1
|
Liu L, Shao M, Huang Y, Qian P, Huang H. Unraveling the roles and mechanisms of mitochondrial translation in normal and malignant hematopoiesis. J Hematol Oncol 2024; 17:95. [PMID: 39396039 PMCID: PMC11470598 DOI: 10.1186/s13045-024-01615-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Accepted: 09/30/2024] [Indexed: 10/14/2024] Open
Abstract
Due to spatial and genomic independence, mitochondria possess a translational mechanism distinct from that of cytoplasmic translation. Several regulators participate in the modulation of mitochondrial translation. Mitochondrial translation is coordinated with cytoplasmic translation through stress responses. Importantly, the inhibition of mitochondrial translation leads to the inhibition of cytoplasmic translation and metabolic disruption. Therefore, defects in mitochondrial translation are closely related to the functions of hematopoietic cells and various immune cells. Finally, the inhibition of mitochondrial translation is a potential therapeutic target for treating multiple hematologic malignancies. Collectively, more in-depth insights into mitochondrial translation not only facilitate our understanding of its functions in hematopoiesis, but also provide a basis for the discovery of new treatments for hematological malignancies and the modulation of immune cell function.
Collapse
Affiliation(s)
- Lianxuan Liu
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Institute of Hematology Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, 310058, China
| | - Mi Shao
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Institute of Hematology Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, 310058, China
| | - Yue Huang
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Institute of Hematology Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, 310058, China
| | - Pengxu Qian
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310058, China.
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China.
- Institute of Hematology Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, 310058, China.
| | - He Huang
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310058, China.
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China.
- Institute of Hematology Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, 310058, China.
| |
Collapse
|
2
|
Gómez-Morón Á, Tsukalov I, Scagnetti C, Pertusa C, Lozano-Prieto M, Martínez-Fleta P, Requena S, Martín P, Alfranca A, Martin-Gayo E, Martin-Cofreces NB. Cytosolic protein translation regulates cell asymmetry and function in early TCR activation of human CD8 + T lymphocytes. Front Immunol 2024; 15:1411957. [PMID: 39114656 PMCID: PMC11303187 DOI: 10.3389/fimmu.2024.1411957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 07/01/2024] [Indexed: 08/10/2024] Open
Abstract
Introduction CD8+ cytotoxic T lymphocytes (CTLs) are highly effective in defending against viral infections and tumours. They are activated through the recognition of peptide-MHC-I complex by the T-cell receptor (TCR) and co-stimulation. This cognate interaction promotes the organisation of intimate cell-cell connections that involve cytoskeleton rearrangement to enable effector function and clearance of the target cell. This is key for the asymmetric transport and mobilisation of lytic granules to the cell-cell contact, promoting directed secretion of lytic mediators such as granzymes and perforin. Mitochondria play a role in regulating CTL function by controlling processes such as calcium flux, providing the necessary energy through oxidative phosphorylation, and its own protein translation on 70S ribosomes. However, the effect of acute inhibition of cytosolic translation in the rapid response after TCR has not been studied in mature CTLs. Methods Here, we investigated the importance of cytosolic protein synthesis in human CTLs after early TCR activation and CD28 co-stimulation for the dynamic reorganisation of the cytoskeleton, mitochondria, and lytic granules through short-term chemical inhibition of 80S ribosomes by cycloheximide and 80S and 70S by puromycin. Results We observed that eukaryotic ribosome function is required to allow proper asymmetric reorganisation of the tubulin cytoskeleton and mitochondria and mTOR pathway activation early upon TCR activation in human primary CTLs. Discussion Cytosolic protein translation is required to increase glucose metabolism and degranulation capacity upon TCR activation and thus to regulate the full effector function of human CTLs.
Collapse
Affiliation(s)
- Álvaro Gómez-Morón
- Immunology Service, Instituto de Investigación Sanitaria del Hospital Universitario La Princesa, IIS- Princesa, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense de Madrid and 12 de Octubre Health Research Institute (imas12), Madrid, Spain
| | - Ilya Tsukalov
- Immunology Service, Instituto de Investigación Sanitaria del Hospital Universitario La Princesa, IIS- Princesa, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Medicine Faculty, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Camila Scagnetti
- Immunology Service, Instituto de Investigación Sanitaria del Hospital Universitario La Princesa, IIS- Princesa, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Videomicroscopy Unit, Instituto de Investigación Sanitaria del Hospital Universitario La Princesa, IIS-Princesa, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Clara Pertusa
- Immunology Service, Instituto de Investigación Sanitaria del Hospital Universitario La Princesa, IIS- Princesa, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Marta Lozano-Prieto
- Immunology Service, Instituto de Investigación Sanitaria del Hospital Universitario La Princesa, IIS- Princesa, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain
| | - Pedro Martínez-Fleta
- Immunology Service, Instituto de Investigación Sanitaria del Hospital Universitario La Princesa, IIS- Princesa, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Silvia Requena
- Immunology Service, Instituto de Investigación Sanitaria del Hospital Universitario La Princesa, IIS- Princesa, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Pilar Martín
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain
- Area of Vascular Pathophysiology, Laboratory of Regulatory Molecules of Inflammatory Processes, Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, Spain
| | - Aranzazu Alfranca
- Immunology Service, Instituto de Investigación Sanitaria del Hospital Universitario La Princesa, IIS- Princesa, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Medicine Faculty, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain
| | - Enrique Martin-Gayo
- Immunology Service, Instituto de Investigación Sanitaria del Hospital Universitario La Princesa, IIS- Princesa, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Medicine Faculty, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red Enfermedades Infecciosas (CIBERINFECC), Instituto de Salud Carlos III, Madrid, Spain
| | - Noa B Martin-Cofreces
- Immunology Service, Instituto de Investigación Sanitaria del Hospital Universitario La Princesa, IIS- Princesa, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Videomicroscopy Unit, Instituto de Investigación Sanitaria del Hospital Universitario La Princesa, IIS-Princesa, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain
- Area of Vascular Pathophysiology, Laboratory of Intercellular Communication, Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, Spain
| |
Collapse
|
3
|
Antolínez-Fernández Á, Esteban-Ramos P, Fernández-Moreno MÁ, Clemente P. Molecular pathways in mitochondrial disorders due to a defective mitochondrial protein synthesis. Front Cell Dev Biol 2024; 12:1410245. [PMID: 38855161 PMCID: PMC11157125 DOI: 10.3389/fcell.2024.1410245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/09/2024] [Indexed: 06/11/2024] Open
Abstract
Mitochondria play a central role in cellular metabolism producing the necessary ATP through oxidative phosphorylation. As a remnant of their prokaryotic past, mitochondria contain their own genome, which encodes 13 subunits of the oxidative phosphorylation system, as well as the tRNAs and rRNAs necessary for their translation in the organelle. Mitochondrial protein synthesis depends on the import of a vast array of nuclear-encoded proteins including the mitochondrial ribosome protein components, translation factors, aminoacyl-tRNA synthetases or assembly factors among others. Cryo-EM studies have improved our understanding of the composition of the mitochondrial ribosome and the factors required for mitochondrial protein synthesis and the advances in next-generation sequencing techniques have allowed for the identification of a growing number of genes involved in mitochondrial pathologies with a defective translation. These disorders are often multisystemic, affecting those tissues with a higher energy demand, and often present with neurodegenerative phenotypes. In this article, we review the known proteins required for mitochondrial translation, the disorders that derive from a defective mitochondrial protein synthesis and the animal models that have been established for their study.
Collapse
Affiliation(s)
- Álvaro Antolínez-Fernández
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
| | - Paula Esteban-Ramos
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
| | - Miguel Ángel Fernández-Moreno
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
| | - Paula Clemente
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
| |
Collapse
|
4
|
Hughes LA, Rackham O, Filipovska A. Illuminating mitochondrial translation through mouse models. Hum Mol Genet 2024; 33:R61-R79. [PMID: 38779771 PMCID: PMC11112386 DOI: 10.1093/hmg/ddae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/22/2024] [Accepted: 01/31/2024] [Indexed: 05/25/2024] Open
Abstract
Mitochondria are hubs of metabolic activity with a major role in ATP conversion by oxidative phosphorylation (OXPHOS). The mammalian mitochondrial genome encodes 11 mRNAs encoding 13 OXPHOS proteins along with 2 rRNAs and 22 tRNAs, that facilitate their translation on mitoribosomes. Maintaining the internal production of core OXPHOS subunits requires modulation of the mitochondrial capacity to match the cellular requirements and correct insertion of particularly hydrophobic proteins into the inner mitochondrial membrane. The mitochondrial translation system is essential for energy production and defects result in severe, phenotypically diverse diseases, including mitochondrial diseases that typically affect postmitotic tissues with high metabolic demands. Understanding the complex mechanisms that underlie the pathologies of diseases involving impaired mitochondrial translation is key to tailoring specific treatments and effectively targeting the affected organs. Disease mutations have provided a fundamental, yet limited, understanding of mitochondrial protein synthesis, since effective modification of the mitochondrial genome has proven challenging. However, advances in next generation sequencing, cryoelectron microscopy, and multi-omic technologies have revealed unexpected and unusual features of the mitochondrial protein synthesis machinery in the last decade. Genome editing tools have generated unique models that have accelerated our mechanistic understanding of mitochondrial translation and its physiological importance. Here we review the most recent mouse models of disease pathogenesis caused by defects in mitochondrial protein synthesis and discuss their value for preclinical research and therapeutic development.
Collapse
Affiliation(s)
- Laetitia A Hughes
- Telethon Kids Institute, Northern Entrance, Perth Children’s Hospital, 15 Hospital Avenue, Nedlands, WA 6009, Australia
- Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, 35 Stirling Highway, Crawley, WA 6009, The University of Western Australia, Crawley, WA 6009, Australia
| | - Oliver Rackham
- Telethon Kids Institute, Northern Entrance, Perth Children’s Hospital, 15 Hospital Avenue, Nedlands, WA 6009, Australia
- Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, 35 Stirling Highway, Crawley, WA 6009, The University of Western Australia, Crawley, WA 6009, Australia
- Curtin Medical School, Curtin University, Kent Street, Bentley, WA 6102, Australia
- Curtin Health Innovation Research Institute, Curtin University, Kent Street, Bentley, WA 6102, Australia
| | - Aleksandra Filipovska
- Telethon Kids Institute, Northern Entrance, Perth Children’s Hospital, 15 Hospital Avenue, Nedlands, WA 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, 35 Stirling Highway, Crawley, WA 6009, The University of Western Australia, Crawley, WA 6009, Australia
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 19 Innovation Walk, Clayton, Clayton, VIC 3168, Australia
| |
Collapse
|
5
|
Krüger A, Kovalchuk D, Shiriaev D, Rorbach J. Decoding the Enigma: Translation Termination in Human Mitochondria. Hum Mol Genet 2024; 33:R42-R46. [PMID: 38779770 PMCID: PMC11112381 DOI: 10.1093/hmg/ddae032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 05/25/2024] Open
Abstract
Mitochondrial translation is a complex process responsible for the synthesis of essential proteins involved in oxidative phosphorylation, a fundamental pathway for cellular energy production. Central to this process is the termination phase, where dedicated factors play a pivotal role in ensuring accurate and timely protein production. This review provides a comprehensive overview of the current understanding of translation termination in human mitochondria, emphasizing structural features and molecular functions of two mitochondrial termination factors mtRF1 and mtRF1a.
