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Brischigliaro M, Krüger A, Moran JC, Antonicka H, Ahn A, Shoubridge EA, Rorbach J, Barrientos A. The human mitochondrial translation factor TACO1 alleviates mitoribosome stalling at polyproline stretches. Nucleic Acids Res 2024; 52:9710-9726. [PMID: 39036954 PMCID: PMC11381339 DOI: 10.1093/nar/gkae645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 07/04/2024] [Accepted: 07/09/2024] [Indexed: 07/23/2024] Open
Abstract
The prokaryotic translation elongation factor P (EF-P) and the eukaryotic/archaeal counterparts eIF5A/aIF5A are proteins that serve a crucial role in mitigating ribosomal stalling during the translation of specific sequences, notably those containing consecutive proline residues (1,2). Although mitochondrial DNA-encoded proteins synthesized by mitochondrial ribosomes also contain polyproline stretches, an EF-P/eIF5A mitochondrial counterpart remains unidentified. Here, we show that the missing factor is TACO1, a protein causative of a juvenile form of neurodegenerative Leigh's syndrome associated with cytochrome c oxidase deficiency, until now believed to be a translational activator of COX1 mRNA. By using a combination of metabolic labeling, puromycin release and mitoribosome profiling experiments, we show that TACO1 is required for the rapid synthesis of the polyproline-rich COX1 and COX3 cytochrome c oxidase subunits, while its requirement is negligible for other mitochondrial DNA-encoded proteins. In agreement with a role in translation efficiency regulation, we show that TACO1 cooperates with the N-terminal extension of the large ribosomal subunit bL27m to provide stability to the peptidyl-transferase center during elongation. This study illuminates the translation elongation dynamics within human mitochondria, a TACO1-mediated biological mechanism in place to mitigate mitoribosome stalling at polyproline stretches during protein synthesis, and the pathological implications of its malfunction.
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Affiliation(s)
- Michele Brischigliaro
- Department of Neurology, University of Miami Miller School of Medicine, 1600 NW 10th Ave., Miami, FL 33136, USA
| | - Annika Krüger
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - J Conor Moran
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 1600 NW 10th Ave., Miami, FL 33136, USA
- The University of Miami Medical Scientist Training Program (MSTP), 1600 NW 10th Ave.,Miami, FL33136, USA
| | - Hana Antonicka
- The Neuro and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Ahram Ahn
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 1600 NW 10th Ave., Miami, FL 33136, USA
| | - Eric A Shoubridge
- The Neuro and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Antoni Barrientos
- Department of Neurology, University of Miami Miller School of Medicine, 1600 NW 10th Ave., Miami, FL 33136, USA
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 1600 NW 10th Ave., Miami, FL 33136, USA
- The Miami Veterans Affairs (VA) Medical System. 1201 NW 16th St, Miami, FL-33125, USA
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2
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Box JM, Higgins ME, Stuart RA. Importance of conserved hydrophobic pocket region in yeast mitoribosomal mL44 protein for mitotranslation and transcript preference. J Biol Chem 2024; 300:107519. [PMID: 38950860 PMCID: PMC11345376 DOI: 10.1016/j.jbc.2024.107519] [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: 01/23/2024] [Revised: 06/14/2024] [Accepted: 06/19/2024] [Indexed: 07/03/2024] Open
Abstract
The mitochondrial ribosome (mitoribosome) is responsible for the synthesis of key oxidative phosphorylation subunits encoded by the mitochondrial genome. Defects in mitoribosomal function therefore can have serious consequences for the bioenergetic capacity of the cell. Mutation of the conserved mitoribosomal mL44 protein has been directly linked to childhood cardiomyopathy and progressive neurophysiology issues. To further explore the functional significance of the mL44 protein in supporting mitochondrial protein synthesis, we have performed a mutagenesis study of the yeast mL44 homolog, the MrpL3/mL44 protein. We specifically investigated the conserved hydrophobic pocket region of the MrpL3/mL44 protein, where the known disease-related residue in the human mL44 protein (L156R) is located. While our findings identify a number of residues in this region critical for MrpL3/mL44's ability to support the assembly of translationally active mitoribosomes, the introduction of the disease-related mutation into the equivalent position in the yeast protein (residue A186) was found to not have a major impact on function. The human and yeast mL44 proteins share many similarities in sequence and structure; however results presented here indicate that these two proteins have diverged somewhat in evolution. Finally, we observed that mutation of the MrpL3/mL44 does not impact the translation of all mitochondrial encoded proteins equally, suggesting the mitochondrial translation system may exhibit a transcript hierarchy and prioritization.
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Affiliation(s)
- Jodie M Box
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Margo E Higgins
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Rosemary A Stuart
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA.
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3
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Moran JC, Brivanlou A, Brischigliaro M, Fontanesi F, Rouskin S, Barrientos A. The human mitochondrial mRNA structurome reveals mechanisms of gene expression. Science 2024; 385:eadm9238. [PMID: 39024447 DOI: 10.1126/science.adm9238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 05/24/2024] [Indexed: 07/20/2024]
Abstract
The human mitochondrial genome encodes crucial oxidative phosphorylation system proteins, pivotal for aerobic energy transduction. They are translated from nine monocistronic and two bicistronic transcripts whose native structures remain unexplored, posing a gap in understanding mitochondrial gene expression. In this work, we devised the mitochondrial dimethyl sulfate mutational profiling with sequencing (mitoDMS-MaPseq) method and applied detection of RNA folding ensembles using expectation-maximization (DREEM) clustering to unravel the native mitochondrial messenger RNA (mt-mRNA) structurome in wild-type (WT) and leucine-rich pentatricopeptide repeat-containing protein (LRPPRC)-deficient cells. Our findings elucidate LRPPRC's role as a holdase contributing to maintaining mt-mRNA folding and efficient translation. mt-mRNA structural insights in WT mitochondria, coupled with metabolic labeling, unveil potential mRNA-programmed translational pausing and a distinct programmed ribosomal frameshifting mechanism. Our data define a critical layer of mitochondrial gene expression regulation. These mt-mRNA folding maps provide a reference for studying mt-mRNA structures in diverse physiological and pathological contexts.
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Affiliation(s)
- J Conor Moran
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA
- University of Miami Medical Scientist Training Program, University of Miami Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA
| | - Amir Brivanlou
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Michele Brischigliaro
- Department of Neurology, University of Miami Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA
| | - Flavia Fontanesi
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA
| | - Silvi Rouskin
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Antoni Barrientos
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA
- Department of Neurology, University of Miami Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA
- The Miami Veterans Affairs (VA) Medical System, 1201 NW 16th Street, Miami, FL 33125, USA
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4
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Lavdovskaia E, Hanitsch E, Linden A, Pašen M, Challa V, Horokhovskyi Y, Roetschke HP, Nadler F, Welp L, Steube E, Heinrichs M, Mai MMQ, Urlaub H, Liepe J, Richter-Dennerlein R. A roadmap for ribosome assembly in human mitochondria. Nat Struct Mol Biol 2024:10.1038/s41594-024-01356-w. [PMID: 38992089 DOI: 10.1038/s41594-024-01356-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 06/17/2024] [Indexed: 07/13/2024]
Abstract
Mitochondria contain dedicated ribosomes (mitoribosomes), which synthesize the mitochondrial-encoded core components of the oxidative phosphorylation complexes. The RNA and protein components of mitoribosomes are encoded on two different genomes (mitochondrial and nuclear) and are assembled into functional complexes with the help of dedicated factors inside the organelle. Defects in mitoribosome biogenesis are associated with severe human diseases, yet the molecular pathway of mitoribosome assembly remains poorly understood. Here, we applied a multidisciplinary approach combining biochemical isolation and analysis of native mitoribosomal assembly complexes with quantitative mass spectrometry and mathematical modeling to reconstitute the entire assembly pathway of the human mitoribosome. We show that, in contrast to its bacterial and cytosolic counterparts, human mitoribosome biogenesis involves the formation of ribosomal protein-only modules, which then assemble on the appropriate ribosomal RNA moiety in a coordinated fashion. The presence of excess protein-only modules primed for assembly rationalizes how mitochondria cope with the challenge of forming a protein-rich ribonucleoprotein complex of dual genetic origin. This study provides a comprehensive roadmap of mitoribosome biogenesis, from very early to late maturation steps, and highlights the evolutionary divergence from its bacterial ancestor.
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Affiliation(s)
- Elena Lavdovskaia
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany
| | - Elisa Hanitsch
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Andreas Linden
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Martin Pašen
- Quantitative and Systems Biology Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Venkatapathi Challa
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Yehor Horokhovskyi
- Quantitative and Systems Biology Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Hanna P Roetschke
- Quantitative and Systems Biology Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Centre for Inflammation Biology and Cancer Immunology & Peter Gorer Department of Immunobiology, King's College London, London, UK
- Francis Crick Institute, London, UK
| | - Franziska Nadler
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Luisa Welp
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Emely Steube
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Marleen Heinrichs
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Mandy Mong-Quyen Mai
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Henning Urlaub
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany.
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
- Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany.
- Göttingen Center for Molecular Biosciences, University of Göttingen, Göttingen, Germany.
| | - Juliane Liepe
- Quantitative and Systems Biology Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| | - Ricarda Richter-Dennerlein
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany.
