1
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Wenger C, Harsman A, Niemann M, Oeljeklaus S, von Känel C, Calderaro S, Warscheid B, Schneider A. The Mba1 homologue of Trypanosoma brucei is involved in the biogenesis of oxidative phosphorylation complexes. Mol Microbiol 2023; 119:537-550. [PMID: 36829306 DOI: 10.1111/mmi.15048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 02/26/2023]
Abstract
Consistent with other eukaryotes, the Trypanosoma brucei mitochondrial genome encodes mainly hydrophobic core subunits of the oxidative phosphorylation system. These proteins must be co-translationally inserted into the inner mitochondrial membrane and are synthesized by the highly unique trypanosomal mitoribosomes, which have a much higher protein to RNA ratio than any other ribosome. Here, we show that the trypanosomal orthologue of the mitoribosome receptor Mba1 (TbMba1) is essential for normal growth of procyclic trypanosomes but redundant in the bloodstream form, which lacks an oxidative phosphorylation system. Proteomic analyses of TbMba1-depleted mitochondria from procyclic cells revealed reduced levels of many components of the oxidative phosphorylation system, most of which belong to the cytochrome c oxidase (Cox) complex, three subunits of which are mitochondrially encoded. However, the integrity of the mitoribosome and its interaction with the inner membrane were not affected. Pull-down experiments showed that TbMba1 forms a dynamic interaction network that includes the trypanosomal Mdm38/Letm1 orthologue and a trypanosome-specific factor that stabilizes the CoxI and CoxII mRNAs. In summary, our study suggests that the function of Mba1 in the biogenesis of membrane subunits of OXPHOS complexes is conserved among yeast, mammals and trypanosomes, which belong to two eukaryotic supergroups.
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Affiliation(s)
- Christoph Wenger
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Anke Harsman
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Moritz Niemann
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Silke Oeljeklaus
- Faculty of Chemistry and Pharmacy, Biochemistry II, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - Corinne von Känel
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Salvatore Calderaro
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Bettina Warscheid
- Faculty of Chemistry and Pharmacy, Biochemistry II, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany.,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - André Schneider
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.,Institute for Advanced Study (Wissenschaftskolleg) Berlin, Berlin, Germany
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2
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Kaiyrzhanov R, Mohammed SEM, Maroofian R, Husain RA, Catania A, Torraco A, Alahmad A, Dutra-Clarke M, Grønborg S, Sudarsanam A, Vogt J, Arrigoni F, Baptista J, Haider S, Feichtinger RG, Bernardi P, Zulian A, Gusic M, Efthymiou S, Bai R, Bibi F, Horga A, Martinez-Agosto JA, Lam A, Manole A, Rodriguez DP, Durigon R, Pyle A, Albash B, Dionisi-Vici C, Murphy D, Martinelli D, Bugiardini E, Allis K, Lamperti C, Reipert S, Risom L, Laugwitz L, Di Nottia M, McFarland R, Vilarinho L, Hanna M, Prokisch H, Mayr JA, Bertini ES, Ghezzi D, Østergaard E, Wortmann SB, Carrozzo R, Haack TB, Taylor RW, Spinazzola A, Nowikovsky K, Houlden H. Bi-allelic LETM1 variants perturb mitochondrial ion homeostasis leading to a clinical spectrum with predominant nervous system involvement. Am J Hum Genet 2022; 109:1692-1712. [PMID: 36055214 PMCID: PMC9502063 DOI: 10.1016/j.ajhg.2022.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 07/01/2022] [Indexed: 11/25/2022] Open
Abstract
Leucine zipper-EF-hand containing transmembrane protein 1 (LETM1) encodes an inner mitochondrial membrane protein with an osmoregulatory function controlling mitochondrial volume and ion homeostasis. The putative association of LETM1 with a human disease was initially suggested in Wolf-Hirschhorn syndrome, a disorder that results from de novo monoallelic deletion of chromosome 4p16.3, a region encompassing LETM1. Utilizing exome sequencing and international gene-matching efforts, we have identified 18 affected individuals from 11 unrelated families harboring ultra-rare bi-allelic missense and loss-of-function LETM1 variants and clinical presentations highly suggestive of mitochondrial disease. These manifested as a spectrum of predominantly infantile-onset (14/18, 78%) and variably progressive neurological, metabolic, and dysmorphic symptoms, plus multiple organ dysfunction associated with neurodegeneration. The common features included respiratory chain complex deficiencies (100%), global developmental delay (94%), optic atrophy (83%), sensorineural hearing loss (78%), and cerebellar ataxia (78%) followed by epilepsy (67%), spasticity (53%), and myopathy (50%). Other features included bilateral cataracts (42%), cardiomyopathy (36%), and diabetes (27%). To better understand the pathogenic mechanism of the identified LETM1 variants, we performed biochemical and morphological studies on mitochondrial K+/H+ exchange activity, proteins, and shape in proband-derived fibroblasts and muscles and in Saccharomyces cerevisiae, which is an important model organism for mitochondrial osmotic regulation. Our results demonstrate that bi-allelic LETM1 variants are associated with defective mitochondrial K+ efflux, swollen mitochondrial matrix structures, and loss of important mitochondrial oxidative phosphorylation protein components, thus highlighting the implication of perturbed mitochondrial osmoregulation caused by LETM1 variants in neurological and mitochondrial pathologies.
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Affiliation(s)
- Rauan Kaiyrzhanov
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK
| | - Sami E M Mohammed
- Department of Biomedical Sciences, Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Reza Maroofian
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK
| | - Ralf A Husain
- Department of Neuropediatrics, Jena University Hospital, Jena 07747, Germany; Center for Rare Diseases, Jena University Hospital, Jena 07747, Germany
| | - Alessia Catania
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20126, Italy
| | - Alessandra Torraco
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome 00146, Italy
| | - Ahmad Alahmad
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK; Kuwait Medical Genetics Centre, Al-Sabah Medical Area 80901, Kuwait
| | - Marina Dutra-Clarke
- Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, the University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Sabine Grønborg
- Center for Rare Diseases, Department of Pediatrics and Department of Genetics, Copenhagen University Hospital Rigshospitalet, Blegdamsvej 9, Copenhagen 2100, Denmark
| | - Annapurna Sudarsanam
- West Midlands Regional Genetics Service, Birmingham Women's and Children's Hospital, Birmingham B15 2TG, UK
| | - Julie Vogt
- West Midlands Regional Genetics Service, Birmingham Women's and Children's Hospital, Birmingham B15 2TG, UK
| | - Filippo Arrigoni
- Paediatric Radiology and Neuroradiology Department, V. Buzzi Children's Hospital, Milan 20154, Italy
| | - Julia Baptista
- Peninsula Medical School, Faculty of Health, University of Plymouth, Plymouth PL4 8AA, UK
| | - Shahzad Haider
- Paediatrics Wah Medical College NUMS, Wah Cantonment, Punjab 44000, Pakistan
| | - René G Feichtinger
- University Children's Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), Salzburg 5020, Austria
| | - Paolo Bernardi
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, Padova 35131, Italy
| | - Alessandra Zulian
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, Padova 35131, Italy
| | - Mirjana Gusic
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg 85764, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich 81675, Germany; Institute of Human Genetics, Technical University of Munich, Munich 81675, Germany
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK
| | | | - Farah Bibi
- Institute of Biochemistry and Biotechnology, Pir Mehar Ali Shah Arid Agriculture University, Rawalpindi 44000, Pakistan
| | - Alejandro Horga
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK; Neuromuscular Diseases Unit, Department of Neurology, Hospital Clinico San Carlos and San Carlos Health Research Institute (IdISSC), Madrid 28040, Spain
| | - Julian A Martinez-Agosto
- Department of Human Genetics, Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Amanda Lam
- Neurometabolic Unit, National Hospital for Neurology and Neurosurgery, London, UK; Department of Chemical Pathology, Great Ormond Street Hospital, WC1N 3BG London, UK
| | - Andreea Manole
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK
| | - Diego-Perez Rodriguez
- Department of Clinical Movement Neurosciences, Royal Free Campus, University College of London, Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Romina Durigon
- Department of Clinical Movement Neurosciences, Royal Free Campus, University College of London, Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Angela Pyle
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK
| | - Buthaina Albash
- Kuwait Medical Genetics Centre, Al-Sabah Medical Area 80901, Kuwait
| | - Carlo Dionisi-Vici
- Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome 00146, Italy
| | - David Murphy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Diego Martinelli
- Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome 00146, Italy
| | - Enrico Bugiardini
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK
| | | | - Costanza Lamperti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20126, Italy
| | - Siegfried Reipert
- Core Facility of Cell Imaging and Ultrastructure Research, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria
| | - Lotte Risom
- Department of Genetics, Copenhagen University Hospital Rigshospitalet Blegdamsvej, Copenhagen 2100, Denmark
| | - Lucia Laugwitz
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72076 Tübingen, Germany; Department of Neuropediatrics, Developmental Neurology and Social Pediatrics, University of Tübingen, Tübingen 72076, Germany
| | - Michela Di Nottia
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome 00146, Italy
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK; NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, UK
| | - Laura Vilarinho
- Unit of Neonatal Screening, Metabolism and Genetics, Department of Human Genetics, National Institute of Health Dr Ricardo Jorge, Porto 4000-055, Portugal
| | - Michael Hanna
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK
| | - Holger Prokisch
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg 85764, Germany; Institute of Human Genetics, Technical University of Munich, Munich 81675, Germany
| | - Johannes A Mayr
- University Children's Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), Salzburg 5020, Austria
| | - Enrico Silvio Bertini
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome 00146, Italy
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20126, Italy; Department of Pathophysiology and Transplantation, University of Milan, Milan 20122, Italy
| | - Elsebet Østergaard
- Department of Genetics, Copenhagen University Hospital Rigshospitalet Blegdamsvej, Copenhagen 2100, Denmark; Institute for Clinical Medicine, University of Copenhagen, Copenhagen 2200, Denmark
| | - Saskia B Wortmann
- University Children's Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), Salzburg 5020, Austria; Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg 85764, Germany; Institute of Human Genetics, Technical University of Munich, Munich 81675, Germany; Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Amalia Children's Hospital, Radboudumc, Nijmegen 6525 EZ, the Netherlands
| | - Rosalba Carrozzo
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome 00146, Italy
| | - Tobias B Haack
- Department of Neuropediatrics, Developmental Neurology and Social Pediatrics, University of Tübingen, Tübingen 72076, Germany; Centre for Rare Diseases, University of Tuebingen, Tübingen 72076, Germany
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK; NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, UK
| | - Antonella Spinazzola
- Department of Clinical Movement Neurosciences, Royal Free Campus, University College of London, Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Karin Nowikovsky
- Department of Biomedical Sciences, Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine Vienna, Vienna 1210, Austria; Department of Internal Medicine I, ASCTR and Comprehensive Cancer Center, Medical University of Vienna, Vienna 1090, Austria.
| | - Henry Houlden
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK.
