023 is defined as binding to a large ribosomal subunit. In other words, it is the molecular function of selectively and non-covalently interacting with the large subunit of a ribosome, which in eukaryotes is the 60S subunit and in bacteria is the 50S subunit. This binding can be transient, as in assembly factors, or stable, as in ribosomal proteins, and it is often a prerequisite for downstream events such as subunit joining, translocation, or recycling.
Why Is ribosomal large subunit binding Important in Cell Biology?
Ribosomal large subunit binding is important because it governs the assembly, quality control, and recycling of the cell's protein synthesis machinery. Defects in this function can lead to impaired translation, activation of stress pathways, and human diseases such as ribosomopathies and cancer. Understanding GO:0043023 helps researchers identify therapeutic targets and interpret genetic variants in ribosome-related genes.
• Controls translation initiation and ribosome assembly.
• Mediates 60S subunit recycling from the ER via UFM1 E3 ligase.
• Regulates stress responses through Gcn2 binding to 60S.
• Maintains nucleolar structure via NPM1 interaction with large subunit precursors.
• Targeted by antimicrobial peptides that disrupt 50S assembly.
• Implicated in ribosomopathies and cancer.
• Essential for bacterial translation initiation via IF3.
• Provides a handle for ribosome export engineering.
• Enables functional genomics of translation control.
• Supports drug discovery targeting ribosome biogenesis.
Molecular Mechanism of ribosomal large subunit binding
Binding to the 60S subunit during stress
In simple terms: Gcn2 is a stress kinase that docks onto the large ribosomal subunit to sense amino acid shortage.
Gcn2 forms a dimer that binds the 60S ribosomal subunit, an interaction that is required for its activation during amino acid starvation. This binding positions Gcn2 to phosphorylate eIF2alpha and inhibit global translation while allowing stress-responsive gene expression.
UFM1 E3 ligase recognition of 60S at the ER
In simple terms: A UFM1-based enzyme complex grabs 60S subunits stuck at the ER and helps release them.
The UFM1 E3 ligase (UFL1-UFBP1) recognizes and binds 60S ribosomal subunits at the ER translocon, leading to their extraction and recycling. This function depends on UFM1 conjugation and is critical for maintaining ER homeostasis and translation fidelity.
NPM1 interaction with large subunit precursors
In simple terms: NPM1 is a nucleolar protein that binds large ribosomal subunit precursors to keep the nucleolus organized.
NPM1 binds precursor forms of the large ribosomal subunit in the nucleolus, and this interaction contributes to maintaining nucleolar structure and ribosome biogenesis. Disruption of this binding alters nucleolar architecture and may affect ribosome output.
Bacterial IF3 binding to the 50S subunit
In simple terms: In bacteria, initiation factor 3 binds the large subunit at a non-canonical site to control translation start.
Initiation factor 3 (IF3) binds the bacterial 50S large ribosomal subunit at a non-canonical site, modulating subunit joining and initiation fidelity. This binding is a validated target for antibiotic development.
Antimicrobial peptide disruption of 50S assembly
In simple terms: Some antibiotics-like peptides bind the large subunit and prevent it from assembling correctly.
The proline-rich antimicrobial peptide Api137 binds the large ribosomal subunit and disrupts its assembly, inducing misfolding and inhibiting bacterial growth. This illustrates how large subunit binding can be exploited for antimicrobial therapy.
Key Genes Involved in GO:0043023 ribosomal large subunit binding
The following genes and proteins are experimentally validated to bind the large ribosomal subunit or regulate this function.
