GO:0070180 large ribosomal subunit rRNA binding: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0070180 (large ribosomal subunit rRNA binding) describes the molecular function of binding to LSU rRNA, such as the 25S rRNA in Saccharomyces cerevisiae.
• This binding activity is essential for the assembly and function of the large ribosomal subunit, impacting translation and cellular growth.
• Key proteins include Mak16, NF45/NF90 heterodimer, and mitoribosome assembly factors like GTPBP8.
• Dysregulation of LSU rRNA binding is linked to ribosomopathies, cancer, and mitochondrial diseases.
• CRISPR knockout, point mutation, knock-in, and overexpression models enable functional dissection of LSU rRNA binding proteins.
• EDITGENE provides comprehensive CRISPR services and bioinformatics to accelerate research on large ribosomal subunit rRNA binding.
Description
The Gene Ontology (GO) term GO:0070180, large ribosomal subunit rRNA binding, defines the molecular function of selectively interacting with the RNA component of the large ribosomal subunit (LSU rRNA), such as the 25S rRNA in Saccharomyces cerevisiae. This binding activity is fundamental to ribosome biogenesis, where ribosomal proteins and assembly factors coordinate the folding, modification, and maturation of rRNA to produce translation-competent subunits. Researchers study this term to understand how mutations or dysregulation in RNA-binding proteins contribute to diseases ranging from cancer to ribosomopathies. The function is conserved across eukaryotes, with mitochondrial ribosomes utilizing a similar binding mechanism for their LSU rRNA. Given its central role in protein synthesis, targeting LSU rRNA binding proteins offers therapeutic potential and serves as a focal point for CRISPR-based functional genomics.
large ribosomal subunit rRNA binding At A Glance
| GO ID | GO:0070180 |
|---|---|
| GO term | large ribosomal subunit rRNA binding |
| Ontology | molecular_function |
| Synonym | 25S rRNA binding, LSU rRNA binding |
| Major function | Binding to LSU rRNA to facilitate ribosome assembly and translation |
| Definition source | QuickGO |
| Related processes | Ribosome biogenesis, translation, mitochondrial translation |
| Key organisms | Saccharomyces cerevisiae, Homo sapiens |
| Disease relevance | Ribosomopathies, cancer, mitochondrial disorders |
What Is GO:0070180?
GO:0070180 large ribosomal subunit rRNA binding is a molecular function term describing the binding to large ribosomal subunit RNA (LSU rRNA), a constituent of the large ribosomal subunit. In Saccharomyces cerevisiae, this is the 25S rRNA. Synonyms include 25S rRNA binding and LSU rRNA binding. This activity is essential for the assembly and stability of the large ribosomal subunit and is carried out by ribosomal proteins and assembly factors.
Why Is large ribosomal subunit rRNA binding Important in Cell Biology?
Understanding large ribosomal subunit rRNA binding is crucial because it underpins the assembly of the large ribosomal subunit, a process that is tightly regulated and essential for protein synthesis in all cells. Defects in this function can lead to impaired ribosome biogenesis, which is associated with human diseases such as ribosomopathies, cancer, and mitochondrial disorders. Moreover, the interaction between assembly factors and LSU rRNA is a target for antibiotics and therapeutic interventions. Research into GO:0070180 provides insights into fundamental cellular mechanisms and offers potential avenues for drug discovery and CRISPR-based gene therapy.
• Essential for large ribosomal subunit assembly and translation.
• Mutations in LSU rRNA binding proteins cause ribosomopathies and cancer.
• Involved in mitochondrial ribosome biogenesis and mitochondrial diseases.
• Target for antibiotics that inhibit ribosome assembly.
• Key to understanding translational control in development and stress.
• Provides biomarkers for cancer diagnosis and prognosis.
• Enables CRISPR screening to identify novel assembly factors.
• Facilitates structural studies of ribosome assembly intermediates.
• Links rRNA modification and quality control pathways.
• Potential therapeutic target for ribosome-related disorders.
What Happens During large ribosomal subunit rRNA binding?
Recognition and Initial Binding
In simple terms: Proteins find and attach to the large ribosomal subunit RNA.
The process begins with the recognition of specific sequences or structures within the LSU rRNA by ribosomal proteins and assembly factors. For example, Mak16, a conserved essential protein, binds to the 25S rRNA in an iron-sulfur cluster-dependent manner, facilitating early assembly steps. Similarly, the NF45/NF90 heterodimer binds to LSU rRNA precursors to promote 60S subunit biogenesis. This initial binding is critical for recruiting other factors and stabilizing rRNA folds.
rRNA Folding and Modification
In simple terms: The RNA shape changes and gets chemical tags added.