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany.
- Göttingen Center for Molecular Biosciences, University of Göttingen, Göttingen, Germany.
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5
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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: 5] [Impact Index Per Article: 5.0] [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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6
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Brischigliaro M, Sierra-Magro A, Ahn A, Barrientos A. Mitochondrial ribosome biogenesis and redox sensing. FEBS Open Bio 2024. [PMID: 38849194 DOI: 10.1002/2211-5463.13844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/06/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024] Open
Abstract
Mitoribosome biogenesis is a complex process involving RNA elements encoded in the mitochondrial genome and mitoribosomal proteins typically encoded in the nuclear genome. This process is orchestrated by extra-ribosomal proteins, nucleus-encoded assembly factors, which play roles across all assembly stages to coordinate ribosomal RNA processing and maturation with the sequential association of ribosomal proteins. Both biochemical studies and recent cryo-EM structures of mammalian mitoribosomes have provided insights into their assembly process. In this article, we will briefly outline the current understanding of mammalian mitoribosome biogenesis pathways and the factors involved. Special attention is devoted to the recent identification of iron-sulfur clusters as structural components of the mitoribosome and a small subunit assembly factor, the existence of redox-sensitive cysteines in mitoribosome proteins and assembly factors, and the role they may play as redox sensor units to regulate mitochondrial translation under stress.
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Affiliation(s)
| | - Ana Sierra-Magro
- Department of Neurology, University of Miami Miller School of Medicine, FL, USA
| | - Ahram Ahn
- Department of Biochemistry and Molecular Biology, 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
- Bruce W. Carter Department of Veterans Affairs VA Medical Center, Miami, FL, USA
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7
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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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8
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Singh V, Itoh Y, Del'Olio S, Hassan A, Naschberger A, Flygaard RK, Nobe Y, Izumikawa K, Aibara S, Andréll J, Whitford PC, Barrientos A, Taoka M, Amunts A. Mitoribosome structure with cofactors and modifications reveals mechanism of ligand binding and interactions with L1 stalk. Nat Commun 2024; 15:4272. [PMID: 38769321 PMCID: PMC11106087 DOI: 10.1038/s41467-024-48163-x] [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: 08/07/2022] [Accepted: 04/19/2024] [Indexed: 05/22/2024] Open
Abstract
The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 Å resolution structure of human mitoribosome together with validated mitoribosomal RNA (rRNA) modifications, including aminoacylated CP-tRNAVal. The structure shows how mitoribosomal proteins stabilise binding of mRNA and tRNA helping to align it in the decoding center, whereas the GDP-bound mS29 stabilizes intersubunit communication. Comparison between different states, with respect to tRNA position, allowed us to characterize a non-canonical L1 stalk, and molecular dynamics simulations revealed how it facilitates tRNA transitions in a way that does not require interactions with rRNA. We also report functionally important polyamines that are depleted when cells are subjected to an antibiotic treatment. The structural, biochemical, and computational data illuminate the principal functional components of the translation mechanism in mitochondria and provide a description of the structure and function of the human mitoribosome.
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Affiliation(s)
- Vivek Singh
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165, Solna, Sweden
| | - Yuzuru Itoh
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165, Solna, Sweden
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 113-0033, Tokyo, Japan
| | - Samuel Del'Olio
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Asem Hassan
- Department of Physics, Northeastern University, Boston, MA, 02115, USA
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, 02115, USA
| | - Andreas Naschberger
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165, Solna, Sweden
- King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Rasmus Kock Flygaard
- Department of Molecular Biology and Genetics, Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Aarhus University, 8000, Aarhus C, Denmark
| | - Yuko Nobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo, 192-0397, Japan
| | - Keiichi Izumikawa
- Department of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan
| | - Shintaro Aibara
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165, Solna, Sweden
| | - Juni Andréll
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Paul C Whitford
- Department of Physics, Northeastern University, Boston, MA, 02115, USA
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, 02115, USA
| | - Antoni Barrientos
- Department of Molecular and Cellular Pharmacology, 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
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo, 192-0397, Japan
| | - Alexey Amunts
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165, Solna, Sweden.
- Westlake University, Hangzhou, China.
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Guo X, Chen H, Tong Y, Wu X, Tang C, Qin X, Guo J, Li P, Wang Z, Liu W, Mo J. A review on the antibiotic florfenicol: Occurrence, environmental fate, effects, and health risks. ENVIRONMENTAL RESEARCH 2024; 244:117934. [PMID: 38109957 DOI: 10.1016/j.envres.2023.117934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/09/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023]
Abstract
Florfenicol, as a replacement for chloramphenicol, can tightly bind to the A site of the 23S rRNA in the 50S subunit of the 70S ribosome, thereby inhibiting protein synthesis and bacterial proliferation. Due to the widespread use in aquaculture and veterinary medicine, florfenicol has been detected in the aquatic environment worldwide. Concerns over the effects and health risks of florfenicol on target and non-target organisms have been raised in recent years. Although the ecotoxicity of florfenicol has been widely reported in different species, no attempt has been made to review the current research progress of florfenicol toxicity, hormesis, and its health risks posed to biota. In this study, a comprehensive literature review was conducted to summarize the effects of florfenicol on various organisms including bacteria, algae, invertebrates, fishes, birds, and mammals. The generation of antibiotic resistant bacteria and spread antibiotic resistant genes, closely associated with hormesis, are pressing environmental health issues stemming from overuse or misuse of antibiotics including florfenicol. Exposure to florfenicol at μg/L-mg/L induced hormetic effects in several algal species, and chromoplasts might serve as a target for florfenicol-induced effects; however, the underlying molecular mechanisms are completely lacking. Exposure to high levels (mg/L) of florfenicol modified the xenobiotic metabolism, antioxidant systems, and energy metabolism, resulting in hepatotoxicity, renal toxicity, immunotoxicity, developmental toxicity, reproductive toxicity, obesogenic effects, and hormesis in different animal species. Mitochondria and the associated energy metabolism are suggested to be the primary targets for florfenicol toxicity in animals, albeit further in-depth investigations are warranted for revealing the long-term effects (e.g., whole-life-cycle impacts, multigenerational effects) of florfenicol, especially at environmental levels, and the underlying mechanisms. This will facilitate the evaluation of potential hormetic effects and construction of adverse outcome pathways for environmental risk assessment and regulation of florfenicol.
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Affiliation(s)
- Xingying Guo
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou, 515063, China
| | - Haibo Chen
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou, 515063, China
| | - Yongqi Tong
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou, 515063, China
| | - Xintong Wu
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou, 515063, China
| | - Can Tang
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou, 515063, China
| | - Xian Qin
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Jiahua Guo
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Ping Li
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou, 515063, China
| | - Zhen Wang
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou, 515063, China
| | - Wenhua Liu
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou, 515063, China
| | - Jiezhang Mo
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou, 515063, China.
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10
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Key J, Gispert S, Koepf G, Steinhoff-Wagner J, Reichlmeir M, Auburger G. Translation Fidelity and Respiration Deficits in CLPP-Deficient Tissues: Mechanistic Insights from Mitochondrial Complexome Profiling. Int J Mol Sci 2023; 24:17503. [PMID: 38139332 PMCID: PMC10743472 DOI: 10.3390/ijms242417503] [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: 11/13/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
The mitochondrial matrix peptidase CLPP is crucial during cell stress. Its loss causes Perrault syndrome type 3 (PRLTS3) with infertility, neurodegeneration, and a growth deficit. Its target proteins are disaggregated by CLPX, which also regulates heme biosynthesis via unfolding ALAS enzymes, providing access for pyridoxal-5'-phosphate (PLP). Despite efforts in diverse organisms with multiple techniques, CLPXP substrates remain controversial. Here, avoiding recombinant overexpression, we employed complexomics in mitochondria from three mouse tissues to identify endogenous targets. A CLPP absence caused the accumulation and dispersion of CLPX-VWA8 as AAA+ unfoldases, and of PLPBP. Similar changes and CLPX-VWA8 co-migration were evident for mitoribosomal central protuberance clusters, translation factors like GFM1-HARS2, the RNA granule components LRPPRC-SLIRP, and enzymes OAT-ALDH18A1. Mitochondrially translated proteins in testes showed reductions to <30% for MTCO1-3, the mis-assembly of the complex IV supercomplex, and accumulated metal-binding assembly factors COX15-SFXN4. Indeed, heavy metal levels were increased for iron, molybdenum, cobalt, and manganese. RT-qPCR showed compensatory downregulation only for Clpx mRNA; most accumulated proteins appeared transcriptionally upregulated. Immunoblots validated VWA8, MRPL38, MRPL18, GFM1, and OAT accumulation. Co-immunoprecipitation confirmed CLPX binding to MRPL38, GFM1, and OAT, so excess CLPX and PLP may affect their activity. Our data mechanistically elucidate the mitochondrial translation fidelity deficits which underlie progressive hearing impairment in PRLTS3.