| Gene | Major Role | Research Relevance |
|---|---|---|
| GCN2 | Binds 60S to sense amino acid stress | Stress response, translation control |
| UFL1 | UFM1 E3 ligase component binding 60S | ER ribosome recycling |
| UFBP1 | UFM1 E3 ligase component binding 60S | ER ribosome recycling |
| UFM1 | Ubiquitin-like modifier for 60S recycling | ER homeostasis |
| NPM1 | Binds large subunit precursors | Nucleolar structure, ribosome biogenesis |
| IF3 | Binds 50S in bacteria | Translation initiation, antibiotics |
| RPL3 | Core 60S ribosomal protein | Ribosome structure |
| RPL4 | Core 60S ribosomal protein | Ribosome structure |
| RPL5 | Core 60S ribosomal protein | Ribosome assembly |
| RPL11 | Core 60S ribosomal protein | Ribosome stress signaling |
| RPL23 | Core 60S ribosomal protein | Ribosome assembly |
| RPL26 | Core 60S ribosomal protein | Translation regulation |
| RPS3 | Small subunit protein, interacts with 60S | Translation initiation |
| RPS10 | Small subunit protein | Ribosome function |
| eIF2alpha | Substrate of Gcn2 after 60S binding | Stress response |
| Api137 target | Bacterial 50S subunit | Antimicrobial development |
| Gcn1 | Activator of Gcn2 on 60S | Stress signaling |
How Is ribosomal large subunit binding Regulated?
Ribosomal large subunit binding is regulated by nutrient availability, ER stress, and the UFM1 conjugation pathway. Gcn2 binding to 60S is triggered by uncharged tRNA during amino acid starvation. UFM1 E3 ligase activity is required for 60S recycling from the ER, and its loss leads to ER stress. NPM1 binding to large subunit precursors is regulated during nucleolar assembly.
ribosomal large subunit binding and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| NPM1 | Leukemia, ribosomopathy | KO/KI in hematopoietic cells |
| GCN2 | Neurodegeneration, stress | KO mice, neuronal cells |
| UFL1 | ER stress, developmental disorders | KO cell lines, zebrafish |
| UFBP1 | ER stress, cancer | KO cell lines |
| IF3 | Bacterial infection | Bacterial KO, antibiotic assays |
Ribosomopathies and nucleolar stress
Mutations affecting large subunit binding proteins such as NPM1 can disrupt nucleolar structure and ribosome biogenesis, contributing to ribosomopathies. Defects in 60S recycling via UFM1 pathway are linked to ER stress and cellular dysfunction.
Cancer
Altered expression of large subunit binding factors like NPM1 is observed in leukemias and solid tumors, where it affects ribosome output and proliferation. Targeting these interactions is a potential therapeutic strategy.
Neurodegeneration and stress
Gcn2 binding to 60S is part of the integrated stress response, which is implicated in neurodegenerative diseases. Dysregulation of this pathway can lead to neuronal death.
Infectious disease
Bacterial IF3 binding to 50S and peptide disruption of 50S assembly are validated antibacterial targets. Inhibiting these interactions can block bacterial translation.
From ribosomal large subunit binding-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does gene X bind 60S? | Tagged knock-in (GFP/HA) + co-IP |
| Is binding required for stress response? | Point mutation in binding domain |
| What is the effect of loss of function? | CRISPR knockout |
| Can binding be restored? | Knock-in of wild-type vs mutant |
| Does overexpression alter translation? | Overexpression cell lines |
| Which domains mediate binding? | Domain deletion mutants |
How to Study the ribosomal large subunit binding Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Ribo-seq | Translation efficiency | Stress response |
| Co-IP/MS | Protein interactions | Identify 60S binders |
| Cryo-EM | 3D structure | Binding interface |
| Polysome profiling | Ribosome assembly | 60S recycling |
| Fluorescence microscopy | Localization | Nucleolar binding |
| CRISPR screen | Gene function | Identify regulators |
| Western blot | Protein levels | Stress signaling |
Ribosome profiling (Ribo-seq)
Ribo-seq measures translation efficiency and can reveal changes in 60S binding factor mutants.
Co-immunoprecipitation and proteomics
Co-IP of tagged binding proteins followed by mass spectrometry identifies large subunit components and interactors.
Cryo-electron microscopy
Cryo-EM resolves the structure of binding complexes, such as Gcn2-60S or IF3-50S, at near-atomic resolution.
Fluorescence imaging
Live-cell imaging of fluorescently tagged ribosomal proteins and binding factors reveals dynamics of large subunit interactions.