Upon binding, assembly factors induce conformational changes in the LSU rRNA, aiding proper folding and modification. For instance, depurination of the sarcin/ricin loop in 25S rRNA is signaled through the small ribosomal subunit, affecting large subunit function. These modifications are essential for catalytic activity and ribosome quality control.
Assembly Intermediate Formation
In simple terms: Proteins and RNA come together to build a pre-ribosome.
Binding of factors like GTPBP8 in human mitochondria is required for the formation of assembly intermediates of the large mitoribosomal subunit. In yeast, late stages of mitoribosome large subunit biogenesis involve sequential binding of assembly factors to rRNA. These intermediates are monitored for correct assembly before proceeding.
Quality Control and Maturation
In simple terms: The cell checks the ribosome and finishes its construction.
Quality control mechanisms ensure that only correctly assembled subunits proceed to translation. The small ribosomal subunit signals depurination of the sarcin/ricin loop in 25S rRNA, leading to degradation of faulty subunits. Additionally, the 5S rRNA plays a role in large subunit assembly, as revealed by antibiotic studies. Maturation involves release of assembly factors and final folding steps.
Key Genes Involved in GO:0070180 large ribosomal subunit rRNA binding
The following genes and proteins are directly implicated in large ribosomal subunit rRNA binding and associated assembly processes.
| Gene | Major Role | Research Relevance |
|---|---|---|
| MAK16 | Binds 25S rRNA; essential for 60S subunit biogenesis | Iron-sulfur cluster-dependent function; knockout lethal in yeast |
| NF45 (ILF2) | Binds LSU rRNA; part of NF45/NF90 heterodimer | Regulates 60S biogenesis and nucleolar morphology |
| NF90 (ILF3) | Binds LSU rRNA; heterodimer partner of NF45 | Influences 60S subunit production and cell growth |
| GTPBP8 | GTPase involved in mitoribosome large subunit assembly | Required for formation of mitoribosomal intermediates |
| MRPL13 | Mitochondrial ribosomal protein of large subunit | Binds mitoribosomal rRNA; mutations linked to mitochondrial disease |
| MRPL44 | Mitochondrial ribosomal protein; binds LSU rRNA | Defects cause oxidative phosphorylation disorders |
| RPL3 | Core large subunit protein; binds 25S rRNA | Mutations affect ribosome assembly and translation |
| RPL4 | Binds LSU rRNA; part of exit tunnel | Target for antibiotics; involved in ribosomopathies |
| RPL22 | Binds 25S rRNA; regulates assembly | Haploinsufficiency linked to cancer |
| RPL5 | Binds 5S rRNA and 25S rRNA | Mutations cause Diamond-Blackfan anemia |
| RPL11 | Binds 5S rRNA and 25S rRNA | Implicated in ribosomopathies and p53 activation |
| RRS1 | Assembly factor binding LSU rRNA | Essential for 60S subunit maturation |
| NOP7 | Assembly factor binding LSU rRNA | Required for pre-rRNA processing |
| EBP2 | Binds LSU rRNA; involved in 60S assembly | Mutations affect ribosome biogenesis |
| SPB1 | Methyltransferase that binds LSU rRNA | Modifies rRNA and influences assembly |
| NSA2 | Assembly factor binding LSU rRNA | Essential for 60S biogenesis |
| TIF6 | Binds LSU rRNA; shuttling factor | Regulates subunit joining |
How Is large ribosomal subunit rRNA binding Regulated?
The binding of proteins to large ribosomal subunit rRNA is regulated at multiple levels. Transcriptional control of ribosomal protein genes and assembly factors ensures stoichiometric production. Post-translational modifications, such as phosphorylation, can modulate binding affinity. The mTOR signaling pathway regulates ribosome biogenesis in response to nutrient availability, affecting LSU rRNA binding indirectly. Additionally, quality control pathways degrade misfolded rRNA or assembly intermediates, providing a checkpoint. In mitochondria, GTPBP8 and other GTPases regulate assembly in a nucleotide-dependent manner.
large ribosomal subunit rRNA binding and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| RPL5 | Diamond-Blackfan anemia | Knockout in hematopoietic stem cells; point mutation knock-in |
| RPL11 | Diamond-Blackfan anemia | Knockout in zebrafish; overexpression in cell lines |
| NF90 (ILF3) | Cancer (overexpression) | Knockout in cancer cell lines; overexpression in normal cells |
| GTPBP8 | Mitochondrial disease | Knockout in HeLa cells; rescue with wild-type and mutant |
| MRPL44 | Leigh syndrome | Knockout in patient fibroblasts; knock-in of patient mutations |
Ribosomopathies
Mutations in genes encoding LSU rRNA binding proteins, such as RPL5 and RPL11, cause ribosomopathies like Diamond-Blackfan anemia, characterized by bone marrow failure and developmental defects. Defective binding leads to impaired 60S subunit assembly and p53-mediated apoptosis.