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3
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Sharma N, Osman C. Yme2, a putative RNA recognition motif and AAA+ domain containing protein, genetically interacts with the mitochondrial protein export machinery. Biol Chem 2022; 403:807-817. [PMID: 35100666 PMCID: PMC9284673 DOI: 10.1515/hsz-2021-0398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/19/2022] [Indexed: 02/04/2023]
Abstract
The mitochondrial respiratory chain is composed of nuclear as well as mitochondrial-encoded subunits. A variety of factors mediate co-translational integration of mtDNA-encoded proteins into the inner membrane. In Saccharomyces cerevisiae, Mdm38 and Mba1 are ribosome acceptors that recruit the mitochondrial ribosome to the inner membrane, where the insertase Oxa1, facilitates membrane integration of client proteins. The protein Yme2 has previously been shown to be localized in the inner mitochondrial membrane and has been implicated in mitochondrial protein biogenesis, but its mode of action remains unclear. Here, we show that multiple copies of Yme2 assemble into a high molecular weight complex. Using a combination of bioinformatics and mutational analyses, we find that Yme2 possesses an RNA recognition motif (RRM), which faces the mitochondrial matrix and a AAA+ domain that is located in the intermembrane space. We further show that YME2 genetically interacts with MDM38, MBA1 and OXA1, which links the function of Yme2 to the mitochondrial protein biogenesis machinery.
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Affiliation(s)
- Nupur Sharma
- Faculty of Biology, Ludwig Maximilian University Munich, D-82152Planegg-Martinsried, Germany
- Graduate School of Life Sciences, Ludwig Maximilian University Munich, D-82152Planegg-Martinsried, Germany
| | - Christof Osman
- Faculty of Biology, Ludwig Maximilian University Munich, D-82152Planegg-Martinsried, Germany
- Graduate School of Life Sciences, Ludwig Maximilian University Munich, D-82152Planegg-Martinsried, Germany
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4
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Medlock AE, Hixon JC, Bhuiyan T, Cobine PA. Prime Real Estate: Metals, Cofactors and MICOS. Front Cell Dev Biol 2022; 10:892325. [PMID: 35669513 PMCID: PMC9163361 DOI: 10.3389/fcell.2022.892325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/02/2022] [Indexed: 12/23/2022] Open
Abstract
Metals are key elements for the survival and normal development of humans but can also be toxic to cells when mishandled. In fact, even mild disruption of metal homeostasis causes a wide array of disorders. Many of the metals essential to normal physiology are required in mitochondria for enzymatic activities and for the formation of essential cofactors. Copper is required as a cofactor in the terminal electron transport chain complex cytochrome c oxidase, iron is required for the for the formation of iron-sulfur (Fe-S) clusters and heme, manganese is required for the prevention of oxidative stress production, and these are only a few examples of the critical roles that mitochondrial metals play. Even though the targets of these metals are known, we are still identifying transporters, investigating the roles of known transporters, and defining regulators of the transport process. Mitochondria are dynamic organelles whose content, structure and localization within the cell vary in different tissues and organisms. Our knowledge of the impact that alterations in mitochondrial physiology have on metal content and utilization in these organelles is very limited. The rates of fission and fusion, the ultrastructure of the organelle, and rates of mitophagy can all affect metal homeostasis and cofactor assembly. This review will focus of the emerging areas of overlap between metal homeostasis, cofactor assembly and the mitochondrial contact site and cristae organizing system (MICOS) that mediates multiple aspects of mitochondrial physiology. Importantly the MICOS complexes may allow for localization and organization of complexes not only involved in cristae formation and contact between the inner and outer mitochondrial membranes but also acts as hub for metal-related proteins to work in concert in cofactor assembly and homeostasis.
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Affiliation(s)
- Amy E. Medlock
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
- Augusta University/University of Georgia Medical Partnership, University of Georgia, Athens, GA, United States
| | - J. Catrice Hixon
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - Tawhid Bhuiyan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Paul A. Cobine
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
- *Correspondence: Paul A. Cobine,
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Arguello T, Peralta S, Antonicka H, Gaidosh G, Diaz F, Tu YT, Garcia S, Shiekhattar R, Barrientos A, Moraes CT. ATAD3A has a scaffolding role regulating mitochondria inner membrane structure and protein assembly. Cell Rep 2021; 37:110139. [PMID: 34936866 PMCID: PMC8785211 DOI: 10.1016/j.celrep.2021.110139] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 09/02/2021] [Accepted: 11/24/2021] [Indexed: 11/30/2022] Open
Abstract
The ATPase Family AAA Domain Containing 3A (ATAD3A), is a mitochondrial inner membrane protein conserved in metazoans. ATAD3A has been associated with several mitochondrial functions, including nucleoid organization, cholesterol metabolism, and mitochondrial translation. To address its primary role, we generated a neuronal-specific conditional knockout (Atad3 nKO) mouse model, which developed a severe encephalopathy by 5 months of age. Pre-symptomatic mice showed aberrant mitochondrial cristae morphogenesis in the cortex as early as 2 months. Using a multi-omics approach in the CNS of 2-to-3-month-old mice, we found early alterations in the organelle membrane structure. We also show that human ATAD3A associates with different components of the inner membrane, including OXPHOS complex I, Letm1, and prohibitin complexes. Stochastic Optical Reconstruction Microscopy (STORM) shows that ATAD3A is regularly distributed along the inner mitochondrial membrane, suggesting a critical structural role in inner mitochondrial membrane and its organization, most likely in an ATPase-dependent manner. Arguello et al. show that deletion of the mitochondrial protein ATAD3 in neurons leads to neuronal loss and death. The earliest phenotype is disruption of the mitochondrial inner membrane structure; OXPHOS complexes are affected later. ATAD3 is regularly spaced and has several interactors at the inner membrane, including CI subunits.
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Affiliation(s)
- Tania Arguello
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Susana Peralta
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Hana Antonicka
- Department of Human Genetics and Montreal Neurological Institute, McGill University, Montreal, QC H3A 0C7, Canada
| | - Gabriel Gaidosh
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Francisca Diaz
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Ya-Ting Tu
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Sofia Garcia
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Ramin Shiekhattar
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Antonio Barrientos
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Carlos T Moraes
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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6
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Heidorn-Czarna M, Heidorn HM, Fernando S, Sanislav O, Jarmuszkiewicz W, Mutzel R, Fisher PR. Chronic Activation of AMPK Induces Mitochondrial Biogenesis through Differential Phosphorylation and Abundance of Mitochondrial Proteins in Dictyostelium discoideum. Int J Mol Sci 2021; 22:ijms222111675. [PMID: 34769115 PMCID: PMC8584165 DOI: 10.3390/ijms222111675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 11/17/2022] Open
Abstract
Mitochondrial biogenesis is a highly controlled process that depends on diverse signalling pathways responding to cellular and environmental signals. AMP-activated protein kinase (AMPK) is a critical metabolic enzyme that acts at a central control point in cellular energy homeostasis. Numerous studies have revealed the crucial roles of AMPK in the regulation of mitochondrial biogenesis; however, molecular mechanisms underlying this process are still largely unknown. Previously, we have shown that, in cellular slime mould Dictyostelium discoideum, the overexpression of the catalytic α subunit of AMPK led to enhanced mitochondrial biogenesis, which was accompanied by reduced cell growth and aberrant development. Here, we applied mass spectrometry-based proteomics of Dictyostelium mitochondria to determine the impact of chronically active AMPKα on the phosphorylation state and abundance of mitochondrial proteins and to identify potential protein targets leading to the biogenesis of mitochondria. Our results demonstrate that enhanced mitochondrial biogenesis is associated with variations in the phosphorylation levels and abundance of proteins related to energy metabolism, protein synthesis, transport, inner membrane biogenesis, and cellular signalling. The observed changes are accompanied by elevated mitochondrial respiratory activity in the AMPK overexpression strain. Our work is the first study reporting on the global phosphoproteome profiling of D. discoideum mitochondria and its changes as a response to constitutively active AMPK. We also propose an interplay between the AMPK and mTORC1 signalling pathways in controlling the cellular growth and biogenesis of mitochondria in Dictyostelium as a model organism.
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Affiliation(s)
- Malgorzata Heidorn-Czarna
- Department of Biology, Chemistry, Pharmacy, Institute for Biology-Microbiology, Freie Universität Berlin, 14195 Berlin, Germany; (H.-M.H.); (R.M.)
- Department of Cellular Molecular Biology, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland
- Correspondence: ; Tel.: +48-71-375-62-73
| | - Herbert-Michael Heidorn
- Department of Biology, Chemistry, Pharmacy, Institute for Biology-Microbiology, Freie Universität Berlin, 14195 Berlin, Germany; (H.-M.H.); (R.M.)
| | - Sanjanie Fernando
- Discipline of Microbiology, Department of Physiology, Anatomy and Microbiology, School of Life Sciences, College of Science, Health and Engineering, La Trobe University, Bundoora, VIC 3086, Australia; (S.F.); (O.S.); (P.R.F.)
| | - Oana Sanislav
- Discipline of Microbiology, Department of Physiology, Anatomy and Microbiology, School of Life Sciences, College of Science, Health and Engineering, La Trobe University, Bundoora, VIC 3086, Australia; (S.F.); (O.S.); (P.R.F.)
| | - Wieslawa Jarmuszkiewicz
- Laboratory of Mitochondrial Biochemistry, Department of Bioenergetics, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland;
| | - Rupert Mutzel
- Department of Biology, Chemistry, Pharmacy, Institute for Biology-Microbiology, Freie Universität Berlin, 14195 Berlin, Germany; (H.-M.H.); (R.M.)
| | - Paul R. Fisher
- Discipline of Microbiology, Department of Physiology, Anatomy and Microbiology, School of Life Sciences, College of Science, Health and Engineering, La Trobe University, Bundoora, VIC 3086, Australia; (S.F.); (O.S.); (P.R.F.)
