1
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Cipullo M, Valentín Gesé G, Gopalakrishna S, Krueger A, Lobo V, Pirozhkova MA, Marks J, Páleníková P, Shiriaev D, Liu Y, Misic J, Cai Y, Nguyen MD, Abdelbagi A, Li X, Minczuk M, Hafner M, Benhalevy D, Sarshad AA, Atanassov I, Hällberg BM, Rorbach J. GTPBP8 plays a role in mitoribosome formation in human mitochondria. Nat Commun 2024; 15:5664. [PMID: 38969660 PMCID: PMC11229512 DOI: 10.1038/s41467-024-50011-x] [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: 08/23/2023] [Accepted: 06/26/2024] [Indexed: 07/07/2024] Open
Abstract
Mitochondrial gene expression relies on mitoribosomes to translate mitochondrial mRNAs. The biogenesis of mitoribosomes is an intricate process involving multiple assembly factors. Among these factors, GTP-binding proteins (GTPBPs) play important roles. In bacterial systems, numerous GTPBPs are required for ribosome subunit maturation, with EngB being a GTPBP involved in the ribosomal large subunit assembly. In this study, we focus on exploring the function of GTPBP8, the human homolog of EngB. We find that ablation of GTPBP8 leads to the inhibition of mitochondrial translation, resulting in significant impairment of oxidative phosphorylation. Structural analysis of mitoribosomes from GTPBP8 knock-out cells shows the accumulation of mitoribosomal large subunit assembly intermediates that are incapable of forming functional monosomes. Furthermore, fPAR-CLIP analysis reveals that GTPBP8 is an RNA-binding protein that interacts specifically with the mitochondrial ribosome large subunit 16 S rRNA. Our study highlights the role of GTPBP8 as a component of the mitochondrial gene expression machinery involved in mitochondrial large subunit maturation.
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Affiliation(s)
- Miriam Cipullo
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Genís Valentín Gesé
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, Stockholm, 17165, Sweden
| | - Shreekara Gopalakrishna
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Annika Krueger
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Vivian Lobo
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE-40530, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530, Gothenburg, Sweden
| | - Maria A Pirozhkova
- Lab for Cellular RNA Biology, Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - James Marks
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Petra Páleníková
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Dmitrii Shiriaev
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Yong Liu
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Jelena Misic
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Yu Cai
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Minh Duc Nguyen
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Abubakar Abdelbagi
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Xinping Li
- Proteomics Core Facility, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931, Cologne, Germany
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel Benhalevy
- Lab for Cellular RNA Biology, Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Aishe A Sarshad
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE-40530, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530, Gothenburg, Sweden
| | - Ilian Atanassov
- Proteomics Core Facility, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931, Cologne, Germany
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, Stockholm, 17165, Sweden
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17165, Sweden.
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2
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Dinh N, Bonnefoy N. Schizosaccharomyces pombe as a fundamental model for research on mitochondrial gene expression: Progress, achievements and outlooks. IUBMB Life 2024; 76:397-419. [PMID: 38117001 DOI: 10.1002/iub.2801] [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: 09/27/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023]
Abstract
Schizosaccharomyces pombe (fission yeast) is an attractive model for mitochondrial research. The organism resembles human cells in terms of mitochondrial inheritance, mitochondrial transport, sugar metabolism, mitogenome structure and dependence of viability on the mitogenome (the petite-negative phenotype). Transcriptions of these genomes produce only a few polycistronic transcripts, which then undergo processing as per the tRNA punctuation model. In general, the machinery for mitochondrial gene expression is structurally and functionally conserved between fission yeast and humans. Furthermore, molecular research on S. pombe is supported by a considerable number of experimental techniques and database resources. Owing to these advantages, fission yeast has significantly contributed to biomedical and fundamental research. Here, we review the current state of knowledge regarding S. pombe mitochondrial gene expression, and emphasise the pertinence of fission yeast as both a model and tool, especially for studies on mitochondrial translation.
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Affiliation(s)
- Nhu Dinh
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette cedex, France
| | - Nathalie Bonnefoy
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette cedex, France
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3
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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.
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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
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4
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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.
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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
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5
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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.
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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
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Nadler F, Lavdovskaia E, Krempler A, Cruz-Zaragoza LD, Dennerlein S, Richter-Dennerlein R. Human mtRF1 terminates COX1 translation and its ablation induces mitochondrial ribosome-associated quality control. Nat Commun 2022; 13:6406. [PMID: 36302763 PMCID: PMC9613700 DOI: 10.1038/s41467-022-34088-w] [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: 05/25/2022] [Accepted: 10/11/2022] [Indexed: 12/25/2022] Open
Abstract
Translation termination requires release factors that read a STOP codon in the decoding center and subsequently facilitate the hydrolysis of the nascent peptide chain from the peptidyl tRNA within the ribosome. In human mitochondria eleven open reading frames terminate in the standard UAA or UAG STOP codon, which can be recognized by mtRF1a, the proposed major mitochondrial release factor. However, two transcripts encoding for COX1 and ND6 terminate in the non-conventional AGA or AGG codon, respectively. How translation termination is achieved in these two cases is not known. We address this long-standing open question by showing that the non-canonical release factor mtRF1 is a specialized release factor that triggers COX1 translation termination, while mtRF1a terminates the majority of other mitochondrial translation events including the non-canonical ND6. Loss of mtRF1 leads to isolated COX deficiency and activates the mitochondrial ribosome-associated quality control accompanied by the degradation of COX1 mRNA to prevent an overload of the ribosome rescue system. Taken together, these results establish the role of mtRF1 in mitochondrial translation, which had been a mystery for decades, and lead to a comprehensive picture of translation termination in human mitochondria.
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Affiliation(s)
- Franziska Nadler
- grid.411984.10000 0001 0482 5331Department of Cellular Biochemistry, University Medical Center Goettingen, D-37073 Goettingen, Germany
| | - Elena Lavdovskaia
- grid.411984.10000 0001 0482 5331Department of Cellular Biochemistry, University Medical Center Goettingen, D-37073 Goettingen, Germany ,grid.7450.60000 0001 2364 4210Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Goettingen, D-37075 Goettingen, Germany
| | - Angelique Krempler
- grid.411984.10000 0001 0482 5331Department of Cellular Biochemistry, University Medical Center Goettingen, D-37073 Goettingen, Germany
| | - Luis Daniel Cruz-Zaragoza
- grid.411984.10000 0001 0482 5331Department of Cellular Biochemistry, University Medical Center Goettingen, D-37073 Goettingen, Germany
| | - Sven Dennerlein
- grid.411984.10000 0001 0482 5331Department of Cellular Biochemistry, University Medical Center Goettingen, D-37073 Goettingen, Germany
| | - Ricarda Richter-Dennerlein
- grid.411984.10000 0001 0482 5331Department of Cellular Biochemistry, University Medical Center Goettingen, D-37073 Goettingen, Germany ,grid.7450.60000 0001 2364 4210Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Goettingen, D-37075 Goettingen, Germany ,grid.7450.60000 0001 2364 4210Goettingen Center for Molecular Biosciences, University of Goettingen, D-37077 Goettingen, Germany
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7
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Mitochondria homeostasis: Biology and involvement in hepatic steatosis to NASH. Acta Pharmacol Sin 2022; 43:1141-1155. [PMID: 35105958 PMCID: PMC9061859 DOI: 10.1038/s41401-022-00864-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/09/2022] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial biology and behavior are central to the physiology of liver. Multiple mitochondrial quality control mechanisms remodel mitochondrial homeostasis under physiological and pathological conditions. Mitochondrial dysfunction and damage induced by overnutrition lead to oxidative stress, inflammation, liver cell death, and collagen production, which advance hepatic steatosis to nonalcoholic steatohepatitis (NASH). Accumulating evidence suggests that specific interventions that target mitochondrial homeostasis, including energy metabolism, antioxidant effects, and mitochondrial quality control, have emerged as promising strategies for NASH treatment. However, clinical translation of these findings is challenging due to the complex and unclear mechanisms of mitochondrial homeostasis in the pathophysiology of NASH.
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8
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Seely SM, Gagnon MG. Mechanisms of ribosome recycling in bacteria and mitochondria: a structural perspective. RNA Biol 2022; 19:662-677. [PMID: 35485608 PMCID: PMC9067457 DOI: 10.1080/15476286.2022.2067712] [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: 10/28/2022] Open
Abstract
In all living cells, the ribosome translates the genetic information carried by messenger RNAs (mRNAs) into proteins. The process of ribosome recycling, a key step during protein synthesis that ensures ribosomal subunits remain available for new rounds of translation, has been largely overlooked. Despite being essential to the survival of the cell, several mechanistic aspects of ribosome recycling remain unclear. In eubacteria and mitochondria, recycling of the ribosome into subunits requires the concerted action of the ribosome recycling factor (RRF) and elongation factor G (EF-G). Recently, the conserved protein HflX was identified in bacteria as an alternative factor that recycles the ribosome under stress growth conditions. The homologue of HflX, the GTP-binding protein 6 (GTPBP6), has a dual role in mitochondrial translation by facilitating ribosome recycling and biogenesis. In this review, mechanisms of ribosome recycling in eubacteria and mitochondria are described based on structural studies of ribosome complexes.
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Affiliation(s)
- Savannah M Seely
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-1019, USA
| | - Matthieu G Gagnon
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-1019, USA.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555-1019, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1019, USA.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas 77555, USA
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9
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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.
