GO:0140978 mitochondrial large ribosomal subunit binding: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0140978 (mitochondrial large ribosomal subunit binding) is a molecular function describing the selective binding of a protein or RNA to the mitochondrial large ribosomal subunit (mt-LSU).
• This binding activity is essential for mitoribosome assembly, translational quality control, and the coordination of mitochondrial protein synthesis [1, 2, 6].
• Key proteins that bind the mt-LSU include mitoribosomal proteins such as bL36m, assembly factors like GTPBP8 and TACO1, and RNA-binding proteins of the large subunit [2, 5, 8].
• Defects in mt-LSU binding proteins are linked to mitochondrial dysfunction, loss of mitochondrial DNA, and human disease including neurodevelopmental disorders and cancer [7, 8].
• CRISPR knockout, point-mutation, and knock-in models are powerful tools to dissect the causal roles of mt-LSU binding proteins in mitochondrial translation and disease [2, 5].
• EDITGENE provides end-to-end CRISPR services, including KO, point mutation, knock-in, overexpression, library screening, and bioinformatics, to accelerate research on mitochondrial large ribosomal subunit binding.
Description
The mitochondrial large ribosomal subunit (mt-LSU) is a specialized ribonucleoprotein complex that catalyzes the synthesis of hydrophobic inner membrane proteins encoded by the mitochondrial genome [1, 3]. The molecular function defined by GO:0140978, mitochondrial large ribosomal subunit binding, refers to the selective interaction of proteins or RNAs with this subunit. This binding activity is fundamental to mitoribosome assembly, translation, and quality control, and its dysregulation has been implicated in a growing number of human pathologies [1, 2, 6]. Understanding the molecular players and mechanisms of mt-LSU binding is therefore critical for researchers in mitochondrial biology, translational medicine, and drug discovery. Historically, RNA-binding proteins of the bovine mitochondrial large subunit were among the first to be biochemically characterized, revealing a complex set of proteins that interact with the mt-LSU. More recent structural and genetic studies have identified essential assembly factors, such as GTPBP8, that transiently bind the mt-LSU to facilitate its maturation. Other proteins, including the zinc-finger protein bL36m, are integral components whose binding is required for optimal assembly and function. The late stages of yeast mitoribosome large subunit biogenesis have been dissected, highlighting a series of ordered binding events that ensure translational competence. Dysfunction in mt-LSU binding proteins can lead to severe consequences. For example, high levels of the mitochondrial large ribosomal subunit protein 40 (MRPL40) prevent the loss of mitochondrial DNA in yeast cells lacking MMF1, linking mt-LSU binding to mitochondrial genome stability. In humans, mutations in TACO1, a mt-LSU binding factor, cause inefficient mitochondrial translation and have been associated with Leigh syndrome. These findings underscore the importance of GO:0140978 in both basic mitochondrial biology and disease mechanisms.
mitochondrial large ribosomal subunit binding At A Glance
| GO ID | GO:0140978 |
|---|---|
| GO term | mitochondrial large ribosomal subunit binding |
| Ontology | molecular_function |
| Synonym | mitochondrial ribosomal large subunit binding |
| Major function | Binding to the mitochondrial large ribosomal subunit, facilitating mitoribosome assembly, translation, and quality control. |
| Related cellular component | Mitochondrial large ribosomal subunit (mt-LSU) |
| Related biological processes | Mitochondrial translation, mitoribosome assembly, mitochondrial quality control |
| Key example proteins | GTPBP8, bL36m, TACO1, MRPL40 |
| Disease relevance | Mitochondrial diseases, neurodevelopmental disorders, cancer |
What Is GO:0140978?
GO:0140978, mitochondrial large ribosomal subunit binding, is a molecular function term defined as the selective binding to a mitochondrial large ribosomal subunit. It encompasses the physical interaction of a protein or RNA molecule with the mt-LSU, which is a key step in mitoribosome assembly, translation, and quality control. This binding can be transient, as in the case of assembly factors, or stable, as with integral mitoribosomal proteins [2, 3, 5].
Why Is mitochondrial large ribosomal subunit binding Important in Cell Biology?
GO:0140978 is critically important because the mitochondrial large ribosomal subunit is the catalytic core of mitochondrial protein synthesis, and its proper assembly and function depend on the precise binding of numerous proteins and RNAs [1, 3]. Defects in these binding events can impair oxidative phosphorylation, leading to a wide range of human diseases, including Leigh syndrome, cardiomyopathy, and cancer [7, 8]. Moreover, mt-LSU binding proteins are emerging as potential therapeutic targets and biomarkers, making this GO term a focal point for both basic and translational research [2, 6].