Collapse
Affiliation(s)
- Annika Krüger
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, Solna 171 65, Sweden
| | - Daria Kovalchuk
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, Solna 171 65, Sweden
| | - Dmitrii Shiriaev
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, Solna 171 65, Sweden
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, Solna 171 65, Sweden
| |
Collapse
|
6
|
Jung SJ, Sridhara S, Ott M. Early steps in the biogenesis of mitochondrially encoded oxidative phosphorylation subunits. IUBMB Life 2024; 76:125-139. [PMID: 37712772 DOI: 10.1002/iub.2784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/10/2023] [Indexed: 09/16/2023]
Abstract
The complexes mediating oxidative phosphorylation (OXPHOS) in the inner mitochondrial membrane consist of proteins encoded in the nuclear or the mitochondrial DNA. The mitochondrially encoded membrane proteins (mito-MPs) represent the catalytic core of these complexes and follow complicated pathways for biogenesis. Owing to their overall hydrophobicity, mito-MPs are co-translationally inserted into the inner membrane by the Oxa1 insertase. After insertion, OXPHOS biogenesis factors mediate the assembly of mito-MPs into complexes and participate in the regulation of mitochondrial translation, while protein quality control factors recognize and degrade faulty or excess proteins. This review summarizes the current understanding of these early steps occurring during the assembly of mito-MPs by concentrating on results obtained in the model organism baker's yeast.
Collapse
Affiliation(s)
- Sung-Jun Jung
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Sagar Sridhara
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Martin Ott
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| |
Collapse
|
7
|
Box JM, Anderson JM, Stuart RA. Mutation of the PEBP-like domain of the mitoribosomal MrpL35/mL38 protein results in production of nascent chains with impaired capacity to assemble into OXPHOS complexes. Mol Biol Cell 2023; 34:ar131. [PMID: 37792492 PMCID: PMC10848944 DOI: 10.1091/mbc.e23-04-0132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023] Open
Abstract
Located in the central protuberance region of the mitoribosome and mitospecific mL38 proteins display homology to PEBP (Phosphatidylethanolamine Binding Protein) proteins, a diverse family of proteins reported to bind anionic substrates/ligands and implicated in cellular signaling and differentiation pathways. In this study, we have performed a mutational analysis of the yeast mitoribosomal protein MrpL35/mL38 and demonstrate that mutation of the PEBP-invariant ligand binding residues Asp(D)232 and Arg(R)288 impacted MrpL35/mL38's ability to support OXPHOS-based growth of the cell. Furthermore, our data indicate these residues exist in a functionally important charged microenvironment, which also includes Asp(D)167 of MrpL35/mL38 and Arg(R)127 of the neighboring Mrp7/bL27m protein. We report that mutation of each of these charged residues resulted in a strong reduction in OXPHOS complex levels that was not attributed to a corresponding inhibition of the mitochondrial translation process. Rather, our findings indicate that a disconnect exists in these mutants between the processes of mitochondrial protein translation and the events required to ensure the competency and/or availability of the newly synthesized proteins to assemble into OXPHOS enzymes. Based on our findings, we postulate that the PEBP-homology domain of MrpL35/mL38, together with its partner Mrp7/bL27m, form a key regulatory region of the mitoribosome.
Collapse
Affiliation(s)
- Jodie M. Box
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233
| | - Jessica M. Anderson
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233
| | - Rosemary A. Stuart
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233
| |
Collapse
|
8
|
Iyer KV, Müller M, Tittel LS, Winz ML. Molecular Highway Patrol for Ribosome Collisions. Chembiochem 2023; 24:e202300264. [PMID: 37382189 DOI: 10.1002/cbic.202300264] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 06/25/2023] [Accepted: 06/28/2023] [Indexed: 06/30/2023]
Abstract
During translation, messenger RNAs (mRNAs) are decoded by ribosomes which can stall for various reasons. These include chemical damage, codon composition, starvation, or translation inhibition. Trailing ribosomes can collide with stalled ribosomes, potentially leading to dysfunctional or toxic proteins. Such aberrant proteins can form aggregates and favor diseases, especially neurodegeneration. To prevent this, both eukaryotes and bacteria have evolved different pathways to remove faulty nascent peptides, mRNAs and defective ribosomes from the collided complex. In eukaryotes, ubiquitin ligases play central roles in triggering downstream responses and several complexes have been characterized that split affected ribosomes and facilitate degradation of the various components. As collided ribosomes signal translation stress to affected cells, in eukaryotes additional stress response pathways are triggered when collisions are sensed. These pathways inhibit translation and modulate cell survival and immune responses. Here, we summarize the current state of knowledge about rescue and stress response pathways triggered by ribosome collisions.
Collapse
Affiliation(s)
- Kaushik Viswanathan Iyer
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Max Müller
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Lena Sophie Tittel
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Marie-Luise Winz
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| |
Collapse
|
9
|
Yadav S, Shah D, Dalai P, Agrawal-Rajput R. The tale of antibiotics beyond antimicrobials: Expanding horizons. Cytokine 2023; 169:156285. [PMID: 37393846 DOI: 10.1016/j.cyto.2023.156285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 06/02/2023] [Accepted: 06/24/2023] [Indexed: 07/04/2023]
Abstract
Antibiotics had proved to be a godsend for mankind since their discovery. They were once the magical solution to the vexing problem of infection-related deaths. German scientist Paul Ehrlich had termed salvarsan as the silver bullet to treatsyphilis.As time passed, the magic of newly discovered silver bullets got tarnished with raging antibiotic resistance among bacteria and associated side-effects. Still, antibiotics remain the primary line of treatment for bacterial infections. Our understanding of their chemical and biological activities has increased immensely with advancement in the research field. Non-antibacterial effects of antibiotics are studied extensively to optimise their safer, broad-range use. These non-antibacterial effects could be both useful and harmful to us. Various researchers across the globe including our lab are studying the direct/indirect effects and molecular mechanisms behind these non-antibacterial effects of antibiotics. So, it is interesting for us to sum up the available literature. In this review, we have briefed the possible reason behind the non-antibacterial effects of antibiotics, owing to the endosymbiotic origin of host mitochondria. We further discuss the physiological and immunomodulatory effects of antibiotics. We then extend the review to discuss molecular mechanisms behind the plausible use of antibiotics as anticancer agents.
Collapse
Affiliation(s)
- Shivani Yadav
- Immunology Lab, Department of Biotechnology and Bioengineering, Indian Institute of Advanced Research, Gandhinagar, India
| | - Dhruvi Shah
- Immunology Lab, Department of Biotechnology and Bioengineering, Indian Institute of Advanced Research, Gandhinagar, India
| | - Parmeswar Dalai
- Immunology Lab, Department of Biotechnology and Bioengineering, Indian Institute of Advanced Research, Gandhinagar, India
| | - Reena Agrawal-Rajput
- Immunology Lab, Department of Biotechnology and Bioengineering, Indian Institute of Advanced Research, Gandhinagar, India.
| |
Collapse
|
10
|
Nadler F, Richter-Dennerlein R. Translation termination in human mitochondria - substrate specificity of mitochondrial release factors. Biol Chem 2023; 404:769-779. [PMID: 37377370 DOI: 10.1515/hsz-2023-0127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 06/19/2023] [Indexed: 06/29/2023]
Abstract
Mitochondria are the essential players in eukaryotic ATP production by oxidative phosphorylation, which relies on the maintenance and accurate expression of the mitochondrial genome. Even though the basic principles of translation are conserved due to the descendance from a bacterial ancestor, some deviations regarding translation factors as well as mRNA characteristics and the applied genetic code are present in human mitochondria. Together, these features are certain challenges during translation the mitochondrion has to handle. Here, we discuss the current knowledge regarding mitochondrial translation focusing on the termination process and the associated quality control mechanisms. We describe how mtRF1a resembles bacterial RF1 mechanistically and summarize in vitro and recent in vivo data leading to the conclusion of mtRF1a being the major mitochondrial release factor. On the other hand, we discuss the ongoing debate about the function of the second codon-dependent mitochondrial release factor mtRF1 regarding its role as a specialized termination factor. Finally, we link defects in mitochondrial translation termination to the activation of mitochondrial rescue mechanisms highlighting the importance of ribosome-associated quality control for sufficient respiratory function and therefore for human health.
Collapse
Affiliation(s)
- Franziska Nadler
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Ricarda Richter-Dennerlein
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, D-37075 Göttingen, Germany
- Goettingen Center for Molecular Biosciences, University of Göttingen, D-37077 Göttingen, Germany
| |
Collapse
|
11
|
Saurer M, Leibundgut M, Nadimpalli HP, Scaiola A, Schönhut T, Lee RG, Siira SJ, Rackham O, Dreos R, Lenarčič T, Kummer E, Gatfield D, Filipovska A, Ban N. Molecular basis of translation termination at noncanonical stop codons in human mitochondria. Science 2023; 380:531-536. [PMID: 37141370 DOI: 10.1126/science.adf9890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The genetic code that specifies the identity of amino acids incorporated into proteins during protein synthesis is almost universally conserved. Mitochondrial genomes feature deviations from the standard genetic code, including the reassignment of two arginine codons to stop codons. The protein required for translation termination at these noncanonical stop codons to release the newly synthesized polypeptides is not currently known. In this study, we used gene editing and ribosomal profiling in combination with cryo-electron microscopy to establish that mitochondrial release factor 1 (mtRF1) detects noncanonical stop codons in human mitochondria by a previously unknown mechanism of codon recognition. We discovered that binding of mtRF1 to the decoding center of the ribosome stabilizes a highly unusual conformation in the messenger RNA in which the ribosomal RNA participates in specific recognition of the noncanonical stop codons.