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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
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10
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Criscuolo D, Avolio R, Matassa DS, Esposito F. Targeting Mitochondrial Protein Expression as a Future Approach for Cancer Therapy. Front Oncol 2021; 11:797265. [PMID: 34888254 PMCID: PMC8650000 DOI: 10.3389/fonc.2021.797265] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/03/2021] [Indexed: 12/20/2022] Open
Abstract
Extensive metabolic remodeling is a fundamental feature of cancer cells. Although early reports attributed such remodeling to a loss of mitochondrial functions, it is now clear that mitochondria play central roles in cancer development and progression, from energy production to synthesis of macromolecules, from redox modulation to regulation of cell death. Biosynthetic pathways are also heavily affected by the metabolic rewiring, with protein synthesis dysregulation at the hearth of cellular transformation. Accumulating evidence in multiple organisms shows that the metabolic functions of mitochondria are tightly connected to protein synthesis, being assembly and activity of respiratory complexes highly dependent on de novo synthesis of their components. In turn, protein synthesis within the organelle is tightly connected with the cytosolic process. This implies an entire network of interactions and fine-tuned regulations that build up a completely under-estimated level of complexity. We are now only preliminarily beginning to reconstitute such regulatory level in human cells, and to perceive its role in diseases. Indeed, disruption or alterations of these connections trigger conditions of proteotoxic and energetic stress that could be potentially exploited for therapeutic purposes. In this review, we summarize the available literature on the coordinated regulation of mitochondrial and cytosolic mRNA translation, and their effects on the integrity of the mitochondrial proteome and functions. Finally, we highlight the potential held by this topic for future research directions and for the development of innovative therapeutic approaches.
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Affiliation(s)
- Daniela Criscuolo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| | - Rosario Avolio
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| | - Danilo Swann Matassa
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| | - Franca Esposito
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
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11
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Friedlander JE, Shen N, Zeng A, Korm S, Feng H. Failure to Guard: Mitochondrial Protein Quality Control in Cancer. Int J Mol Sci 2021; 22:ijms22158306. [PMID: 34361072 PMCID: PMC8348654 DOI: 10.3390/ijms22158306] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 07/20/2021] [Accepted: 07/27/2021] [Indexed: 02/07/2023] Open
Abstract
Mitochondria are energetic and dynamic organelles with a crucial role in bioenergetics, metabolism, and signaling. Mitochondrial proteins, encoded by both nuclear and mitochondrial DNA, must be properly regulated to ensure proteostasis. Mitochondrial protein quality control (MPQC) serves as a critical surveillance system, employing different pathways and regulators as cellular guardians to ensure mitochondrial protein quality and quantity. In this review, we describe key pathways and players in MPQC, such as mitochondrial protein translocation-associated degradation, mitochondrial stress responses, chaperones, and proteases, and how they work together to safeguard mitochondrial health and integrity. Deregulated MPQC leads to proteotoxicity and dysfunctional mitochondria, which contributes to numerous human diseases, including cancer. We discuss how alterations in MPQC components are linked to tumorigenesis, whether they act as drivers, suppressors, or both. Finally, we summarize recent advances that seek to target these alterations for the development of anti-cancer drugs.
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Affiliation(s)
- Joseph E. Friedlander
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA; (J.E.F.); (N.S.); (A.Z.); (S.K.)
| | - Ning Shen
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA; (J.E.F.); (N.S.); (A.Z.); (S.K.)
- Department of Medicine, Section of Hematology and Medical Oncology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Aozhuo Zeng
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA; (J.E.F.); (N.S.); (A.Z.); (S.K.)
| | - Sovannarith Korm
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA; (J.E.F.); (N.S.); (A.Z.); (S.K.)
| | - Hui Feng
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA; (J.E.F.); (N.S.); (A.Z.); (S.K.)
- Department of Medicine, Section of Hematology and Medical Oncology, Boston University School of Medicine, Boston, MA 02118, USA
- Correspondence: ; Tel.: +1-617-358-4688; Fax: +1-617-358-1599
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12
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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.
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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
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13
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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.
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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
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14
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Koripella RK, Deep A, Agrawal EK, Keshavan P, Banavali NK, Agrawal RK. Distinct mechanisms of the human mitoribosome recycling and antibiotic resistance. Nat Commun 2021; 12:3607. [PMID: 34127662 PMCID: PMC8203779 DOI: 10.1038/s41467-021-23726-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/14/2021] [Indexed: 11/16/2022] Open
Abstract
Ribosomes are recycled for a new round of translation initiation by dissociation of ribosomal subunits, messenger RNA and transfer RNA from their translational post-termination complex. Here we present cryo-EM structures of the human 55S mitochondrial ribosome (mitoribosome) and the mitoribosomal large 39S subunit in complex with mitoribosome recycling factor (RRFmt) and a recycling-specific homolog of elongation factor G (EF-G2mt). These structures clarify an unusual role of a mitochondria-specific segment of RRFmt, identify the structural distinctions that confer functional specificity to EF-G2mt, and show that the deacylated tRNA remains with the dissociated 39S subunit, suggesting a distinct sequence of events in mitoribosome recycling. Furthermore, biochemical and structural analyses reveal that the molecular mechanism of antibiotic fusidic acid resistance for EF-G2mt is markedly different from that of mitochondrial elongation factor EF-G1mt, suggesting that the two human EF-Gmts have evolved diversely to negate the effect of a bacterial antibiotic. High-resolution cryo-EM structures and biochemical analyses of the human mitoribosome, in complex with mitochondria-specific factors mediating mitoribosome recycling, RRFmt and EF-G2mt, offer insight into mechanisms of mitoribosome recycling and resistance to antibiotic fusidic acid.
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Affiliation(s)
- Ravi Kiran Koripella
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY, USA
| | - Ayush Deep
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY, USA
| | - Ekansh K Agrawal
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY, USA
| | - Pooja Keshavan
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY, USA
| | - Nilesh K Banavali
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY, USA.,Department of Biomedical Sciences, University at Albany, Albany, NY, USA
| | - Rajendra K Agrawal
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY, USA. .,Department of Biomedical Sciences, University at Albany, Albany, NY, USA.
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15
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Wang YP, Sharda A, Xu SN, van Gastel N, Man CH, Choi U, Leong WZ, Li X, Scadden DT. Malic enzyme 2 connects the Krebs cycle intermediate fumarate to mitochondrial biogenesis. Cell Metab 2021; 33:1027-1041.e8. [PMID: 33770508 PMCID: PMC10472834 DOI: 10.1016/j.cmet.2021.03.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/21/2020] [Accepted: 03/03/2021] [Indexed: 12/13/2022]
Abstract
Mitochondria have an independent genome (mtDNA) and protein synthesis machinery that coordinately activate for mitochondrial generation. Here, we report that the Krebs cycle intermediate fumarate links metabolism to mitobiogenesis through binding to malic enzyme 2 (ME2). Mechanistically, fumarate binds ME2 with two complementary consequences. First, promoting the formation of ME2 dimers, which activate deoxyuridine 5'-triphosphate nucleotidohydrolase (DUT). DUT fosters thymidine generation and an increase of mtDNA. Second, fumarate-induced ME2 dimers abrogate ME2 monomer binding to mitochondrial ribosome protein L45, freeing it for mitoribosome assembly and mtDNA-encoded protein production. Methylation of the ME2-fumarate binding site by protein arginine methyltransferase-1 inhibits fumarate signaling to constrain mitobiogenesis. Notably, acute myeloid leukemia is highly dependent on mitochondrial function and is sensitive to targeting of the fumarate-ME2 axis. Therefore, mitobiogenesis can be manipulated in normal and malignant cells through ME2, an unanticipated governor of mitochondrial biomass production that senses nutrient availability through fumarate.
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Affiliation(s)
- Yi-Ping Wang
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Key Laboratory of Breast Cancer in Shanghai, Cancer Institute, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College, Fudan University, Shanghai 20032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 20032, China
| | - Azeem Sharda
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Shuang-Nian Xu
- Department of Hematology, Southwest Hospital, Army Medical University, Chongqing 400038, China
| | - Nick van Gastel
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Cheuk Him Man
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Una Choi
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Wei Zhong Leong
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Xi Li
- Department of Hematology, Southwest Hospital, Army Medical University, Chongqing 400038, China
| | - David T Scadden
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.
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16
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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: 28] [Impact Index Per Article: 9.3] [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.
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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.
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17
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Gonçalves AM, Pereira-Santos AR, Esteves AR, Cardoso SM, Empadinhas N. The Mitochondrial Ribosome: A World of Opportunities for Mitochondrial Dysfunction Toward Parkinson's Disease. Antioxid Redox Signal 2021; 34:694-711. [PMID: 32098485 DOI: 10.1089/ars.2019.7997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Significance: Mitochondrial ribosomes (mitoribosomes) are organelles that translate mitochondrial messenger RNA in the matrix and, in mammals, have evolved to translate 13 polypeptides of the pathway that performs oxidative phosphorylation (OXPHOS). Although a number of devastating diseases result from defects in this mitochondrial translation apparatus, most are associated with genetic mutations and little is known about allelopathic defects caused by antibiotics, toxins, or nonproteinogenic amino acids. Recent Advances: The levels of mitochondrial ribosomal subunits 12S and 16S ribosomal RNA (rRNA) in cells/tissues from patients carrying mutations in these genes have been associated with alterations in mitochondrial translation efficiency and with impaired OXPHOS activities, as well as with the severity of clinical phenotypes. In recent decades, important studies revealed a prominent role of mitochondrial dysfunction in Parkinson's disease (PD); however, the involvement of mitoribosomes remains largely unknown. Critical Issues: Considering that mitoribosomal structure and function can determine the efficiency of OXPHOS and that an impaired mitochondrial respiratory chain is a common finding in PD, we argue that the mitoribosome may be key to disease onset and progression. With this review, we comprehensively integrate the available knowledge on the composition, assembly, and role of the mitoribosome in mitochondrial efficiency, reflecting on its possible involvement in the etiopathogenesis of this epidemic disease as an appealing research avenue. Future Directions: If a direct correlation between mitoribosome failure and PD pathology is demonstrated, these mitochondrial organelles will provide valuable early clinical markers and potentially attractive targets for the development of innovative PD-directed therapeutic agents.