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7
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Abstract
The uptake of calcium into and extrusion of calcium from the mitochondrial matrix is a fundamental biological process that has critical effects on cellular metabolism, signaling, and survival. Disruption of mitochondrial calcium (mCa2+) cycling is implicated in numerous acquired diseases such as heart failure, stroke, neurodegeneration, diabetes, and cancer, and is genetically linked to several inherited neuromuscular disorders. Understanding the mechanisms responsible for mCa2+ exchange therefore holds great promise for the treatment of these diseases. The past decade has seen the genetic identification of many of the key proteins that mediate mitochondrial calcium uptake and efflux. Here, we present an overview of the phenomenon of mCa2+ transport, and a comprehensive examination of the molecular machinery that mediates calcium flux across the inner mitochondrial membrane: the mitochondrial uniporter complex (consisting of MCU, EMRE, MICU1, MICU2, MICU3, MCUB, and MCUR1), NCLX, LETM1, the mitochondrial ryanodine receptor, and the mitochondrial permeability transition pore. We then consider the physiological implications of mCa2+ flux and evaluate how alterations in mCa2+ homeostasis contribute to human disease. This review concludes by highlighting opportunities and challenges for therapeutic intervention in pathologies characterized by aberrant mCa2+ handling and by summarizing critical unanswered questions regarding the biology of mCa2+ flux.
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Affiliation(s)
- Joanne F Garbincius
- Center for Translational Medicine, Center for Translational Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
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8
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Srinivasan K, Banerjee A, Baid P, Dhur A, Sengupta J. Ribosome-membrane crosstalk: Co-translational targeting pathways of proteins across membranes in prokaryotes and eukaryotes. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 128:163-198. [PMID: 35034718 DOI: 10.1016/bs.apcsb.2021.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Ribosomes are the molecular machine of living cells designed for decoding mRNA-encoded genetic information into protein. Being sophisticated machinery, both in design and function, the ribosome not only carries out protein synthesis, but also coordinates several other ribosome-associated cellular processes. One such process is the translocation of proteins across or into the membrane depending on their secretory or membrane-associated nature. These proteins comprise a large portion of a cell's proteome and act as key factors for cellular survival as well as several crucial functional pathways. Protein transport to extra- and intra-cytosolic compartments (across the eukaryotic endoplasmic reticulum (ER) or across the prokaryotic plasma membrane) or insertion into membranes majorly occurs through an evolutionarily conserved protein-conducting channel called translocon (eukaryotic Sec61 or prokaryotic SecYEG channels). Targeting proteins to the membrane-bound translocon may occur via post-translational or co-translational modes and it is often mediated by recognition of an N-terminal signal sequence in the newly synthesizes polypeptide chain. Co-translational translocation is coupled to protein synthesis where the ribosome-nascent chain complex (RNC) itself is targeted to the translocon. Here, in the light of recent advances in structural and functional studies, we discuss our current understanding of the mechanistic models of co-translational translocation, coordinated by the actively translating ribosomes, in prokaryotes and eukaryotes.
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Affiliation(s)
- Krishnamoorthi Srinivasan
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Aneek Banerjee
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Priya Baid
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Ankit Dhur
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Jayati Sengupta
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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9
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Itoh Y, Andréll J, Choi A, Richter U, Maiti P, Best RB, Barrientos A, Battersby BJ, Amunts A. Mechanism of membrane-tethered mitochondrial protein synthesis. Science 2021; 371:846-849. [PMID: 33602856 PMCID: PMC7610362 DOI: 10.1126/science.abe0763] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 12/24/2020] [Indexed: 12/11/2022]
Abstract
Mitochondrial ribosomes (mitoribosomes) are tethered to the mitochondrial inner membrane to facilitate the cotranslational membrane insertion of the synthesized proteins. We report cryo-electron microscopy structures of human mitoribosomes with nascent polypeptide, bound to the insertase oxidase assembly 1-like (OXA1L) through three distinct contact sites. OXA1L binding is correlated with a series of conformational changes in the mitoribosomal large subunit that catalyze the delivery of newly synthesized polypeptides. The mechanism relies on the folding of mL45 inside the exit tunnel, forming two specific constriction sites that would limit helix formation of the nascent chain. A gap is formed between the exit and the membrane, making the newly synthesized proteins accessible. Our data elucidate the basis by which mitoribosomes interact with the OXA1L insertase to couple protein synthesis and membrane delivery.
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Affiliation(s)
- Yuzuru Itoh
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165 Solna, Stockholm, Sweden.
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Juni Andréll
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165 Solna, Stockholm, Sweden.
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Austin Choi
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
| | - Uwe Richter
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland.
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Priyanka Maiti
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Antoni Barrientos
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
| | - Brendan J Battersby
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland.
| | - Alexey Amunts
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165 Solna, Stockholm, Sweden.
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
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10
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Hierro-Yap C, Šubrtová K, Gahura O, Panicucci B, Dewar C, Chinopoulos C, Schnaufer A, Zíková A. Bioenergetic consequences of F oF 1-ATP synthase/ATPase deficiency in two life cycle stages of Trypanosoma brucei. J Biol Chem 2021; 296:100357. [PMID: 33539923 PMCID: PMC7949148 DOI: 10.1016/j.jbc.2021.100357] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 12/23/2020] [Accepted: 01/28/2021] [Indexed: 12/17/2022] Open
Abstract
Mitochondrial ATP synthase is a reversible nanomotor synthesizing or hydrolyzing ATP depending on the potential across the membrane in which it is embedded. In the unicellular parasite Trypanosoma brucei, the direction of the complex depends on the life cycle stage of this digenetic parasite: in the midgut of the tsetse fly vector (procyclic form), the FoF1–ATP synthase generates ATP by oxidative phosphorylation, whereas in the mammalian bloodstream form, this complex hydrolyzes ATP and maintains mitochondrial membrane potential (ΔΨm). The trypanosome FoF1–ATP synthase contains numerous lineage-specific subunits whose roles remain unknown. Here, we seek to elucidate the function of the lineage-specific protein Tb1, the largest membrane-bound subunit. In procyclic form cells, Tb1 silencing resulted in a decrease of FoF1–ATP synthase monomers and dimers, rerouting of mitochondrial electron transfer to the alternative oxidase, reduced growth rate and cellular ATP levels, and elevated ΔΨm and total cellular reactive oxygen species levels. In bloodstream form parasites, RNAi silencing of Tb1 by ∼90% resulted in decreased FoF1–ATPase monomers and dimers, but it had no apparent effect on growth. The same findings were obtained by silencing of the oligomycin sensitivity-conferring protein, a conserved subunit in T. brucei FoF1–ATP synthase. However, as expected, nearly complete Tb1 or oligomycin sensitivity-conferring protein suppression was lethal because of the inability to sustain ΔΨm. The diminishment of FoF1–ATPase complexes was further accompanied by a decreased ADP/ATP ratio and reduced oxygen consumption via the alternative oxidase. Our data illuminate the often diametrically opposed bioenergetic consequences of FoF1–ATP synthase loss in insect versus mammalian forms of the parasite.
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Affiliation(s)
- Carolina Hierro-Yap
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic; Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Karolína Šubrtová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic; Institute of Immunology and Infection Research, University of Edinburgh, United Kingdom
| | - Ondřej Gahura
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Brian Panicucci
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Caroline Dewar
- Institute of Immunology and Infection Research, University of Edinburgh, United Kingdom
| | | | - Achim Schnaufer
- Institute of Immunology and Infection Research, University of Edinburgh, United Kingdom
| | - Alena Zíková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic; Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic.
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11
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Zhang F, Bian J, Chen X, Huang J, Smith N, Lu W, Xu Y, Lee J, Wu X. Roles for intracellular cation transporters in respiratory growth of yeast. Metallomics 2020; 11:1667-1678. [PMID: 31402362 DOI: 10.1039/c9mt00145j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Potassium is involved in copper and iron metabolism in eukaryotic Golgi apparatus, but it is not clear yet whether potassium distributions in other vesicles also affect copper and iron metabolism. Here we show that respiratory growth and iron acquisition by the yeast Saccharomyces cerevisiae relies on potassium (K+) compartmentalization to the mitochondria, as well as the vacuole and late endosome via K+/H+ exchangers Mdm38p, Vnx1p and Nhx1p, respectively. The data indicate that NHX1 and VNX1 knock-out cells grow better than wild type cells on non-fermentable YPEG media, while MDM38 knock-out cells display a growth defect on YPEG media. The over expression of the KHA1 gene located on the Golgi apparatus partially compensates for the growth defect of the MDM38 knock-out strain. The results suggest that the vacuole and late endosome are important potassium storage vesicles and Mdm38p affects the mitochondrial function by regulating copper and iron metabolism. Our study reveals potassium compartmentalization to the subcellular vesicles is relevant for respiratory growth by improving copper utilization and promoting iron absorption.
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Affiliation(s)
- Feng Zhang
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
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12
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Gray MW, Burger G, Derelle R, Klimeš V, Leger MM, Sarrasin M, Vlček Č, Roger AJ, Eliáš M, Lang BF. The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome. BMC Biol 2020; 18:22. [PMID: 32122349 PMCID: PMC7050145 DOI: 10.1186/s12915-020-0741-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 01/21/2020] [Indexed: 01/02/2023] Open
Abstract
Background Comparative analyses have indicated that the mitochondrion of the last eukaryotic common ancestor likely possessed all the key core structures and functions that are widely conserved throughout the domain Eucarya. To date, such studies have largely focused on animals, fungi, and land plants (primarily multicellular eukaryotes); relatively few mitochondrial proteomes from protists (primarily unicellular eukaryotic microbes) have been examined. To gauge the full extent of mitochondrial structural and functional complexity and to identify potential evolutionary trends in mitochondrial proteomes, more comprehensive explorations of phylogenetically diverse mitochondrial proteomes are required. In this regard, a key group is the jakobids, a clade of protists belonging to the eukaryotic supergroup Discoba, distinguished by having the most gene-rich and most bacteria-like mitochondrial genomes discovered to date. Results In this study, we assembled the draft nuclear genome sequence for the jakobid Andalucia godoyi and used a comprehensive in silico approach to infer the nucleus-encoded portion of the mitochondrial proteome of this protist, identifying 864 candidate mitochondrial proteins. The A. godoyi mitochondrial proteome has a complexity that parallels that of other eukaryotes, while exhibiting an unusually large number of ancestral features that have been lost particularly in opisthokont (animal and fungal) mitochondria. Notably, we find no evidence that the A. godoyi nuclear genome has or had a gene encoding a single-subunit, T3/T7 bacteriophage-like RNA polymerase, which functions as the mitochondrial transcriptase in all eukaryotes except the jakobids. Conclusions As genome and mitochondrial proteome data have become more widely available, a strikingly punctuate phylogenetic distribution of different mitochondrial components has been revealed, emphasizing that the pathways of mitochondrial proteome evolution are likely complex and lineage-specific. Unraveling this complexity will require comprehensive comparative analyses of mitochondrial proteomes from a phylogenetically broad range of eukaryotes, especially protists. The systematic in silico approach described here offers a valuable adjunct to direct proteomic analysis (e.g., via mass spectrometry), particularly in cases where the latter approach is constrained by sample limitation or other practical considerations.