Collapse
Affiliation(s)
- Martin Saurer
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Marc Leibundgut
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | | | - Alain Scaiola
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Tanja Schönhut
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Richard G Lee
- Harry Perkins Institute of Medical Research, The University of Western Australia, Nedlands, Western Australia 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, The University of Western Australia, Nedlands, Western Australia 6009, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, Western Australia, Australia
| | - Stefan J Siira
- Harry Perkins Institute of Medical Research, The University of Western Australia, Nedlands, Western Australia 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, The University of Western Australia, Nedlands, Western Australia 6009, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, The University of Western Australia, Nedlands, Western Australia 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, The University of Western Australia, Nedlands, Western Australia 6009, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, Western Australia, Australia
- Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia 6102, Australia
| | - René Dreos
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Tea Lenarčič
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Eva Kummer
- Novo Nordisk Foundation Center for Protein Research, Protein Structure and Function Program, Blegdamsvej 3B, 2200 København N, Denmark
| | - David Gatfield
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, The University of Western Australia, Nedlands, Western Australia 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, The University of Western Australia, Nedlands, Western Australia 6009, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, Western Australia, Australia
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| |
Collapse
|
12
|
Krüger A, Remes C, Shiriaev DI, Liu Y, Spåhr H, Wibom R, Atanassov I, Nguyen MD, Cooperman BS, Rorbach J. Human mitochondria require mtRF1 for translation termination at non-canonical stop codons. Nat Commun 2023; 14:30. [PMID: 36596788 PMCID: PMC9810596 DOI: 10.1038/s41467-022-35684-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/19/2022] [Indexed: 01/04/2023] Open
Abstract
The mitochondrial translation machinery highly diverged from its bacterial counterpart. This includes deviation from the universal genetic code, with AGA and AGG codons lacking cognate tRNAs in human mitochondria. The locations of these codons at the end of COX1 and ND6 open reading frames, respectively, suggest they might function as stop codons. However, while the canonical stop codons UAA and UAG are known to be recognized by mtRF1a, the release mechanism at AGA and AGG codons remains a debated issue. Here, we show that upon the loss of another member of the mitochondrial release factor family, mtRF1, mitoribosomes accumulate specifically at AGA and AGG codons. Stalling of mitoribosomes alters COX1 transcript and protein levels, but not ND6 synthesis. In addition, using an in vitro reconstituted mitochondrial translation system, we demonstrate the specific peptide release activity of mtRF1 at the AGA and AGG codons. Together, our results reveal the role of mtRF1 in translation termination at non-canonical stop codons in mitochondria.
Collapse
Affiliation(s)
- Annika Krüger
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65, Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Cristina Remes
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Dmitrii Igorevich Shiriaev
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65, Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Yong Liu
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65, Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Spåhr
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65, Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Rolf Wibom
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ilian Atanassov
- Proteomics Core Facility, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931, Cologne, Germany
| | - Minh Duc Nguyen
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65, Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Barry S Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65, Solna, Sweden. .,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden. .,S.T.I.A.S: Stellenbosch Institute for Advanced Study, Marais Rd, Mostertsdrift, Stellenbosch, 7600, South Africa.
| |
Collapse
|
13
|
Chrzanowska-Lightowlers ZM, Lightowlers RN. Translation in Mitochondrial Ribosomes. Methods Mol Biol 2023; 2661:53-72. [PMID: 37166631 DOI: 10.1007/978-1-0716-3171-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Mitochondrial protein synthesis is essential for the life of aerobic eukaryotes. Without it, oxidative phosphorylation cannot be coupled. Evolution has shaped a battery of factors and machinery that are key to production of just a handful of critical proteins. In this general concept chapter, we attempt to briefly summarize our current knowledge of the overall process in mitochondria from a variety of species, breaking this down to the four parts of translation: initiation, elongation, termination, and recycling. Where appropriate, we highlight differences between species and emphasize gaps in our understanding. Excitingly, with the current revolution in cryoelectron microscopy and mitochondrial genome editing, it is highly likely that many of these gaps will be resolved in the near future. However, the absence of a faithful in vitro reconstituted system to study mitochondrial translation is still problematic.
Collapse
Affiliation(s)
- Zofia M Chrzanowska-Lightowlers
- Wellcome Centre for Mitochondrial Research, Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, UK.
| | - Robert N Lightowlers
- Wellcome Centre for Mitochondrial Research, Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, UK
| |
Collapse
|
14
|
Ng KY, Lutfullahoglu Bal G, Richter U, Safronov O, Paulin L, Dunn CD, Paavilainen VO, Richer J, Newman WG, Taylor RW, Battersby BJ. Nonstop mRNAs generate a ground state of mitochondrial gene expression noise. SCIENCE ADVANCES 2022; 8:eabq5234. [PMID: 36399564 PMCID: PMC9674279 DOI: 10.1126/sciadv.abq5234] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 10/22/2022] [Indexed: 05/29/2023]
Abstract
A stop codon within the mRNA facilitates coordinated termination of protein synthesis, releasing the nascent polypeptide from the ribosome. This essential step in gene expression is impeded with transcripts lacking a stop codon, generating nonstop ribosome complexes. Here, we use deep sequencing to investigate sources of nonstop mRNAs generated from the human mitochondrial genome. We identify diverse types of nonstop mRNAs on mitochondrial ribosomes that are resistant to translation termination by canonical release factors. Failure to resolve these aberrations by the mitochondrial release factor in rescue (MTRFR) imparts a negative regulatory effect on protein synthesis that is associated with human disease. Our findings reveal a source of underlying noise in mitochondrial gene expression and the importance of responsive ribosome quality control mechanisms for cell fitness and human health.
Collapse
Affiliation(s)
- Kah Ying Ng
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Guleycan Lutfullahoglu Bal
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Uwe Richter
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Omid Safronov
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- DNA Sequencing and Genomics Laboratory, University of Helsinki, Helsinki, Finland
| | - Cory D. Dunn
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ville O. Paavilainen
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Julie Richer
- Department of Medical Genetics, Children’s Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - William G. Newman
- Manchester Centre for Genomic Medicine, St. Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Brendan J. Battersby
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| |
Collapse
|
15
|
Soto I, Couvillion M, Hansen KG, McShane E, Moran JC, Barrientos A, Churchman LS. Balanced mitochondrial and cytosolic translatomes underlie the biogenesis of human respiratory complexes. Genome Biol 2022; 23:170. [PMID: 35945592 PMCID: PMC9361522 DOI: 10.1186/s13059-022-02732-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 07/18/2022] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Oxidative phosphorylation (OXPHOS) complexes consist of nuclear and mitochondrial DNA-encoded subunits. Their biogenesis requires cross-compartment gene regulation to mitigate the accumulation of disproportionate subunits. To determine how human cells coordinate mitochondrial and nuclear gene expression processes, we tailored ribosome profiling for the unique features of the human mitoribosome. RESULTS We resolve features of mitochondrial translation initiation and identify a small ORF in the 3' UTR of MT-ND5. Analysis of ribosome footprints in five cell types reveals that average mitochondrial synthesis levels correspond precisely to cytosolic levels across OXPHOS complexes, and these average rates reflect the relative abundances of the complexes. Balanced mitochondrial and cytosolic synthesis does not rely on rapid feedback between the two translation systems, and imbalance caused by mitochondrial translation deficiency is associated with the induction of proteotoxicity pathways. CONCLUSIONS Based on our findings, we propose that human OXPHOS complexes are synthesized proportionally to each other, with mitonuclear balance relying on the regulation of OXPHOS subunit translation across cellular compartments, which may represent a proteostasis vulnerability.
Collapse
Affiliation(s)
- Iliana Soto
- Blavatnik Institute, Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Mary Couvillion
- Blavatnik Institute, Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Katja G Hansen
- Blavatnik Institute, Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Erik McShane
- Blavatnik Institute, Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - J Conor Moran
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Antoni Barrientos
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - L Stirling Churchman
- Blavatnik Institute, Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
| |
Collapse
|
16
|
Organization and expression of the mammalian mitochondrial genome. Nat Rev Genet 2022; 23:606-623. [PMID: 35459860 DOI: 10.1038/s41576-022-00480-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 02/07/2023]
Abstract
The mitochondrial genome encodes core subunits of the respiratory chain that drives oxidative phosphorylation and is, therefore, essential for energy conversion. Advances in high-throughput sequencing technologies and cryoelectron microscopy have shed light on the structure and organization of the mitochondrial genome and revealed unique mechanisms of mitochondrial gene regulation. New animal models of impaired mitochondrial protein synthesis have shown how the coordinated regulation of the cytoplasmic and mitochondrial translation machineries ensures the correct assembly of the respiratory chain complexes. These new technologies and disease models are providing a deeper understanding of mitochondrial genome organization and expression and of the diseases caused by impaired energy conversion, including mitochondrial, neurodegenerative, cardiovascular and metabolic diseases. They also provide avenues for the development of treatments for these conditions.
Collapse
|
17
|
Mammalian HEMK1 methylates glutamine residue of the GGQ motif of mitochondrial release factors. Sci Rep 2022; 12:4104. [PMID: 35260756 PMCID: PMC8904536 DOI: 10.1038/s41598-022-08061-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 03/01/2022] [Indexed: 02/04/2023] Open
Abstract
Despite limited reports on glutamine methylation, methylated glutamine is found to be highly conserved in a "GGQ" motif in both prokaryotes and eukaryotes. In bacteria, glutamine methylation of peptide chain release factors 1/2 (RF1/2) by the enzyme PrmC is essential for translational termination and transcript recycling. Two PrmC homologs, HEMK1 and HEMK2, are found in mammals. In contrast to those of HEMK2, the biochemical properties and biological significance of HEMK1 remain largely unknown. In this study, we demonstrated that HEMK1 is an active methyltransferase for the glutamine residue of the GGQ motif of all four putative mitochondrial release factors (mtRFs)-MTRF1, MTRF1L, MRPL58, and MTRFR. In HEMK1-deficient HeLa cells, GGQ motif glutamine methylation was absent in all the mtRFs. We examined cell growth and mitochondrial properties, but disruption of the HEMK1 gene had no considerable impact on the overall cell growth, mtDNA copy number, mitochondrial membrane potential, and mitochondrial protein synthesis under regular culture condition with glucose as a carbon source. Furthermore, cell growth potential of HEMK1 KO cells was still maintained in the respiratory condition with galactose medium. Our results suggest that HEMK1 mediates the GGQ methylation of all four mtRFs in human cells; however, this specific modification seems mostly dispensable in cell growth and mitochondrial protein homeostasis at least for HeLa cells under fermentative culture condition.
