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Lavdovskaia E, Hanitsch E, Linden A, Pašen M, Challa V, Horokhovskyi Y, Roetschke HP, Nadler F, Welp L, Steube E, Heinrichs M, Mai MMQ, Urlaub H, Liepe J, Richter-Dennerlein R. A roadmap for ribosome assembly in human mitochondria. Nat Struct Mol Biol 2024:10.1038/s41594-024-01356-w. [PMID: 38992089 DOI: 10.1038/s41594-024-01356-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 06/17/2024] [Indexed: 07/13/2024]
Abstract
Mitochondria contain dedicated ribosomes (mitoribosomes), which synthesize the mitochondrial-encoded core components of the oxidative phosphorylation complexes. The RNA and protein components of mitoribosomes are encoded on two different genomes (mitochondrial and nuclear) and are assembled into functional complexes with the help of dedicated factors inside the organelle. Defects in mitoribosome biogenesis are associated with severe human diseases, yet the molecular pathway of mitoribosome assembly remains poorly understood. Here, we applied a multidisciplinary approach combining biochemical isolation and analysis of native mitoribosomal assembly complexes with quantitative mass spectrometry and mathematical modeling to reconstitute the entire assembly pathway of the human mitoribosome. We show that, in contrast to its bacterial and cytosolic counterparts, human mitoribosome biogenesis involves the formation of ribosomal protein-only modules, which then assemble on the appropriate ribosomal RNA moiety in a coordinated fashion. The presence of excess protein-only modules primed for assembly rationalizes how mitochondria cope with the challenge of forming a protein-rich ribonucleoprotein complex of dual genetic origin. This study provides a comprehensive roadmap of mitoribosome biogenesis, from very early to late maturation steps, and highlights the evolutionary divergence from its bacterial ancestor.
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Affiliation(s)
- Elena Lavdovskaia
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany
| | - Elisa Hanitsch
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Andreas Linden
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Martin Pašen
- Quantitative and Systems Biology Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Venkatapathi Challa
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Yehor Horokhovskyi
- Quantitative and Systems Biology Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Hanna P Roetschke
- Quantitative and Systems Biology Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Centre for Inflammation Biology and Cancer Immunology & Peter Gorer Department of Immunobiology, King's College London, London, UK
- Francis Crick Institute, London, UK
| | - Franziska Nadler
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Luisa Welp
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Emely Steube
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Marleen Heinrichs
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Mandy Mong-Quyen Mai
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Henning Urlaub
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany.
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
- Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany.
- Göttingen Center for Molecular Biosciences, University of Göttingen, Göttingen, Germany.
| | - Juliane Liepe
- Quantitative and Systems Biology Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| | - Ricarda Richter-Dennerlein
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany.
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany.
- Göttingen Center for Molecular Biosciences, University of Göttingen, Göttingen, Germany.
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2
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Thompson K, Stroud DA, Thorburn DR, Taylor RW. Investigation of oxidative phosphorylation activity and complex composition in mitochondrial disease. HANDBOOK OF CLINICAL NEUROLOGY 2023; 194:127-139. [PMID: 36813309 DOI: 10.1016/b978-0-12-821751-1.00008-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
A multidisciplinary approach to the laboratory diagnosis of mitochondrial disease has long been applied, with crucial information provided by deep clinical phenotyping, blood investigations, and biomarker screening as well as histopathological and biochemical testing of biopsy material to support molecular genetic screening. In an era of second and third generation sequencing technologies, traditional diagnostic algorithms for mitochondrial disease have been replaced by gene agnostic, genomic strategies including whole-exome sequencing (WES) and whole-genome sequencing (WGS), increasingly supported by other 'omics technologies (Alston et al., 2021). Whether a primary testing strategy, or one used to validate and interpret candidate genetic variants, the availability of a range of tests aimed at determining mitochondrial function (i.e., the assessment of individual respiratory chain enzyme activities in a tissue biopsy or cellular respiration in a patient cell line) remains an important part of the diagnostic armory. In this chapter, we summarize several disciplines used in the laboratory investigation of suspected mitochondrial disease, including the histopathological and biochemical assessment of mitochondrial function, as well as protein-based techniques to assess the steady-state levels of oxidative phosphorylation (OXPHOS) subunits and assembly of OXPHOS complexes via traditional (immunoblotting) and cutting-edge (quantitative proteomic) approaches.