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Affiliation(s)
- Michael W Gray
- Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Sir Charles Tupper Medical Building, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, B3H 4R2, Canada.
| | - Gertraud Burger
- Département de Biochimie and Robert-Cedergren Center for Bioinformatics and Genomics, Université de Montréal, Montréal, QC, Canada
| | - Romain Derelle
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Vladimír Klimeš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Michelle M Leger
- Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Sir Charles Tupper Medical Building, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, B3H 4R2, Canada.,Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Matt Sarrasin
- Département de Biochimie and Robert-Cedergren Center for Bioinformatics and Genomics, Université de Montréal, Montréal, QC, Canada
| | - Čestmír Vlček
- Current address: Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Sir Charles Tupper Medical Building, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - B Franz Lang
- Département de Biochimie and Robert-Cedergren Center for Bioinformatics and Genomics, Université de Montréal, Montréal, QC, Canada
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13
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LETM1: Essential for Mitochondrial Biology and Cation Homeostasis? Trends Biochem Sci 2019; 44:648-658. [DOI: 10.1016/j.tibs.2019.04.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 02/28/2019] [Accepted: 04/03/2019] [Indexed: 12/28/2022]
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14
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Durigon R, Mitchell AL, Jones AW, Manole A, Mennuni M, Hirst EM, Houlden H, Maragni G, Lattante S, Doronzio PN, Dalla Rosa I, Zollino M, Holt IJ, Spinazzola A. LETM1 couples mitochondrial DNA metabolism and nutrient preference. EMBO Mol Med 2019; 10:emmm.201708550. [PMID: 30012579 PMCID: PMC6127893 DOI: 10.15252/emmm.201708550] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The diverse clinical phenotypes of Wolf–Hirschhorn syndrome (WHS) are the result of haploinsufficiency of several genes, one of which, LETM1, encodes a protein of the mitochondrial inner membrane of uncertain function. Here, we show that LETM1 is associated with mitochondrial ribosomes, is required for mitochondrial DNA distribution and expression, and regulates the activity of an ancillary metabolic enzyme, pyruvate dehydrogenase. LETM1 deficiency in WHS alters mitochondrial morphology and DNA organization, as does substituting ketone bodies for glucose in control cells. While this change in nutrient availability leads to the death of fibroblasts with normal amounts of LETM1, WHS‐derived fibroblasts survive on ketone bodies, which can be attributed to their reduced dependence on glucose oxidation. Thus, remodeling of mitochondrial nucleoprotein complexes results from the inability of mitochondria to use specific substrates for energy production and is indicative of mitochondrial dysfunction. However, the dysfunction could be mitigated by a modified diet—for WHS, one high in lipids and low in carbohydrates.
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Affiliation(s)
- Romina Durigon
- Department of Clinical and Movement Neurosciences, UCL Institute of Neurology, London, UK
| | - Alice L Mitchell
- Department of Clinical and Movement Neurosciences, UCL Institute of Neurology, London, UK
| | - Aleck We Jones
- Department of Clinical and Movement Neurosciences, UCL Institute of Neurology, London, UK
| | - Andreea Manole
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, London, UK.,Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Mara Mennuni
- Department of Clinical and Movement Neurosciences, UCL Institute of Neurology, London, UK
| | | | - Henry Houlden
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, London, UK.,Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | | | - Serena Lattante
- Institute of Genomic Medicine, Catholic University, Rome, Italy
| | | | - Ilaria Dalla Rosa
- Department of Clinical and Movement Neurosciences, UCL Institute of Neurology, London, UK
| | | | - Ian J Holt
- Department of Clinical and Movement Neurosciences, UCL Institute of Neurology, London, UK.,Biodonostia Health Research Institute, San Sebastián, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Antonella Spinazzola
- Department of Clinical and Movement Neurosciences, UCL Institute of Neurology, London, UK .,MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, London, UK
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15
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Cogliati S, Lorenzi I, Rigoni G, Caicci F, Soriano ME. Regulation of Mitochondrial Electron Transport Chain Assembly. J Mol Biol 2018; 430:4849-4873. [DOI: 10.1016/j.jmb.2018.09.016] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/20/2018] [Accepted: 09/25/2018] [Indexed: 12/26/2022]
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16
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Vargas Möller-Hergt B, Carlström A, Suhm T, Ott M. Insertion Defects of Mitochondrially Encoded Proteins Burden the Mitochondrial Quality Control System. Cells 2018; 7:cells7100172. [PMID: 30336542 PMCID: PMC6211022 DOI: 10.3390/cells7100172] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/07/2018] [Accepted: 10/16/2018] [Indexed: 12/31/2022] Open
Abstract
The mitochondrial proteome contains proteins from two different genetic systems. Proteins are either synthesized in the cytosol and imported into the different compartments of the organelle or directly produced in the mitochondrial matrix. To ensure proteostasis, proteins are monitored by the mitochondrial quality control system, which will degrade non-native polypeptides. Defective mitochondrial membrane proteins are degraded by membrane-bound AAA-proteases. These proteases are regulated by factors promoting protein turnover or preventing their degradation. Here we determined genetic interactions between the mitoribosome receptors Mrx15 and Mba1 with the quality control system. We show that simultaneous absence of Mrx15 and the regulators of the i-AAA protease Mgr1 and Mgr3 provokes respiratory deficiency. Surprisingly, mutants lacking Mrx15 were more tolerant against proteotoxic stress. Furthermore, yeast cells became hypersensitive against proteotoxic stress upon deletion of MBA1. Contrary to Mrx15, Mba1 cooperates with the regulators of the m-AAA and i-AAA proteases. Taken together, these results suggest that membrane protein insertion and mitochondrial AAA-proteases are functionally coupled, possibly reflecting an early quality control step during mitochondrial protein synthesis.
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Affiliation(s)
| | - Andreas Carlström
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden.
| | - Tamara Suhm
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden.
| | - Martin Ott
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden.
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17
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Abstract
Mitochondria contain their own genome that encodes for a small number of proteins, while the vast majority of mitochondrial proteins is produced on cytosolic ribosomes. The formation of respiratory chain complexes depends on the coordinated biogenesis of mitochondrially encoded and nuclear-encoded subunits. In this review, we describe pathways that adjust mitochondrial protein synthesis and import of nuclear-encoded subunits to the assembly of respiratory chain complexes. Furthermore, we outline how defects in protein import into mitochondria affect nuclear gene expression to maintain protein homeostasis under physiological and stress conditions.
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Affiliation(s)
- Chantal Priesnitz
- Institute of Biochemistry and Molecular Biology, Center for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Center for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104 Freiburg, Germany
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18
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Möller-Hergt BV, Carlström A, Stephan K, Imhof A, Ott M. The ribosome receptors Mrx15 and Mba1 jointly organize cotranslational insertion and protein biogenesis in mitochondria. Mol Biol Cell 2018; 29:2386-2396. [PMID: 30091672 PMCID: PMC6233058 DOI: 10.1091/mbc.e18-04-0227] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Mitochondrial gene expression in Saccharomyces cerevisiae is responsible for the production of highly hydrophobic subunits of the oxidative phosphorylation system. Membrane insertion occurs cotranslationally on membrane-bound mitochondrial ribosomes. Here, by employing a systematic mass spectrometry–based approach, we discovered the previously uncharacterized membrane protein Mrx15 that interacts via a soluble C-terminal domain with the large ribosomal subunit. Mrx15 contacts mitochondrial translation products during their synthesis and plays, together with the ribosome receptor Mba1, an overlapping role in cotranslational protein insertion. Taken together, our data reveal how these ribosome receptors organize membrane protein biogenesis in mitochondria.
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Affiliation(s)
| | - Andreas Carlström
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
| | - Katharina Stephan
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
| | - Axel Imhof
- Protein Analysis Unit, Biomedical Center, Faculty of Medicine, Ludwig Maximilian University of Munich, DE-82152 Planegg-Martinsried, Germany
| | - Martin Ott
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
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19
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Zeng R, Smith E, Barrientos A. Yeast Mitoribosome Large Subunit Assembly Proceeds by Hierarchical Incorporation of Protein Clusters and Modules on the Inner Membrane. Cell Metab 2018. [PMID: 29514071 PMCID: PMC5951612 DOI: 10.1016/j.cmet.2018.01.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Mitoribosomes are specialized for the synthesis of hydrophobic membrane proteins encoded by mtDNA, all essential for oxidative phosphorylation. Despite their linkage to human mitochondrial diseases and the recent cryoelectron microscopy reconstruction of yeast and mammalian mitoribosomes, how they are assembled remains obscure. Here, we dissected the yeast mitoribosome large subunit (mtLSU) assembly process by systematic genomic deletion of 44 mtLSU proteins (MRPs). Analysis of the strain collection unveiled 37 proteins essential for functional mtLSU assembly, three of which are critical for mtLSU 21S rRNA stability. Hierarchical cluster analysis of mtLSU subassemblies accumulated in mutant strains revealed co-operative assembly of protein sets forming structural clusters and preassembled modules. It also indicated crucial roles for mitochondrion-specific membrane-binding MRPs in anchoring newly transcribed 21S rRNA to the inner membrane, where assembly proceeds. Our results define the yeast mtLSU assembly landscape in vivo and provide a foundation for studies of mitoribosome assembly across evolution.
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Affiliation(s)
- Rui Zeng
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 1420 NW 9th Ave, Miami, FL 33136, USA
| | - Erin Smith
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 1420 NW 9th Ave, Miami, FL 33136, USA
| | - Antoni Barrientos
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 1420 NW 9th Ave, Miami, FL 33136, USA; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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20
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Ribosome-Associated Mba1 Escorts Cox2 from Insertion Machinery to Maturing Assembly Intermediates. Mol Cell Biol 2016; 36:2782-2793. [PMID: 27550809 PMCID: PMC5086520 DOI: 10.1128/mcb.00361-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 07/08/2016] [Accepted: 08/17/2016] [Indexed: 01/25/2023] Open
Abstract
The three conserved core subunits of the cytochrome c oxidase are encoded by mitochondria in close to all eukaryotes. The Cox2 subunit spans the inner membrane twice, exposing the N and C termini to the intermembrane space. For this, the N terminus is exported cotranslationally by Oxa1 and subsequently undergoes proteolytic maturation in Saccharomyces cerevisiae. Little is known about the translocation of the C terminus, but Cox18 has been identified to be a critical protein in this process. Here we find that the scaffold protein Cox20, which promotes processing of Cox2, is in complex with the ribosome receptor Mba1 and translating mitochondrial ribosomes in a Cox2-dependent manner. The Mba1-Cox20 complex accumulates when export of the C terminus of Cox2 is blocked by the loss of the Cox18 protein. While Cox20 engages with Cox18, Mba1 is no longer present at this stage. Our analyses indicate that Cox20 associates with nascent Cox2 and Mba1 to promote Cox2 maturation cotranslationally. We suggest that Mba1 stabilizes the Cox20-ribosome complex and supports the handover of Cox2 to the Cox18 tail export machinery.