Collapse
|
18
|
Apostolopoulos A, Iwasaki S. Into the matrix: current methods for mitochondrial translation studies. J Biochem 2022; 171:379-387. [PMID: 35080613 DOI: 10.1093/jb/mvac005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 01/18/2022] [Indexed: 11/12/2022] Open
Abstract
In addition to the cytoplasmic translation system, eukaryotic cells house additional protein synthesis machinery in mitochondria. The importance of this in organello translation is exemplified by clinical pathologies associated with mutations in mitochondrial translation factors. Although a detailed understanding of mitochondrial translation has long been awaited, quantitative, comprehensive, and spatiotemporal measurements have posed analytic challenges. The recent development of novel approaches for studying mitochondrial protein synthesis has overcome these issues and expands our understanding of the unique translation system. Here, we review the current technologies for the investigation of mitochondrial translation and the insights provided by their application.
Collapse
Affiliation(s)
- Antonios Apostolopoulos
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan.,RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Shintaro Iwasaki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan.,RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| |
Collapse
|
19
|
Nadler F, Lavdovskaia E, Richter-Dennerlein R. Maintaining mitochondrial ribosome function: The role of ribosome rescue and recycling factors. RNA Biol 2021; 19:117-131. [PMID: 34923906 PMCID: PMC8786322 DOI: 10.1080/15476286.2021.2015561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
The universally conserved process of protein biosynthesis is crucial for maintaining cellular homoeostasis and in eukaryotes, mitochondrial translation is essential for aerobic energy production. Mitochondrial ribosomes (mitoribosomes) are highly specialized to synthesize 13 core subunits of the oxidative phosphorylation (OXPHOS) complexes. Although the mitochondrial translation machinery traces its origin from a bacterial ancestor, it has acquired substantial differences within this endosymbiotic environment. The cycle of mitoribosome function proceeds through the conserved canonical steps of initiation, elongation, termination and mitoribosome recycling. However, when mitoribosomes operate in the context of limited translation factors or on aberrant mRNAs, they can become stalled and activation of rescue mechanisms is required. This review summarizes recent advances in the understanding of protein biosynthesis in mitochondria, focusing especially on the mechanistic and physiological details of translation termination, and mitoribosome recycling and rescue.
Collapse
Affiliation(s)
- Franziska Nadler
- Department of Cellular Biochemistry, University Medical Center Goettingen, Goettingen, Germany
| | - Elena Lavdovskaia
- Department of Cellular Biochemistry, University Medical Center Goettingen, Goettingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Goettingen, Germany
| | - Ricarda Richter-Dennerlein
- Department of Cellular Biochemistry, University Medical Center Goettingen, Goettingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Goettingen, Germany
| |
Collapse
|
20
|
Korostelev AA. Diversity and Similarity of Termination and Ribosome Rescue in Bacterial, Mitochondrial, and Cytoplasmic Translation. BIOCHEMISTRY (MOSCOW) 2021; 86:1107-1121. [PMID: 34565314 DOI: 10.1134/s0006297921090066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
When a ribosome encounters the stop codon of an mRNA, it terminates translation, releases the newly made protein, and is recycled to initiate translation on a new mRNA. Termination is a highly dynamic process in which release factors (RF1 and RF2 in bacteria; eRF1•eRF3•GTP in eukaryotes) coordinate peptide release with large-scale molecular rearrangements of the ribosome. Ribosomes stalled on aberrant mRNAs are rescued and recycled by diverse bacterial, mitochondrial, or cytoplasmic quality control mechanisms. These are catalyzed by rescue factors with peptidyl-tRNA hydrolase activity (bacterial ArfA•RF2 and ArfB, mitochondrial ICT1 and mtRF-R, and cytoplasmic Vms1), that are distinct from each other and from release factors. Nevertheless, recent structural studies demonstrate a remarkable similarity between translation termination and ribosome rescue mechanisms. This review describes how these pathways rely on inherent ribosome dynamics, emphasizing the active role of the ribosome in all translation steps.
Collapse
Affiliation(s)
- Andrei A Korostelev
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, USA.
| |
Collapse
|
21
|
Chicherin IV, Dukhalin SV, Khannanov RA, Baleva MV, Levitskii SA, Patrushev MV, Sergiev PV, Kamenski P. Functional Diversity of Mitochondrial Peptidyl-tRNA Hydrolase ICT1 in Human Cells. Front Mol Biosci 2021; 8:716885. [PMID: 34336930 PMCID: PMC8322449 DOI: 10.3389/fmolb.2021.716885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 06/30/2021] [Indexed: 11/13/2022] Open
Abstract
Mitochondria are energy producing organelles of the eukaryotic cell, involved in the synthesis of key metabolites, calcium homeostasis and apoptosis. Protein biosynthesis in these organelles is a relic of its endosymbiotic origin. While mitochondrial translational factors have homologues among prokaryotes, they possess a number of unique traits. Remarkably as many as four mammalian mitochondrial proteins possess a clear similarity with translation termination factors. The review focuses on the ICT1, which combines several functions. It is a non-canonical termination factor for protein biosynthesis, a rescue factor for stalled mitochondrial ribosomes, a structural protein and a regulator of proliferation, cell cycle, and apoptosis. Such a diversity of roles demonstrates the high functionality of mitochondrial translation associated proteins and their relationship with numerous processes occurring in a living cell.
Collapse
Affiliation(s)
- I V Chicherin
- Department of Molecular Biology, M.V.Lomonosov Moscow State University, Moscow, Russia.,National Research Center "Kurchatov Institute", NBICS Center, Moscow, Russia
| | - S V Dukhalin
- Department of Molecular Biology, M.V.Lomonosov Moscow State University, Moscow, Russia
| | - R A Khannanov
- Department of Molecular Biology, M.V.Lomonosov Moscow State University, Moscow, Russia
| | - M V Baleva
- Department of Molecular Biology, M.V.Lomonosov Moscow State University, Moscow, Russia
| | - S A Levitskii
- Department of Molecular Biology, M.V.Lomonosov Moscow State University, Moscow, Russia
| | - M V Patrushev
- National Research Center "Kurchatov Institute", NBICS Center, Moscow, Russia
| | - P V Sergiev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russia.,Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Institute of Functional Genomics, Lomonosov Moscow State University, Moscow, Russia
| | - P Kamenski
- Department of Molecular Biology, M.V.Lomonosov Moscow State University, Moscow, Russia
| |
Collapse
|
22
|
Wang F, Zhang D, Zhang D, Li P, Gao Y. Mitochondrial Protein Translation: Emerging Roles and Clinical Significance in Disease. Front Cell Dev Biol 2021; 9:675465. [PMID: 34277617 PMCID: PMC8280776 DOI: 10.3389/fcell.2021.675465] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/09/2021] [Indexed: 12/28/2022] Open
Abstract
Mitochondria are one of the most important organelles in cells. Mitochondria are semi-autonomous organelles with their own genetic system, and can independently replicate, transcribe, and translate mitochondrial DNA. Translation initiation, elongation, termination, and recycling of the ribosome are four stages in the process of mitochondrial protein translation. In this process, mitochondrial protein translation factors and translation activators, mitochondrial RNA, and other regulatory factors regulate mitochondrial protein translation. Mitochondrial protein translation abnormalities are associated with a variety of diseases, including cancer, cardiovascular diseases, and nervous system diseases. Mutation or deletion of various mitochondrial protein translation factors and translation activators leads to abnormal mitochondrial protein translation. Mitochondrial tRNAs and mitochondrial ribosomal proteins are essential players during translation and mutations in genes encoding them represent a large fraction of mitochondrial diseases. Moreover, there is crosstalk between mitochondrial protein translation and cytoplasmic translation, and the imbalance between mitochondrial protein translation and cytoplasmic translation can affect some physiological and pathological processes. This review summarizes the regulation of mitochondrial protein translation factors, mitochondrial ribosomal proteins, mitochondrial tRNAs, and mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) in the mitochondrial protein translation process and its relationship with diseases. The regulation of mitochondrial protein translation and cytoplasmic translation in multiple diseases is also summarized.
Collapse
Affiliation(s)
- Fei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Deyu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.,Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, China
| |
Collapse
|
23
|
Kummer E, Schubert KN, Schoenhut T, Scaiola A, Ban N. Structural basis of translation termination, rescue, and recycling in mammalian mitochondria. Mol Cell 2021; 81:2566-2582.e6. [PMID: 33878294 DOI: 10.1016/j.molcel.2021.03.042] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/12/2021] [Accepted: 03/24/2021] [Indexed: 12/26/2022]
Abstract
The mitochondrial translation system originates from a bacterial ancestor but has substantially diverged in the course of evolution. Here, we use single-particle cryo-electron microscopy (cryo-EM) as a screening tool to identify mitochondrial translation termination mechanisms and to describe them in molecular detail. We show how mitochondrial release factor 1a releases the nascent chain from the ribosome when it encounters the canonical stop codons UAA and UAG. Furthermore, we define how the peptidyl-tRNA hydrolase ICT1 acts as a rescue factor on mitoribosomes that have stalled on truncated messages to recover them for protein synthesis. Finally, we present structural models detailing the process of mitochondrial ribosome recycling to explain how a dedicated elongation factor, mitochondrial EFG2 (mtEFG2), has specialized for cooperation with the mitochondrial ribosome recycling factor to dissociate the mitoribosomal subunits at the end of the translation process.
Collapse
Affiliation(s)
- Eva Kummer
- Swiss Federal Institute of Technology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland.
| | - Katharina Noel Schubert
- Swiss Federal Institute of Technology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Tanja Schoenhut
- Swiss Federal Institute of Technology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Alain Scaiola
- Swiss Federal Institute of Technology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Nenad Ban
- Swiss Federal Institute of Technology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland.
| |
Collapse
|
24
|
Zarechenskaia AS, Sergiev PV, Osterman IA. Quality Control Mechanisms in Bacterial Translation. Acta Naturae 2021; 13:32-44. [PMID: 34377554 PMCID: PMC8327144 DOI: 10.32607/actanaturae.11401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 05/15/2021] [Indexed: 12/24/2022] Open
Abstract
Ribosome stalling during translation significantly reduces cell viability, because cells have to spend resources on the synthesis of new ribosomes. Therefore, all bacteria have developed various mechanisms of ribosome rescue. Usually, the release of ribosomes is preceded by hydrolysis of the tRNA-peptide bond, but, in some cases, the ribosome can continue translation thanks to the activity of certain factors. This review describes the mechanisms of ribosome rescue thanks to trans-translation and the activity of the ArfA, ArfB, BrfA, ArfT, HflX, and RqcP/H factors, as well as continuation of translation via the action of EF-P, EF-4, and EttA. Despite the ability of some systems to duplicate each other, most of them have their unique functional role, related to the quality control of bacterial translation in certain abnormalities caused by mutations, stress cultivation conditions, or antibiotics.