• Essential for mitoribosome assembly and mitochondrial translation [2, 6].
• Required for translational quality control and rescue of stalled mitoribosomes.
• Linked to mitochondrial DNA stability and maintenance.
• Implicated in human mitochondrial diseases such as Leigh syndrome.
• Associated with cancer cell metabolism and survival.
• Provides targets for antibiotic development and mitochondrial medicine.
• Key to understanding neurodevelopmental disorders with mitochondrial dysfunction.
• Enables mechanistic studies of protein-RNA interactions in mitochondria [3, 5].
• Facilitates the development of CRISPR-based disease models [2, 5].
• Supports the discovery of novel biomarkers for mitochondrial disease.
Molecular Mechanism of mitochondrial large ribosomal subunit binding
Substrate recognition and initial binding
In simple terms: Proteins that bind the mitochondrial large ribosomal subunit first recognize specific features on its surface.
The mitochondrial large ribosomal subunit (mt-LSU) presents a complex surface of ribosomal RNA and proteins. Binding proteins, such as assembly factors and ribosomal proteins, recognize these features through electrostatic and shape complementarity. For instance, RNA-binding proteins of the bovine mt-LSU were shown to interact with specific rRNA regions, suggesting a lock-and-key mechanism. This initial recognition is critical for the subsequent steps of assembly and translation.
Assembly factor-mediated maturation
In simple terms: Helper proteins bind transiently to the large subunit to help it mature into a working machine.
Assembly factors like GTPBP8 transiently bind the mt-LSU to facilitate its maturation. GTPBP8 plays a role in mitoribosome formation in human mitochondria, likely by coordinating the incorporation of ribosomal proteins and the processing of rRNA. Similarly, the late stages of yeast mitoribosome large subunit biogenesis involve a series of assembly factors that bind and release the subunit in an ordered fashion. These transient interactions ensure that the mt-LSU achieves its functional conformation.
Stable incorporation of ribosomal proteins
In simple terms: Some proteins become permanent parts of the large subunit, and their binding is essential for its function.
Integral mitoribosomal proteins, such as bL36m, bind stably to the mt-LSU. The zinc finger motif in bL36m is essential for optimal yeast mitoribosome assembly and function, indicating that specific structural motifs mediate stable binding. Similarly, the mitochondrial large ribosomal subunit protein 40 (MRPL40) is a stable component whose high levels prevent loss of mitochondrial DNA in mmf1-null yeast cells. These stable interactions are crucial for the structural integrity and catalytic activity of the mitoribosome.
Quality control and stalled ribosome rescue
In simple terms: When translation stalls, quality control factors bind the large subunit to rescue and recycle it.
Elongational stalling activates mitoribosome-associated quality control, which involves the binding of quality control factors to the mt-LSU. These factors recognize stalled ribosomes and initiate rescue pathways, preventing the accumulation of aberrant translation products. This binding activity is essential for maintaining mitochondrial proteostasis and is a key aspect of GO:0140978.
Coordination with small subunit and translation initiation
In simple terms: The large subunit must join with the small subunit to start translation, and binding proteins help coordinate this.
The mechanism of mitoribosomal small subunit biogenesis and preinitiation involves interactions that ultimately lead to the joining of the large and small subunits. Proteins that bind the mt-LSU may also participate in this coordination, ensuring that translation initiates correctly. TACO1, for example, mediates efficient mitochondrial translation, likely by stabilizing the mt-LSU or facilitating its interaction with mRNA.
Key Genes Involved in GO:0140978 mitochondrial large ribosomal subunit binding
The following genes encode proteins that bind the mitochondrial large ribosomal subunit and are central to GO:0140978.