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Affiliation(s)
- Jana Key
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Suzana Gispert
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Gabriele Koepf
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Julia Steinhoff-Wagner
- TUM School of Life Sciences, Animal Nutrition and Metabolism, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising-Weihenstephan, Germany;
| | - Marina Reichlmeir
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Georg Auburger
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
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11
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Zhong H, Janer A, Khalimonchuk O, Antonicka H, Shoubridge E, Barrientos A. BOLA3 and NFU1 link mitoribosome iron-sulfur cluster assembly to multiple mitochondrial dysfunctions syndrome. Nucleic Acids Res 2023; 51:11797-11812. [PMID: 37823603 PMCID: PMC10681725 DOI: 10.1093/nar/gkad842] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 09/08/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023] Open
Abstract
The human mitochondrial ribosome contains three [2Fe-2S] clusters whose assembly pathway, role, and implications for mitochondrial and metabolic diseases are unknown. Here, structure-function correlation studies show that the clusters play a structural role during mitoribosome assembly. To uncover the assembly pathway, we have examined the effect of silencing the expression of Fe-S cluster biosynthetic and delivery factors on mitoribosome stability. We find that the mitoribosome receives its [2Fe-2S] clusters from the GLRX5-BOLA3 node. Additionally, the assembly of the small subunit depends on the mitoribosome biogenesis factor METTL17, recently reported containing a [4Fe-4S] cluster, which we propose is inserted via the ISCA1-NFU1 node. Consistently, fibroblasts from subjects suffering from 'multiple mitochondrial dysfunction' syndrome due to mutations in BOLA3 or NFU1 display previously unrecognized attenuation of mitochondrial protein synthesis that contributes to their cellular and pathophysiological phenotypes. Finally, we report that, in addition to their structural role, one of the mitoribosomal [2Fe-2S] clusters and the [4Fe-4S] cluster in mitoribosome assembly factor METTL17 sense changes in the redox environment, thus providing a way to regulate organellar protein synthesis accordingly.
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Affiliation(s)
- Hui Zhong
- Department of Biochemistry and Molecular Biology. University of Miami Miller School of Medicine, 1600 NW 10Ave. Miami, FL 33136, USA
| | - Alexandre Janer
- The Neuro and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Oleh Khalimonchuk
- Department of Biochemistry. University of Nebraska-Lincoln; 1901 Vine St. Beadle Center, Lincoln, NE 68588, USA
- Nebraska Redox Biology Center. University of Nebraska-Lincoln; 1901 Vine St. Beadle Center, Lincoln, NE 68588, USA
| | - Hana Antonicka
- The Neuro and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Eric A Shoubridge
- The Neuro and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Antoni Barrientos
- Department of Biochemistry and Molecular Biology. University of Miami Miller School of Medicine, 1600 NW 10Ave. Miami, FL 33136, USA
- Department of Neurology. University of Miami Miller School of Medicine; 1600 NW 10 Ave., Miami, FL 33136, USA
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12
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Conor Moran J, Brivanlou A, Brischigliaro M, Fontanesi F, Rouskin S, Barrientos A. The human mitochondrial mRNA structurome reveals mechanisms of gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.31.564750. [PMID: 37961485 PMCID: PMC10635011 DOI: 10.1101/2023.10.31.564750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The mammalian mitochondrial genome encodes thirteen oxidative phosphorylation system proteins, crucial in aerobic energy transduction. These proteins are translated from 9 monocistronic and 2 bicistronic transcripts, whose native structures remain unexplored, leaving fundamental molecular determinants of mitochondrial gene expression unknown. To address this gap, we developed a mitoDMS-MaPseq approach and used DREEM clustering to resolve the native human mitochondrial mt-mRNA structurome. We gained insights into mt-mRNA biology and translation regulatory mechanisms, including a unique programmed ribosomal frameshifting for the ATP8/ATP6 transcript. Furthermore, absence of the mt-mRNA maintenance factor LRPPRC led to a mitochondrial transcriptome structured differently, with specific mRNA regions exhibiting increased or decreased structuredness. This highlights the role of LRPPRC in maintaining mRNA folding to promote mt-mRNA stabilization and efficient translation. In conclusion, our mt-mRNA folding maps reveal novel mitochondrial gene expression mechanisms, serving as a detailed reference and tool for studying them in different physiological and pathological contexts.
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13
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Gruffaz C, Smirnov A. GTPase Era at the heart of ribosome assembly. Front Mol Biosci 2023; 10:1263433. [PMID: 37860580 PMCID: PMC10582724 DOI: 10.3389/fmolb.2023.1263433] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
Ribosome biogenesis is a key process in all organisms. It relies on coordinated work of multiple proteins and RNAs, including an array of assembly factors. Among them, the GTPase Era stands out as an especially deeply conserved protein, critically required for the assembly of bacterial-type ribosomes from Escherichia coli to humans. In this review, we bring together and critically analyze a wealth of phylogenetic, biochemical, structural, genetic and physiological data about this extensively studied but still insufficiently understood factor. We do so using a comparative and, wherever possible, synthetic approach, by confronting observations from diverse groups of bacteria and eukaryotic organelles (mitochondria and chloroplasts). The emerging consensus posits that Era intervenes relatively early in the small subunit biogenesis and is essential for the proper shaping of the platform which, in its turn, is a prerequisite for efficient translation. The timing of Era action on the ribosome is defined by its interactions with guanosine nucleotides [GTP, GDP, (p)ppGpp], ribosomal RNA, and likely other factors that trigger or delay its GTPase activity. As a critical nexus of the small subunit biogenesis, Era is subject to sophisticated regulatory mechanisms at the transcriptional, post-transcriptional, and post-translational levels. Failure of these mechanisms or a deficiency in Era function entail dramatic generalized consequences for the protein synthesis and far-reaching, pleiotropic effects on the organism physiology, such as the Perrault syndrome in humans.
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Affiliation(s)
- Christelle Gruffaz
- UMR7156- Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, Centre National de la Recherche Scientifique (CNRS), Strasbourg, France
| | - Alexandre Smirnov
- UMR7156- Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, Centre National de la Recherche Scientifique (CNRS), Strasbourg, France
- University of Strasbourg Institute for Advanced Study (USIAS), Strasbourg, France
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14
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Amarasekera SSC, Hock DH, Lake NJ, Calvo SE, Grønborg SW, Krzesinski EI, Amor DJ, Fahey MC, Simons C, Wibrand F, Mootha VK, Lek M, Lunke S, Stark Z, Østergaard E, Christodoulou J, Thorburn DR, Stroud DA, Compton AG. Multi-omics identifies large mitoribosomal subunit instability caused by pathogenic MRPL39 variants as a cause of pediatric onset mitochondrial disease. Hum Mol Genet 2023; 32:2441-2454. [PMID: 37133451 PMCID: PMC10360397 DOI: 10.1093/hmg/ddad069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 03/20/2023] [Accepted: 04/24/2023] [Indexed: 05/04/2023] Open
Abstract
MRPL39 encodes one of 52 proteins comprising the large subunit of the mitochondrial ribosome (mitoribosome). In conjunction with 30 proteins in the small subunit, the mitoribosome synthesizes the 13 subunits of the mitochondrial oxidative phosphorylation (OXPHOS) system encoded by mitochondrial Deoxyribonucleic acid (DNA). We used multi-omics and gene matching to identify three unrelated individuals with biallelic variants in MRPL39 presenting with multisystem diseases with severity ranging from lethal, infantile-onset (Leigh syndrome spectrum) to milder with survival into adulthood. Clinical exome sequencing of known disease genes failed to diagnose these patients; however quantitative proteomics identified a specific decrease in the abundance of large but not small mitoribosomal subunits in fibroblasts from the two patients with severe phenotype. Re-analysis of exome sequencing led to the identification of candidate single heterozygous variants in mitoribosomal genes MRPL39 (both patients) and MRPL15. Genome sequencing identified a shared deep intronic MRPL39 variant predicted to generate a cryptic exon, with transcriptomics and targeted studies providing further functional evidence for causation. The patient with the milder disease was homozygous for a missense variant identified through trio exome sequencing. Our study highlights the utility of quantitative proteomics in detecting protein signatures and in characterizing gene-disease associations in exome-unsolved patients. We describe Relative Complex Abundance analysis of proteomics data, a sensitive method that can identify defects in OXPHOS disorders to a similar or greater sensitivity to the traditional enzymology. Relative Complex Abundance has potential utility for functional validation or prioritization in many hundreds of inherited rare diseases where protein complex assembly is disrupted.