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21
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22
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Affiliation(s)
- Martin Ott
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden;
| | - Alexey Amunts
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden;
- Science for Life Laboratory, Stockholm University, SE-171 21 Solna, Sweden;
| | - Alan Brown
- Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 0QH, United Kingdom;
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23
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Wagner S, De Bortoli S, Schwarzländer M, Szabò I. Regulation of mitochondrial calcium in plants versus animals. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3809-29. [PMID: 27001920 DOI: 10.1093/jxb/erw100] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Ca(2+) acts as an important cellular second messenger in eukaryotes. In both plants and animals, a wide variety of environmental and developmental stimuli trigger Ca(2+) transients of a specific signature that can modulate gene expression and metabolism. In animals, mitochondrial energy metabolism has long been considered a hotspot of Ca(2+) regulation, with a range of pathophysiology linked to altered Ca(2+) control. Recently, several molecular players involved in mitochondrial Ca(2+) signalling have been identified, including those of the mitochondrial Ca(2+) uniporter. Despite strong evidence for sophisticated Ca(2+) regulation in plant mitochondria, the picture has remained much less clear. This is currently changing aided by live imaging and genetic approaches which allow dissection of subcellular Ca(2+) dynamics and identification of the proteins involved. We provide an update on our current understanding in the regulation of mitochondrial Ca(2+) and signalling by comparing work in plants and animals. The significance of mitochondrial Ca(2+) control is discussed in the light of the specific metabolic and energetic needs of plant and animal cells.
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Affiliation(s)
- Stephan Wagner
- Plant Energy Biology Lab, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Friedrich-Ebert-Allee 144, D-53113 Bonn, Germany
| | - Sara De Bortoli
- Department of Biology and CNR Institute of Neurosciences, University of Padova, Viale G. Colombo 3, 35121 Padova, Italy
| | - Markus Schwarzländer
- Plant Energy Biology Lab, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Friedrich-Ebert-Allee 144, D-53113 Bonn, Germany
| | - Ildikò Szabò
- Department of Biology and CNR Institute of Neurosciences, University of Padova, Viale G. Colombo 3, 35121 Padova, Italy
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24
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Bareth B, Nikolov M, Lorenzi I, Hildenbeutel M, Mick DU, Helbig C, Urlaub H, Ott M, Rehling P, Dennerlein S. Oms1 associates with cytochrome c oxidase assembly intermediates to stabilize newly synthesized Cox1. Mol Biol Cell 2016; 27:1570-80. [PMID: 27030670 PMCID: PMC4865315 DOI: 10.1091/mbc.e15-12-0811] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/23/2016] [Accepted: 03/24/2016] [Indexed: 12/18/2022] Open
Abstract
The mitochondrial cytochrome c oxidase assembles in the inner membrane from subunits of dual genetic origin. The assembly process of the enzyme is initiated by membrane insertion of the mitochondria-encoded Cox1 subunit. During complex maturation, transient assembly intermediates, consisting of structural subunits and specialized chaperone-like assembly factors, are formed. In addition, cofactors such as heme and copper have to be inserted into the nascent complex. To regulate the assembly process, the availability of Cox1 is under control of a regulatory feedback cycle in which translation of COX1 mRNA is stalled when assembly intermediates of Cox1 accumulate through inactivation of the translational activator Mss51. Here we isolate a cytochrome c oxidase assembly intermediate in preparatory scale from coa1Δ mutant cells, using Mss51 as bait. We demonstrate that at this stage of assembly, the complex has not yet incorporated the heme a cofactors. Using quantitative mass spectrometry, we define the protein composition of the assembly intermediate and unexpectedly identify the putative methyltransferase Oms1 as a constituent. Our analyses show that Oms1 participates in cytochrome c oxidase assembly by stabilizing newly synthesized Cox1.
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Affiliation(s)
- Bettina Bareth
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Miroslav Nikolov
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Isotta Lorenzi
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Markus Hildenbeutel
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - David U Mick
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Christin Helbig
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany Bioanalytik Group, Department of Clinical Chemistry, University Medical Center Göttingen, D-37075 Göttingen, Germany
| | - Martin Ott
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Sven Dennerlein
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
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25
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Carraretto L, Checchetto V, De Bortoli S, Formentin E, Costa A, Szabó I, Teardo E. Calcium Flux across Plant Mitochondrial Membranes: Possible Molecular Players. FRONTIERS IN PLANT SCIENCE 2016; 7:354. [PMID: 27065186 PMCID: PMC4814809 DOI: 10.3389/fpls.2016.00354] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 03/07/2016] [Indexed: 05/24/2023]
Abstract
Plants, being sessile organisms, have evolved the ability to integrate external stimuli into metabolic and developmental signals. A wide variety of signals, including abiotic, biotic, and developmental stimuli, were observed to evoke specific spatio-temporal Ca(2+) transients which are further transduced by Ca(2+) sensor proteins into a transcriptional and metabolic response. Most of the research on Ca(2+) signaling in plants has been focused on the transport mechanisms for Ca(2+) across the plasma- and the vacuolar membranes as well as on the components involved in decoding of cytoplasmic Ca(2+) signals, but how intracellular organelles such as mitochondria are involved in the process of Ca(2+) signaling is just emerging. The combination of the molecular players and the elicitors of Ca(2+) signaling in mitochondria together with newly generated detection systems for measuring organellar Ca(2+) concentrations in plants has started to provide fruitful grounds for further discoveries. In the present review we give an updated overview of the currently identified/hypothesized pathways, such as voltage-dependent anion channels, homologs of the mammalian mitochondrial uniporter (MCU), LETM1, a plant glutamate receptor family member, adenine nucleotide/phosphate carriers and the permeability transition pore (PTP), that may contribute to the transport of Ca(2+) across the outer and inner mitochondrial membranes in plants. We briefly discuss the relevance of the mitochondrial Ca(2+) homeostasis for ensuring optimal bioenergetic performance of this organelle.
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Affiliation(s)
| | - Vanessa Checchetto
- Department of Biology, University of PadovaPadova, Italy
- Department of Biomedical Sciences, University of PadovaPadova, Italy
| | | | - Elide Formentin
- Department of Biology, University of PadovaPadova, Italy
- Department of Life Science and Biotechnology, University of FerraraFerrara, Italy
| | - Alex Costa
- Department of Biosciences, University of MilanMilan, Italy
- CNR, Institute of Biophysics, Consiglio Nazionale delle RicercheMilan, Italy
| | - Ildikó Szabó
- Department of Biology, University of PadovaPadova, Italy
- CNR, Institute of NeurosciencesPadova, Italy
| | - Enrico Teardo
- Department of Biology, University of PadovaPadova, Italy
- CNR, Institute of NeurosciencesPadova, Italy
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26
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Abstract
Mitochondrial ribosomes (mitoribosomes) perform protein synthesis inside mitochondria, the organelles responsible for energy conversion and adenosine triphosphate production in eukaryotic cells. Throughout evolution, mitoribosomes have become functionally specialized for synthesizing mitochondrial membrane proteins, and this has been accompanied by large changes to their structure and composition. We review recent high-resolution structural data that have provided unprecedented insight into the structure and function of mitoribosomes in mammals and fungi.
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Affiliation(s)
- Basil J Greber
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland; .,*Present address: California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720-3220
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland;
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27
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Breiman A, Fieulaine S, Meinnel T, Giglione C. The intriguing realm of protein biogenesis: Facing the green co-translational protein maturation networks. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:531-50. [PMID: 26555180 DOI: 10.1016/j.bbapap.2015.11.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/05/2015] [Indexed: 01/13/2023]
Abstract
The ribosome is the cell's protein-making factory, a huge protein-RNA complex, that is essential to life. Determining the high-resolution structures of the stable "core" of this factory was among the major breakthroughs of the past decades, and was awarded the Nobel Prize in 2009. Now that the mysteries of the ribosome appear to be more traceable, detailed understanding of the mechanisms that regulate protein synthesis includes not only the well-known steps of initiation, elongation, and termination but also the less comprehended features of the co-translational events associated with the maturation of the nascent chains. The ribosome is a platform for co-translational events affecting the nascent polypeptide, including protein modifications, folding, targeting to various cellular compartments for integration into membrane or translocation, and proteolysis. These events are orchestrated by ribosome-associated protein biogenesis factors (RPBs), a group of a dozen or more factors that act as the "welcoming committee" for the nascent chain as it emerges from the ribosome. In plants these factors have evolved to fit the specificity of different cellular compartments: cytoplasm, mitochondria and chloroplast. This review focuses on the current state of knowledge of these factors and their interaction around the exit tunnel of dedicated ribosomes. Particular attention has been accorded to the plant system, highlighting the similarities and differences with other organisms.
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Affiliation(s)
- Adina Breiman
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay 91198 Gif-sur-Yvette cedex, France; Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
| | - Sonia Fieulaine
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay 91198 Gif-sur-Yvette cedex, France
| | - Thierry Meinnel
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay 91198 Gif-sur-Yvette cedex, France
| | - Carmela Giglione
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay 91198 Gif-sur-Yvette cedex, France.
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28
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Roloff GA, Henry MF. Mam33 promotes cytochrome c oxidase subunit I translation in Saccharomyces cerevisiae mitochondria. Mol Biol Cell 2015; 26:2885-94. [PMID: 26108620 PMCID: PMC4571327 DOI: 10.1091/mbc.e15-04-0222] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 06/16/2015] [Indexed: 12/22/2022] Open
Abstract
Expression of genes encoded by the mitochondrial genome is dependent on gene-specific translational activators. Mam33, the yeast homologue of p32/gC1qR/C1QBP/HABP1, promotes the translation of Cox1, a core catalytic subunit of respiratory chain complex IV. Three mitochondrial DNA–encoded proteins, Cox1, Cox2, and Cox3, comprise the core of the cytochrome c oxidase complex. Gene-specific translational activators ensure that these respiratory chain subunits are synthesized at the correct location and in stoichiometric ratios to prevent unassembled protein products from generating free oxygen radicals. In the yeast Saccharomyces cerevisiae, the nuclear-encoded proteins Mss51 and Pet309 specifically activate mitochondrial translation of the largest subunit, Cox1. Here we report that Mam33 is a third COX1 translational activator in yeast mitochondria. Mam33 is required for cells to adapt efficiently from fermentation to respiration. In the absence of Mam33, Cox1 translation is impaired, and cells poorly adapt to respiratory conditions because they lack basal fermentative levels of Cox1.