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Affiliation(s)
- Ana Mafalda Gonçalves
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Ana Raquel Pereira-Santos
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Ana Raquel Esteves
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Sandra M Cardoso
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Nuno Empadinhas
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,IIIUC-Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
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18
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Cipullo M, Pearce SF, Lopez Sanchez IG, Gopalakrishna S, Krüger A, Schober F, Busch JD, Li X, Wredenberg A, Atanassov I, Rorbach J. Human GTPBP5 is involved in the late stage of mitoribosome large subunit assembly. Nucleic Acids Res 2021; 49:354-370. [PMID: 33283228 PMCID: PMC7797037 DOI: 10.1093/nar/gkaa1131] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/02/2020] [Accepted: 11/10/2020] [Indexed: 12/12/2022] Open
Abstract
Human mitoribosomes are macromolecular complexes essential for translation of 11 mitochondrial mRNAs. The large and the small mitoribosomal subunits undergo a multistep maturation process that requires the involvement of several factors. Among these factors, GTP-binding proteins (GTPBPs) play an important role as GTP hydrolysis can provide energy throughout the assembly stages. In bacteria, many GTPBPs are needed for the maturation of ribosome subunits and, of particular interest for this study, ObgE has been shown to assist in the 50S subunit assembly. Here, we characterize the role of a related human Obg-family member, GTPBP5. We show that GTPBP5 interacts specifically with the large mitoribosomal subunit (mt-LSU) proteins and several late-stage mitoribosome assembly factors, including MTERF4:NSUN4 complex, MRM2 methyltransferase, MALSU1 and MTG1. Interestingly, we find that interaction of GTPBP5 with the mt-LSU is compromised in the presence of a non-hydrolysable analogue of GTP, implying a different mechanism of action of this protein in contrast to that of other Obg-family GTPBPs. GTPBP5 ablation leads to severe impairment in the oxidative phosphorylation system, concurrent with a decrease in mitochondrial translation and reduced monosome formation. Overall, our data indicate an important role of GTPBP5 in mitochondrial function and suggest its involvement in the late-stage of mt-LSU maturation.
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Affiliation(s)
- Miriam Cipullo
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Sarah F Pearce
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Isabel G Lopez Sanchez
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden.,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, 32 Gisborne Street, East Melbourne, 3002 Victoria, Australia
| | - Shreekara Gopalakrishna
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Annika Krüger
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Florian Schober
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital, Solna (L1:00), 171 76 Stockholm, Sweden
| | - Jakob D Busch
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Xinping Li
- Proteomics Core Facility, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Anna Wredenberg
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden.,Max Planck Institute 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
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
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19
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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: 23] [Impact Index Per Article: 7.7] [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.
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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
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20
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Ferrari A, Del'Olio S, Barrientos A. The Diseased Mitoribosome. FEBS Lett 2020; 595:1025-1061. [PMID: 33314036 DOI: 10.1002/1873-3468.14024] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/03/2020] [Accepted: 12/06/2020] [Indexed: 12/17/2022]
Abstract
Mitochondria control life and death in eukaryotic cells. Harboring a unique circular genome, a by-product of an ancient endosymbiotic event, mitochondria maintains a specialized and evolutionary divergent protein synthesis machinery, the mitoribosome. Mitoribosome biogenesis depends on elements encoded in both the mitochondrial genome (the RNA components) and the nuclear genome (all ribosomal proteins and assembly factors). Recent cryo-EM structures of mammalian mitoribosomes have illuminated their composition and provided hints regarding their assembly and elusive mitochondrial translation mechanisms. A growing body of literature involves the mitoribosome in inherited primary mitochondrial disorders. Mutations in genes encoding mitoribosomal RNAs, proteins, and assembly factors impede mitoribosome biogenesis, causing protein synthesis defects that lead to respiratory chain failure and mitochondrial disorders such as encephalo- and cardiomyopathy, deafness, neuropathy, and developmental delays. In this article, we review the current fundamental understanding of mitoribosome assembly and function, and the clinical landscape of mitochondrial disorders driven by mutations in mitoribosome components and assembly factors, to portray how basic and clinical studies combined help us better understand both mitochondrial biology and medicine.
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Affiliation(s)
- Alberto Ferrari
- Department of Neurology, University of Miami Miller School of Medicine, FL, USA
| | - Samuel Del'Olio
- Department of Neurology, University of Miami Miller School of Medicine, FL, USA.,Molecular and Cellular Pharmacology Graduate Program, University of Miami Miller School of Medicine, FL, USA
| | - Antoni Barrientos
- Department of Neurology, University of Miami Miller School of Medicine, FL, USA.,Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, FL, USA
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21
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Anturaniemi J, Zaldívar-López S, Savelkoul HFJ, Elo K, Hielm-Björkman A. The Effect of Atopic Dermatitis and Diet on the Skin Transcriptome in Staffordshire Bull Terriers. Front Vet Sci 2020; 7:552251. [PMID: 33178726 PMCID: PMC7596200 DOI: 10.3389/fvets.2020.552251] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 09/08/2020] [Indexed: 12/22/2022] Open
Abstract
Canine atopic dermatitis (CAD) has a hereditary basis that is modified by interactions with the environment, including diet. Differentially expressed genes in non-lesional skin, determined by RNA sequencing before and after a dietary intervention, were compared between dogs with naturally occurring CAD (n = 4) and healthy dogs (n = 4). The dogs were fed either a common commercial heat-processed high carbohydrate food (kibble diet) (n = 4), or a non-processed high fat food (raw meat-based diet) (n = 4). At the end of the diet intervention, 149 differentially expressed transcripts were found between the atopic and healthy dogs. The main canonical pathways altered by the dysregulation of these genes were angiopoietin signaling, epidermal growth factor signaling, activation of angiogenesis, and alterations in keratinocyte proliferation and lipid metabolism. On the other hand, 33 differently expressed transcripts were found between the two diet groups, of which 8 encode genes that are annotated in the current version of the dog genome: immunoglobulin heavy constant mu (IGHM), immunoglobulin lambda-like polypeptide 5 (IGLL5), B-cell antigen receptor complex-associated protein beta chain (CD79B), polymeric immunoglobulin receptor (PIGR), cystathionine β-synthase (CBS), argininosuccinate synthase 1 (ASS1), secretory leukocyte peptidase inhibitor (SLPI), and mitochondrial ribosome recycling factor (MRRF). All genes were upregulated in the raw diet group. In conclusion the findings of this study suggest alterations in lipid and keratinocyte metabolism as well as angiogenesis in the skin of atopic dogs. Additionally, a possible enhancement of innate immunity and decrease in oxidative stress was seen in raw food fed dogs, which could have an important role in preventing hypersensitivities and disturbed immunity at young age.
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Affiliation(s)
- Johanna Anturaniemi
- Faculty of Veterinary Medicine, Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
| | - Sara Zaldívar-López
- Genomics and Animal Breeding Group, Department of Genetics, Faculty of Veterinary Medicine, University of Córdoba, Córdoba, Spain
| | - Huub F J Savelkoul
- Cell Biology and Immunology Group, Wageningen University, Wageningen, Netherlands
| | - Kari Elo
- Faculty of Agriculture and Forestry, Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Anna Hielm-Björkman
- Faculty of Veterinary Medicine, Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
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22
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Koripella RK, Sharma MR, Bhargava K, Datta PP, Kaushal PS, Keshavan P, Spremulli LL, Banavali NK, Agrawal RK. Structures of the human mitochondrial ribosome bound to EF-G1 reveal distinct features of mitochondrial translation elongation. Nat Commun 2020; 11:3830. [PMID: 32737313 PMCID: PMC7395135 DOI: 10.1038/s41467-020-17715-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023] Open
Abstract
The mammalian mitochondrial ribosome (mitoribosome) and its associated translational factors have evolved to accommodate greater participation of proteins in mitochondrial translation. Here we present the 2.68-3.96 Å cryo-EM structures of the human 55S mitoribosome in complex with the human mitochondrial elongation factor G1 (EF-G1mt) in three distinct conformational states, including an intermediate state and a post-translocational state. These structures reveal the role of several mitochondria-specific (mito-specific) mitoribosomal proteins (MRPs) and a mito-specific segment of EF-G1mt in mitochondrial tRNA (tRNAmt) translocation. In particular, the mito-specific C-terminal extension in EF-G1mt is directly involved in translocation of the acceptor arm of the A-site tRNAmt. In addition to the ratchet-like and independent head-swiveling motions exhibited by the small mitoribosomal subunit, we discover significant conformational changes in MRP mL45 at the nascent polypeptide-exit site within the large mitoribosomal subunit that could be critical for tethering of the elongating mitoribosome onto the inner-mitochondrial membrane.