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Affiliation(s)
- Sumudu S C Amarasekera
- Murdoch Children’s Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Daniella H Hock
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Nicole J Lake
- Murdoch Children’s Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510 USA
| | - Sarah E Calvo
- Broad Institute, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02446, USA
| | - Sabine W Grønborg
- Department of Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen 2100, Denmark
- Center for Inherited Metabolic Disease, Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen 2100, Denmark
| | - Emma I Krzesinski
- Monash Genetics, Monash Health, Melbourne, VIC 3168 Australia
- Department of Paediatrics, Monash University, Melbourne, VIC 3168 Australia
| | - David J Amor
- Murdoch Children’s Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Michael C Fahey
- Monash Genetics, Monash Health, Melbourne, VIC 3168 Australia
- Department of Paediatrics, Monash University, Melbourne, VIC 3168 Australia
| | - Cas Simons
- Murdoch Children’s Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Flemming Wibrand
- Department of Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen 2100, Denmark
| | - Vamsi K Mootha
- Broad Institute, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02446, USA
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510 USA
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Australian Genomics Health Alliance, Melbourne, VIC 3052, Australia
- Department of Pathology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Zornitza Stark
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Australian Genomics Health Alliance, Melbourne, VIC 3052, Australia
| | - Elsebet Østergaard
- Department of Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen 2100, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen 2200, Denmark
| | - John Christodoulou
- Murdoch Children’s Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Australian Genomics Health Alliance, Melbourne, VIC 3052, Australia
- Discipline of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - David R Thorburn
- Murdoch Children’s Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Australian Genomics Health Alliance, Melbourne, VIC 3052, Australia
| | - David A Stroud
- Murdoch Children’s Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
| | - Alison G Compton
- Murdoch Children’s Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
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15
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Singh V, Itoh Y, Del'Olio S, Hassan A, Naschberger A, Flygaard RK, Nobe Y, Izumikawa K, Aibara S, Andréll J, Whitford PC, Barrientos A, Taoka M, Amunts A. Structure of mitoribosome reveals mechanism of mRNA binding, tRNA interactions with L1 stalk, roles of cofactors and rRNA modifications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.24.542018. [PMID: 37503168 PMCID: PMC10369894 DOI: 10.1101/2023.05.24.542018] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 Å resolution structure of human mitoribosome together with validated mitoribosomal RNA (rRNA) modifications, including aminoacylated CP-tRNA Val . The structure shows how mitoribosomal proteins stabilise binding of mRNA and tRNA helping to align it in the decoding center, whereas the GDP-bound mS29 stabilizes intersubunit communication. Comparison between different states, with respect to tRNA position, allowed to characterize a non-canonical L1 stalk, and molecular dynamics simulations revealed how it facilitates tRNA transition in a way that does not require interactions with rRNA. We also report functionally important polyamines that are depleted when cells are subjected to an antibiotic treatment. The structural, biochemical, and computational data illuminate the principal functional components of the translation mechanism in mitochondria and provide the most complete description so far of the structure and function of the human mitoribosome.
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16
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Del Giudice L, Pontieri P, Aletta M, Calcagnile M. Mitochondrial Neurodegenerative Diseases: Three Mitochondrial Ribosomal Proteins as Intermediate Stage in the Pathway That Associates Damaged Genes with Alzheimer's and Parkinson's. BIOLOGY 2023; 12:972. [PMID: 37508402 PMCID: PMC10376763 DOI: 10.3390/biology12070972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023]
Abstract
Currently, numerous research endeavors are dedicated to unraveling the intricate nature of neurodegenerative diseases. These conditions are characterized by the gradual and progressive impairment of specific neuronal systems that exhibit anatomical or physiological connections. In particular, in the last twenty years, remarkable efforts have been made to elucidate neurodegenerative disorders such as Alzheimer's disease and Parkinson's disease. However, despite extensive research endeavors, no cure or effective treatment has been discovered thus far. With the emergence of studies shedding light on the contribution of mitochondria to the onset and advancement of mitochondrial neurodegenerative disorders, researchers are now directing their investigations toward the development of therapies. These therapies include molecules designed to protect mitochondria and neurons from the detrimental effects of aging, as well as mutant proteins. Our objective is to discuss and evaluate the recent discovery of three mitochondrial ribosomal proteins linked to Alzheimer's and Parkinson's diseases. These proteins represent an intermediate stage in the pathway connecting damaged genes to the two mitochondrial neurological pathologies. This discovery potentially could open new avenues for the production of medicinal substances with curative potential for the treatment of these diseases.
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Affiliation(s)
- Luigi Del Giudice
- Istituto di Bioscienze e BioRisorse-UOS Napoli-CNR c/o Dipartimento di Biologia, Sezione di Igiene, 80134 Napoli, Italy
| | - Paola Pontieri
- Istituto di Bioscienze e BioRisorse-UOS Napoli-CNR c/o Dipartimento di Biologia, Sezione di Igiene, 80134 Napoli, Italy
| | | | - Matteo Calcagnile
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali, Università del Salento, 73100 Lecce, Italy
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17
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Mo D, Liu C, Chen Y, Cheng X, Shen J, Zhao L, Zhang J. The mitochondrial ribosomal protein mRpL4 regulates Notch signaling. EMBO Rep 2023; 24:e55764. [PMID: 37009823 PMCID: PMC10240210 DOI: 10.15252/embr.202255764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 03/07/2023] [Accepted: 03/18/2023] [Indexed: 04/04/2023] Open
Abstract
Mitochondrial ribosomal proteins (MRPs) assemble as specialized ribosome to synthesize mtDNA-encoded proteins, which are essential for mitochondrial bioenergetic and metabolic processes. MRPs are required for fundamental cellular activities during animal development, but their roles beyond mitochondrial protein translation are poorly understood. Here, we report a conserved role of the mitochondrial ribosomal protein L4 (mRpL4) in Notch signaling. Genetic analyses demonstrate that mRpL4 is required in the Notch signal-receiving cells to permit target gene transcription during Drosophila wing development. We find that mRpL4 physically and genetically interacts with the WD40 repeat protein wap and activates the transcription of Notch signaling targets. We show that human mRpL4 is capable of replacing fly mRpL4 during wing development. Furthermore, knockout of mRpL4 in zebrafish leads to downregulated expression of Notch signaling components. Thus, we have discovered a previously unknown function of mRpL4 during animal development.
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Affiliation(s)
- Dongqing Mo
- Department of Plant Biosecurity and MOA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Chenglin Liu
- Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
- College of FisheriesOcean University of ChinaQingdaoChina
- Key Laboratory of Mariculture (OUC)Ministry of EducationQingdaoChina
| | - Yao Chen
- Department of Plant Biosecurity and MOA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Xinkai Cheng
- Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
- College of FisheriesOcean University of ChinaQingdaoChina
- Key Laboratory of Mariculture (OUC)Ministry of EducationQingdaoChina
| | - Jie Shen
- Department of Plant Biosecurity and MOA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Long Zhao
- Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
- College of FisheriesOcean University of ChinaQingdaoChina
- Key Laboratory of Mariculture (OUC)Ministry of EducationQingdaoChina
| | - Junzheng Zhang
- Department of Plant Biosecurity and MOA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant ProtectionChina Agricultural UniversityBeijingChina
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18
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Bakhshalizadeh S, Hock DH, Siddall NA, Kline BL, Sreenivasan R, Bell KM, Casagranda F, Kamalanathan S, Sahoo J, Narayanan N, Naik D, Suryadevara V, Compton AG, Amarasekera SSC, Kapoor R, Jaillard S, Simpson A, Robevska G, van den Bergen J, Pachernegg S, Ayers KL, Thorburn DR, Stroud DA, Hime GR, Sinclair AH, Tucker EJ. Deficiency of the mitochondrial ribosomal subunit, MRPL50, causes autosomal recessive syndromic premature ovarian insufficiency. Hum Genet 2023:10.1007/s00439-023-02563-z. [PMID: 37148394 DOI: 10.1007/s00439-023-02563-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/19/2023] [Indexed: 05/08/2023]
Abstract
Premature ovarian insufficiency (POI) is a common cause of infertility in women, characterised by amenorrhea and elevated FSH under the age of 40 years. In some cases, POI is syndromic in association with other features such as sensorineural hearing loss in Perrault syndrome. POI is a heterogeneous disease with over 80 causative genes known so far; however, these explain only a minority of cases. Using whole-exome sequencing (WES), we identified a MRPL50 homozygous missense variant (c.335T > A; p.Val112Asp) shared by twin sisters presenting with POI, bilateral high-frequency sensorineural hearing loss, kidney and heart dysfunction. MRPL50 encodes a component of the large subunit of the mitochondrial ribosome. Using quantitative proteomics and western blot analysis on patient fibroblasts, we demonstrated a loss of MRPL50 protein and an associated destabilisation of the large subunit of the mitochondrial ribosome whilst the small subunit was preserved. The mitochondrial ribosome is responsible for the translation of subunits of the mitochondrial oxidative phosphorylation machinery, and we found patient fibroblasts have a mild but significant decrease in the abundance of mitochondrial complex I. These data support a biochemical phenotype associated with MRPL50 variants. We validated the association of MRPL50 with the clinical phenotype by knockdown/knockout of mRpL50 in Drosophila, which resulted abnormal ovarian development. In conclusion, we have shown that a MRPL50 missense variant destabilises the mitochondrial ribosome, leading to oxidative phosphorylation deficiency and syndromic POI, highlighting the importance of mitochondrial support in ovarian development and function.