How CRISPR Can Be Used to Study GO:0043023 ribosomal large subunit binding
Knockout
CRISPR knockout of genes like UFL1 or NPM1 abolishes large subunit binding and reveals loss-of-function phenotypes such as ER stress or nucleolar disruption.
Point Mutation
Point mutations in the binding interface of Gcn2 or IF3 can dissect which residues are required for 60S or 50S binding without affecting protein stability.
Knock-in
Knock-in of tagged versions (e.g., GFP, HA) of binding proteins enables live-cell imaging and co-IP to study endogenous interactions.
Overexpression
Overexpression of large subunit binding proteins can test sufficiency for translation reprogramming or stress resistance.
How EDITGENE Supports ribosomal large subunit binding Research
Researchers studying ribosomal large subunit binding-related genes often need to determine whether a candidate gene is causally involved in ribosome function, stress response, or disease. EDITGENE provides validated CRISPR models to test these hypotheses.
Contact EDITGENE today to design your custom CRISPR model for ribosomal large subunit binding research.
Frequently Asked Questions About ribosomal large subunit binding
What is GO:0043023?
GO:0043023 is the Gene Ontology molecular function term for ribosomal large subunit binding, defined as binding to a large ribosomal subunit.
What genes are involved in ribosomal large subunit binding?
Key genes include GCN2, UFL1, UFBP1, UFM1, NPM1, and bacterial IF3.
How is ribosomal large subunit binding studied?
Common methods include co-IP, cryo-EM, Ribo-seq, and CRISPR knockout models.
What diseases are linked to ribosomal large subunit binding?
Ribosomopathies, cancer, neurodegeneration, and bacterial infections.
What is the role of Gcn2 in large subunit binding?
Gcn2 binds the 60S subunit to sense amino acid stress and activate the integrated stress response.
How does UFM1 regulate 60S recycling?
UFM1 E3 ligase binds and extracts 60S subunits from the ER translocon for recycling.
What is the function of NPM1 in ribosome biogenesis?
NPM1 binds large subunit precursors and maintains nucleolar structure.
Can CRISPR be used to study large subunit binding?
Yes, CRISPR knockout, knock-in, and point mutation models are widely used.
What is the bacterial equivalent of GO:0043023?
In bacteria, it refers to binding the 50S subunit, as seen with IF3.
Why is ribosomal large subunit binding important for drug discovery?
It is a target for antibiotics and cancer therapeutics.
Conclusion
GO:0043023 ribosomal large subunit binding is a fundamental molecular function that connects ribosome assembly, translation control, and stress signaling. Its dysregulation contributes to diverse diseases, making it a rich area for functional genomics and therapeutic development. CRISPR-based models and advanced omics are accelerating discoveries in this field.
References
- 1. Paternoga H et al.. 2025. Structure of a Gcn2 dimer in complex with the large 60S ribosomal subunit.. Proc Natl Acad Sci U S A 122(15):e2415807122 PMID: 40198700
- 2. DaRosa PA et al.. 2024. UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER.. Nature 627(8003):445-452 PMID: 38383785
- 3. Makhlouf L et al.. 2024. The UFM1 E3 ligase recognizes and releases 60S ribosomes from ER translocons.. Nature 627(8003):437-444 PMID: 38383789
- 5. Okuwaki M et al.. 2021. The interaction between nucleophosmin/NPM1 and the large ribosomal subunit precursors contribute to maintaining the nucleolar structure.. Biochim Biophys Acta Mol Cell Res 1868(1):118879 PMID: 33039556
- 6. Lauer SM et al.. 2025. The proline-rich antimicrobial peptide Api137 disrupts large ribosomal subunit assembly and induces misfolding.. Nat Commun 16(1):567 PMID: 39794318
- 7. Lo KY et al.. 2009. Reengineering ribosome export.. Mol Biol Cell 20(5):1545-54 PMID: 19144820
- 8. Goyal A et al.. 2017. Non-canonical Binding Site for Bacterial Initiation Factor 3 on the Large Ribosomal Subunit.. Cell Rep 20(13):3113-3122 PMID: 28954228