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MESH Headings
- Amino Acid Sequence
- Binding Sites
- Cryoelectron Microscopy
- HEK293 Cells
- Humans
- Mitochondria/metabolism
- Mitochondria/ultrastructure
- Mitochondrial Membranes/metabolism
- Mitochondrial Membranes/ultrastructure
- Mitochondrial Proteins/chemistry
- Mitochondrial Proteins/genetics
- Mitochondrial Proteins/metabolism
- Models, Molecular
- Nucleic Acid Conformation
- Peptide Chain Elongation, Translational
- Peptide Elongation Factor G/chemistry
- Peptide Elongation Factor G/genetics
- Peptide Elongation Factor G/metabolism
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- RNA, Mitochondrial/chemistry
- RNA, Mitochondrial/genetics
- RNA, Mitochondrial/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosomes/metabolism
- Ribosomes/ultrastructure
- Sequence Alignment
- Sequence Homology, Amino Acid
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Affiliation(s)
- Ravi Kiran Koripella
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY, 12201, USA
| | - Manjuli R Sharma
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY, 12201, USA
| | - Kalpana Bhargava
- Department of Chemistry, Campus Box 3290, University of North Carolina, Chapel Hill, NC, USA
- High Energy Material Research Lab, Defense Research and Development Organization, Sutarwadi, Pashan, Pune, Maharashtra, 411021, India
| | - Partha P Datta
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY, 12201, USA
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, 741246, India
| | - Prem S Kaushal
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY, 12201, USA
- Regional Centre for Biotechnology, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box # 3, Faridabad, Haryana, 121001, India
| | - Pooja Keshavan
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY, 12201, USA
| | - Linda L Spremulli
- Department of Chemistry, Campus Box 3290, University of North Carolina, Chapel Hill, NC, USA
| | - Nilesh K Banavali
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY, 12201, USA
- Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY, 12201-0509, USA
| | - Rajendra K Agrawal
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY, 12201, USA.
- Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY, 12201-0509, USA.
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23
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Mitochondrial OXPHOS Biogenesis: Co-Regulation of Protein Synthesis, Import, and Assembly Pathways. Int J Mol Sci 2020; 21:ijms21113820. [PMID: 32481479 PMCID: PMC7312649 DOI: 10.3390/ijms21113820] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/21/2020] [Accepted: 05/25/2020] [Indexed: 02/07/2023] Open
Abstract
The assembly of mitochondrial oxidative phosphorylation (OXPHOS) complexes is an intricate process, which—given their dual-genetic control—requires tight co-regulation of two evolutionarily distinct gene expression machineries. Moreover, fine-tuning protein synthesis to the nascent assembly of OXPHOS complexes requires regulatory mechanisms such as translational plasticity and translational activators that can coordinate mitochondrial translation with the import of nuclear-encoded mitochondrial proteins. The intricacy of OXPHOS complex biogenesis is further evidenced by the requirement of many tightly orchestrated steps and ancillary factors. Early-stage ancillary chaperones have essential roles in coordinating OXPHOS assembly, whilst late-stage assembly factors—also known as the LYRM (leucine–tyrosine–arginine motif) proteins—together with the mitochondrial acyl carrier protein (ACP)—regulate the incorporation and activation of late-incorporating OXPHOS subunits and/or co-factors. In this review, we describe recent discoveries providing insights into the mechanisms required for optimal OXPHOS biogenesis, including the coordination of mitochondrial gene expression with the availability of nuclear-encoded factors entering via mitochondrial protein import systems.
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24
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Gopalakrishna S, Pearce SF, Dinan AM, Schober FA, Cipullo M, Spåhr H, Khawaja A, Maffezzini C, Freyer C, Wredenberg A, Atanassov I, Firth AE, Rorbach J. C6orf203 is an RNA-binding protein involved in mitochondrial protein synthesis. Nucleic Acids Res 2019; 47:9386-9399. [PMID: 31396629 PMCID: PMC6755124 DOI: 10.1093/nar/gkz684] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/22/2019] [Accepted: 07/26/2019] [Indexed: 01/17/2023] Open
Abstract
In all biological systems, RNAs are associated with RNA-binding proteins (RBPs), forming complexes that control gene regulatory mechanisms, from RNA synthesis to decay. In mammalian mitochondria, post-transcriptional regulation of gene expression is conducted by mitochondrial RBPs (mt-RBPs) at various stages of mt-RNA metabolism, including polycistronic transcript production, its processing into individual transcripts, mt-RNA modifications, stability, translation and degradation. To date, only a handful of mt-RBPs have been characterized. Here, we describe a putative human mitochondrial protein, C6orf203, that contains an S4-like domain-an evolutionarily conserved RNA-binding domain previously identified in proteins involved in translation. Our data show C6orf203 to bind highly structured RNA in vitro and associate with the mitoribosomal large subunit in HEK293T cells. Knockout of C6orf203 leads to a decrease in mitochondrial translation and consequent OXPHOS deficiency, without affecting mitochondrial RNA levels. Although mitoribosome stability is not affected in C6orf203-depleted cells, mitoribosome profiling analysis revealed a global disruption of the association of mt-mRNAs with the mitoribosome, suggesting that C6orf203 may be required for the proper maturation and functioning of the mitoribosome. We therefore propose C6orf203 to be a novel RNA-binding protein involved in mitochondrial translation, expanding the repertoire of factors engaged in this process.
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Affiliation(s)
- Shreekara Gopalakrishna
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 77 Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Sarah F Pearce
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 77 Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Adam M Dinan
- Department of Pathology, University of Cambridge, CB2 0QQ Cambridge, UK
| | - Florian A Schober
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, 171 77 Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Miriam Cipullo
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 77 Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Henrik Spåhr
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 77 Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Anas Khawaja
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 77 Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Camilla Maffezzini
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 77 Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Christoph Freyer
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 77 Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Anna Wredenberg
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 77 Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Ilian Atanassov
- Proteomics Core Facility, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Andrew E Firth
- Department of Pathology, University of Cambridge, CB2 0QQ Cambridge, UK
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 77 Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, 171 77 Stockholm, Sweden
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25
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Rudler DL, Hughes LA, Perks KL, Richman TR, Kuznetsova I, Ermer JA, Abudulai LN, Shearwood AMJ, Viola HM, Hool LC, Siira SJ, Rackham O, Filipovska A. Fidelity of translation initiation is required for coordinated respiratory complex assembly. SCIENCE ADVANCES 2019; 5:eaay2118. [PMID: 31903419 PMCID: PMC6924987 DOI: 10.1126/sciadv.aay2118] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/30/2019] [Indexed: 05/22/2023]
Abstract
Mammalian mitochondrial ribosomes are unique molecular machines that translate 11 leaderless mRNAs; however, it is not clear how mitoribosomes initiate translation, since mitochondrial mRNAs lack untranslated regions. Mitochondrial translation initiation shares similarities with prokaryotes, such as the formation of a ternary complex of fMet-tRNAMet, mRNA and the 28S subunit, but differs in the requirements for initiation factors. Mitochondria have two initiation factors: MTIF2, which closes the decoding center and stabilizes the binding of the fMet-tRNAMet to the leaderless mRNAs, and MTIF3, whose role is not clear. We show that MTIF3 is essential for survival and that heart- and skeletal muscle-specific loss of MTIF3 causes cardiomyopathy. We identify increased but uncoordinated mitochondrial protein synthesis in mice lacking MTIF3, resulting in loss of specific respiratory complexes. Ribosome profiling shows that MTIF3 is required for recognition and regulation of translation initiation of mitochondrial mRNAs and for coordinated assembly of OXPHOS complexes in vivo.
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Affiliation(s)
- Danielle L. Rudler
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
| | - Laetitia A. Hughes
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
| | - Kara L. Perks
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
| | - Tara R. Richman
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
| | - Irina Kuznetsova
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
| | - Judith A. Ermer
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
| | - Laila N. Abudulai
- Centre for Microscopy, Characterisation and Analysis and School of Biomedical Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Anne-Marie J. Shearwood
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
| | - Helena M. Viola
- School of Human Sciences (Physiology), The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Livia C. Hool
- School of Human Sciences (Physiology), The University of Western Australia, Crawley, Western Australia 6009, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia
| | - Stefan J. Siira
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, Western Australia 6102, Australia
- Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia 6102, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
- Corresponding author.
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26
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Toompuu M, Tuomela T, Laine P, Paulin L, Dufour E, Jacobs HT. Polyadenylation and degradation of structurally abnormal mitochondrial tRNAs in human cells. Nucleic Acids Res 2019. [PMID: 29518244 PMCID: PMC6007314 DOI: 10.1093/nar/gky159] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
RNA 3' polyadenylation is known to serve diverse purposes in biology, in particular, regulating mRNA stability and translation. Here we determined that, upon exposure to high levels of the intercalating agent ethidium bromide (EtBr), greater than those required to suppress mitochondrial transcription, mitochondrial tRNAs in human cells became polyadenylated. Relaxation of the inducing stress led to rapid turnover of the polyadenylated tRNAs. The extent, kinetics and duration of tRNA polyadenylation were EtBr dose-dependent, with mitochondrial tRNAs differentially sensitive to the stress. RNA interference and inhibitor studies indicated that ongoing mitochondrial ATP synthesis, plus the mitochondrial poly(A) polymerase and SUV3 helicase were required for tRNA polyadenylation, while polynucleotide phosphorylase counteracted the process and was needed, along with SUV3, for degradation of the polyadenylated tRNAs. Doxycycline treatment inhibited both tRNA polyadenylation and turnover, suggesting a possible involvement of the mitoribosome, although other translational inhibitors had only minor effects. The dysfunctional tRNALeu(UUR) bearing the pathological A3243G mutation was constitutively polyadenylated at a low level, but this was markedly enhanced after doxycycline treatment. We propose that polyadenylation of structurally and functionally abnormal mitochondrial tRNAs entrains their PNPase/SUV3-mediated destruction, and that this pathway could play an important role in mitochondrial diseases associated with tRNA mutations.