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Affiliation(s)
- Gabrielle A Roloff
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, and Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ 08084
| | - Michael F Henry
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, and Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ 08084
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29
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De Silva D, Tu YT, Amunts A, Fontanesi F, Barrientos A. Mitochondrial ribosome assembly in health and disease. Cell Cycle 2015; 14:2226-50. [PMID: 26030272 DOI: 10.1080/15384101.2015.1053672] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The ribosome is a structurally and functionally conserved macromolecular machine universally responsible for catalyzing protein synthesis. Within eukaryotic cells, mitochondria contain their own ribosomes (mitoribosomes), which synthesize a handful of proteins, all essential for the biogenesis of the oxidative phosphorylation system. High-resolution cryo-EM structures of the yeast, porcine and human mitoribosomal subunits and of the entire human mitoribosome have uncovered a wealth of new information to illustrate their evolutionary divergence from their bacterial ancestors and their adaptation to synthesis of highly hydrophobic membrane proteins. With such structural data becoming available, one of the most important remaining questions is that of the mitoribosome assembly pathway and factors involved. The regulation of mitoribosome biogenesis is paramount to mitochondrial respiration, and thus to cell viability, growth and differentiation. Moreover, mutations affecting the rRNA and protein components produce severe human mitochondrial disorders. Despite its biological and biomedical significance, knowledge on mitoribosome biogenesis and its deviations from the much-studied bacterial ribosome assembly processes is scarce, especially the order of rRNA processing and assembly events and the regulatory factors required to achieve fully functional particles. This article focuses on summarizing the current available information on mitoribosome assembly pathway, factors that form the mitoribosome assembly machinery, and the effect of defective mitoribosome assembly on human health.
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Affiliation(s)
- Dasmanthie De Silva
- a Department of Biochemistry and Molecular Biology ; University of Miami Miller School of Medicine ; Miami , FL USA
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30
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Pfeffer S, Woellhaf MW, Herrmann JM, Förster F. Organization of the mitochondrial translation machinery studied in situ by cryoelectron tomography. Nat Commun 2015; 6:6019. [PMID: 25609543 DOI: 10.1038/ncomms7019] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 12/02/2014] [Indexed: 11/09/2022] Open
Abstract
Whereas the structure and function of cytosolic ribosomes have been studied in great detail, we know surprisingly little about the structural basis of mitochondrial protein synthesis. Here we used cryoelectron tomography and subtomogram analysis to visualize mitoribosomes in isolated yeast mitochondria, avoiding perturbations during ribosomal purification. Most mitoribosomes reside in immediate proximity to the inner mitochondrial membrane, in line with their specialization in the synthesis of hydrophobic membrane proteins. The subtomogram average of membrane-associated mitoribosomes reveals two distinct membrane contact sites, formed by the 21S rRNA expansion segment 96-ES1 and the inner membrane protein Mba1. On the basis of our data, we further hypothesize that Mba1 is not just a passive mitoribosome receptor on the inner membrane, but that it spatially aligns mitoribosomes with the membrane insertion machinery. This study reveals detailed insights into the supramolecular organization of the mitochondrial translation machinery and its association with the inner membrane in translation-competent mitochondria.
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Affiliation(s)
- Stefan Pfeffer
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Michael W Woellhaf
- Cell Biology, University of Kaiserslautern, Erwin-Schrodinger-Strasse 13, 67663 Kaiserslautern, Germany
| | - Johannes M Herrmann
- Cell Biology, University of Kaiserslautern, Erwin-Schrodinger-Strasse 13, 67663 Kaiserslautern, Germany
| | - Friedrich Förster
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
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31
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Abstract
The pyruvate dehydrogenase complex (PDC) catalyzes the conversion of pyruvate into acetyl-CoA, a critical step in metabolism. Sutendra et al. now demonstrate that PDC can translocate from the mitochondria to the nucleus to provide acetyl-CoA necessary for histone acetylation, suggesting a new pathway for mitochondrial-nuclear communication.
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Affiliation(s)
- Vincent C J de Boer
- Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; Department of Pediatrics, Emma Children's Hospital, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
| | - Sander M Houten
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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32
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Zamudio-Ochoa A, Camacho-Villasana Y, García-Guerrero AE, Pérez-Martínez X. The Pet309 pentatricopeptide repeat motifs mediate efficient binding to the mitochondrial COX1 transcript in yeast. RNA Biol 2014; 11:953-67. [PMID: 25181249 PMCID: PMC4179968 DOI: 10.4161/rna.29780] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Mitochondrial synthesis of Cox1, the largest subunit of the cytochrome c oxidase complex, is controlled by Mss51 and Pet309, two mRNA-specific translational activators that act via the COX1 mRNA 5′-UTR through an unknown mechanism. Pet309 belongs to the pentatricopeptide repeat (PPR) protein family, which is involved in RNA metabolism in mitochondria and chloroplasts, and its sequence predicts at least 12 PPR motifs in the central portion of the protein. Deletion of these motifs selectively disrupted translation but not accumulation of the COX1 mRNA. We used RNA coimmunoprecipitation assays to show that Pet309 interacts with the COX1 mRNA in vivo and that this association is present before processing of the COX1 mRNA from the ATP8/6 polycistronic mRNA. This association was not affected by deletion of 8 of the PPR motifs but was undetectable after deletion of the entire 12-PPR region. However, interaction of the Pet309 protein lacking 12 PPR motifs with the COX1 mRNA was detected after overexpression of the mutated form of the protein, suggesting that deletion of this region decreased the binding affinity for the COX1 mRNA without abolishing it entirely. Moreover, binding of Pet309 to the COX1 mRNA was affected by deletion of Mss51. This work demonstrates an in vivo physical interaction between a yeast mitochondrial translational activator and its target mRNA and shows the cooperativity of the PPR domains of Pet309 in interaction with the COX1 mRNA.
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Affiliation(s)
- Angélica Zamudio-Ochoa
- Departamento de Genética Molecular; Instituto de Fisiología Celular; Universidad Nacional Autónoma de México; México
| | - Yolanda Camacho-Villasana
- Departamento de Genética Molecular; Instituto de Fisiología Celular; Universidad Nacional Autónoma de México; México
| | - Aldo E García-Guerrero
- Departamento de Genética Molecular; Instituto de Fisiología Celular; Universidad Nacional Autónoma de México; México
| | - Xochitl Pérez-Martínez
- Departamento de Genética Molecular; Instituto de Fisiología Celular; Universidad Nacional Autónoma de México; México
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33
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Ng S, De Clercq I, Van Aken O, Law SR, Ivanova A, Willems P, Giraud E, Van Breusegem F, Whelan J. Anterograde and retrograde regulation of nuclear genes encoding mitochondrial proteins during growth, development, and stress. MOLECULAR PLANT 2014; 7:1075-93. [PMID: 24711293 DOI: 10.1093/mp/ssu037] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Mitochondrial biogenesis and function in plants require the expression of over 1000 nuclear genes encoding mitochondrial proteins (NGEMPs). The expression of these genes is regulated by tissue-specific, developmental, internal, and external stimuli that result in a dynamic organelle involved in both metabolic and a variety of signaling processes. Although the metabolic and biosynthetic machinery of mitochondria is relatively well understood, the factors that regulate these processes and the various signaling pathways involved are only beginning to be identified at a molecular level. The molecular components of anterograde (nuclear to mitochondrial) and retrograde (mitochondrial to nuclear) signaling pathways that regulate the expression of NGEMPs interact with chloroplast-, growth-, and stress-signaling pathways in the cell at a variety of levels, with common components involved in transmission and execution of these signals. This positions mitochondria as important hubs for signaling in the cell, not only in direct signaling of mitochondrial function per se, but also in sensing and/or integrating a variety of other internal and external signals. This integrates and optimizes growth with energy metabolism and stress responses, which is required in both photosynthetic and non-photosynthetic cells.
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Affiliation(s)
- Sophia Ng
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Australia Joint Research Laboratory in Genomics and Nutriomics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, P.R. China
| | - Inge De Clercq
- Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
| | - Olivier Van Aken
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Australia
| | - Simon R Law
- Department of Botany, ARC Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University, Bundoora 3086, Victoria, Australia
| | - Aneta Ivanova
- Department of Botany, ARC Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University, Bundoora 3086, Victoria, Australia
| | - Patrick Willems
- Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium Department of Medical Protein Research and Department of Biochemistry, 9000 Ghent, Belgium
| | - Estelle Giraud
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Australia Present address: Illumina, ANZ, 1 International Court, Scoresby Victoria 3179, Australia
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
| | - James Whelan
- Department of Botany, ARC Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University, Bundoora 3086, Victoria, Australia
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34
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Dalla Rosa I, Durigon R, Pearce SF, Rorbach J, Hirst EMA, Vidoni S, Reyes A, Brea-Calvo G, Minczuk M, Woellhaf MW, Herrmann JM, Huynen MA, Holt IJ, Spinazzola A. MPV17L2 is required for ribosome assembly in mitochondria. Nucleic Acids Res 2014; 42:8500-15. [PMID: 24948607 PMCID: PMC4117752 DOI: 10.1093/nar/gku513] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MPV17 is a mitochondrial protein of unknown function, and mutations in MPV17 are associated with mitochondrial deoxyribonucleic acid (DNA) maintenance disorders. Here we investigated its most similar relative, MPV17L2, which is also annotated as a mitochondrial protein. Mitochondrial fractionation analyses demonstrate MPV17L2 is an integral inner membrane protein, like MPV17. However, unlike MPV17, MPV17L2 is dependent on mitochondrial DNA, as it is absent from ρ(0) cells, and co-sediments on sucrose gradients with the large subunit of the mitochondrial ribosome and the monosome. Gene silencing of MPV17L2 results in marked decreases in the monosome and both subunits of the mitochondrial ribosome, leading to impaired protein synthesis in the mitochondria. Depletion of MPV17L2 also induces mitochondrial DNA aggregation. The DNA and ribosome phenotypes are linked, as in the absence of MPV17L2 proteins of the small subunit of the mitochondrial ribosome are trapped in the enlarged nucleoids, in contrast to a component of the large subunit. These findings suggest MPV17L2 contributes to the biogenesis of the mitochondrial ribosome, uniting the two subunits to create the translationally competent monosome, and provide evidence that assembly of the small subunit of the mitochondrial ribosome occurs at the nucleoid.