Cancer
Altered expression of LSU rRNA binding proteins, including NF45/NF90, is observed in various cancers. Overexpression of NF90 promotes 60S biogenesis and cell proliferation, contributing to tumorigenesis. RPL22 haploinsufficiency is linked to cancer predisposition.
Mitochondrial Disorders
Mutations in mitoribosomal proteins like MRPL13 and MRPL44, which bind LSU rRNA, cause oxidative phosphorylation deficiencies and mitochondrial diseases such as Leigh syndrome. GTPBP8 defects impair mitoribosome assembly and mitochondrial translation.
Neurodegeneration
Impaired ribosome assembly and LSU rRNA binding have been implicated in neurodegenerative diseases, though the exact mechanisms remain under investigation. Depurination of 25S rRNA signals stress responses that may contribute to neuronal death.
From large ribosomal subunit rRNA binding-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Is MAK16 essential for LSU rRNA binding? | CRISPR knockout in S. cerevisiae; rescue with wild-type and mutant |
| Does NF90 overexpression drive 60S biogenesis? | CRISPR overexpression in HEK293T cells; RNA-seq and polysome profiling |
| What is the role of GTPBP8 in mitoribosome assembly? | CRISPR knockout in HeLa cells; mitochondrial translation assays |
| How do point mutations in RPL5 affect rRNA binding? | CRISPR point mutation knock-in in iPSCs; ribosome profiling |
| Can tagged RPL3 be used to purify pre-ribosomes? | CRISPR knock-in of FLAG tag in yeast; affinity purification |
| Does RPL22 haploinsufficiency cause cancer? | CRISPR knockout in mouse models; tumorigenesis assays |
How to Study the large ribosomal subunit rRNA binding Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Ribo-seq | Translation efficiency and ribosome occupancy | Detect defects in LSU rRNA binding mutants |
| RIP/CLIP | Direct protein-RNA interactions | Confirm binding of factors to 25S rRNA |
| Polysome profiling | Distribution of ribosomal subunits and polysomes | Assess 60S assembly defects |
| CRISPR knockout screen | Gene essentiality and growth phenotypes | Identify novel LSU rRNA binding factors |
| Proteomics (AP-MS) | Protein-protein interactions in pre-ribosomes | Map assembly intermediates |
| Cryo-EM | High-resolution structure of ribosome assembly intermediates | Visualize LSU rRNA binding |
| Northern blot | rRNA processing intermediates | Monitor pre-rRNA processing |
| Mitochondrial translation assay | Mitochondrial protein synthesis | Study mitoribosome assembly defects |
Ribosome Profiling (Ribo-seq)
Ribo-seq measures translation efficiency and ribosome occupancy at codon resolution. It can reveal defects in large subunit assembly caused by mutations in LSU rRNA binding proteins. For example, depurination of 25S rRNA affects translation elongation, detectable by Ribo-seq.
RNA Immunoprecipitation (RIP) and CLIP
RIP and CLIP identify direct binding between proteins and LSU rRNA. These methods use antibodies against candidate proteins to pull down RNA-protein complexes, followed by RT-qPCR or sequencing. They are essential to confirm GO:0070180 activity in vivo.
Sucrose Gradient Polysome Profiling
Polysome profiling separates ribosomal subunits, monosomes, and polysomes on sucrose gradients. It detects assembly defects in 60S subunits due to impaired LSU rRNA binding. This method is widely used to study ribosomopathies.
CRISPR Screening and Functional Genomics
Genome-wide CRISPR knockout screens can identify genes required for LSU rRNA binding and 60S assembly. Cells with defects in this function show growth arrest or altered translation, which can be quantified by sequencing. This approach is powerful for discovering novel assembly factors.
How CRISPR Can Be Used to Study GO:0070180 large ribosomal subunit rRNA binding
Knockout
CRISPR knockout of genes encoding LSU rRNA binding proteins, such as MAK16 or GTPBP8, can reveal their essentiality and impact on ribosome assembly. For example, MAK16 knockout in yeast is lethal, and rescue with wild-type or mutant alleles can dissect domain functions. In human cells, GTPBP8 knockout impairs mitoribosome formation and mitochondrial translation.
Point Mutation
CRISPR point mutation knock-in allows precise introduction of disease-associated or functional mutations. For instance, mutations in the iron-sulfur cluster ligands of MAK16 can be introduced to test their role in LSU rRNA binding. Similarly, point mutations in RPL5 found in Diamond-Blackfan anemia can be modeled to study rRNA binding defects.