Collapse
Affiliation(s)
- A. S. Zarechenskaia
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Moscow, 119992 Russia
| | - P. V. Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143028 Russia
- Lomonosov Moscow State University, Institute of functional genomics, Moscow, 119992 Russia
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119992 Russia
| | - I. A. Osterman
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143028 Russia
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119992 Russia
- Sirius University of Science and Technology, Genetics and Life Sciences Research Center, Sochi, 354340 Russia
| |
Collapse
|
25
|
Müller C, Crowe-McAuliffe C, Wilson DN. Ribosome Rescue Pathways in Bacteria. Front Microbiol 2021; 12:652980. [PMID: 33815344 PMCID: PMC8012679 DOI: 10.3389/fmicb.2021.652980] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/23/2021] [Indexed: 12/18/2022] Open
Abstract
Ribosomes that become stalled on truncated or damaged mRNAs during protein synthesis must be rescued for the cell to survive. Bacteria have evolved a diverse array of rescue pathways to remove the stalled ribosomes from the aberrant mRNA and return them to the free pool of actively translating ribosomes. In addition, some of these pathways target the damaged mRNA and the incomplete nascent polypeptide chain for degradation. This review highlights the recent developments in our mechanistic understanding of bacterial ribosomal rescue systems, including drop-off, trans-translation mediated by transfer-messenger RNA and small protein B, ribosome rescue by the alternative rescue factors ArfA and ArfB, as well as Bacillus ribosome rescue factor A, an additional rescue system found in some Gram-positive bacteria, such as Bacillus subtilis. Finally, we discuss the recent findings of ribosome-associated quality control in particular bacterial lineages mediated by RqcH and RqcP. The importance of rescue pathways for bacterial survival suggests they may represent novel targets for the development of new antimicrobial agents against multi-drug resistant pathogenic bacteria.
Collapse
Affiliation(s)
| | | | - Daniel N. Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| |
Collapse
|
26
|
Hoshino S, Kanemura R, Kurita D, Soutome Y, Himeno H, Takaine M, Watanabe M, Nameki N. A stalled-ribosome rescue factor Pth3 is required for mitochondrial translation against antibiotics in Saccharomyces cerevisiae. Commun Biol 2021; 4:300. [PMID: 33686140 PMCID: PMC7940416 DOI: 10.1038/s42003-021-01835-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 02/09/2021] [Indexed: 11/09/2022] Open
Abstract
Mitochondrial translation appears to involve two stalled-ribosome rescue factors (srRFs). One srRF is an ICT1 protein from humans that rescues a "non-stop" type of mitochondrial ribosomes (mitoribosomes) stalled on mRNA lacking a stop codon, while the other, C12orf65, reportedly has functions that overlap with those of ICT1; however, its primary role remains unclear. We herein demonstrated that the Saccharomyces cerevisiae homolog of C12orf65, Pth3 (Rso55), preferentially rescued antibiotic-dependent stalled mitoribosomes, which appear to represent a "no-go" type of ribosomes stalled on intact mRNA. On media containing a non-fermentable carbon source, which requires mitochondrial gene expression, respiratory growth was impaired significantly more by the deletion of PTH3 than that of the ICT1 homolog PTH4 in the presence of antibiotics that inhibit mitochondrial translation, such as tetracyclines and macrolides. Additionally, the in organello labeling of mitochondrial translation products and quantification of mRNA levels by quantitative RT-PCR suggested that in the presence of tetracycline, the deletion of PTH3, but not PTH4, reduced the protein expression of all eight mtDNA-encoded genes at the post-transcriptional or translational level. These results indicate that Pth3 can function as a mitochondrial srRF specific for ribosomes stalled by antibiotics and plays a role in antibiotic resistance in fungi.
Collapse
Affiliation(s)
- Soichiro Hoshino
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma, Japan
| | - Ryohei Kanemura
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma, Japan
| | - Daisuke Kurita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
| | - Yukihiro Soutome
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma, Japan
| | - Hyouta Himeno
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
| | - Masak Takaine
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Maebashi, Japan.,Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan
| | - Masakatsu Watanabe
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Nobukazu Nameki
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma, Japan.
| |
Collapse
|
27
|
Mechanisms and regulation of protein synthesis in mitochondria. Nat Rev Mol Cell Biol 2021; 22:307-325. [PMID: 33594280 DOI: 10.1038/s41580-021-00332-2] [Citation(s) in RCA: 167] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2021] [Indexed: 02/06/2023]
Abstract
Mitochondria are cellular organelles responsible for generation of chemical energy in the process called oxidative phosphorylation. They originate from a bacterial ancestor and maintain their own genome, which is expressed by designated, mitochondrial transcription and translation machineries that differ from those operating for nuclear gene expression. In particular, the mitochondrial protein synthesis machinery is structurally and functionally very different from that governing eukaryotic, cytosolic translation. Despite harbouring their own genetic information, mitochondria are far from being independent of the rest of the cell and, conversely, cellular fitness is closely linked to mitochondrial function. Mitochondria depend heavily on the import of nuclear-encoded proteins for gene expression and function, and hence engage in extensive inter-compartmental crosstalk to regulate their proteome. This connectivity allows mitochondria to adapt to changes in cellular conditions and also mediates responses to stress and mitochondrial dysfunction. With a focus on mammals and yeast, we review fundamental insights that have been made into the biogenesis, architecture and mechanisms of the mitochondrial translation apparatus in the past years owing to the emergence of numerous near-atomic structures and a considerable amount of biochemical work. Moreover, we discuss how cellular mitochondrial protein expression is regulated, including aspects of mRNA and tRNA maturation and stability, roles of auxiliary factors, such as translation regulators, that adapt mitochondrial translation rates, and the importance of inter-compartmental crosstalk with nuclear gene expression and cytosolic translation and how it enables integration of mitochondrial translation into the cellular context.
Collapse
|
28
|
Lee M, Matsunaga N, Akabane S, Yasuda I, Ueda T, Takeuchi-Tomita N. Reconstitution of mammalian mitochondrial translation system capable of correct initiation and long polypeptide synthesis from leaderless mRNA. Nucleic Acids Res 2021; 49:371-382. [PMID: 33300043 PMCID: PMC7797035 DOI: 10.1093/nar/gkaa1165] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/12/2020] [Accepted: 11/16/2020] [Indexed: 12/31/2022] Open
Abstract
Mammalian mitochondria have their own dedicated protein synthesis system, which produces 13 essential subunits of the oxidative phosphorylation complexes. We have reconstituted an in vitro translation system from mammalian mitochondria, utilizing purified recombinant mitochondrial translation factors, 55S ribosomes from pig liver mitochondria, and a tRNA mixture from either Escherichia coli or yeast. The system is capable of translating leaderless mRNAs encoding model proteins (DHFR and nanoLuciferase) or some mtDNA-encoded proteins. We show that a leaderless mRNA, encoding nanoLuciferase, is faithfully initiated without the need for any auxiliary factors other than IF-2mt and IF-3mt. We found that the ribosome-dependent GTPase activities of both the translocase EF-G1mt and the recycling factor EF-G2mt are insensitive to fusidic acid (FA), the translation inhibitor that targets bacterial EF-G homologs, and consequently the system is resistant to FA. Moreover, we demonstrate that a polyproline sequence in the protein causes 55S mitochondrial ribosome stalling, yielding ribosome nascent chain complexes. Analyses of the effects of the Mg concentration on the polyproline-mediated ribosome stalling suggested the unique regulation of peptide elongation by the mitoribosome. This system will be useful for analyzing the mechanism of translation initiation, and the interactions between the nascent peptide chain and the mitochondrial ribosome.
Collapse
Affiliation(s)
- Muhoon Lee
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Noriko Matsunaga
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Shiori Akabane
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan.,Department of Life Science, Rikkyo University, Tokyo, 171-8501, Japan
| | - Ippei Yasuda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Takuya Ueda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan.,Department of Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, Tokyo, Shinjuku 162-8480, Japan
| | - Nono Takeuchi-Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| |
Collapse
|
29
|
Lavdovskaia E, Denks K, Nadler F, Steube E, Linden A, Urlaub H, Rodnina MV, Richter-Dennerlein R. Dual function of GTPBP6 in biogenesis and recycling of human mitochondrial ribosomes. Nucleic Acids Res 2021; 48:12929-12942. [PMID: 33264405 PMCID: PMC7736812 DOI: 10.1093/nar/gkaa1132] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/19/2020] [Accepted: 11/09/2020] [Indexed: 01/01/2023] Open
Abstract
Translation and ribosome biogenesis in mitochondria require auxiliary factors that ensure rapid and accurate synthesis of mitochondrial proteins. Defects in translation are associated with oxidative phosphorylation deficiency and cause severe human diseases, but the exact roles of mitochondrial translation-associated factors are not known. Here we identify the functions of GTPBP6, a homolog of the bacterial ribosome-recycling factor HflX, in human mitochondria. Similarly to HflX, GTPBP6 facilitates the dissociation of ribosomes in vitro and in vivo. In contrast to HflX, GTPBP6 is also required for the assembly of mitochondrial ribosomes. GTPBP6 ablation leads to accumulation of late assembly intermediate(s) of the large ribosomal subunit containing ribosome biogenesis factors MTERF4, NSUN4, MALSU1 and the GTPases GTPBP5, GTPBP7 and GTPBP10. Our data show that GTPBP6 has a dual function acting in ribosome recycling and biogenesis. These findings contribute to our understanding of large ribosomal subunit assembly as well as ribosome recycling pathway in mitochondria.
Collapse
Affiliation(s)
- Elena Lavdovskaia
- Department of Cellular Biochemistry, University Medical Center Goettingen, D-37073 Goettingen, Germany.,Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Goettingen, Goettingen, Germany
| | - Kärt Denks
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Goettingen, Goettingen, Germany.,Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Goettingen, Germany
| | - Franziska Nadler
- Department of Cellular Biochemistry, University Medical Center Goettingen, D-37073 Goettingen, Germany
| | - Emely Steube
- Department of Cellular Biochemistry, University Medical Center Goettingen, D-37073 Goettingen, Germany
| | - Andreas Linden
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, D-37077 Goettingen, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Goettingen, D-37073 Goettingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, D-37077 Goettingen, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Goettingen, D-37073 Goettingen, Germany
| | - Marina V Rodnina
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Goettingen, Goettingen, Germany.,Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Goettingen, Germany
| | - Ricarda Richter-Dennerlein
- Department of Cellular Biochemistry, University Medical Center Goettingen, D-37073 Goettingen, Germany.,Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Goettingen, Goettingen, Germany
| |
Collapse
|
30
|
Carbone CE, Demo G, Madireddy R, Svidritskiy E, Korostelev AA. ArfB can displace mRNA to rescue stalled ribosomes. Nat Commun 2020; 11:5552. [PMID: 33144582 PMCID: PMC7641280 DOI: 10.1038/s41467-020-19370-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/08/2020] [Indexed: 12/16/2022] Open
Abstract
Ribosomes stalled during translation must be rescued to replenish the pool of translation-competent ribosomal subunits. Bacterial alternative rescue factor B (ArfB) releases nascent peptides from ribosomes stalled on mRNAs truncated at the A site, allowing ribosome recycling. Prior structural work revealed that ArfB recognizes such ribosomes by inserting its C-terminal α-helix into the vacant mRNA tunnel. In this work, we report that ArfB can efficiently recognize a wider range of mRNA substrates, including longer mRNAs that extend beyond the A-site codon. Single-particle cryo-EM unveils that ArfB employs two modes of function depending on the mRNA length. ArfB acts as a monomer to accommodate a shorter mRNA in the ribosomal A site. By contrast, longer mRNAs are displaced from the mRNA tunnel by more than 20 Å and are stabilized in the intersubunit space by dimeric ArfB. Uncovering distinct modes of ArfB function resolves conflicting biochemical and structural studies, and may lead to re-examination of other ribosome rescue pathways, whose functions depend on mRNA lengths.