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Affiliation(s)
- Shabnam Bakhshalizadeh
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Daniella H Hock
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia
| | - Nicole A Siddall
- Department of Anatomy and Physiology, University of Melbourne, Parkville, Australia
| | | | - Rajini Sreenivasan
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Katrina M Bell
- Department of Bioinformatics, Murdoch Children's Research Institute, Melbourne, Australia
| | - Franca Casagranda
- Department of Anatomy and Physiology, University of Melbourne, Parkville, Australia
| | - Sadishkumar Kamalanathan
- Department of Endocrinology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, 605006, India
| | - Jayaprakash Sahoo
- Department of Endocrinology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, 605006, India
| | - Niya Narayanan
- Department of Endocrinology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, 605006, India
| | - Dukhabandhu Naik
- Department of Endocrinology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, 605006, India
| | - Varun Suryadevara
- Department of Endocrinology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, 605006, India
| | - Alison G Compton
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, Australia
| | - Sumudu S C Amarasekera
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Ridam Kapoor
- Department of Anatomy and Physiology, University of Melbourne, Parkville, Australia
| | - Sylvie Jaillard
- Univ Rennes, CHU Rennes, INSERM, EHESP, IRSET (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, 35000, Rennes, France
- CHU Rennes, Service de Cytogénétique et Biologie Cellulaire, 35033, Rennes, France
| | - Andrea Simpson
- School of Allied Health, College of Science, Health and Engineering, La Trobe University, Bundoora, VIC, Australia
- College of Health and Human Services, Charles Darwin University, Darwin, NT, Australia
| | | | | | - Svenja Pachernegg
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Katie L Ayers
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - David R Thorburn
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, Australia
| | - David A Stroud
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia
- Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, Australia
| | - Gary R Hime
- Department of Anatomy and Physiology, University of Melbourne, Parkville, Australia.
| | - Andrew H Sinclair
- Murdoch Children's Research Institute, Melbourne, Australia.
- Department of Paediatrics, University of Melbourne, Melbourne, Australia.
| | - Elena J Tucker
- Murdoch Children's Research Institute, Melbourne, Australia.
- Department of Paediatrics, University of Melbourne, Melbourne, Australia.
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19
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Jerome MS, Nanjappa DP, Chakraborty A, Chakrabarty S. Molecular etiology of defective nuclear and mitochondrial ribosome biogenesis: Clinical phenotypes and therapy. Biochimie 2023; 207:122-136. [PMID: 36336106 DOI: 10.1016/j.biochi.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/27/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022]
Abstract
Ribosomopathies are rare congenital disorders associated with defective ribosome biogenesis due to pathogenic variations in genes that encode proteins related to ribosome function and biogenesis. Defects in ribosome biogenesis result in a nucleolar stress response involving the TP53 tumor suppressor protein and impaired protein synthesis leading to a deregulated translational output. Despite the accepted notion that ribosomes are omnipresent and essential for all cells, most ribosomopathies show tissue-specific phenotypes affecting blood cells, hair, spleen, or skin. On the other hand, defects in mitochondrial ribosome biogenesis are associated with a range of clinical manifestations affecting more than one organ. Intriguingly, the deregulated ribosomal function is also a feature in several human malignancies with a selective upregulation or downregulation of specific ribosome components. Here, we highlight the clinical conditions associated with defective ribosome biogenesis in the nucleus and mitochondria with a description of the affected genes and the implicated pathways, along with a note on the treatment strategies currently available for these disorders.
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Affiliation(s)
- Maria Sona Jerome
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Dechamma Pandyanda Nanjappa
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to Be University), Deralakate, Mangaluru, 575018, India
| | - Anirban Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to Be University), Deralakate, Mangaluru, 575018, India.
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.
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20
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Brischigliaro M, Fernandez-Vizarra E, Viscomi C. Mitochondrial Neurodegeneration: Lessons from Drosophila melanogaster Models. Biomolecules 2023; 13:378. [PMID: 36830747 PMCID: PMC9953451 DOI: 10.3390/biom13020378] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/19/2023] Open
Abstract
The fruit fly-i.e., Drosophila melanogaster-has proven to be a very useful model for the understanding of basic physiological processes, such as development or ageing. The availability of straightforward genetic tools that can be used to produce engineered individuals makes this model extremely interesting for the understanding of the mechanisms underlying genetic diseases in physiological models. Mitochondrial diseases are a group of yet-incurable genetic disorders characterized by the malfunction of the oxidative phosphorylation system (OXPHOS), which is the highly conserved energy transformation system present in mitochondria. The generation of D. melanogaster models of mitochondrial disease started relatively recently but has already provided relevant information about the molecular mechanisms and pathological consequences of mitochondrial dysfunction. Here, we provide an overview of such models and highlight the relevance of D. melanogaster as a model to study mitochondrial disorders.
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Affiliation(s)
- Michele Brischigliaro
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
- Veneto Institute of Molecular Medicine, 35129 Padova, Italy
| | - Erika Fernandez-Vizarra
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
- Veneto Institute of Molecular Medicine, 35129 Padova, Italy
| | - Carlo Viscomi
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
- Veneto Institute of Molecular Medicine, 35129 Padova, Italy
- Centre for the Study of Neurodegeneration (CESNE), University of Padova, 35131 Padova, Italy
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21
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He L, Tronstad KJ, Maheshwari A. Mitochondrial Dynamics during Development. NEWBORN (CLARKSVILLE, MD.) 2023; 2:19-44. [PMID: 37206581 PMCID: PMC10193651 DOI: 10.5005/jp-journals-11002-0053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Mitochondria are dynamic membrane-bound organelles in eukaryotic cells. These are important for the generation of chemical energy needed to power various cellular functions and also support metabolic, energetic, and epigenetic regulation in various cells. These organelles are also important for communication with the nucleus and other cellular structures, to maintain developmental sequences and somatic homeostasis, and for cellular adaptation to stress. Increasing information shows mitochondrial defects as an important cause of inherited disorders in different organ systems. In this article, we provide an extensive review of ontogeny, ultrastructural morphology, biogenesis, functional dynamics, important clinical manifestations of mitochondrial dysfunction, and possibilities for clinical intervention. We present information from our own clinical and laboratory research in conjunction with information collected from an extensive search in the databases PubMed, EMBASE, and Scopus.
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Affiliation(s)
- Ling He
- Department of Pediatrics and Pharmacology, Johns Hopkins University, Baltimore, United States of America
| | | | - Akhil Maheshwari
- Founding Chairman, Global Newborn Society, Clarksville, Maryland, United States of America
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22
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Conor Moran J, Del'Olio S, Choi A, Zhong H, Barrientos A. Mitoribosome Biogenesis. Methods Mol Biol 2023; 2661:23-51. [PMID: 37166630 PMCID: PMC10639111 DOI: 10.1007/978-1-0716-3171-3_3] [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] [Indexed: 05/12/2023]
Abstract
Mitoribosome biogenesis is a complex and energetically costly process that involves RNA elements encoded in the mitochondrial genome and mitoribosomal proteins most frequently encoded in the nuclear genome. The process is catalyzed by extra-ribosomal proteins, nucleus-encoded assembly factors that act in all stages of the assembly process to coordinate the processing and maturation of ribosomal RNAs with the hierarchical association of ribosomal proteins. Biochemical studies and recent cryo-EM structures of mammalian mitoribosomes have provided hints regarding their assembly. In this general concept chapter, we will briefly describe the current knowledge, mainly regarding the mammalian mitoribosome biogenesis pathway and factors involved, and will emphasize the biological sources and approaches that have been applied to advance the field.
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Affiliation(s)
- J Conor Moran
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Samuel Del'Olio
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Austin Choi
- Department of Neurology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Hui Zhong
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Antoni Barrientos
- Department of Neurology and Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA.
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23
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Ng KY, Battersby BJ. Sucrose Gradient Analysis of Human Mitochondrial Ribosomes and RNA. Methods Mol Biol 2023; 2661:101-117. [PMID: 37166634 DOI: 10.1007/978-1-0716-3171-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Faithful expression of the mitochondrial genome is required for the synthesis of the oxidative phosphorylation complexes and cell fitness. In humans, mitochondrial DNA (mtDNA) encodes 13 essential subunits of four oxidative phosphorylation complexes along with tRNAs and rRNAs needed for the translation of these proteins. Protein synthesis occurs on unique ribosomes within the organelle. Over the last decade, the revolution in genetic diagnostics has identified disruptions to the faithful synthesis of these 13 mitochondrial proteins as the largest group of inherited human mitochondrial pathologies. All of the molecular steps required for mitochondrial protein synthesis can be affected, from the genome to protein, including cotranslational quality control. Here, we describe methodologies for the biochemical separation of mitochondrial ribosomes from cultured human cells for RNA and protein analysis. Our method has been optimized to facilitate analysis for low-level sample material and thus does not require prior organelle enrichment.
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Affiliation(s)
- Kah Ying Ng
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Brendan J Battersby
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.
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24
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Del'Olio S, Barrientos A. Systematic Analysis of Assembly Intermediates in Yeast to Decipher the Mitoribosome Assembly Pathway. Methods Mol Biol 2023; 2661:163-191. [PMID: 37166638 PMCID: PMC10654547 DOI: 10.1007/978-1-0716-3171-3_11] [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] [Indexed: 05/12/2023]
Abstract
Studies of yeast mitoribosome assembly have been historically hampered by the difficulty of generating mitoribosome protein-coding gene deletion strains with a stable mitochondrial genome. The identification of mitochondrial DNA-stabilizing approaches allows for the generation of a complete set of yeast deletion strains covering all mitoribosome proteins and known assembly factors. These strains can be used to analyze the integrity and assembly state of mitoribosomes by determining the sedimentation profile of these structures by sucrose gradient centrifugation of mitochondrial extracts, coupled to mass spectrometry analysis of mitoribosome composition. Subsequent hierarchical cluster analysis of mitoribosome subassemblies accumulated in mutant strains reveals details regarding the order of protein association during the mitoribosome biogenetic process. These strains also allow the expression of truncated protein variants to probe the role of mitochondrion-specific protein extensions, the relevance of protein cofactors, or the importance of RNA-protein interactions in functional sites of the mitoribosome. In this chapter, we will detail the methodology involved in these studies.