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Affiliation(s)
- Kyle Thompson
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - David A Stroud
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, Australia; Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - David R Thorburn
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia; Mitochondrial Laboratory, Victorian Clinical Genetic Services, Melbourne, VIC, Australia
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom; NHS Highly Specialised Services for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom.
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3
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Imami K, Selbach M, Ishihama Y. Monitoring mitochondrial translation by pulse SILAC. J Biol Chem 2023; 299:102865. [PMID: 36603763 PMCID: PMC9922817 DOI: 10.1016/j.jbc.2022.102865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 12/27/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023] Open
Abstract
Mitochondrial ribosomes are specialized to translate the 13 membrane proteins encoded in the mitochondrial genome, which shapes the oxidative phosphorylation complexes essential for cellular energy metabolism. Despite the importance of mitochondrial translation (MT) control, it is challenging to identify and quantify the mitochondrial-encoded proteins because of their hydrophobic nature and low abundance. Here, we introduce a mass spectrometry-based proteomic method that combines biochemical isolation of mitochondria with pulse stable isotope labeling by amino acids in cell culture. Our method provides the highest protein identification rate with the shortest measurement time among currently available methods, enabling us to quantify 12 of the 13 mitochondrial-encoded proteins. We applied this method to uncover the global picture of (post-)translational regulation of both mitochondrial- and nuclear-encoded subunits of oxidative phosphorylation complexes. We found that inhibition of MT led to degradation of orphan nuclear-encoded subunits that are considered to form subcomplexes with the mitochondrial-encoded subunits. This method should be readily applicable to study MT programs in many contexts, including oxidative stress and mitochondrial disease.
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Affiliation(s)
- Koshi Imami
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan; RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
| | - Matthias Selbach
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan; Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, Japan.
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Koc ZC, Sollars VE, Bou Zgheib N, Rankin GO, Koc EC. Evaluation of mitochondrial biogenesis and ROS generation in high-grade serous ovarian cancer. Front Oncol 2023; 13:1129352. [PMID: 36937395 PMCID: PMC10014927 DOI: 10.3389/fonc.2023.1129352] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/08/2023] [Indexed: 03/05/2023] Open
Abstract
Introduction Ovarian cancer is one of the leading causes of death for women with cancer worldwide. Energy requirements for tumor growth in epithelial high-grade serous ovarian cancer (HGSOC) are fulfilled by a combination of aerobic glycolysis and oxidative phosphorylation (OXPHOS). Although reduced OXPHOS activity has emerged as one of the significant contributors to tumor aggressiveness and chemoresistance, up-regulation of mitochondrial antioxidant capacity is required for matrix detachment and colonization into the peritoneal cavity to form malignant ascites in HGSOC patients. However, limited information is available about the mitochondrial biogenesis regulating OXPHOS capacity and generation of mitochondrial reactive oxygen species (mtROS) in HGSOC. Methods To evaluate the modulation of OXPHOS in HGSOC tumor samples and ovarian cancer cell lines, we performed proteomic analyses of proteins involved in mitochondrial energy metabolism and biogenesis and formation of mtROS by immunoblotting and flow cytometry, respectively. Results and discussion We determined that the increased steady-state expression levels of mitochondrial- and nuclear-encoded OXPHOS subunits were associated with increased mitochondrial biogenesis in HGSOC tumors and ovarian cancer cell lines. The more prominent increase in MT-COII expression was in agreement with significant increase in mitochondrial translation factors, TUFM and DARS2. On the other hand, the ovarian cancer cell lines with reduced OXPHOS subunit expression and mitochondrial translation generated the highest levels of mtROS and significantly reduced SOD2 expression. Evaluation of mitochondrial biogenesis suggested that therapies directed against mitochondrial targets, such as those involved in transcription and translation machineries, should be considered in addition to the conventional chemotherapies in HGSOC treatment.