Collapse
Affiliation(s)
- Christine E Carbone
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts, 01605, United States
| | - Gabriel Demo
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts, 01605, United States
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Rohini Madireddy
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts, 01605, United States
- Medicago Inc., 7 Triangle drive, Durham, NC, 27713, USA
| | - Egor Svidritskiy
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts, 01605, United States.
- Sanofi, 49 New York Ave, Suite 3660, Framingham, MA, 01701, USA.
| | - Andrei A Korostelev
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts, 01605, United States.
| |
Collapse
|
31
|
Chan KH, Petrychenko V, Mueller C, Maracci C, Holtkamp W, Wilson DN, Fischer N, Rodnina MV. Mechanism of ribosome rescue by alternative ribosome-rescue factor B. Nat Commun 2020; 11:4106. [PMID: 32796827 PMCID: PMC7427801 DOI: 10.1038/s41467-020-17853-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/15/2020] [Indexed: 12/11/2022] Open
Abstract
Alternative ribosome-rescue factor B (ArfB) rescues ribosomes stalled on non-stop mRNAs by releasing the nascent polypeptide from the peptidyl-tRNA. By rapid kinetics we show that ArfB selects ribosomes stalled on short truncated mRNAs, rather than on longer mRNAs mimicking pausing on rare codon clusters. In combination with cryo-electron microscopy we dissect the multistep rescue pathway of ArfB, which first binds to ribosomes very rapidly regardless of the mRNA length. The selectivity for shorter mRNAs arises from the subsequent slow engagement step, as it requires longer mRNA to shift to enable ArfB binding. Engagement results in specific interactions of the ArfB C-terminal domain with the mRNA entry channel, which activates peptidyl-tRNA hydrolysis by the N-terminal domain. These data reveal how protein dynamics translate into specificity of substrate recognition and provide insights into the action of a putative rescue factor in mitochondria. Rescue of ribosomes stalled on non-stop mRNA is essential for cell viability, and several rescue systems to resolve stalling exist in bacteria. Here, the authors use rapid kinetics and cryo-EM to reveal the pathway and selectivity mechanism of ArfB-mediated ribosome rescue.
Collapse
Affiliation(s)
- Kai-Hsin Chan
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Valentyn Petrychenko
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Claudia Mueller
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Cristina Maracci
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Wolf Holtkamp
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.,Paul-Ehrlich-Institut, Paul-Ehrlich-Straße 51-59, 63225, Langen, Germany
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Niels Fischer
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
| |
Collapse
|
32
|
Žihala D, Salamonová J, Eliáš M. Evolution of the genetic code in the mitochondria of Labyrinthulea (Stramenopiles). Mol Phylogenet Evol 2020; 152:106908. [PMID: 32702525 DOI: 10.1016/j.ympev.2020.106908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/30/2020] [Accepted: 07/15/2020] [Indexed: 02/02/2023]
Abstract
Mitochondrial translation often exhibits departures from the standard genetic code, but the full spectrum of these changes has certainly not yet been described and the molecular mechanisms behind the changes in codon meaning are rarely studied. Here we report a detailed analysis of the mitochondrial genetic code in the stramenopile group Labyrinthulea (Labyrinthulomycetes) and their relatives. In the genus Aplanochytrium, UAG is not a termination codon but encodes tyrosine, in contrast to the unaffected meaning of the UAA codon. This change is evolutionarily independent of the reassignment of both UAG and UAA as tyrosine codons recently reported from two uncultivated labyrinthuleans (S2 and S4), which we show are not thraustochytrids as proposed before, but represent the clade LAB14 previously recognised in environmental 18S rRNA gene surveys. We provide rigorous evidence that the UUA codon in the mitochondria of all labyrinthuleans serves as a termination codon instead of encoding leucine, and propose that a sense-to-stop reassignment has also affected the AGG and AGA codons in the LAB14 clade. The distribution of the different forms of sense-to-stop and stop-to-sense reassignments correlates with specific modifications of the mitochondrial release factor mtRF2a in different subsets of labyrinthuleans, and with the unprecedented loss of mtRF1a in Aplanochytrium and perhaps also in the LAB14 clade, pointing towards a possible mechanistic basis of the code changes observed. Curiously, we show that labyrinthulean mitochondria also exhibit a sense-to-sense codon reassignment, manifested as AUA encoding methionine instead of isoleucine. Furthermore, we show that this change evolved independently in the uncultivated stramenopile lineage MAST8b, together with the reassignment of the AGR codons from arginine to serine. Altogether, our study has uncovered novel variants of the mitochondrial genetic code and previously unknown modifications of the mitochondrial translation machinery, further enriching our understanding of the rules governing the evolution of one of the central molecular process in the cell.
Collapse
Affiliation(s)
- David Žihala
- Department of Biology and Ecology & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Jana Salamonová
- Department of Biology and Ecology & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Marek Eliáš
- Department of Biology and Ecology & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic.
| |
Collapse
|
33
|
Alonso-Garrido M, Manyes L, Pralea IE, Iuga CA. Mitochondrial proteomics profile points oxidative phosphorylation as main target for beauvericin and enniatin B mixture. Food Chem Toxicol 2020; 141:111432. [PMID: 32407736 DOI: 10.1016/j.fct.2020.111432] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 05/04/2020] [Accepted: 05/09/2020] [Indexed: 01/01/2023]
Abstract
Beauvericin (BEA) and enniatin B (EN B) are non-legislated Fusarium mycotoxins usually found in cereal and cereal-based products all around the world. By the proteomic analysis of mitochondria enriched extracts from Jurkat cells exposed for 24 h to three concentrations of BEA:EN B (0.01-0.1-0.5 μM), a number of 1821 proteins (202 mitochondrial) were identified and relatively quantified. 340 proteins (59 mitochondrial) were statistically significant altered in our samples (Anova p-value ≤ 0.05 and fold change (FC) ≥1.5). The protein mitochondrial translational release factor 1 like (MTRF1L) was the most abundant protein in the three mycotoxin exposures studied. The mycotoxins mixture exposure induced concentration dependent changes at mitochondrial proteins levels that mainly involve inner and outer membrane complexes, Electron Transport Chain (ETC) and ribosomes. These results showed alteration of proteins levels related to oxidative phosphorylation, metabolic and neurodegenerative diseases related pathways.
Collapse
Affiliation(s)
- M Alonso-Garrido
- Laboratory of Food Chemistry and Toxicology, Faculty of Pharmacy, University of Valencia, Burjassot, Spain.
| | - L Manyes
- Laboratory of Food Chemistry and Toxicology, Faculty of Pharmacy, University of Valencia, Burjassot, Spain
| | - I E Pralea
- Department of Proteomics and Metabolomics, MedFuture Research Center for Advanced Medicine, "Iuliu Hațieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - C A Iuga
- Department of Proteomics and Metabolomics, MedFuture Research Center for Advanced Medicine, "Iuliu Hațieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania; Department of Pharmaceutical Analysis, Faculty of Pharmacy, "Iuliu Hațieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| |
Collapse
|
34
|
Ayyub SA, Gao F, Lightowlers RN, Chrzanowska-Lightowlers ZM. Rescuing stalled mammalian mitoribosomes - what can we learn from bacteria? J Cell Sci 2020; 133:133/1/jcs231811. [PMID: 31896602 DOI: 10.1242/jcs.231811] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In the canonical process of translation, newly completed proteins escape from the ribosome following cleavage of the ester bond that anchors the polypeptide to the P-site tRNA, after which the ribosome can be recycled to initiate a new round of translation. Not all protein synthesis runs to completion as various factors can impede the progression of ribosomes. Rescuing of stalled ribosomes in mammalian mitochondria, however, does not share the same mechanisms that many bacteria use. The classic method for rescuing bacterial ribosomes is trans-translation. The key components of this system are absent from mammalian mitochondria; however, four members of a translation termination factor family are present, with some evidence of homology to members of a bacterial back-up rescue system. To date, there is no definitive demonstration of any other member of this family functioning in mitoribosome rescue. Here, we provide an overview of the processes and key players of canonical translation termination in both bacteria and mammalian mitochondria, followed by a perspective of the bacterial systems used to rescue stalled ribosomes. We highlight any similarities or differences with the mitochondrial translation release factors, and suggest potential roles for these proteins in ribosome rescue in mammalian mitochondria.