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Affiliation(s)
- Samuel Del'Olio
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Antoni Barrientos
- Department of Neurology and Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA.
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25
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Mechanisms and players of mitoribosomal biogenesis revealed in trypanosomatids. Trends Parasitol 2022; 38:1053-1067. [PMID: 36075844 DOI: 10.1016/j.pt.2022.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 01/13/2023]
Abstract
Translation in mitochondria is mediated by mitochondrial ribosomes, or mitoribosomes, complex ribonucleoprotein machines with dual genetic origin. Mitoribosomes in trypanosomatid parasites diverged markedly from their bacterial ancestors and other eukaryotic lineages in terms of protein composition, rRNA content, and overall architecture, yet their core functional elements remained conserved. Recent cryo-electron microscopy studies provided atomic models of trypanosomatid large and small mitoribosomal subunits and their precursors, making these parasites the organisms with the best-understood biogenesis of mitoribosomes. The structures revealed molecular mechanisms and players involved in the assembly of mitoribosomes not only in the parasites, but also in eukaryotes in general.
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26
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Chagas Disease Megaesophagus Patients Carrying Variant MRPS18B P260A Display Nitro-Oxidative Stress and Mitochondrial Dysfunction in Response to IFN-γ Stimulus. Biomedicines 2022; 10:biomedicines10092215. [PMID: 36140315 PMCID: PMC9496350 DOI: 10.3390/biomedicines10092215] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
Chagas disease (CD), caused by the protozoan parasite Trypanosoma cruzi, affects 8 million people, and around 1/3 develop chronic cardiac (CCC) or digestive disease (megaesophagus/megacolon), while the majority remain asymptomatic, in the indeterminate form of Chagas disease (ASY). Most CCC cases in families with multiple Chagas disease patients carry damaging mutations in mitochondrial genes. We searched for exonic mutations associated to chagasic megaesophagus (CME) in genes essential to mitochondrial processes. We performed whole exome sequencing of 13 CME and 45 ASY patients. We found the damaging variant MRPS18B 688C > G P230A, in five out of the 13 CME patients (one of them being homozygous; 38.4%), while the variant appeared in one out of 45 ASY patients (2.2%). We analyzed the interferon (IFN)-γ-induced nitro-oxidative stress and mitochondrial function of EBV-transformed lymphoblastoid cell lines. We found the CME carriers of the mutation displayed increased levels of nitrite and nitrated proteins; in addition, the homozygous (G/G) CME patient also showed increased mitochondrial superoxide and reduced levels of ATP production. The results suggest that pathogenic mitochondrial mutations may contribute to cytokine-induced nitro-oxidative stress and mitochondrial dysfunction. We hypothesize that, in mutation carriers, IFN-γ produced in the esophageal myenteric plexus might cause nitro-oxidative stress and mitochondrial dysfunction in neurons, contributing to megaesophagus.
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27
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Abstract
The human brain consumes five orders of magnitude more energy than the sun by unit of mass and time. This staggering bioenergetic cost serves mostly synaptic transmission and actin cytoskeleton dynamics. The peak of both brain bioenergetic demands and the age of onset for neurodevelopmental disorders is approximately 5 years of age. This correlation suggests that defects in the machinery that provides cellular energy would be causative and/or consequence of neurodevelopmental disorders. We explore this hypothesis from the perspective of the machinery required for the synthesis of the electron transport chain, an ATP-producing and NADH-consuming enzymatic cascade. The electron transport chain is constituted by nuclear- and mitochondrial-genome-encoded subunits. These subunits are synthesized by the 80S and the 55S ribosomes, which are segregated to the cytoplasm and the mitochondrial matrix, correspondingly. Mitochondrial protein synthesis by the 55S ribosome is the rate-limiting step in the synthesis of electron transport chain components, suggesting that mitochondrial protein synthesis is a bottleneck for tissues with high bionergetic demands. We discuss genetic defects in the human nuclear and mitochondrial genomes that affect these protein synthesis machineries and cause a phenotypic spectrum spanning autism spectrum disorders to neurodegeneration during neurodevelopment. We propose that dysregulated mitochondrial protein synthesis is a chief, yet understudied, causative mechanism of neurodevelopmental and behavioral disorders.
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28
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The Bacterial ClpXP-ClpB Family Is Enriched with RNA-Binding Protein Complexes. Cells 2022; 11:cells11152370. [PMID: 35954215 PMCID: PMC9368063 DOI: 10.3390/cells11152370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/23/2022] [Accepted: 07/28/2022] [Indexed: 11/17/2022] Open
Abstract
In the matrix of bacteria/mitochondria/chloroplasts, Lon acts as the degradation machine for soluble proteins. In stress periods, however, proteostasis and survival depend on the strongly conserved Clp/Hsp100 family. Currently, the targets of ATP-powered unfoldases/disaggregases ClpB and ClpX and of peptidase ClpP heptameric rings are still unclear. Trapping experiments and proteome profiling in multiple organisms triggered confusion, so we analyzed the consistency of ClpP-trap targets in bacteria. We also provide meta-analyses of protein interactions in humans, to elucidate where Clp family members are enriched. Furthermore, meta-analyses of mouse complexomics are provided. Genotype–phenotype correlations confirmed our concept. Trapping, proteome, and complexome data retrieved consistent coaccumulation of CLPXP with GFM1 and TUFM orthologs. CLPX shows broad interaction selectivity encompassing mitochondrial translation elongation, RNA granules, and nucleoids. CLPB preferentially attaches to mitochondrial RNA granules and translation initiation components; CLPP is enriched with them all and associates with release/recycling factors. Mutations in CLPP cause Perrault syndrome, with phenotypes similar to defects in mtDNA/mtRNA. Thus, we propose that CLPB and CLPXP are crucial to counteract misfolded insoluble protein assemblies that contain nucleotides. This insight is relevant to improve ClpP-modulating drugs that block bacterial growth and for the treatment of human infertility, deafness, and neurodegeneration.
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29
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Mitochondrial rRNA Methylation by Mettl15 Contributes to the Exercise and Learning Capability in Mice. Int J Mol Sci 2022; 23:ijms23116056. [PMID: 35682734 PMCID: PMC9181494 DOI: 10.3390/ijms23116056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/22/2022] [Accepted: 05/26/2022] [Indexed: 02/01/2023] Open
Abstract
Mitochondrial translation is a unique relic of the symbiotic origin of the organelle. Alterations of its components cause a number of severe human diseases. Hereby we report a study of mice devoid of Mettl15 mitochondrial 12S rRNA methyltransferase, responsible for the formation of m4C839 residue (human numbering). Homozygous Mettl15−/− mice appeared to be viable in contrast to other mitochondrial rRNA methyltransferase knockouts reported earlier. The phenotype of Mettl15−/− mice is much milder than that of other mutants of mitochondrial translation apparatus. In agreement with the results obtained earlier for cell cultures with an inactivated Mettl15 gene, we observed accumulation of the RbfA factor, normally associated with the precursor of the 28S subunit, in the 55S mitochondrial ribosome fraction of knockout mice. A lack of Mettl15 leads to a lower blood glucose level after physical exercise relative to that of the wild-type mice. Mettl15−/− mice demonstrated suboptimal muscle performance and lower levels of Cox3 protein synthesized by mitoribosomes in the oxidative soleus muscles. Additionally, we detected decreased learning capabilities in the Mettl15−/− knockout mice in the tests with both positive and negative reinforcement. Such properties make Mettl15−/− knockout mice a suitable model for mild mitochondriopathies.