| Gene | Major Role | Research Relevance |
|---|---|---|
| GTPBP8 | Assembly factor for mitoribosome formation | Knockout leads to defective mitoribosome assembly |
| MRPL36 (bL36m) | Mitochondrial large ribosomal subunit protein | Zinc finger motif essential for assembly and function |
| TACO1 | Translational activator of cytochrome c oxidase I | Mutations cause Leigh syndrome and inefficient translation |
| MRPL40 | Mitochondrial large ribosomal subunit protein | Prevents loss of mitochondrial DNA in mmf1-null cells |
| MRPL3 | Mitochondrial large ribosomal subunit protein | RNA-binding protein of the large subunit |
| MRPL4 | Mitochondrial large ribosomal subunit protein | RNA-binding protein of the large subunit |
| MRPL13 | Mitochondrial large ribosomal subunit protein | Component of the mt-LSU |
| MRPL20 | Mitochondrial large ribosomal subunit protein | Component of the mt-LSU |
| MRPL22 | Mitochondrial large ribosomal subunit protein | Component of the mt-LSU |
| MRPL24 | Mitochondrial large ribosomal subunit protein | Component of the mt-LSU |
| MRPL37 | Mitochondrial large ribosomal subunit protein | Component of the mt-LSU |
| MRPL39 | Mitochondrial large ribosomal subunit protein | Component of the mt-LSU |
| MRPL44 | Mitochondrial large ribosomal subunit protein | Component of the mt-LSU |
| MRPL47 | Mitochondrial large ribosomal subunit protein | Component of the mt-LSU |
| MRPL49 | Mitochondrial large ribosomal subunit protein | Component of the mt-LSU |
| MRPL51 | Mitochondrial large ribosomal subunit protein | Component of the mt-LSU |
| MRPL55 | Mitochondrial large ribosomal subunit protein | Component of the mt-LSU |
How Is mitochondrial large ribosomal subunit binding Regulated?
The binding of proteins to the mitochondrial large ribosomal subunit is regulated at multiple levels. Transcriptional and translational control of mitoribosomal protein genes ensures stoichiometric production of subunits. Post-translational modifications, such as phosphorylation, may modulate binding affinity. Additionally, the availability of assembly factors like GTPBP8 is tightly regulated to match mitoribosome demand. Quality control pathways, such as the mitoribosome-associated quality control activated by elongational stalling, also regulate the interaction of rescue factors with the mt-LSU. Furthermore, the zinc finger motif in bL36m is essential for optimal assembly, suggesting that metal homeostasis may influence binding.
mitochondrial large ribosomal subunit binding and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| TACO1 | Leigh syndrome with COX deficiency | Knockout in human cells, point mutation knock-in |
| GTPBP8 | Mitoribosome assembly defects, potential mtDNA depletion | Knockout and rescue in human cells |
| MRPL40 | Mitochondrial DNA instability, cancer metabolism | Overexpression in yeast and human cells |
| MRPL36 (bL36m) | Mitoribosome dysfunction, potential ribosomopathy | Point mutation of zinc finger motif in yeast |
| MRPL3 | RNA-binding defects, potential mitochondrial disease | Knockout in human cells |
Mitochondrial large ribosomal subunit binding in neurodevelopmental disorders
Mutations in genes encoding mt-LSU binding proteins can cause severe neurodevelopmental disorders. For example, mutations in TACO1, a mt-LSU binding factor, lead to Leigh syndrome, a progressive neurodegenerative disorder characterized by bilateral brain lesions and mitochondrial dysfunction. TACO1 is required for efficient translation of cytochrome c oxidase subunit I (COX1), and its loss results in isolated COX deficiency. This highlights the critical role of mt-LSU binding in neuronal survival and energy metabolism.
Mitochondrial large ribosomal subunit binding and cancer
Altered mitochondrial translation is increasingly recognized as a hallmark of cancer. Overexpression of mt-LSU proteins, such as MRPL40, has been observed in various cancers and may support the high metabolic demands of tumor cells. In yeast, high levels of MRPL40 prevent loss of mitochondrial DNA, suggesting a role in mitochondrial genome maintenance that could be co-opted by cancer cells. Targeting mt-LSU binding proteins may therefore offer novel therapeutic strategies for cancer treatment.
Mitochondrial large ribosomal subunit binding in mitochondrial DNA instability syndromes
Defects in mt-LSU binding can lead to mitochondrial DNA (mtDNA) instability. In Saccharomyces cerevisiae, the absence of MMF1 causes loss of mtDNA, but high levels of MRPL40 suppress this phenotype, indicating that mt-LSU binding proteins can influence mtDNA maintenance. In humans, mutations in mt-LSU assembly factors like GTPBP8 may contribute to mtDNA depletion syndromes, although direct evidence is still emerging. These findings link GO:0140978 to the broader family of mitochondrial genome maintenance disorders.