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Affiliation(s)
- Marina Toompuu
- Faculty of Medicine and Life Sciences, BioMediTech Institute and Tampere University Hospital, FI-33014 University of Tampere, Finland
| | - Tea Tuomela
- Faculty of Medicine and Life Sciences, BioMediTech Institute and Tampere University Hospital, FI-33014 University of Tampere, Finland
| | - Pia Laine
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Eric Dufour
- Faculty of Medicine and Life Sciences, BioMediTech Institute and Tampere University Hospital, FI-33014 University of Tampere, Finland
| | - Howard T Jacobs
- Faculty of Medicine and Life Sciences, BioMediTech Institute and Tampere University Hospital, FI-33014 University of Tampere, Finland.,Institute of Biotechnology, FI-00014 University of Helsinki, Finland
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27
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Durigon R, Mitchell AL, Jones AW, Manole A, Mennuni M, Hirst EM, Houlden H, Maragni G, Lattante S, Doronzio PN, Dalla Rosa I, Zollino M, Holt IJ, Spinazzola A. LETM1 couples mitochondrial DNA metabolism and nutrient preference. EMBO Mol Med 2019; 10:emmm.201708550. [PMID: 30012579 PMCID: PMC6127893 DOI: 10.15252/emmm.201708550] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The diverse clinical phenotypes of Wolf–Hirschhorn syndrome (WHS) are the result of haploinsufficiency of several genes, one of which, LETM1, encodes a protein of the mitochondrial inner membrane of uncertain function. Here, we show that LETM1 is associated with mitochondrial ribosomes, is required for mitochondrial DNA distribution and expression, and regulates the activity of an ancillary metabolic enzyme, pyruvate dehydrogenase. LETM1 deficiency in WHS alters mitochondrial morphology and DNA organization, as does substituting ketone bodies for glucose in control cells. While this change in nutrient availability leads to the death of fibroblasts with normal amounts of LETM1, WHS‐derived fibroblasts survive on ketone bodies, which can be attributed to their reduced dependence on glucose oxidation. Thus, remodeling of mitochondrial nucleoprotein complexes results from the inability of mitochondria to use specific substrates for energy production and is indicative of mitochondrial dysfunction. However, the dysfunction could be mitigated by a modified diet—for WHS, one high in lipids and low in carbohydrates.
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Affiliation(s)
- Romina Durigon
- Department of Clinical and Movement Neurosciences, UCL Institute of Neurology, London, UK
| | - Alice L Mitchell
- Department of Clinical and Movement Neurosciences, UCL Institute of Neurology, London, UK
| | - Aleck We Jones
- Department of Clinical and Movement Neurosciences, UCL Institute of Neurology, London, UK
| | - Andreea Manole
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, London, UK.,Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Mara Mennuni
- Department of Clinical and Movement Neurosciences, UCL Institute of Neurology, London, UK
| | | | - Henry Houlden
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, London, UK.,Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | | | - Serena Lattante
- Institute of Genomic Medicine, Catholic University, Rome, Italy
| | | | - Ilaria Dalla Rosa
- Department of Clinical and Movement Neurosciences, UCL Institute of Neurology, London, UK
| | | | - Ian J Holt
- Department of Clinical and Movement Neurosciences, UCL Institute of Neurology, London, UK.,Biodonostia Health Research Institute, San Sebastián, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Antonella Spinazzola
- Department of Clinical and Movement Neurosciences, UCL Institute of Neurology, London, UK .,MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, London, UK
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28
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Structural insights into unique features of the human mitochondrial ribosome recycling. Proc Natl Acad Sci U S A 2019; 116:8283-8288. [PMID: 30962385 PMCID: PMC6486771 DOI: 10.1073/pnas.1815675116] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing proteins that are essential for oxidative phosphorylation (ATP generation). Despite their common ancestry with bacteria, the composition and structure of the human mitoribosome and its translational factors are significantly different from those of their bacterial counterparts. The mammalian mitoribosome recycling factor (RRFmt) carries a mito-specific N terminus extension (NTE), which is necessary for the function of RRFmt Here we present a 3.9-Å resolution cryo-electron microscopic (cryo-EM) structure of the human 55S mitoribosome-RRFmt complex, which reveals α-helix and loop structures for the NTE that makes multiple mito-specific interactions with functionally critical regions of the mitoribosome. These include ribosomal RNA segments that constitute the peptidyl transferase center (PTC) and those that connect PTC with the GTPase-associated center and with mitoribosomal proteins L16 and L27. Our structure reveals the presence of a tRNA in the pe/E position and a rotation of the small mitoribosomal subunit on RRFmt binding. In addition, we observe an interaction between the pe/E tRNA and a mito-specific protein, mL64. These findings help understand the unique features of mitoribosome recycling.
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29
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Kim HJ, Barrientos A. MTG1 couples mitoribosome large subunit assembly with intersubunit bridge formation. Nucleic Acids Res 2018; 46:8435-8453. [PMID: 30085276 PMCID: PMC6144824 DOI: 10.1093/nar/gky672] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 07/11/2018] [Accepted: 07/13/2018] [Indexed: 02/06/2023] Open
Abstract
Mammalian mitochondrial ribosomes (mitoribosomes) synthesize 13 proteins, essential components of the oxidative phosphorylation system. They are linked to mitochondrial disorders, often involving cardiomyopathy. Mitoribosome biogenesis is assisted by multiple cofactors whose specific functions remain largely uncharacterized. Here, we examined the role of human MTG1, a conserved ribosome assembly guanosine triphosphatase. MTG1-silencing in human cardiomyocytes and developing zebrafish revealed early cardiovascular lesions. A combination of gene-editing and biochemical approaches using HEK293T cells demonstrated that MTG1 binds to the large subunit (mtLSU) 16S ribosomal RNA to facilitate incorporation of late-assembly proteins. Furthermore, MTG1 interacts with mtLSU uL19 protein and mtSSU mS27, a putative guanosine triphosphate-exchange factor (GEF), to enable MTG1 release and the formation of the mB6 intersubunit bridge. In this way, MTG1 establishes a quality control checkpoint in mitoribosome assembly. In conclusion, MTG1 controls mitochondrial translation by coupling mtLSU assembly with intersubunit bridge formation using the intrinsic GEF activity acquired by the mtSSU through mS27, a unique occurrence in translational systems.
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Affiliation(s)
- Hyun-Jung Kim
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Antoni Barrientos
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
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30
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Mitochondrial transcription and translation: overview. Essays Biochem 2018; 62:309-320. [PMID: 30030363 PMCID: PMC6056719 DOI: 10.1042/ebc20170102] [Citation(s) in RCA: 165] [Impact Index Per Article: 27.5] [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.
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31
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Impact of spliceosome mutations on RNA splicing in myelodysplasia: dysregulated genes/pathways and clinical associations. Blood 2018; 132:1225-1240. [PMID: 29930011 DOI: 10.1182/blood-2018-04-843771] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/11/2018] [Indexed: 12/14/2022] Open
Abstract
SF3B1, SRSF2, and U2AF1 are the most frequently mutated splicing factor genes in the myelodysplastic syndromes (MDS). We have performed a comprehensive and systematic analysis to determine the effect of these commonly mutated splicing factors on pre-mRNA splicing in the bone marrow stem/progenitor cells and in the erythroid and myeloid precursors in splicing factor mutant MDS. Using RNA-seq, we determined the aberrantly spliced genes and dysregulated pathways in CD34+ cells of 84 patients with MDS. Splicing factor mutations result in different alterations in splicing and largely affect different genes, but these converge in common dysregulated pathways and cellular processes, focused on RNA splicing, protein synthesis, and mitochondrial dysfunction, suggesting common mechanisms of action in MDS. Many of these dysregulated pathways and cellular processes can be linked to the known disease pathophysiology associated with splicing factor mutations in MDS, whereas several others have not been previously associated with MDS, such as sirtuin signaling. We identified aberrantly spliced events associated with clinical variables, and isoforms that independently predict survival in MDS and implicate dysregulation of focal adhesion and extracellular exosomes as drivers of poor survival. Aberrantly spliced genes and dysregulated pathways were identified in the MDS-affected lineages in splicing factor mutant MDS. Functional studies demonstrated that knockdown of the mitosis regulators SEPT2 and AKAP8, aberrantly spliced target genes of SF3B1 and SRSF2 mutations, respectively, led to impaired erythroid cell growth and differentiation. This study illuminates the effect of the common spliceosome mutations on the MDS phenotype and provides novel insights into disease pathophysiology.
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32
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Abstract
Mitochondria are intracellular organelles responsible for adenosine triphosphate production. The strict control of intracellular energy needs require proper mitochondrial functioning. The mitochondria are under dual controls of mitochondrial DNA (mtDNA) and nuclear DNA (nDNA). Mitochondrial dysfunction can arise from changes in either mtDNA or nDNA genes regulating function. There are an estimated ∼1500 proteins in the mitoproteome, whereas the mtDNA genome has 37 proteins. There are, to date, ∼275 genes shown to give rise to disease. The unique physiology of mitochondrial functioning contributes to diverse gene expression. The onset and range of phenotypic expression of disease is diverse, with onset from neonatal to seventh decade of life. The range of dysfunction is heterogeneous, ranging from single organ to multisystem involvement. The complexity of disease expression has severely limited gene discovery. Combining phenotypes with improvements in gene sequencing strategies are improving the diagnosis process. This chapter focuses on the interplay of the unique physiology and gene discovery in the current knowledge of genetically derived mitochondrial disease.
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Affiliation(s)
- Russell P Saneto
- Seattle Children's Hospital/University of Washington, Seattle, WA, United States.
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33
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Abstract
Mitochondria play fundamental roles in the regulation of life and death of eukaryotic cells. They mediate aerobic energy conversion through the oxidative phosphorylation (OXPHOS) system, and harbor and control the intrinsic pathway of apoptosis. As a descendant of a bacterial endosymbiont, mitochondria retain a vestige of their original genome (mtDNA), and its corresponding full gene expression machinery. Proteins encoded in the mtDNA, all components of the multimeric OXPHOS enzymes, are synthesized in specialized mitochondrial ribosomes (mitoribosomes). Mitoribosomes are therefore essential in the regulation of cellular respiration. Additionally, an increasing body of literature has been reporting an alternative role for several mitochondrial ribosomal proteins as apoptosis-inducing factors. No surprisingly, the expression of genes encoding for mitoribosomal proteins, mitoribosome assembly factors and mitochondrial translation factors is modified in numerous cancers, a trait that has been linked to tumorigenesis and metastasis. In this article, we will review the current knowledge regarding the dual function of mitoribosome components in protein synthesis and apoptosis and their association with cancer susceptibility and development. We will also highlight recent developments in targeting mitochondrial ribosomes for the treatment of cancer.