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30
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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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31
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Hu D, Zhang B, Suo Y, Li Z, Wan Z, Zhao W, Chen L, Yin Z, Ning H, Ge Y, Li W. Molecular Mechanisms Underlying the Inhibition of Proliferation and Differentiation by Florfenicol in P19 Stem Cells: Transcriptome Analysis. Front Pharmacol 2022; 13:779664. [PMID: 35422703 PMCID: PMC9002123 DOI: 10.3389/fphar.2022.779664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Florfenicol (FLO), which is widely used in veterinary clinics and aquaculture, can disrupt the protein synthesis of bacteria and mitochondria and, thus, lead to antibacterial and toxic effects in plants, insects, and mammals. FLO was found to repress chicken embryonic development and induce early embryonic death previously, but the underlying mechanism is not fully understood. Clarifying the mechanism of FLO-induced embryonic toxicity is important to the research and development of new drugs and the rational use of FLO to ensure human and animal health and ecological safety. In this study, the effects of FLO on pluripotency, proliferation, and differentiation were investigated in P19 stem cells (P19SCs). We also identified differentially expressed genes and performed bioinformatics analysis to obtain hub genes and conducted some functional analysis. FLO inhibited the proliferation and pluripotency of P19SCs and repressed the formation of embryoid bodies derived from P19SCs. A total of 2,396 DEGs were identified using RNA-Seq in FLO-treated P19SCs, and these genes were significantly enriched in biological processes, such as angiogenesis, embryonic organ development, and morphogenesis of organs. Kyoto encyclopedia of genes and genome-based pathway analysis also showed that five relevant pathways, especially the canonical Wnt pathway, were engaged in FLO-induced toxicity of pluripotent stem cells. We further analyzed modules and hub genes and found the involvement of ubiquitin-mediated proteolysis, DNA replication, and cell cycle machinery in regulating the pluripotency and proliferation of FLO-treated P19SCs. In summary, our data suggest that FLO disrupts the signaling transduction of pathways, especially the canonical Wnt pathway, and further inhibits the expression of target genes involved in regulating DNA replication, cell cycle, and pluripotency. This phenomenon leads to the inhibition of proliferation and differentiation in FLO-treated P19SCs. However, further experiments are required to validate our findings and elucidate the potential mechanisms underlying FLO-induced embryonic toxicity.
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Affiliation(s)
- Dongfang Hu
- Postdoctoral Research Station in Biological Sciences, Henan Normal University, Xinxiang, China.,College of Animal Science and Technology, Henan Institute of Science and Technology, Xinxiang, China.,Postdoctoral Research Base, Henan Institute of Science and Technology, Xinxiang, China
| | - Bin Zhang
- College of Animal Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Yu Suo
- College of Animal Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Zhiyue Li
- College of Animal Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Zhishuai Wan
- College of Animal Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Weihua Zhao
- College of Animal Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Lingli Chen
- College of Animal Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Zhihong Yin
- College of Animal Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Hongmei Ning
- College of Animal Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Yaming Ge
- College of Animal Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Weiguo Li
- Postdoctoral Research Station in Biological Sciences, Henan Normal University, Xinxiang, China
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32
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Santos B, Zeng R, Jorge SF, Ferreira-Junior JR, Barrientos A, Barros MH. Functional analyses of mitoribosome 54S subunit devoid of mitochondria-specific protein sequences. Yeast 2022; 39:208-229. [PMID: 34713496 PMCID: PMC8969203 DOI: 10.1002/yea.3678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 12/17/2022] Open
Abstract
In Saccharomyces cerevisiae, mitoribosomes are composed of a 54S large subunit (mtLSU) and a 37S small subunit (mtSSU). The two subunits altogether contain 73 mitoribosome proteins (MRPs) and two ribosomal RNAs (rRNAs). Although mitoribosomes preserve some similarities with their bacterial counterparts, they have significantly diverged by acquiring new proteins, protein extensions, and new RNA segments, adapting the mitoribosome to the synthesis of highly hydrophobic membrane proteins. In this study, we investigated the functional relevance of mitochondria-specific protein extensions at the C-terminus (C) or N-terminus (N) present in 19 proteins of the mtLSU. The studied mitochondria-specific extensions consist of long tails and loops extending from globular domains that mainly interact with mitochondria-specific proteins and 21S rRNA moieties extensions. The expression of variants devoid of extensions in uL4 (C), uL5 (N), uL13 (N), uL13 (C), uL16 (C), bL17 (N), bL17 (C), bL21 (24), uL22 (N), uL23 (N), uL23 (C), uL24 (C), bL27 (C), bL28 (N), bL28 (C), uL29 (N), uL29 (C), uL30 (C), bL31 (C), and bL32 (C) did not rescue the mitochondrial protein synthesis capacities and respiratory growth of the respective null mutants. On the contrary, the truncated form of the mitoribosome exit tunnel protein uL24 (N) yields a partially functional mitoribosome. Also, the removal of mitochondria-specific sequences from uL1 (N), uL3 (N), uL16 (N), bL9 (N), bL19 (C), uL29 (C), and bL31 (N) did not affect the mitoribosome function and respiratory growth. The collection of mutants described here provides new means to study and evaluate defective assembly modules in the mitoribosome biogenesis process.
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Affiliation(s)
- Barbara Santos
- Departamento de Microbiologia, Universidade de São Paulo, São Paulo, Brazil
| | - Rui Zeng
- Department of Neurology University of Miami Miller School of Medicine, Miami, USA
| | - Sasa F. Jorge
- Departamento de Microbiologia, Universidade de São Paulo, São Paulo, Brazil
| | | | - Antoni Barrientos
- Department of Neurology University of Miami Miller School of Medicine, Miami, USA
| | - Mario H. Barros
- Departamento de Microbiologia, Universidade de São Paulo, São Paulo, Brazil
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33
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Dennerlein S, Poerschke S, Oeljeklaus S, Wang C, Richter-Dennerlein R, Sattmann J, Bauermeister D, Hanitsch E, Stoldt S, Langer T, Jakobs S, Warscheid B, Rehling P. Defining the interactome of the human mitochondrial ribosome identifies SMIM4 and TMEM223 as respiratory chain assembly factors. eLife 2021; 10:68213. [PMID: 34969438 PMCID: PMC8719881 DOI: 10.7554/elife.68213] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 12/17/2021] [Indexed: 12/20/2022] Open
Abstract
Human mitochondria express a genome that encodes thirteen core subunits of the oxidative phosphorylation system (OXPHOS). These proteins insert into the inner membrane co-translationally. Therefore, mitochondrial ribosomes engage with the OXA1L-insertase and membrane-associated proteins, which support membrane insertion of translation products and early assembly steps into OXPHOS complexes. To identify ribosome-associated biogenesis factors for the OXPHOS system, we purified ribosomes and associated proteins from mitochondria. We identified TMEM223 as a ribosome-associated protein involved in complex IV biogenesis. TMEM223 stimulates the translation of COX1 mRNA and is a constituent of early COX1 assembly intermediates. Moreover, we show that SMIM4 together with C12ORF73 interacts with newly synthesized cytochrome b to support initial steps of complex III biogenesis in complex with UQCC1 and UQCC2. Our analyses define the interactome of the human mitochondrial ribosome and reveal novel assembly factors for complex III and IV biogenesis that link early assembly stages to the translation machinery.
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Affiliation(s)
- Sven Dennerlein
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Sabine Poerschke
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Silke Oeljeklaus
- Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Cong Wang
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Ricarda Richter-Dennerlein
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Johannes Sattmann
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Diana Bauermeister
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Elisa Hanitsch
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Stefan Stoldt
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.,Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Thomas Langer
- Department of Mitochondrial Proteostasis, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Stefan Jakobs
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.,Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Department of Neurology, University Medical Center Göttingen, Göttingen, Germany.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Translational Neuroinflammation and Automated Microscopy, Göttingen, Germany
| | - Bettina Warscheid
- Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Translational Neuroinflammation and Automated Microscopy, Göttingen, Germany.,Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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34
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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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35
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Herbert CJ, Labarre-Mariotte S, Cornu D, Sophie C, Panozzo C, Michel T, Dujardin G, Bonnefoy N. Translational activators and mitoribosomal isoforms cooperate to mediate mRNA-specific translation in Schizosaccharomyces pombe mitochondria. Nucleic Acids Res 2021; 49:11145-11166. [PMID: 34634819 PMCID: PMC8565316 DOI: 10.1093/nar/gkab789] [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: 04/07/2021] [Revised: 08/24/2021] [Accepted: 10/05/2021] [Indexed: 11/12/2022] Open
Abstract
Mitochondrial mRNAs encode key subunits of the oxidative phosphorylation complexes that produce energy for the cell. In Saccharomyces cerevisiae, mitochondrial translation is under the control of translational activators, specific to each mRNA. In Schizosaccharomyces pombe, which more closely resembles the human system by its mitochondrial DNA structure and physiology, most translational activators appear to be either lacking, or recruited for post-translational functions. By combining bioinformatics, genetic and biochemical approaches we identified two interacting factors, Cbp7 and Cbp8, controlling Cytb production in S. pombe. We show that their absence affects cytb mRNA stability and impairs the detection of the Cytb protein. We further identified two classes of Cbp7/Cbp8 partners and showed that they modulated Cytb or Cox1 synthesis. First, two isoforms of bS1m, a protein of the small mitoribosomal subunit, that appear mutually exclusive and confer translational specificity. Second, a complex of four proteins dedicated to Cox1 synthesis, which includes an RNA helicase that interacts with the mitochondrial ribosome. Our results suggest that S. pombe contains, in addition to complexes of translational activators, a heterogeneous population of mitochondrial ribosomes that could specifically modulate translation depending on the mRNA translated, in order to optimally balance the production of different respiratory complex subunits.