From mitochondrial large ribosomal subunit binding-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does loss of GTPBP8 impair mitoribosome assembly? | CRISPR knockout of GTPBP8 in HEK293T cells |
| Is the zinc finger of bL36m required for mt-LSU binding? | Point mutation knock-in of bL36m in yeast |
| Can TACO1 rescue COX deficiency in patient cells? | Knock-in of wild-type TACO1 in patient fibroblasts |
| Where does MRPL40 localize in live cells? | Tagged knock-in of MRPL40 with GFP |
| Does overexpression of MRPL40 stabilize mtDNA? | Overexpression of MRPL40 in mmf1-null yeast |
| What proteins bind the mt-LSU during stalling? | CRISPR knockout of quality control factors followed by proteomics |
How to Study the mitochondrial large ribosomal subunit binding Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Ribo-seq | Ribosome occupancy and translation efficiency | Assessing impact of mt-LSU binding protein KO on mitochondrial translation |
| AP-MS | Protein-protein interactions | Identifying novel mt-LSU binding proteins |
| Cryo-EM | High-resolution structure of mt-LSU complexes | Visualizing binding interfaces and assembly intermediates |
| Live-cell imaging | Localization and dynamics of tagged proteins | Tracking mt-LSU assembly in real time |
| RNA-seq | Transcript abundance | Measuring changes in mitoribosomal gene expression |
| Western blot | Protein levels | Validating knockout or overexpression efficiency |
| Blue native PAGE | Intact mitoribosome complexes | Assessing mt-LSU assembly state |
| Seahorse assay | Mitochondrial respiration | Linking mt-LSU binding to oxidative phosphorylation |
Ribosome profiling (Ribo-seq)
Ribo-seq provides a genome-wide snapshot of mitochondrial translation by sequencing ribosome-protected mRNA fragments. It can be used to assess the impact of mt-LSU binding protein knockouts on translation efficiency and stalling. For example, elongational stalling activates mitoribosome-associated quality control, which can be monitored by Ribo-seq.
Proteomics and interactomics
Affinity purification coupled with mass spectrometry (AP-MS) can identify proteins that bind the mt-LSU. This approach has been used to characterize RNA-binding proteins of the bovine mitochondrial large subunit. Quantitative proteomics can also reveal changes in mt-LSU composition upon genetic perturbation.
Structural biology (cryo-EM)
Cryo-electron microscopy (cryo-EM) enables high-resolution visualization of mt-LSU binding events. Recent studies have elucidated the mechanism of mitoribosomal small subunit biogenesis and preinitiation, providing structural insights into how binding proteins interact with the mt-LSU. Structural analysis of TACO1-mediated translation has also revealed key binding interfaces.
Live-cell imaging
Fluorescence microscopy of tagged mt-LSU proteins allows real-time tracking of their localization and dynamics. Tagged knock-in models, such as MRPL40-GFP, can be used to study mt-LSU assembly and mitochondrial morphology. This method is particularly useful for assessing the effects of point mutations on binding.
How CRISPR Can Be Used to Study GO:0140978 mitochondrial large ribosomal subunit binding
Knockout
CRISPR knockout of genes encoding mt-LSU binding proteins, such as GTPBP8, allows researchers to assess their essentiality for mitoribosome assembly and mitochondrial translation. Knockout cell lines can be used in rescue experiments to confirm specificity and to map functional domains.
Point Mutation
Point mutation knock-in can be used to dissect the role of specific residues in mt-LSU binding. For example, mutating the zinc finger motif of bL36m in yeast revealed its essential role in optimal mitoribosome assembly and function. Similar approaches can be applied to human mt-LSU proteins to model disease-associated mutations.
Knock-in
Knock-in of tagged versions of mt-LSU proteins, such as GFP or FLAG fusions, enables affinity purification and imaging studies. Knock-in of disease-relevant mutations, like those in TACO1, can create isogenic models to study pathogenic mechanisms.
Overexpression
Overexpression of mt-LSU binding proteins can be used to test gain-of-function effects. For instance, overexpression of MRPL40 in mmf1-null yeast prevented loss of mitochondrial DNA, demonstrating a protective role. Overexpression models are valuable for studying dosage-sensitive interactions and for drug screening.
How EDITGENE Supports mitochondrial large ribosomal subunit binding Research
Researchers studying mitochondrial large ribosomal subunit binding-related genes often need to determine whether a candidate gene is causally involved in mitoribosome assembly, translation, or disease. This requires precise genetic models that can isolate the function of individual binding proteins and their domains.
Contact EDITGENE today to design your custom CRISPR model for mitochondrial large ribosomal subunit binding research.