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Abstract
SIGNIFICANCE In the last years, metabolic reprogramming, fluctuations in bioenergetic fuels, and modulation of oxidative stress became new key hallmarks of tumor development. In cancer, elevated glucose uptake and high glycolytic rate, as a source of adenosine triphosphate, constitute a growth advantage for tumors. This represents the universally known Warburg effect, which gave rise to one major clinical application for detecting cancer cells using glucose analogs: the positron emission tomography scan imaging. Recent Advances: Glucose utilization and carbon sources in tumors are much more heterogeneous than initially thought. Indeed, new studies emerged and revealed a dual capacity of tumor cells for glycolytic and oxidative phosphorylation (OXPHOS) metabolism. OXPHOS metabolism, which relies predominantly on mitochondrial respiration, exhibits fine-tuned regulation of respiratory chain complexes and enhanced antioxidant response or detoxification capacity. CRITICAL ISSUES OXPHOS-dependent cancer cells use alternative oxidizable substrates, such as glutamine and fatty acids. The diversity of carbon substrates fueling neoplastic cells is indicative of metabolic heterogeneity, even within tumors sharing the same clinical diagnosis. Metabolic switch supports cancer cell stemness and their bioenergy-consuming functions, such as proliferation, survival, migration, and invasion. Moreover, reactive oxygen species-induced mitochondrial metabolism and nutrient availability are important for interaction with tumor microenvironment components. Carcinoma-associated fibroblasts and immune cells participate in the metabolic interplay with neoplastic cells. They collectively adapt in a dynamic manner to the metabolic needs of cancer cells, thus participating in tumorigenesis and resistance to treatments. FUTURE DIRECTIONS Characterizing the reciprocal metabolic interplay between stromal, immune, and neoplastic cells will provide a better understanding of treatment resistance. Antioxid. Redox Signal. 26, 462-485.
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Affiliation(s)
- Géraldine Gentric
- 1 Stress and Cancer Laboratory, Équipe Labelisée LNCC, Institut Curie , Paris, France .,2 Inserm , U830, Paris, France
| | - Virginie Mieulet
- 1 Stress and Cancer Laboratory, Équipe Labelisée LNCC, Institut Curie , Paris, France .,2 Inserm , U830, Paris, France
| | - Fatima Mechta-Grigoriou
- 1 Stress and Cancer Laboratory, Équipe Labelisée LNCC, Institut Curie , Paris, France .,2 Inserm , U830, Paris, France
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Differential contribution of the mitochondrial translation pathway to the survival of diffuse large B-cell lymphoma subsets. Cell Death Differ 2016; 24:251-262. [PMID: 27768122 DOI: 10.1038/cdd.2016.116] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 09/08/2016] [Accepted: 09/13/2016] [Indexed: 12/13/2022] Open
Abstract
Diffuse large B-cell lymphomas (DLBCLs) are a highly heterogeneous group of tumors in which subsets share molecular features revealed by gene expression profiles and metabolic fingerprints. While B-cell receptor (BCR)-dependent DLBCLs are glycolytic, OxPhos-DLBCLs rely on mitochondrial energy transduction and nutrient utilization pathways that provide pro-survival benefits independent of BCR signaling. Integral to these metabolic distinctions is elevated mitochondrial electron transport chain (ETC) activity in OxPhos-DLBCLs compared with BCR-DLBCLs, which is linked to greater protein abundance of ETC components. To gain insights into molecular determinants of the selective increase in ETC activity and dependence on mitochondrial energy metabolism in OxPhos-DLBCLs, we examined the mitochondrial translation pathway in charge of the synthesis of mitochondrial DNA encoded ETC subunits. Quantitative mass spectrometry identified increased expression of mitochondrial translation factors in OxPhos-DLBCL as compared with the BCR subtype. Biochemical and functional assays indicate that the mitochondrial translation pathway is required for increased ETC activity and mitochondrial energy reserves in OxPhos-DLBCL. Importantly, molecular depletion of several mitochondrial translation proteins using RNA interference or pharmacological perturbation of the mitochondrial translation pathway with the FDA-approved inhibitor tigecycline (Tigecyl) is selectively toxic to OxPhos-DLBCL cell lines and primary tumors. These findings provide additional molecular insights into the metabolic characteristics of OxPhos-DLBCLs, and mark the mitochondrial translation pathway as a potential therapeutic target in these tumors.
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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.
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Lao X, Feng Q, He G, Ji M, Zhu D, Xu P, Tang W, Xu J, Qin X. Immature Colon Carcinoma Transcript-1 (ICT1) Expression Correlates with Unfavorable Prognosis and Survival in Patients with Colorectal Cancer. Ann Surg Oncol 2016; 23:3924-3933. [PMID: 27411551 DOI: 10.1245/s10434-016-5305-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Indexed: 01/03/2023]
Abstract
BACKGROUND Colorectal cancer (CRC) is the third leading cause of death from cancer worldwide. Immature colon carcinoma transcript-1 (ICT1) has been reported to be correlated with lung cancer; however, whether ICT1 is a functional gene in CRC, as well as the molecular mechanism underlying ICT1 mediation of colorectal-tumor formation, remains unknown. METHODS The expression of ICT1 was firstly determined by using immunohistochemistry in 861 CRC specimens. The correlation of ICT1 expression with clinicopathological parameters and the survival rate was analyzed. Furthermore, we investigated the effect of ICT1 silencing on CRC cell proliferation and migration by MTT, colony formation, flow cytometry, and transwell in vitro. RESULTS ICT1 is highly expressed in a cohort of human CRCs, and that higher ICT1 expression may lead to reduced overall survival rate of CRC. Likewise, ICT1 silencing lowered the cell viability through cell-cycle arrest, inhibited cell migration, and induced apoptosis in CRC. We further revealed a novel mechanism in which ICT1 promoted CRC growth via the intracellular AMPK, SAPK/JNK, and PARP signaling pathways. CONCLUSIONS Our data showed that ICT1 could be an important target for CRC diagnosis and treatment.
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Affiliation(s)
- Xinyuan Lao
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Qingyang Feng
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Guodong He
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Meiling Ji
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Dexiang Zhu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Pingping Xu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Wentao Tang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jianmin Xu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
| | - Xinyu Qin
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
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Ostojić J, Panozzo C, Bourand-Plantefol A, Herbert CJ, Dujardin G, Bonnefoy N. Ribosome recycling defects modify the balance between the synthesis and assembly of specific subunits of the oxidative phosphorylation complexes in yeast mitochondria. Nucleic Acids Res 2016; 44:5785-97. [PMID: 27257059 PMCID: PMC4937339 DOI: 10.1093/nar/gkw490] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 05/20/2016] [Indexed: 01/07/2023] Open
Abstract
Mitochondria have their own translation machinery that produces key subunits of the OXPHOS complexes. This machinery relies on the coordinated action of nuclear-encoded factors of bacterial origin that are well conserved between humans and yeast. In humans, mutations in these factors can cause diseases; in yeast, mutations abolishing mitochondrial translation destabilize the mitochondrial DNA. We show that when the mitochondrial genome contains no introns, the loss of the yeast factors Mif3 and Rrf1 involved in ribosome recycling neither blocks translation nor destabilizes mitochondrial DNA. Rather, the absence of these factors increases the synthesis of the mitochondrially-encoded subunits Cox1, Cytb and Atp9, while strongly impairing the assembly of OXPHOS complexes IV and V. We further show that in the absence of Rrf1, the COX1 specific translation activator Mss51 accumulates in low molecular weight forms, thought to be the source of the translationally-active form, explaining the increased synthesis of Cox1. We propose that Rrf1 takes part in the coordination between translation and OXPHOS assembly in yeast mitochondria. These interactions between general and specific translation factors might reveal an evolutionary adaptation of the bacterial translation machinery to the set of integral membrane proteins that are translated within mitochondria.
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Affiliation(s)
- Jelena Ostojić
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, UEVE, 91198, Gif-sur-Yvette cedex, France
| | - Cristina Panozzo
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, UEVE, 91198, Gif-sur-Yvette cedex, France
| | - Alexa Bourand-Plantefol
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, UEVE, 91198, Gif-sur-Yvette cedex, France
| | - Christopher J Herbert
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, UEVE, 91198, Gif-sur-Yvette cedex, France
| | - Geneviève Dujardin
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, UEVE, 91198, Gif-sur-Yvette cedex, France
| | - Nathalie Bonnefoy
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, UEVE, 91198, Gif-sur-Yvette cedex, France
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Ficociello G, Salemme A, Uccelletti D, Fiorito S, Togna AR, Vallan L, González-Domínguez JM, Da Ros T, Francisci S, Montanari A. Evaluation of the efficacy of carbon nanotubes for delivering peptides into mitochondria. RSC Adv 2016. [DOI: 10.1039/c6ra14254k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Future therapy for mitochondrial pathologies: CKKSFLSPRTALINFLVK peptide from mitochondrial-LeuRS has a mitochondrial targeting activity when conjugated with multi-walled carbon nanotubes.