Collapse
Affiliation(s)
- Shreya Ahana Ayyub
- The Wellcome Centre for Mitochondrial Research, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Fei Gao
- The Wellcome Centre for Mitochondrial Research, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Robert N Lightowlers
- The Wellcome Centre for Mitochondrial Research, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Zofia M Chrzanowska-Lightowlers
- The Wellcome Centre for Mitochondrial Research, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| |
Collapse
|
35
|
Busch JD, Cipullo M, Atanassov I, Bratic A, Silva Ramos E, Schöndorf T, Li X, Pearce SF, Milenkovic D, Rorbach J, Larsson NG. MitoRibo-Tag Mice Provide a Tool for In Vivo Studies of Mitoribosome Composition. Cell Rep 2019; 29:1728-1738.e9. [PMID: 31693908 PMCID: PMC6859486 DOI: 10.1016/j.celrep.2019.09.080] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 08/14/2019] [Accepted: 09/26/2019] [Indexed: 11/16/2022] Open
Abstract
Mitochondria harbor specialized ribosomes (mitoribosomes) necessary for the synthesis of key membrane proteins of the oxidative phosphorylation (OXPHOS) machinery located in the mitochondrial inner membrane. To date, no animal model exists to study mitoribosome composition and mitochondrial translation coordination in mammals in vivo. Here, we create MitoRibo-Tag mice as a tool enabling affinity purification and proteomics analyses of mitoribosomes and their interactome in different tissues. We also define the composition of an assembly intermediate formed in the absence of MTERF4, necessary for a late step in mitoribosomal biogenesis. We identify the orphan protein PUSL1, which interacts with a large subunit assembly intermediate, and demonstrate that it is an inner-membrane-associated mitochondrial matrix protein required for efficient mitochondrial translation. This work establishes MitoRibo-Tag mice as a powerful tool to study mitoribosomes in vivo, enabling future studies on the mitoribosome interactome under different physiological states, as well as in disease and aging. MitoRibo-Tag mice with a tag on mL62 were generated to study mitoribosomes in vivo The mitoribosome interactome of different mouse tissues was defined with proteomics PUSL1 was identified as a mitoribosome-interacting protein using MitoRibo-Tag mice MitoRibo-Tag mice allow mitoribosome analysis under different conditions and setups
Collapse
Affiliation(s)
- Jakob D Busch
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany; Faculty of Mathematics and Natural Sciences, University of Cologne, Albertus-Magnus-Platz, 50923 Cologne, Germany
| | - Miriam Cipullo
- Department of Medical Biochemistry and Biophysics, Research Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden; Max-Planck-Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Ilian Atanassov
- Proteomics Core Facility, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Ana Bratic
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Eduardo Silva Ramos
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Thomas Schöndorf
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany; Faculty of Mathematics and Natural Sciences, University of Cologne, Albertus-Magnus-Platz, 50923 Cologne, Germany
| | - Xinping Li
- Proteomics Core Facility, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Sarah F Pearce
- Department of Medical Biochemistry and Biophysics, Research Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden; Max-Planck-Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Dusanka Milenkovic
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Research Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden; Max-Planck-Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden.
| | - Nils-Göran Larsson
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany; Department of Medical Biochemistry and Biophysics, Research Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden; Max-Planck-Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
36
|
Lind C, Esguerra M, Jespers W, Satpati P, Gutierrez-de-Terán H, Åqvist J. Free energy calculations of RNA interactions. Methods 2019; 162-163:85-95. [DOI: 10.1016/j.ymeth.2019.02.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/01/2019] [Accepted: 02/15/2019] [Indexed: 01/19/2023] Open
|
37
|
Kuroha K, Zinoviev A, Hellen CUT, Pestova TV. Release of Ubiquitinated and Non-ubiquitinated Nascent Chains from Stalled Mammalian Ribosomal Complexes by ANKZF1 and Ptrh1. Mol Cell 2018; 72:286-302.e8. [PMID: 30244831 DOI: 10.1016/j.molcel.2018.08.022] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/24/2018] [Accepted: 08/15/2018] [Indexed: 01/08/2023]
Abstract
The ribosome-associated quality control (RQC) pathway degrades nascent chains (NCs) arising from interrupted translation. First, recycling factors split stalled ribosomes, yielding NC-tRNA/60S ribosome-nascent chain complexes (60S RNCs). 60S RNCs associate with NEMF, which recruits the E3 ubiquitin ligase Listerin that ubiquitinates NCs. The mechanism of subsequent ribosomal release of Ub-NCs remains obscure. We found that, in non-ubiquitinated 60S RNCs and 80S RNCs formed on non-stop mRNAs, tRNA is not firmly fixed in the P site, which allows peptidyl-tRNA hydrolase Ptrh1 to cleave NC-tRNA, suggesting the existence of a pathway involving release of non-ubiquitinated NCs. Association with NEMF and Listerin and ubiquitination of NCs results in accommodation of NC-tRNA, rendering 60S RNCs resistant to Ptrh1 but susceptible to ANKZF1, which induces specific cleavage in the tRNA acceptor arm, releasing proteasome-degradable Ub-NCs linked to four 3'-terminal tRNA nucleotides. We also found that TCF25, a poorly characterized RQC component, ensures preferential formation of the K48-ubiquitin linkage.
Collapse
Affiliation(s)
- Kazushige Kuroha
- Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY 11203, USA.
| | - Alexandra Zinoviev
- Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY 11203, USA
| | | | - Tatyana V Pestova
- Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY 11203, USA.
| |
Collapse
|
38
|
Mitochondrial transcription and translation: overview. Essays Biochem 2018; 62:309-320. [PMID: 30030363 PMCID: PMC6056719 DOI: 10.1042/ebc20170102] [Citation(s) in RCA: 172] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/14/2018] [Accepted: 05/14/2018] [Indexed: 12/13/2022]
Abstract
Mitochondria are the major source of ATP in the cell. Five multi-subunit complexes in the inner membrane of the organelle are involved in the oxidative phosphorylation required for ATP production. Thirteen subunits of these complexes are encoded by the mitochondrial genome often referred to as mtDNA. For this reason, the expression of mtDNA is vital for the assembly and functioning of the oxidative phosphorylation complexes. Defects of the mechanisms regulating mtDNA gene expression have been associated with deficiencies in assembly of these complexes, resulting in mitochondrial diseases. Recently, numerous factors involved in these processes have been identified and characterized leading to a deeper understanding of the mechanisms that underlie mitochondrial diseases.
Collapse
|
39
|
Ferreira N, Rackham O, Filipovska A. Regulation of a minimal transcriptome by repeat domain proteins. Semin Cell Dev Biol 2018; 76:132-141. [DOI: 10.1016/j.semcdb.2017.08.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/15/2017] [Accepted: 08/18/2017] [Indexed: 01/19/2023]
|
40
|
Cultured bloodstream Trypanosoma brucei adapt to life without mitochondrial translation release factor 1. Sci Rep 2018; 8:5135. [PMID: 29572512 PMCID: PMC5865105 DOI: 10.1038/s41598-018-23472-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 03/13/2018] [Indexed: 01/07/2023] Open
Abstract
Trypanosoma brucei is an extracellular parasite that alternates between an insect vector (procyclic form) and the bloodstream of a mammalian host (bloodstream form). While it was previously reported that mitochondrial release factor 1 (TbMrf1) is essential in cultured procyclic form cells, we demonstrate here that in vitro bloodstream form cells can tolerate the elimination of TbMrf1. Therefore, we explored if this discrepancy is due to the unique bioenergetics of the parasite since procyclic form cells rely on oxidative phosphorylation; whereas bloodstream form cells utilize glycolysis for ATP production and FoF1-ATPase to maintain the essential mitochondrial membrane potential. The observed disruption of intact bloodstream form FoF1-ATPases serves as a proxy to indicate that the translation of its mitochondrially encoded subunit A6 is impaired without TbMrf1. While these null mutants have a decreased mitochondrial membrane potential, they have adapted by increasing their dependence on the electrogenic contributions of the ADP/ATP carrier to maintain the mitochondrial membrane potential above the minimum threshold required for T. brucei viability in vitro. However, this inefficient compensatory mechanism results in avirulent mutants in mice. Finally, the depletion of the codon-independent release factor TbPth4 in the TbMrf1 knockouts further exacerbates the characterized mitchondrial phenotypes.
Collapse
|
41
|
Umbaugh CS, Diaz-Quiñones A, Neto MF, Shearer JJ, Figueiredo ML. A dock derived compound against laminin receptor (37 LR) exhibits anti-cancer properties in a prostate cancer cell line model. Oncotarget 2017; 9:5958-5978. [PMID: 29464047 PMCID: PMC5814187 DOI: 10.18632/oncotarget.23236] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/16/2017] [Indexed: 11/25/2022] Open
Abstract
Laminin receptor (67 LR) is a 67 kDa protein derived from a 37 kDa precursor (37 LR). 37/67 LR is a strong clinical correlate for progression, aggression, and chemotherapeutic relapse of several cancers including breast, prostate, and colon. The ability of 37/67 LR to promote cancer cell aggressiveness is further increased by its ability to transduce physiochemical and mechanosensing signals in endothelial cells and modulate angiogenesis. Recently, it was demonstrated that 37/67 LR modulates the anti-angiogenic potential of the secreted glycoprotein pigment epithelium-derived factor (PEDF). Restoration of PEDF balance is a desirable therapeutic outcome, and we sought to identify a small molecule that could recapitulate known signaling properties of PEDF but without the additional complications of peptide formulation or gene delivery safety validation. We used an in silico drug discovery approach to target the interaction interface between PEDF and 37 LR. Following cell based counter screening and binding validation, we characterized a hit compound's anti-viability, activation of PEDF signaling-related genes, anti-wound healing, and anti-cancer signaling properties. This hit compound has potential for future development as a lead compound for treating tumor growth and inhibiting angiogenesis.
Collapse
Affiliation(s)
- Charles Samuel Umbaugh
- Department of Basic Medical Sciences, Purdue University College of Veterinary Medicine, West Lafayette, IN 47907, USA
| | - Adriana Diaz-Quiñones
- Department of Basic Medical Sciences, Purdue University College of Veterinary Medicine, West Lafayette, IN 47907, USA
| | - Manoel Figueiredo Neto
- Department of Basic Medical Sciences, Purdue University College of Veterinary Medicine, West Lafayette, IN 47907, USA
| | - Joseph J Shearer
- Department of Basic Medical Sciences, Purdue University College of Veterinary Medicine, West Lafayette, IN 47907, USA
| | - Marxa L Figueiredo
- Department of Basic Medical Sciences, Purdue University College of Veterinary Medicine, West Lafayette, IN 47907, USA
| |
Collapse
|
42
|
Bock LV, Kolář MH, Grubmüller H. Molecular simulations of the ribosome and associated translation factors. Curr Opin Struct Biol 2017; 49:27-35. [PMID: 29202442 DOI: 10.1016/j.sbi.2017.11.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/15/2017] [Accepted: 11/16/2017] [Indexed: 01/15/2023]
Abstract
The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM), the structure of the ribosome was resolved at atomic resolution in many functional and conformational states. Molecular dynamics simulations have added information on dynamics and energetics to the available structural information, thereby have bridged the gap to the kinetics obtained from single-molecule and bulk experiments. Here, we review recent computational studies that brought notable insights into ribosomal structure and function.