Frequently Asked Questions About mitochondrial large ribosomal subunit binding
What is GO:0140978?
GO:0140978 is a Gene Ontology molecular function term defined as binding to a mitochondrial large ribosomal subunit. It encompasses the selective interaction of proteins or RNAs with the mt-LSU, which is essential for mitoribosome assembly and translation.
What genes are involved in mitochondrial large ribosomal subunit binding?
Key genes include GTPBP8, MRPL36 (bL36m), TACO1, MRPL40, and many other MRPL genes encoding mitochondrial ribosomal proteins [2, 3, 5, 7, 8].
How is mitochondrial large ribosomal subunit binding studied?
Common methods include Ribo-seq, affinity purification mass spectrometry, cryo-EM, live-cell imaging, and CRISPR knockout models [1, 3, 4, 7].
Why is mitochondrial large ribosomal subunit binding important?
It is critical for mitochondrial protein synthesis, quality control, and cellular energy metabolism. Defects can cause Leigh syndrome, mitochondrial DNA instability, and cancer [1, 7, 8].
What diseases are associated with defects in mitochondrial large ribosomal subunit binding?
Diseases include Leigh syndrome, neurodevelopmental disorders, mitochondrial DNA depletion syndromes, and cancer [7, 8].
What is the role of GTPBP8 in mitochondrial large ribosomal subunit binding?
GTPBP8 is an assembly factor that transiently binds the mt-LSU to facilitate mitoribosome formation in human mitochondria.
How does TACO1 function in mitochondrial translation?
TACO1 binds the mt-LSU and mediates efficient translation of cytochrome c oxidase subunit I (COX1). Mutations in TACO1 cause Leigh syndrome.
Can CRISPR be used to study mitochondrial large ribosomal subunit binding?
Yes, CRISPR knockout, point mutation, knock-in, and overexpression models are powerful tools to dissect the function of mt-LSU binding proteins [2, 5, 7].
What is the zinc finger motif in bL36m?
The zinc finger motif in bL36m is a structural domain essential for optimal yeast mitoribosome assembly and function, likely by mediating stable binding to the mt-LSU.
How does MRPL40 prevent loss of mitochondrial DNA?
High levels of MRPL40 prevent loss of mitochondrial DNA in mmf1-null Saccharomyces cerevisiae cells, suggesting a role in mitochondrial genome maintenance.
Conclusion
GO:0140978, mitochondrial large ribosomal subunit binding, is a fundamental molecular function that underpins mitochondrial translation and cellular energy metabolism. The precise binding of proteins and RNAs to the mt-LSU is essential for mitoribosome assembly, quality control, and the coordination of translation with cellular demands [1, 2, 6]. Dysregulation of these interactions leads to a spectrum of human diseases, including Leigh syndrome, mitochondrial DNA instability, and cancer [7, 8]. Continued research using advanced CRISPR models and multi-omics approaches will further illuminate the mechanistic details and therapeutic potential of targeting mt-LSU binding proteins.
References
- 1. Desai N et al.. 2020. Elongational stalling activates mitoribosome-associated quality control.. Science 370(6520):1105-1110 PMID: 33243891
- 2. Cipullo M et al.. 2024. GTPBP8 plays a role in mitoribosome formation in human mitochondria.. Nat Commun 15(1):5664 PMID: 38969660
- 3. Piatyszek MA et al.. 1988. RNA binding proteins of the large subunit of bovine mitochondrial ribosomes.. Nucleic Acids Res 16(6):2565-83 PMID: 3129699
- 4. Itoh Y et al.. 2022. Mechanism of mitoribosomal small subunit biogenesis and preinitiation.. Nature 606(7914):603-608 PMID: 35676484
- 5. Zhong H et al.. 2024. The zinc finger motif in the mitochondrial large ribosomal subunit protein bL36m is essential for optimal yeast mitoribosome assembly and function.. Biochim Biophys Acta Mol Cell Res 1871(4):119707 PMID: 38493895
- 6. 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
- 7. Accardi R et al.. 2004. High levels of the mitochondrial large ribosomal subunit protein 40 prevent loss of mitochondrial DNA in null mmf1 Saccharomyces cerevisiae cells.. Yeast 21(7):539-48 PMID: 15164357
- 8. Wang S et al.. 2026. Structural basis of TACO1-mediated efficient mitochondrial translation.. Nat Commun 17(1) PMID: 41663403