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Affiliation(s)
- Christopher J Herbert
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Sylvie Labarre-Mariotte
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - David Cornu
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Cyrielle Sophie
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Cristina Panozzo
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Thomas Michel
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Geneviève Dujardin
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Nathalie Bonnefoy
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
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36
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Hilander T, Jackson CB, Robciuc M, Bashir T, Zhao H. The roles of assembly factors in mammalian mitoribosome biogenesis. Mitochondrion 2021; 60:70-84. [PMID: 34339868 DOI: 10.1016/j.mito.2021.07.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 02/08/2023]
Abstract
As ancient bacterial endosymbionts of eukaryotic cells, mitochondria have retained their own circular DNA as well as protein translation system including mitochondrial ribosomes (mitoribosomes). In recent years, methodological advancements in cryoelectron microscopy and mass spectrometry have revealed the extent of the evolutionary divergence of mitoribosomes from their bacterial ancestors and their adaptation to the synthesis of 13 mitochondrial DNA encoded oxidative phosphorylation complex subunits. In addition to the structural data, the first assembly pathway maps of mitoribosomes have started to emerge and concomitantly also the assembly factors involved in this process to achieve fully translational competent particles. These transiently associated factors assist in the intricate assembly process of mitoribosomes by enhancing protein incorporation, ribosomal RNA folding and modification, and by blocking premature or non-native protein binding, for example. This review focuses on summarizing the current understanding of the known mammalian mitoribosome assembly factors and discussing their possible roles in the assembly of small or large mitoribosomal subunits.
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Affiliation(s)
- Taru Hilander
- Faculty of Biological and Environmental Sciences, University of Helsinki, Finland.
| | - Christopher B Jackson
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Finland.
| | - Marius Robciuc
- Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
| | - Tanzeela Bashir
- Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
| | - Hongxia Zhao
- Faculty of Biological and Environmental Sciences, University of Helsinki, Finland; Key Laboratory of Stem Cell and Biopharmaceutical Technology, School of Life Sciences, Guangxi Normal University, Guangxi, China.
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37
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Cheng J, Berninghausen O, Beckmann R. A distinct assembly pathway of the human 39S late pre-mitoribosome. Nat Commun 2021; 12:4544. [PMID: 34315873 PMCID: PMC8316566 DOI: 10.1038/s41467-021-24818-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/01/2021] [Indexed: 02/03/2023] Open
Abstract
Assembly of the mitoribosome is largely enigmatic and involves numerous assembly factors. Little is known about their function and the architectural transitions of the pre-ribosomal intermediates. Here, we solve cryo-EM structures of the human 39S large subunit pre-ribosomes, representing five distinct late states. Besides the MALSU1 complex used as bait for affinity purification, we identify several assembly factors, including the DDX28 helicase, MRM3, GTPBP10 and the NSUN4-mTERF4 complex, all of which keep the 16S rRNA in immature conformations. The late transitions mainly involve rRNA domains IV and V, which form the central protuberance, the intersubunit side and the peptidyltransferase center of the 39S subunit. Unexpectedly, we find deacylated tRNA in the ribosomal E-site, suggesting a role in 39S assembly. Taken together, our study provides an architectural inventory of the distinct late assembly phase of the human 39S mitoribosome.
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Affiliation(s)
- Jingdong Cheng
- Gene Center and Department for Biochemistry, LMU Munich, München, Germany.
| | - Otto Berninghausen
- Gene Center and Department for Biochemistry, LMU Munich, München, Germany
| | - Roland Beckmann
- Gene Center and Department for Biochemistry, LMU Munich, München, Germany.
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38
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Chacinska A, Rehling P. Molecular bases of mitochondrial disorders. FEBS Lett 2021; 595:973-975. [PMID: 33908035 DOI: 10.1002/1873-3468.14086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Agnieszka Chacinska
- ReMedy International Research Agenda Unit, University of Warsaw, Poland.,IMol Polish Academy of Sciences, Warsaw, Poland
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Germany.,Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Germany.,Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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39
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Molecular Insights into Mitochondrial Protein Translocation and Human Disease. Genes (Basel) 2021; 12:genes12071031. [PMID: 34356047 PMCID: PMC8305315 DOI: 10.3390/genes12071031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/27/2021] [Accepted: 06/30/2021] [Indexed: 12/11/2022] Open
Abstract
In human mitochondria, mtDNA encodes for only 13 proteins, all components of the OXPHOS system. The rest of the mitochondrial components, which make up approximately 99% of its proteome, are encoded in the nuclear genome, synthesized in cytosolic ribosomes and imported into mitochondria. Different import machineries translocate mitochondrial precursors, depending on their nature and the final destination inside the organelle. The proper and coordinated function of these molecular pathways is critical for mitochondrial homeostasis. Here, we will review molecular details about these pathways, which components have been linked to human disease and future perspectives on the field to expand the genetic landscape of mitochondrial diseases.
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40
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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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41
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Lenarčič T, Jaskolowski M, Leibundgut M, Scaiola A, Schönhut T, Saurer M, Lee RG, Rackham O, Filipovska A, Ban N. Stepwise maturation of the peptidyl transferase region of human mitoribosomes. Nat Commun 2021; 12:3671. [PMID: 34135320 PMCID: PMC8208988 DOI: 10.1038/s41467-021-23811-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/07/2021] [Indexed: 02/08/2023] Open
Abstract
Mitochondrial ribosomes are specialized for the synthesis of membrane proteins responsible for oxidative phosphorylation. Mammalian mitoribosomes have diverged considerably from the ancestral bacterial ribosomes and feature dramatically reduced ribosomal RNAs. The structural basis of the mammalian mitochondrial ribosome assembly is currently not well understood. Here we present eight distinct assembly intermediates of the human large mitoribosomal subunit involving seven assembly factors. We discover that the NSUN4-MTERF4 dimer plays a critical role in the process by stabilizing the 16S rRNA in a conformation that exposes the functionally important regions of rRNA for modification by the MRM2 methyltransferase and quality control interactions with the conserved mitochondrial GTPase MTG2 that contacts the sarcin-ricin loop and the immature active site. The successive action of these factors leads to the formation of the peptidyl transferase active site of the mitoribosome and the folding of the surrounding rRNA regions responsible for interactions with tRNAs and the small ribosomal subunit.
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Affiliation(s)
- Tea Lenarčič
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Mateusz Jaskolowski
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Marc Leibundgut
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Alain Scaiola
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Tanja Schönhut
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Martin Saurer
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Richard G Lee
- Harry Perkins Institute of Medical Research, QEII Medical Centre, University of Western Australia, Nedlands, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, University of Western Australia, Nedlands, WA, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, QEII Medical Centre, University of Western Australia, Nedlands, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, University of Western Australia, Nedlands, WA, Australia
- Curtin Health Innovation Research Institute and Curtin Medical School, Curtin University, Bentley, WA, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, WA, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, QEII Medical Centre, University of Western Australia, Nedlands, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, University of Western Australia, Nedlands, WA, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, WA, Australia
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
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42
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Mechanisms and regulation of protein synthesis in mitochondria. Nat Rev Mol Cell Biol 2021; 22:307-325. [PMID: 33594280 DOI: 10.1038/s41580-021-00332-2] [Citation(s) in RCA: 159] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2021] [Indexed: 02/06/2023]
Abstract
Mitochondria are cellular organelles responsible for generation of chemical energy in the process called oxidative phosphorylation. They originate from a bacterial ancestor and maintain their own genome, which is expressed by designated, mitochondrial transcription and translation machineries that differ from those operating for nuclear gene expression. In particular, the mitochondrial protein synthesis machinery is structurally and functionally very different from that governing eukaryotic, cytosolic translation. Despite harbouring their own genetic information, mitochondria are far from being independent of the rest of the cell and, conversely, cellular fitness is closely linked to mitochondrial function. Mitochondria depend heavily on the import of nuclear-encoded proteins for gene expression and function, and hence engage in extensive inter-compartmental crosstalk to regulate their proteome. This connectivity allows mitochondria to adapt to changes in cellular conditions and also mediates responses to stress and mitochondrial dysfunction. With a focus on mammals and yeast, we review fundamental insights that have been made into the biogenesis, architecture and mechanisms of the mitochondrial translation apparatus in the past years owing to the emergence of numerous near-atomic structures and a considerable amount of biochemical work. Moreover, we discuss how cellular mitochondrial protein expression is regulated, including aspects of mRNA and tRNA maturation and stability, roles of auxiliary factors, such as translation regulators, that adapt mitochondrial translation rates, and the importance of inter-compartmental crosstalk with nuclear gene expression and cytosolic translation and how it enables integration of mitochondrial translation into the cellular context.
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43
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Role of GTPases in Driving Mitoribosome Assembly. Trends Cell Biol 2021; 31:284-297. [PMID: 33419649 DOI: 10.1016/j.tcb.2020.12.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/01/2020] [Accepted: 12/11/2020] [Indexed: 01/08/2023]
Abstract
Mitoribosomes catalyze essential protein synthesis within mitochondria. Mitoribosome biogenesis is assisted by an increasing number of assembly factors, among which guanosine triphosphate hydrolases (GTPases) are the most abundant class. Here, we review recent progress in our understanding of mitoribosome assembly GTPases. We describe their shared and specific features and mechanisms of action, compare them with their bacterial counterparts, and discuss their possible roles in the assembly of small or large mitoribosomal subunits and the formation of the monosome by establishing quality-control checkpoints during these processes. Furthermore, following the recent unification of the nomenclature for the mitoribosomal proteins, we also propose a unified nomenclature for mitoribosome assembly GTPases.
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