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Affiliation(s)
- Ilaria Dalla Rosa
- MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Romina Durigon
- MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Sarah F Pearce
- MRC Mitochondrial Biology Unit, Wellcome Trust-MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Joanna Rorbach
- MRC Mitochondrial Biology Unit, Wellcome Trust-MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | | | - Sara Vidoni
- MRC Mitochondrial Biology Unit, Wellcome Trust-MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Aurelio Reyes
- MRC Mitochondrial Biology Unit, Wellcome Trust-MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Gloria Brea-Calvo
- MRC Mitochondrial Biology Unit, Wellcome Trust-MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, Wellcome Trust-MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Michael W Woellhaf
- Cell Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | | | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Geert Grooteplein Zuid 26-28, 6525 GA Nijmegen, Netherlands
| | - Ian J Holt
- MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
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35
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Kuzmenko AV, Levitskii SA, Vinogradova EN, Atkinson GC, Hauryliuk V, Zenkin N, Kamenski PA. Protein biosynthesis in mitochondria. BIOCHEMISTRY (MOSCOW) 2014; 78:855-66. [PMID: 24228873 DOI: 10.1134/s0006297913080014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Translation, that is biosynthesis of polypeptides in accordance with information encoded in the genome, is one of the most important processes in the living cell, and it has been in the spotlight of international research for many years. The mechanisms of protein biosynthesis in bacteria and in the eukaryotic cytoplasm are now understood in great detail. However, significantly less is known about translation in eukaryotic mitochondria, which is characterized by a number of unusual features. In this review, we summarize current knowledge about mitochondrial translation in different organisms while paying special attention to the aspects of this process that differ from cytoplasmic protein biosynthesis.
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Affiliation(s)
- A V Kuzmenko
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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36
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Weckbecker D, Herrmann JM. Methods to study the biogenesis of membrane proteins in yeast mitochondria. Methods Mol Biol 2014; 1033:307-22. [PMID: 23996186 DOI: 10.1007/978-1-62703-487-6_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
The biogenesis of mitochondrial membrane proteins is an intricate process that relies on the import and submitochondrial sorting of nuclear-encoded preproteins and on the synthesis of mitochondrial translation products in the matrix. Subsequently, these polypeptides need to be inserted into the outer and the inner membranes of the organelle where many of them assemble into multisubunit complexes. In this chapter we provide established protocols to study these different processes experimentally using mitochondria of budding yeast. In particular, methods are described in detail to purify mitochondria, to study mitochondrial protein synthesis, to follow the import of radiolabeled preproteins into isolated mitochondria, and to assess membrane association and the aggregation of mitochondrial proteins by fractionation. These protocols and a list of dos and don'ts shall enable beginners and experienced scientists to address the targeting and assembly of mitochondrial membrane proteins.
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37
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Hashimi H, McDonald L, Stríbrná E, Lukeš J. Trypanosome Letm1 protein is essential for mitochondrial potassium homeostasis. J Biol Chem 2013; 288:26914-25. [PMID: 23893410 DOI: 10.1074/jbc.m113.495119] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Letm1 is a conserved protein in eukaryotes bearing energized mitochondria. Hemizygous deletion of its gene has been implicated in symptoms of the human disease Wolf-Hirschhorn syndrome. Studies almost exclusively performed in opisthokonts have attributed several roles to Letm1, including maintaining mitochondrial morphology, mediating either calcium or potassium/proton antiport, and facilitating mitochondrial translation. We address the ancestral function of Letm1 in the highly diverged protist and significant pathogen, Trypanosoma brucei. We demonstrate that Letm1 is involved in maintaining mitochondrial volume via potassium/proton exchange across the inner membrane. This role is essential in the vector-dwelling procyclic and mammal-infecting bloodstream stages as well as in Trypanosoma brucei evansi, a form of the latter stage lacking an organellar genome. In the pathogenic bloodstream stage, the mitochondrion consumes ATP to maintain an energized state, whereas that of T. brucei evansi also lacks a conventional proton-driven membrane potential. Thus, Letm1 performs its function in different physiological states, suggesting that ion homeostasis is among the few characterized essential pathways of the mitochondrion at this T. brucei life stage. Interestingly, Letm1 depletion in the procyclic stage can be complemented by exogenous expression of its human counterpart, highlighting the conservation of protein function between highly divergent species. Furthermore, although mitochondrial translation is affected upon Letm1 ablation, it is an indirect consequence of K(+) accumulation in the matrix.
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Affiliation(s)
- Hassan Hashimi
- From the Institute of Parasitology, Biology Centre, Czech Academy of Sciences and
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Kotani T, Akabane S, Takeyasu K, Ueda T, Takeuchi N. Human G-proteins, ObgH1 and Mtg1, associate with the large mitochondrial ribosome subunit and are involved in translation and assembly of respiratory complexes. Nucleic Acids Res 2013; 41:3713-22. [PMID: 23396448 PMCID: PMC3616715 DOI: 10.1093/nar/gkt079] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The bacterial homologues of ObgH1 and Mtg1, ObgE and RbgA, respectively, have been suggested to be involved in the assembly of large ribosomal subunits. We sought to elucidate the functions of ObgH1 and Mtg1 in ribosome biogenesis in human mitochondria. ObgH1 and Mtg1 are localized in mitochondria in association with the inner membrane, and are exposed on the matrix side. Mtg1 and ObgH1 specifically associate with the large subunit of the mitochondrial ribosome in GTP-dependent manner. The large ribosomal subunit stimulated the GTPase activity of Mtg1, whereas only the intrinsic GTPase activity was detectable with ObgH1. The knockdown of Mtg1 decreased the overall mitochondrial translation activity, and caused defects in the formation of respiratory complexes. On the other hand, the depletion of ObgH1 led to the specific activation of the translation of subunits of Complex V, and disrupted its proper formation. Our results suggested that Mtg1 and ObgH1 function with the large subunit of the mitochondrial ribosome, and are also involved in both the translation and assembly of respiratory complexes. The fine coordination of ribosome assembly, translation and respiratory complex formation in mammalian mitochondria is affirmed.
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Affiliation(s)
- Tetsuya Kotani
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
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Nowikovsky K, Pozzan T, Rizzuto R, Scorrano L, Bernardi P. Perspectives on: SGP symposium on mitochondrial physiology and medicine: the pathophysiology of LETM1. ACTA ACUST UNITED AC 2013; 139:445-54. [PMID: 22641639 PMCID: PMC3362517 DOI: 10.1085/jgp.201110757] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Karin Nowikovsky
- Department of Internal Medicine 1, Anna Spiegel Center of Translational Research, Medical University Vienna, 1090 Wien, Austria.
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Funes S, Westerburg H, Jaimes-Miranda F, Woellhaf MW, Aguilar-Lopez JL, Janßen L, Bonnefoy N, Kauff F, Herrmann JM. Partial suppression of Oxa1 mutants by mitochondria-targeted signal recognition particle provides insights into the evolution of the cotranslational insertion systems. FEBS J 2013. [PMID: 23198851 DOI: 10.1111/febs.12082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The biogenesis of hydrophobic membrane proteins involves their cotranslational membrane integration in order to prevent their unproductive aggregation. In the cytosol of bacteria and eukaryotes, membrane targeting of ribosomes that synthesize membrane proteins is achieved by signal recognition particles (SRPs) and their cognate membrane-bound receptors. As is evident from the genomes of fully sequenced eukaryotes, mitochondria generally lack an SRP system. Instead, mitochondrial ribosomes are physically associated with the protein insertion machinery in the inner membrane. Accordingly, deletion of ribosome-binding sites on the Oxa1 insertase and the Mba1 ribosome receptor in yeast leads to severe defects in cotranslational protein insertion and results in respiration-deficient mutants. In this study, we expressed mitochondria-targeted versions of the bacterial SRP protein Ffh and its receptor FtsY in these yeast mutants. Interestingly, Ffh was found to bind to the large subunit of mitochondrial ribosomes, and could relieve, to some degree, the defect of these insertion mutants. Although FtsY could also bind to mitochondrial membranes, it did not improve membrane protein biogenesis in this strain, presumably because of its inability to interact with Ffh. Hence, mitochondrial ribosomes are still able to interact physically and functionally with the bacterial SRP system. Our observations are consistent with a model according to which the protein insertion system in mitochondria evolved in three steps. The loss of genes for hydrophilic polypeptides (step 1) allowed the development of ribosome-binding sites on membrane proteins (step 2), which finally made the existence of an SRP-mediated system dispensable (step 3).
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Affiliation(s)
- Soledad Funes
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Ciudad Universitaria, Universidad Nacional Autónoma de México, Distrito Federal, Mexico.
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41
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Zhang B, Carrie C, Ivanova A, Narsai R, Murcha MW, Duncan O, Wang Y, Law SR, Albrecht V, Pogson B, Giraud E, Van Aken O, Whelan J. LETM proteins play a role in the accumulation of mitochondrially encoded proteins in Arabidopsis thaliana and AtLETM2 displays parent of origin effects. J Biol Chem 2012; 287:41757-73. [PMID: 23043101 PMCID: PMC3516725 DOI: 10.1074/jbc.m112.383836] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 10/01/2012] [Indexed: 11/06/2022] Open
Abstract
The Arabidopsis thaliana genome contains two genes with homology to the mitochondrial protein LETM1 (leucine zipper-EF-hand-containing transmembrane protein). Inactivation of both genes, Atletm1 and Atletm2, together is lethal. Plants that are hemizygous for AtLETM2 and homozygous for Atletm1 (letm1(-/-) LETM2(+/-)) displayed a mild retarded growth phenotype during early seedling growth. It was shown that accumulation of mitochondrial proteins was reduced in hemizygous (letm1(-/-) LETM2(+/-)) plants. Examination of respiratory chain proteins by Western blotting, blue native PAGE, and enzymatic activity assays revealed that the steady state level of ATP synthase was reduced in abundance, whereas the steady state levels of other respiratory chain proteins remained unchanged. The absence of a functional maternal AtLETM2 allele in an Atletm1 mutant background resulted in early seed abortion. Reciprocal crosses revealed that maternally, but not paternally, derived AtLETM2 was absolutely required for seed development. This requirement for a functional maternal allele of AtLETM2 was confirmed using direct sequencing of reciprocal crosses of Col-0 and Ler accessions. Furthermore, AtLETM2 promoter β-glucuronidase constructs displayed exclusive maternal expression patterns.