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Affiliation(s)
- Graziella Ficociello
- Department of Biology and Biotechnologies “Charles Darwin”
- Sapienza University of Rome
- 5-00185 Rome
- Italy
| | - Adele Salemme
- Department of Physiology and Pharmacology “Vittorio Erspamer”
- Sapienza University of Rome
- 5-00185 Rome
- Italy
| | - Daniela Uccelletti
- Department of Biology and Biotechnologies “Charles Darwin”
- Sapienza University of Rome
- 5-00185 Rome
- Italy
| | - Silvana Fiorito
- Institute of Translational Pharmacology – CNR
- 100-00133 Rome
- Italy
| | - Anna Rita Togna
- Department of Physiology and Pharmacology “Vittorio Erspamer”
- Sapienza University of Rome
- 5-00185 Rome
- Italy
| | - Lorenzo Vallan
- INSTM Unit of Trieste
- Department of Chemical and Pharmaceutical Sciences
- University of Trieste
- 1-34127 Trieste
- Italy
| | - Jose M. González-Domínguez
- INSTM Unit of Trieste
- Department of Chemical and Pharmaceutical Sciences
- University of Trieste
- 1-34127 Trieste
- Italy
| | - Tatiana Da Ros
- INSTM Unit of Trieste
- Department of Chemical and Pharmaceutical Sciences
- University of Trieste
- 1-34127 Trieste
- Italy
| | - Silvia Francisci
- Department of Biology and Biotechnologies “Charles Darwin”
- Sapienza University of Rome
- 5-00185 Rome
- Italy
| | - Arianna Montanari
- Department of Biology and Biotechnologies “Charles Darwin”
- Sapienza University of Rome
- 5-00185 Rome
- Italy
- Pasteur Institute – Cenci Bolognetti Foundation
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Bond ME, Brown R, Rallis C, Bähler J, Mole SE. A central role for TOR signalling in a yeast model for juvenile CLN3 disease. MICROBIAL CELL 2015; 2:466-480. [PMID: 28357272 PMCID: PMC5354605 DOI: 10.15698/mic2015.12.241] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Yeasts provide an excellent genetically tractable eukaryotic system for investigating the function of genes in their biological context, and are especially relevant for those conserved genes that cause disease. We study the role of btn1, the orthologue of a human gene that underlies an early onset neurodegenerative disease (juvenile CLN3 disease, neuronal ceroid lipofuscinosis (NCLs) or Batten disease) in the fission yeast Schizosaccharomyces pombe. A global screen for genetic interactions with btn1 highlighted a conserved key signalling hub in which multiple components functionally relate to this conserved disease gene. This signalling hub includes two major mitogen-activated protein kinase (MAPK) cascades, and centers on the Tor kinase complexes TORC1 and TORC2. We confirmed that yeast cells modelling CLN3 disease exhibit features consistent with dysfunction in the TORC pathways, and showed that modulating TORC function leads to a comprehensive rescue of defects in this yeast disease model. The same pathways may be novel targets in the development of therapies for the NCLs and related diseases.
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Affiliation(s)
- Michael E Bond
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Rachel Brown
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Charalampos Rallis
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK. ; Institute of Healthy Ageing, University College London, London WC1E 6BT, UK
| | - Jürg Bähler
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK. ; Institute of Healthy Ageing, University College London, London WC1E 6BT, UK
| | - Sara E Mole
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK. ; UCL Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK. ; Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
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Brown TA, Tkachuk AN, Clayton DA. Mitochondrial Transcription Factor A (TFAM) Binds to RNA Containing 4-Way Junctions and Mitochondrial tRNA. PLoS One 2015; 10:e0142436. [PMID: 26545237 PMCID: PMC4636309 DOI: 10.1371/journal.pone.0142436] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/21/2015] [Indexed: 11/26/2022] Open
Abstract
Mitochondrial DNA (mtDNA) is maintained within nucleoprotein complexes known as nucleoids. These structures are highly condensed by the DNA packaging protein, mitochondrial Transcription Factor A (TFAM). Nucleoids also include RNA, RNA:DNA hybrids, and are associated with proteins involved with RNA processing and mitochondrial ribosome biogenesis. Here we characterize the ability of TFAM to bind various RNA containing substrates in order to determine their role in TFAM distribution and function within the nucleoid. We find that TFAM binds to RNA-containing 4-way junctions but does not bind appreciably to RNA hairpins, internal loops, or linear RNA:DNA hybrids. Therefore the RNA within nucleoids largely excludes TFAM, and its distribution is not grossly altered with removal of RNA. Within the cell, TFAM binds to mitochondrial tRNAs, consistent with our RNA 4-way junction data. Kinetic binding assays and RNase-insensitive TFAM distribution indicate that DNA remains the preferred substrate within the nucleoid. However, TFAM binds to tRNA with nanomolar affinity and these complexes are not rare. TFAM-immunoprecipitated tRNAs have processed ends, suggesting that binding is not specific to RNA precursors. The amount of each immunoprecipitated tRNA is not well correlated with tRNA celluar abundance, indicating unequal TFAM binding preferences. TFAM-mt-tRNA interaction suggests potentially new functions for this protein.
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Affiliation(s)
- Timothy A. Brown
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
- * E-mail:
| | - Ariana N. Tkachuk
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - David A. Clayton
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
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Xie R, Zhang Y, Shen C, Cao X, Gu S, Che X. Knockdown of immature colon carcinoma transcript-1 inhibits proliferation of glioblastoma multiforme cells through Gap 2/mitotic phase arrest. Onco Targets Ther 2015; 8:1119-27. [PMID: 26056476 PMCID: PMC4446011 DOI: 10.2147/ott.s75864] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
“Glioblastoma multiforme” (GBM) is the frequent form of malignant glioma. Immature colon carcinoma transcript-1 (ICT1) is essential for cell vitality and mitochondrial function and has been recognized in several human cancers. In the study reported here, we attempted to evaluate the functional role of ICT1 in GBM cells. Lentivirus-mediated RNA interference (RNAi) was applied to silence ICT1 expression in human GBM cell lines U251 and U87. Cell proliferation was measured by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and colony-formation assays. Cell-cycle progression was determined by flow cytometry with propidium iodide staining. The results revealed that lentivirus-mediated short hairpin RNA (shRNA) can specifically suppress the expression of ICT1 in U251 and U87 cells. Functional investigations proved for the first time, as far as we are aware, that ICT1 knockdown significantly inhibited the proliferation of both cell lines. Moreover, the cell cycle of U251 cells was arrested at Gap 2 (G2)/mitotic (M) phase after ICT1 knockdown, with a concomitant accumulation of cells in the Sub-Gap 1 (G1) phase. This study highlights the crucial role of ICT1 in promoting GBM cell proliferation, and provides a foundation for further study into the clinical potential of lentivirus-mediated silencing of ICT1 for GBM therapy.
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Affiliation(s)
- Rong Xie
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Yichao Zhang
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Chao Shen
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Xiaoyun Cao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Shixin Gu
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Xiaoming Che
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
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Rajala N, Hensen F, Wessels HJCT, Ives D, Gloerich J, Spelbrink JN. Whole cell formaldehyde cross-linking simplifies purification of mitochondrial nucleoids and associated proteins involved in mitochondrial gene expression. PLoS One 2015; 10:e0116726. [PMID: 25695250 PMCID: PMC4335056 DOI: 10.1371/journal.pone.0116726] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 12/13/2014] [Indexed: 11/19/2022] Open
Abstract
Mitochondrial DNA/protein complexes (nucleoids) appear as discrete entities inside the mitochondrial network when observed by live-cell imaging and immunofluorescence. This somewhat trivial observation in recent years has spurred research towards isolation of these complexes and the identification of nucleoid-associated proteins. Here we show that whole cell formaldehyde crosslinking combined with affinity purification and tandem mass-spectrometry provides a simple and reproducible method to identify potential nucleoid associated proteins. The method avoids spurious mitochondrial isolation and subsequent multifarious nucleoid enrichment protocols and can be implemented to allow for label-free quantification (LFQ) by mass-spectrometry. Using expression of a Flag-tagged Twinkle helicase and appropriate controls we show that this method identifies many previously identified nucleoid associated proteins. Using LFQ to compare HEK293 cells with and without mtDNA, but both expressing Twinkle-FLAG, identifies many proteins that are reduced or absent in the absence of mtDNA. This set not only includes established mtDNA maintenance proteins but also many proteins involved in mitochondrial RNA metabolism and translation and therefore represents what can be considered an mtDNA gene expression proteome. Our data provides a very valuable resource for both basic mitochondrial researchers as well as clinical geneticists working to identify novel disease genes on the basis of exome sequence data.