Collapse
Affiliation(s)
- Lars V Bock
- Department of Theoretical and Computational Biophysics, Am Faßberg 11, Göttingen, Germany
| | - Michal H Kolář
- Department of Theoretical and Computational Biophysics, Am Faßberg 11, Göttingen, Germany
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Am Faßberg 11, Göttingen, Germany.
| |
Collapse
|
43
|
Mitochondrial diseases: the contribution of organelle stress responses to pathology. Nat Rev Mol Cell Biol 2017; 19:77-92. [DOI: 10.1038/nrm.2017.66] [Citation(s) in RCA: 264] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
44
|
Huter P, Müller C, Arenz S, Beckert B, Wilson DN. Structural Basis for Ribosome Rescue in Bacteria. Trends Biochem Sci 2017. [PMID: 28629612 DOI: 10.1016/j.tibs.2017.05.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Ribosomes that translate mRNAs lacking stop codons become stalled at the 3' end of the mRNA. Recycling of these stalled ribosomes is essential for cell viability. In bacteria three ribosome rescue systems have been identified so far, with the most ubiquitous and best characterized being the trans-translation system mediated by transfer-messenger RNA (tmRNA) and small protein B (SmpB). The two additional rescue systems present in some bacteria employ alternative rescue factor (Arf) A and release factor (RF) 2 or ArfB. Recent structures have revealed how ArfA mediates ribosome rescue by recruiting the canonical termination factor RF2 to ribosomes stalled on truncated mRNAs. This now provides us with the opportunity to compare and contrast the available structures of all three bacterial ribosome rescue systems.
Collapse
Affiliation(s)
- Paul Huter
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Feodor-Lynenstr. 25, 81377 München, Germany
| | - Claudia Müller
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Feodor-Lynenstr. 25, 81377 München, Germany
| | - Stefan Arenz
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Feodor-Lynenstr. 25, 81377 München, Germany
| | - Bertrand Beckert
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Feodor-Lynenstr. 25, 81377 München, Germany; Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Daniel N Wilson
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Feodor-Lynenstr. 25, 81377 München, Germany; Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany.
| |
Collapse
|
45
|
Wang C, Liang C, Feng W, Xia X, Chen F, Qiao E, Zhang X, Chen D, Ling Z, Yang H. ICT1 knockdown inhibits breast cancer cell growth via induction of cell cycle arrest and apoptosis. Int J Mol Med 2017; 39:1037-1045. [PMID: 28290601 DOI: 10.3892/ijmm.2017.2913] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/23/2017] [Indexed: 11/05/2022] Open
Abstract
The protein encoded by immature colon carcinoma transcript 1 (ICT1) is a component of the human mitochondrial ribosome, and is reported to be implicated in cell proliferation, viability and apoptosis of HeLa cells. This study was conducted to investigate the role of ICT1 in human breast cancer. Oncomine database was used to investigate ICT1 expression in human breast cancer tissues compared to normal tissues. The results showed that ICT1 was highly overexpressed in various human breast cancer subtypes. Then short hairpin RNA (shRNA)-mediated knockdown of ICT1 was performed in human breast cancer ZR-75-30 and T-47D cells. A series of functional analysis, including MTT, colony formation and flow cytometry assays were conducted after ICT1 knockdown. Our results demonstrated that knockdown of ICT1 significantly suppressed cell viability and proliferation through cell cycle arrest at the G2/M phase and induced apoptosis in breast cancer cells. Furthermore, knockdown of ICT1 altered signaling pathways associated with cell growth and apoptosis, including phospho‑BAD (Ser112), phospho-PRAS40 (Thr246) and induction of phospho‑AMPKα (Thr172). Additionally, it was further confirmed by western blot analysis that ICT1 knockdown altered the expression of apoptosis- or cell cycle‑related proteins such as Bcl-2, caspase-3, CDK1, CDK2 and cyclin B. In conclusion, targeting ICT1 in breast cancer cells may provide a new strategy for breast cancer gene therapy.
Collapse
Affiliation(s)
- Chen Wang
- Department of Oncology, First Clinical Medical College, Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Chenlu Liang
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Weiliang Feng
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Xianghou Xia
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Feng Chen
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Enqi Qiao
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Xiping Zhang
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Daobao Chen
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Zhiqiang Ling
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Hongjian Yang
- Department of Oncology, First Clinical Medical College, Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| |
Collapse
|
46
|
Dealing with an Unconventional Genetic Code in Mitochondria: The Biogenesis and Pathogenic Defects of the 5-Formylcytosine Modification in Mitochondrial tRNA Met. Biomolecules 2017; 7:biom7010024. [PMID: 28257121 PMCID: PMC5372736 DOI: 10.3390/biom7010024] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/24/2017] [Indexed: 01/13/2023] Open
Abstract
Human mitochondria contain their own genome, which uses an unconventional genetic code. In addition to the standard AUG methionine codon, the single mitochondrial tRNA Methionine (mt-tRNAMet) also recognises AUA during translation initiation and elongation. Post-transcriptional modifications of tRNAs are important for structure, stability, correct folding and aminoacylation as well as decoding. The unique 5-formylcytosine (f5C) modification of position 34 in mt-tRNAMet has been long postulated to be crucial for decoding of unconventional methionine codons and efficient mitochondrial translation. However, the enzymes responsible for the formation of mitochondrial f5C have been identified only recently. The first step of the f5C pathway consists of methylation of cytosine by NSUN3. This is followed by further oxidation by ABH1. Here, we review the role of f5C, the latest breakthroughs in our understanding of the biogenesis of this unique mitochondrial tRNA modification and its involvement in human disease.
Collapse
|
47
|
Abstract
Oxidative phosphorylation (OXPHOS) is the mechanism whereby ATP, the major energy source for the cell, is produced by harnessing cellular respiration in the mitochondrion. This is facilitated by five multi-subunit complexes housed within the inner mitochondrial membrane. These complexes, with the exception of complex II, are of a dual genetic origin, requiring expression from nuclear and mitochondrial genes. Mitochondrially encoded mRNA is translated on the mitochondrial ribosome (mitoribosome) and the recent release of the near atomic resolution structure of the mammalian mitoribosome has highlighted its peculiar features. However, whereas some aspects of mitochondrial translation are understood, much is to be learnt about the presentation of mitochondrial mRNA to the mitoribosome, the biogenesis of the machinery, the exact role of the membrane, the constitution of the translocon/insertion machinery and the regulation of translation in the mitochondrion. This review addresses our current knowledge of mammalian mitochondrial gene expression, highlights key questions and indicates how defects in this process can result in profound mitochondrial disease.
Collapse
|
48
|
Affiliation(s)
- Martin Ott
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden;
| | - Alexey Amunts
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden;
- Science for Life Laboratory, Stockholm University, SE-171 21 Solna, Sweden;
| | - Alan Brown
- Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 0QH, United Kingdom;
| |
Collapse
|
49
|
Vaishya S, Kumar V, Gupta A, Siddiqi MI, Habib S. Polypeptide release factors and stop codon recognition in the apicoplast and mitochondrion of Plasmodium falciparum. Mol Microbiol 2016; 100:1080-95. [PMID: 26946524 DOI: 10.1111/mmi.13369] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2016] [Indexed: 11/30/2022]
Abstract
Correct termination of protein synthesis would be a critical step in translation of organellar open reading frames (ORFs) of the apicoplast and mitochondrion of the malaria parasite. We identify release factors (RFs) responsible for recognition of the UAA and UGA stop-codons of apicoplast ORFs and the sole UAA stop-codon that terminates translation from the three mitochondrial ORFs. A single nuclear-encoded canonical RF2, PfRF2Api , localizes to the apicoplast. It has a conserved tripeptide motif (SPF) for stop-codon recognition and is sufficient for peptidyl-tRNA hydrolysis (PTH) from both UAA and UGA. Two RF family proteins are targeted to the parasite mitochondrion; a canonical RF1, PfRF1Mit , with a variant codon-recognition motif (PxN instead of the conserved RF1 PxT) is the major peptidyl-hydrolase with specific recognition of the UAA codon relevant to mitochondrial ORFs. Mutation of the N residue of the PfRF1Mit PxN motif and two other conserved residues of the codon recognition domain lowers PTH activity from pre-termination ribosomes indicating their role in codon-recognition. The second RF imported by the mitochondrion is the non-canonical PfICT1 that functions as a dimer and mediates codon nonspecific peptide release. Our results help delineate a critical step in organellar translation in Plasmodium, which is an important target for anti-malarials.
Collapse
Affiliation(s)
- Suniti Vaishya
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Vikash Kumar
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Ankit Gupta
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Mohammad Imran Siddiqi
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Saman Habib
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| |
Collapse
|
50
|
Feaga HA, Quickel MD, Hankey-Giblin PA, Keiler KC. Human Cells Require Non-stop Ribosome Rescue Activity in Mitochondria. PLoS Genet 2016; 12:e1005964. [PMID: 27029019 PMCID: PMC4814080 DOI: 10.1371/journal.pgen.1005964] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/07/2016] [Indexed: 12/04/2022] Open
Abstract
Bacteria use trans-translation and the alternative rescue factors ArfA (P36675) and ArfB (Q9A8Y3) to hydrolyze peptidyl-tRNA on ribosomes that stall near the 3' end of an mRNA during protein synthesis. The eukaryotic protein ICT1 (Q14197) is homologous to ArfB. In vitro ribosome rescue assays of human ICT1 and Caulobacter crescentus ArfB showed that these proteins have the same activity and substrate specificity. Both ArfB and ICT1 hydrolyze peptidyl-tRNA on nonstop ribosomes or ribosomes stalled with ≤6 nucleotides extending past the A site, but are unable to hydrolyze peptidyl-tRNA when the mRNA extends ≥14 nucleotides past the A site. ICT1 provided sufficient ribosome rescue activity to support viability in C. crescentus cells that lacked both trans-translation and ArfB. Likewise, expression of ArfB protected human cells from death when ICT1 was silenced with siRNA. These data indicate that ArfB and ICT1 are functionally interchangeable, and demonstrate that ICT1 is a ribosome rescue factor. Because ICT1 is essential in human cells, these results suggest that ribosome rescue activity in mitochondria is required in humans. Ribosomes can stall during protein synthesis on truncated or damaged mRNAs that lack a stop codon. In bacteria, these “non-stop” ribosomes are rescued by trans-translation or by an alternative rescue factor, ArfA or ArfB. Most eukaryotes do not have trans-translation, but mammals have a homolog of ArfB named ICT1. ICT1 is targeted to mitochondria, and is essential in human cells. Here, we show that human ICT1 and ArfB from the bacterium Caulobacter crescentus have the same biochemical activity and specificity. We also demonstrate that ICT1 and ArfB are functionally interchangeable in both bacteria and human cells. Collectively, this work demonstrates a new essential function in human cells—rescue of mitochondrial non-stop translation complexes.
Collapse
Affiliation(s)
- Heather A. Feaga
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Michael D. Quickel
- Department of Veterinary and Biomedical Science, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Pamela A. Hankey-Giblin
- Department of Veterinary and Biomedical Science, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Kenneth C. Keiler
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|