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Affiliation(s)
- Botao Zhang
- From the Australian Research Council Centre of Excellence in Plant Energy Biology and
| | - Chris Carrie
- From the Australian Research Council Centre of Excellence in Plant Energy Biology and
| | - Aneta Ivanova
- From the Australian Research Council Centre of Excellence in Plant Energy Biology and
| | - Reena Narsai
- From the Australian Research Council Centre of Excellence in Plant Energy Biology and
- Centre for Computational Systems Biology, Bayliss Building M316 University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia and
| | - Monika W. Murcha
- From the Australian Research Council Centre of Excellence in Plant Energy Biology and
| | - Owen Duncan
- From the Australian Research Council Centre of Excellence in Plant Energy Biology and
| | - Yan Wang
- From the Australian Research Council Centre of Excellence in Plant Energy Biology and
| | - Simon R. Law
- From the Australian Research Council Centre of Excellence in Plant Energy Biology and
| | - Verónica Albrecht
- the Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton 2601, Australian Capital Territory, Australia
| | - Barry Pogson
- the Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton 2601, Australian Capital Territory, Australia
| | - Estelle Giraud
- From the Australian Research Council Centre of Excellence in Plant Energy Biology and
| | - Olivier Van Aken
- From the Australian Research Council Centre of Excellence in Plant Energy Biology and
| | - James Whelan
- From the Australian Research Council Centre of Excellence in Plant Energy Biology and
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Keil M, Bareth B, Woellhaf MW, Peleh V, Prestele M, Rehling P, Herrmann JM. Oxa1-ribosome complexes coordinate the assembly of cytochrome C oxidase in mitochondria. J Biol Chem 2012; 287:34484-93. [PMID: 22904327 DOI: 10.1074/jbc.m112.382630] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The terminal enzyme of the respiratory chain, cytochrome c oxidase, consists of a hydrophobic reaction center formed by three mitochondrially encoded subunits with which 9-10 nuclear encoded subunits are associated. The three core subunits are synthesized on mitochondrial ribosomes and inserted into the inner membrane in a co-translational reaction facilitated by the Oxa1 insertase. Oxa1 consists of an N-terminal insertase domain and a C-terminal ribosome-binding region. Mutants lacking the C-terminal region show specific defects in co-translational insertion, suggesting that the close contact of the ribosome with the insertase promotes co-translational insertion of nascent chains. In this study, we inserted flexible linkers of 100 or 200 amino acid residues between the insertase domain and ribosome-binding region of Oxa1 of Saccharomyces cerevisiae. In the absence of the ribosome receptor Mba1, these linkers caused a length-dependent decrease in mitochondrial respiratory activity caused by diminished levels of cytochrome c oxidase. Interestingly, considerable amounts of mitochondrial translation products were still integrated into the inner membrane in these linker mutants. However, they showed severe defects in later stages of the biogenesis process, presumably during assembly into functional complexes. Our observations suggest that the close proximity of Oxa1 to ribosomes is not only used to improve membrane insertion but is also critical for the productive assembly of the subunits of the cytochrome c oxidase. This points to a role for Oxa1 in the spatial coordination of the ribosome with assembly factors that are critical for enzyme biogenesis.
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Affiliation(s)
- Melanie Keil
- Department of Cell Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
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Tan YF, Millar AH, Taylor NL. Components of mitochondrial oxidative phosphorylation vary in abundance following exposure to cold and chemical stresses. J Proteome Res 2012; 11:3860-79. [PMID: 22574745 DOI: 10.1021/pr3003535] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Plant mitochondria are highly responsive organelles that vary their metabolism in response to a wide range of chemical and environmental conditions. Quantitative proteomics studies have begun to allow the analysis of these large-scale protein changes in mitochondria. However studies of the integral membrane proteome of plant mitochondria, arguably the site responsible for the most fundamental mitochondrial processes of oxidative phosphorylation, protein import and metabolite transport, remain a technical challenge. Here we have investigated the changes in protein abundance in response to a number of chemical stresses and cold. In addition to refining the subcellular localization of 66 proteins, we have been able to characterize 596 protein × treatment combinations following a range of stresses. To date it has been assumed that the main mitochondrial response to stress involved the induction of alternative respiratory proteins such as AOX, UCPs, and alternative NAD(P)H dehydrogenases; we now provide evidence for a number of very specific protein abundance changes that have not been highlighted previously by transcript studies. This includes both previously characterized stress responsive proteins as well as major components of oxidative phosphorylation, protein import/export, and metabolite transport.
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Affiliation(s)
- Yew-Foon Tan
- ARC Centre of Excellence in Plant Energy Biology, MCS Building M316, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Western Australia, Australia
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Herrmann JM, Woellhaf MW, Bonnefoy N. Control of protein synthesis in yeast mitochondria: the concept of translational activators. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1833:286-94. [PMID: 22450032 DOI: 10.1016/j.bbamcr.2012.03.007] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 03/01/2012] [Accepted: 03/08/2012] [Indexed: 12/18/2022]
Abstract
Mitochondria contain their own genome which codes for a small number of proteins. Most mitochondrial translation products are part of the membrane-embedded reaction centers of the respiratory chain complexes. In the yeast Saccharomyces cerevisiae, the expression of these proteins is regulated by translational activators that bind mitochondrial mRNAs, in most cases to their 5'-untranslated regions, and each mitochondrial mRNA appears to have its own translational activator(s). Recent studies showed that these translational activators can be part of feedback control loops which only permit translation if the downstream assembly of nascent translation products can occur. In several cases, the accumulation of a non-assembled protein prevents further synthesis of this protein but not translation in general. These control loops prevent the synthesis of potentially harmful assembly intermediates of the reaction centers of mitochondrial enzymes. Since such regulatory feedback loops only work if translation occurs in the compartment in which the complexes of the respiratory chain are assembled, these control mechanisms require the presence of a translation machinery in mitochondria. This might explain why eukaryotic cells maintained DNA in mitochondria during the last two billion years of evolution. This review gives an overview of the mitochondrial translation system and summarizes the current knowledge on translational activators and their role in the regulation of mitochondrial protein synthesis. This article is part of a Special Issue entitled: Protein import and quality control in mitochondria and plastids.
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Affiliation(s)
- Johannes M Herrmann
- Cell Biology, Erwin-Schrödinger-Strasse 13, University of Kaiserslautern, 67663 Kaiserslautern, Germany.
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Abstract
Depending on the organism, mitochondria consist approximately of 500-1,400 different proteins. By far most of these proteins are encoded by nuclear genes and synthesized on cytosolic ribosomes. Targeting signals direct these proteins into mitochondria and there to their respective subcompartment: the outer membrane, the intermembrane space (IMS), the inner membrane, and the matrix. Membrane-embedded translocation complexes allow the translocation of proteins across and, in the case of membrane proteins, the insertion into mitochondrial membranes. A small number of proteins are encoded by the mitochondrial genome: Most mitochondrial translation products represent hydrophobic proteins of the inner membrane which-together with many nuclear-encoded proteins-form the respiratory chain complexes. This chapter gives an overview on the mitochondrial protein translocases and the mechanisms by which they drive the transport and assembly of mitochondrial proteins.
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Lupo D, Vollmer C, Deckers M, Mick DU, Tews I, Sinning I, Rehling P. Mdm38 is a 14-3-3-like receptor and associates with the protein synthesis machinery at the inner mitochondrial membrane. Traffic 2011; 12:1457-66. [PMID: 21718401 DOI: 10.1111/j.1600-0854.2011.01239.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mitochondrial ribosomes synthesize core subunits of the inner membrane respiratory chain complexes. In mitochondria, translation is regulated by mRNA-specific activator proteins and occurs on membrane-associated ribosomes. Mdm38/Letm1 is a conserved membrane receptor for mitochondrial ribosomes and specifically involved in respiratory chain biogenesis. In addition, Mdm38 and its higher eukaryotic homolog Letm1, function as K(+)/H(+) or Ca(2+)/H(+) antiporters in the inner membrane. Here, we identify the conserved ribosome-binding domain (RBD) of Mdm38 and determine the crystal structure at 2.1 Å resolution. Surprisingly, Mdm38(RBD) displays a 14-3-3-like fold despite any similarity to 14-3-3-proteins at the primary sequence level and thus represents the first 14-3-3-like protein in mitochondria. The 14-3-3-like domain is critical for respiratory chain assembly through regulation of Cox1 and Cytb translation. We show that this function can be spatially separated from the ion transport activity of the membrane integrated portion of Mdm38. On the basis of the phenotypes observed for mdm38Δ as compared to Mdm38 lacking the RBD, we suggest a model that combining ion transport and translational regulation into one molecule allows for direct coupling of ion flux across the inner membrane, and serves as a signal for the translation of mitochondrial membrane proteins via its direct association with the protein synthesis machinery.
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Affiliation(s)
- Domenico Lupo
- Biochemie-Zentrum der Universität Heidelberg, INF328, Heidelberg 69120, Germany
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47
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Inventory control: cytochrome c oxidase assembly regulates mitochondrial translation. Nat Rev Mol Cell Biol 2011; 12:14-20. [PMID: 21179059 DOI: 10.1038/nrm3029] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mitochondria maintain genome and translation machinery to synthesize a small subset of subunits of the oxidative phosphorylation system. To build up functional enzymes, these organellar gene products must assemble with imported subunits that are encoded in the nucleus. New findings on the early steps of cytochrome c oxidase assembly reveal how the mitochondrial translation of its core component, cytochrome c oxidase subunit 1 (Cox1), is directly coupled to the assembly of this respiratory complex.
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Gruschke S, Ott M. The polypeptide tunnel exit of the mitochondrial ribosome is tailored to meet the specific requirements of the organelle. Bioessays 2010; 32:1050-7. [PMID: 20967780 DOI: 10.1002/bies.201000081] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The ribosomal polypeptide tunnel exit is the site where a variety of factors interact with newly synthesized proteins to guide them through the early steps of their biogenesis. In mitochondrial ribosomes, this site has been considerably modified in the course of evolution. In contrast to all other translation systems, mitochondrial ribosomes are responsible for the synthesis of only a few hydrophobic membrane proteins that are essential subunits of the mitochondrial respiratory chain. Membrane insertion of these proteins occurs co-translationally and is connected to a sophisticated assembly process that not only includes the assembly of the different subunits but also the acquisition of redox co-factors. Here, we describe how mitochondrial translation is organized in the context of respiratory chain assembly and speculate how alteration of the ribosomal tunnel exit might allow the establishment of a subset of specialized ribosomes that individually organize the early steps in the biogenesis of distinct mitochondrially-encoded proteins.
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Affiliation(s)
- Steffi Gruschke
- Research Group Membrane Biogenesis, University of Kaiserslautern, Kaiserslautern, Germany
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