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Affiliation(s)
- Nina Rajala
- Mitochondrial DNA Maintenance Group, BioMediTech, FI-33014 University of Tampere, Tampere, Finland
| | - Fenna Hensen
- Department of Pediatrics, Nijmegen Centre for Mitochondrial Disorders, Radboud University Medical Centre, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Hans J. C. T. Wessels
- Department of Pediatrics, Nijmegen Centre for Mitochondrial Disorders, Radboud University Medical Centre, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Radboud Proteomics Centre, Department of Laboratory Medicine, Laboratory of Genetic Endocrine and Metabolic Disorders, Radboud University Medical Centre, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Daniel Ives
- MRC-National Institute for Medical Research, Mill Hill, London, United Kingdom
| | - Jolein Gloerich
- Department of Pediatrics, Nijmegen Centre for Mitochondrial Disorders, Radboud University Medical Centre, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Radboud Proteomics Centre, Department of Laboratory Medicine, Laboratory of Genetic Endocrine and Metabolic Disorders, Radboud University Medical Centre, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Johannes N. Spelbrink
- Mitochondrial DNA Maintenance Group, BioMediTech, FI-33014 University of Tampere, Tampere, Finland
- Department of Pediatrics, Nijmegen Centre for Mitochondrial Disorders, Radboud University Medical Centre, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- * E-mail:
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44
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Recent advances in biochemistry and biotechnological synthesis of avermectins and their derivatives. Appl Microbiol Biotechnol 2014; 98:7747-59. [DOI: 10.1007/s00253-014-5926-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 06/29/2014] [Accepted: 07/01/2014] [Indexed: 10/24/2022]
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45
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Wesolowska MT, Richter-Dennerlein R, Lightowlers RN, Chrzanowska-Lightowlers ZMA. Overcoming stalled translation in human mitochondria. Front Microbiol 2014; 5:374. [PMID: 25101074 PMCID: PMC4103422 DOI: 10.3389/fmicb.2014.00374] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 07/03/2014] [Indexed: 12/30/2022] Open
Abstract
Protein synthesis is central to life and maintaining a highly accurate and efficient mechanism is essential. What happens when a translating ribosome stalls on a messenger RNA? Many highly intricate processes have been documented in the cytosol of numerous species, but how does organellar protein synthesis resolve this stalling issue? Mammalian mitochondria synthesize just thirteen highly hydrophobic polypeptides. These proteins are all integral components of the machinery that couples oxidative phosphorylation. Consequently, it is essential that stalled mitochondrial ribosomes can be efficiently recycled. To date, there is no evidence to support any particular molecular mechanism to resolve this problem. However, here we discuss the observation that there are four predicted members of the mitochondrial translation release factor family and that only one member, mtRF1a, is necessary to terminate the translation of all thirteen open reading frames in the mitochondrion. Could the other members be involved in the process of recycling stalled mitochondrial ribosomes?
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Affiliation(s)
| | | | | | - Zofia M. A. Chrzanowska-Lightowlers
- Wellcome Trust Centre for Mitochondrial Research, Institute for Cell and Molecular Biosciences, Newcastle University, Medical SchoolNewcastle upon Tyne, UK
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Rorbach J, Boesch P, Gammage PA, Nicholls TJJ, Pearce SF, Patel D, Hauser A, Perocchi F, Minczuk M. MRM2 and MRM3 are involved in biogenesis of the large subunit of the mitochondrial ribosome. Mol Biol Cell 2014; 25:2542-55. [PMID: 25009282 PMCID: PMC4148245 DOI: 10.1091/mbc.e14-01-0014] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Defects of the translation apparatus in human mitochondria are known to cause disease, yet details of how protein synthesis is regulated in this organelle remain to be unveiled. Ribosome production in all organisms studied thus far entails a complex, multistep pathway involving a number of auxiliary factors. This includes several RNA processing and modification steps required for correct rRNA maturation. Little is known about the maturation of human mitochondrial 16S rRNA and its role in biogenesis of the mitoribosome. Here we investigate two methyltransferases, MRM2 (also known as RRMJ2, encoded by FTSJ2) and MRM3 (also known as RMTL1, encoded by RNMTL1), that are responsible for modification of nucleotides of the 16S rRNA A-loop, an essential component of the peptidyl transferase center. Our studies show that inactivation of MRM2 or MRM3 in human cells by RNA interference results in respiratory incompetence as a consequence of diminished mitochondrial translation. Ineffective translation in MRM2- and MRM3-depleted cells results from aberrant assembly of the large subunit of the mitochondrial ribosome (mt-LSU). Our findings show that MRM2 and MRM3 are human mitochondrial methyltransferases involved in the modification of 16S rRNA and are important factors for the biogenesis and function of the large subunit of the mitochondrial ribosome.
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Affiliation(s)
- Joanna Rorbach
- MRC Mitochondrial Biology Unit, Cambridge CB2 0XY, United Kingdom
| | - Pierre Boesch
- MRC Mitochondrial Biology Unit, Cambridge CB2 0XY, United Kingdom
| | - Payam A Gammage
- MRC Mitochondrial Biology Unit, Cambridge CB2 0XY, United Kingdom
| | | | - Sarah F Pearce
- MRC Mitochondrial Biology Unit, Cambridge CB2 0XY, United Kingdom
| | - Dipali Patel
- MRC Mitochondrial Biology Unit, Cambridge CB2 0XY, United Kingdom
| | - Andreas Hauser
- Gene Center Munich, Ludwig-Maximilians University, 81377 Munich, Germany
| | - Fabiana Perocchi
- Gene Center Munich, Ludwig-Maximilians University, 81377 Munich, Germany Institute of Human Genetics, Helmholtz Zentrum Munich, 85764 Munich, Germany
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, Cambridge CB2 0XY, United Kingdom
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Lightowlers RN, Rozanska A, Chrzanowska-Lightowlers ZM. Mitochondrial protein synthesis: figuring the fundamentals, complexities and complications, of mammalian mitochondrial translation. FEBS Lett 2014; 588:2496-503. [PMID: 24911204 PMCID: PMC4099522 DOI: 10.1016/j.febslet.2014.05.054] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 05/28/2014] [Accepted: 05/29/2014] [Indexed: 12/28/2022]
Abstract
Mitochondrial protein synthesis is essential for all mammals, being responsible for providing key components of the oxidative phosphorylation complexes. Although only thirteen different polypeptides are made, the molecular details of this deceptively simple process remain incomplete. Central to this process is a non-canonical ribosome, the mitoribosome, which has evolved to address its unique mandate. In this review, we integrate the current understanding of the molecular aspects of mitochondrial translation with recent advances in structural biology. We identify numerous key questions that we will need to answer if we are to increase our knowledge of the molecular mechanisms underlying mitochondrial protein synthesis.
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Affiliation(s)
- Robert N Lightowlers
- The Wellcome Trust Centre for Mitochondrial Research, Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.
| | - Agata Rozanska
- The Wellcome Trust Centre for Mitochondrial Research, Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Zofia M Chrzanowska-Lightowlers
- The Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.
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Hensen F, Cansiz S, Gerhold JM, Spelbrink JN. To be or not to be a nucleoid protein: A comparison of mass-spectrometry based approaches in the identification of potential mtDNA-nucleoid associated proteins. Biochimie 2014; 100:219-26. [DOI: 10.1016/j.biochi.2013.09.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 09/17/2013] [Indexed: 01/09/2023]
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Bogenhagen DF, Martin DW, Koller A. Initial steps in RNA processing and ribosome assembly occur at mitochondrial DNA nucleoids. Cell Metab 2014; 19:618-29. [PMID: 24703694 DOI: 10.1016/j.cmet.2014.03.013] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 12/17/2013] [Accepted: 02/06/2014] [Indexed: 10/25/2022]
Abstract
Mammalian mitochondrial DNA (mtDNA) resides in compact nucleoids, where it is replicated and transcribed into long primary transcripts processed to generate rRNAs, tRNAs, and mRNAs encoding 13 proteins. This situation differs from bacteria and eukaryotic nucleoli, which have dedicated rRNA transcription units. The assembly of rRNAs into mitoribosomes has received little study. We show that mitochondrial RNA processing enzymes involved in tRNA excision, ribonuclease P (RNase P) and ELAC2, as well as a subset of nascent mitochondrial ribosomal proteins (MRPs) associate with nucleoids to initiate RNA processing and ribosome assembly. SILAC pulse-chase labeling experiments show that nascent MRPs recruited to the nucleoid fraction were highly labeled after the pulse in a transcription-dependent manner and decreased in labeling intensity during the chase. These results provide insight into the landscape of binding events required for mitochondrial ribosome assembly and firmly establish the mtDNA nucleoid as a control center for mitochondrial biogenesis.
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Affiliation(s)
- Daniel F Bogenhagen
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA.
| | - Dwight W Martin
- Department of Medicine, Stony Brook University, Stony Brook, NY 11794-8160, USA; Proteomics Center, Stony Brook University, Stony Brook, NY 11794-8691, USA
| | - Antonius Koller
- Proteomics Center, Stony Brook University, Stony Brook, NY 11794-8691, USA
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Rackham O, Filipovska A. Supernumerary proteins of mitochondrial ribosomes. Biochim Biophys Acta Gen Subj 2013; 1840:1227-32. [PMID: 23958563 DOI: 10.1016/j.bbagen.2013.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 08/08/2013] [Accepted: 08/13/2013] [Indexed: 01/13/2023]
Abstract
BACKGROUND Messenger RNAs encoded by mitochondrial genomes are translated on mitochondrial ribosomes that have unique structure and protein composition compared to prokaryotic and cytoplasmic ribosomes. Mitochondrial ribosomes are a patchwork of core proteins that share homology with prokaryotic ribosomal proteins and new, supernumerary proteins that can be unique to different organisms. In mammals, there are specific supernumerary ribosomal proteins that are not present in other eukaryotes. SCOPE OF REVIEW Here we discuss the roles of supernumerary proteins in the regulation of mitochondrial gene expression and compare them among different eukaryotic systems. Furthermore, we consider if differences in the structure and organization of mitochondrial genomes may have contributed to the acquisition of mitochondrial ribosomal proteins with new functions. MAJOR CONCLUSIONS The distinct and diverse compositions of mitochondrial ribosomes illustrate the high evolutionary divergence found between mitochondrial genetic systems. GENERAL SIGNIFICANCE Elucidating the role of the organism-specific supernumerary proteins may provide a window into the regulation of mitochondrial gene expression through evolution in response to distinct evolutionary paths taken by mitochondria in different organisms. This article is part of a Special Issue entitled Frontiers of Mitochondrial Research.
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Affiliation(s)
- Oliver Rackham
- Western Australian Institute for Medical Research, Western Australia 6000, Australia; School of Chemistry and Biochemistry, The University of Western Australia, Western Australia 6009, Australia
| | - Aleksandra Filipovska
- Western Australian Institute for Medical Research, Western Australia 6000, Australia; School of Chemistry and Biochemistry, The University of Western Australia, Western Australia 6009, Australia.
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