Knock-in
Knock-in of epitope tags (e.g., FLAG, HA) into endogenous loci enables purification of protein-RNA complexes. Tagged RPL3 or NF45 can be used for RIP or affinity purification to identify bound LSU rRNA regions. Knock-in of reporter genes can also monitor assembly factor expression.
Overexpression
CRISPR activation (CRISPRa) or cDNA overexpression can drive high-level expression of LSU rRNA binding proteins. Overexpression of NF90 promotes 60S biogenesis and cell proliferation, providing a model for cancer studies. Conversely, overexpression of dominant-negative mutants can inhibit assembly.
How EDITGENE Supports large ribosomal subunit rRNA binding Research
Researchers studying large ribosomal subunit rRNA binding-related genes often need to determine whether a candidate gene is causally involved in ribosome assembly, translation, or disease. EDITGENE provides a comprehensive suite of CRISPR services to enable precise genetic manipulation and functional interrogation of these genes in relevant cell models.
Contact EDITGENE today to design your custom CRISPR model for large ribosomal subunit rRNA binding research.
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Frequently Asked Questions About large ribosomal subunit rRNA binding
What is GO:0070180 large ribosomal subunit rRNA binding?
GO:0070180 is a Gene Ontology molecular function term describing the binding to large ribosomal subunit RNA (LSU rRNA), such as 25S rRNA in yeast, essential for ribosome assembly.
What genes are involved in large ribosomal subunit rRNA binding?
Key genes include MAK16, NF45/NF90, GTPBP8, RPL3, RPL5, RPL11, and many mitoribosomal proteins like MRPL13 and MRPL44.
How is large ribosomal subunit rRNA binding studied?
Common methods include Ribo-seq, RIP/CLIP, polysome profiling, CRISPR screens, and cryo-EM.
Why is large ribosomal subunit rRNA binding important?
It is essential for building the large ribosomal subunit, and defects cause ribosomopathies, cancer, and mitochondrial diseases.
What diseases are linked to defects in LSU rRNA binding?
Diamond-Blackfan anemia, cancer, Leigh syndrome, and other mitochondrial disorders.
Can CRISPR be used to study large ribosomal subunit rRNA binding?
Yes, CRISPR knockout, point mutation, knock-in, and overexpression models enable functional dissection of these genes.
What is the role of MAK16 in LSU rRNA binding?
MAK16 binds 25S rRNA in an iron-sulfur cluster-dependent manner and is essential for 60S subunit biogenesis.
How does NF45/NF90 heterodimer contribute to LSU rRNA binding?
NF45/NF90 binds LSU rRNA precursors to promote 60S subunit biogenesis and influences nucleolar morphology.
What is the function of GTPBP8 in mitoribosome assembly?
GTPBP8 is a GTPase required for the formation of large mitoribosomal subunit intermediates in human mitochondria.
What experimental models are available for studying LSU rRNA binding?
Models include CRISPR knockout/knock-in in yeast and human cells, mitochondrial translation assays, and polysome profiling.
Conclusion
GO:0070180 large ribosomal subunit rRNA binding is a fundamental molecular function required for ribosome assembly and translation. Dysregulation of this process leads to a spectrum of human diseases, including ribosomopathies, cancer, and mitochondrial disorders. Advances in CRISPR technology and functional genomics have enabled precise dissection of the genes and mechanisms involved. EDITGENE offers comprehensive services to support researchers in modeling and studying large ribosomal subunit rRNA binding, from knockout to overexpression and screening.
References
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- 2. Metelev VG et al.. 2025. The NeverEnding E-Story.. Biochemistry (Mosc) 90(11):1553-1565 PMID: 41354069
- 3. Rathore S et al.. 2025. The late stages of yeast mitoribosome large subunit biogenesis.. Biochim Biophys Acta Mol Cell Res 1872(8):120051 PMID: 40865570
- 4. Cipullo M et al.. 2024. GTPBP8 plays a role in mitoribosome formation in human mitochondria.. Nat Commun 15(1):5664 PMID: 38969660
- 5. Itoh Y et al.. 2022. Mechanism of mitoribosomal small subunit biogenesis and preinitiation.. Nature 606(7914):603-608 PMID: 35676484
- 6. Prashar T et al.. 2025. Depurination of sarcin/ricin loop 25S rRNA is signaled through the small ribosomal subunit during translation.. RNA 31(12):1812-1825 PMID: 40987586
- 7. Khaitovich P et al.. 1999. Effect of antibiotics on large ribosomal subunit assembly reveals possible function of 5 S rRNA.. J Mol Biol 291(5):1025-34 PMID: 10518940
- 8. Wandrey F et al.. 2015. The NF45/NF90 Heterodimer Contributes to the Biogenesis of 60S Ribosomal Subunits and Influences Nucleolar Morphology.. Mol Cell Biol 35(20):3491-503 PMID: 26240280