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Affiliation(s)
- Zeynep C. Koc
- Department of Obstetrics, Gynecology and Reproductive Sciences, Temple University, Philadelphia, PA, United States
| | - Vincent E. Sollars
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, United States
| | - Nadim Bou Zgheib
- Edwards Comprehensive Cancer Center, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, United States
| | - Gary O. Rankin
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, United States
| | - Emine C. Koc
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, United States
- *Correspondence: Emine C. Koc,
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Meng F, Jia Z, Zheng J, Ji Y, Wang J, Xiao Y, Fu Y, Wang M, Ling F, Guan MX. A deafness-associated mitochondrial DNA mutation caused pleiotropic effects on DNA replication and tRNA metabolism. Nucleic Acids Res 2022; 50:9453-9469. [PMID: 36039763 PMCID: PMC9458427 DOI: 10.1093/nar/gkac720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 08/09/2022] [Indexed: 12/24/2022] Open
Abstract
In this report, we investigated the molecular mechanism underlying a deafness-associated m.5783C > T mutation that affects the canonical C50-G63 base-pairing of TΨC stem of tRNACys and immediately adjacent to 5' end of light-strand origin of mitochondrial DNA (mtDNA) replication (OriL). Two dimensional agarose gel electrophoresis revealed marked decreases in the replication intermediates including ascending arm of Y-fork arcs spanning OriL in the mutant cybrids bearing m.5783C > T mutation. mtDNA replication alterations were further evidenced by decreased levels of PolγA, Twinkle and SSBP1, newly synthesized mtDNA and mtDNA contents in the mutant cybrids. The m.5783C > T mutation altered tRNACys structure and function, including decreased melting temperature, conformational changes, instability and deficient aminoacylation of mutated tRNACys. The m.5783C > T mutation impaired the 5' end processing efficiency of tRNACys precursors and reduced the levels of tRNACys and downstream tRNATyr. The aberrant tRNA metabolism impaired mitochondrial translation, which was especially pronounced effects in the polypeptides harboring higher numbers of cysteine and tyrosine codons. These alterations led to deficient oxidative phosphorylation including instability and reduced activities of the respiratory chain enzyme complexes I, III, IV and intact supercomplexes overall. Our findings highlight the impact of mitochondrial dysfunction on deafness arising from defects in mitochondrial DNA replication and tRNA metabolism.
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Affiliation(s)
| | | | - Jing Zheng
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China,Zhejiang Provincial Key Lab of Genetic and Developmental Disorder, Hangzhou, Zhejiang, China
| | - Yanchun Ji
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China,Zhejiang Provincial Key Lab of Genetic and Developmental Disorder, Hangzhou, Zhejiang, China
| | - Jing Wang
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yun Xiao
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yong Fu
- Division of Otolaryngology-Head and Neck Surgery, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Meng Wang
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China,Zhejiang Provincial Key Lab of Genetic and Developmental Disorder, Hangzhou, Zhejiang, China
| | - Feng Ling
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Hirosawa 2-1, Wako, Saitama, Japan
| | - Min-Xin Guan
- To whom correspondence should be addressed. Tel: +86 571 88206916; Fax: +86 571 88982377;
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Koc EC, Koc FC, Kartal F, Tirona M, Koc H. Role of mitochondrial translation in remodeling of energy metabolism in ER/PR(+) breast cancer. Front Oncol 2022; 12:897207. [PMID: 36119536 PMCID: PMC9472243 DOI: 10.3389/fonc.2022.897207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Remodeling of mitochondrial energy metabolism is essential for the survival of tumor cells in limited nutrient availability and hypoxic conditions. Defects in oxidative phosphorylation (OXPHOS) and mitochondrial biogenesis also cause a switch in energy metabolism from oxidative to aerobic glycolysis contributing to the tumor heterogeneity in cancer. Specifically, the aberrant expressions of mitochondrial translation components such as ribosomal proteins (MRPs) and translation factors have been increasingly associated with many different cancers including breast cancer. The mitochondrial translation is responsible for the synthesis 13 of mitochondrial-encoded OXPHOS subunits of complexes. In this study, we investigated the contribution of mitochondrial translation in the remodeling of oxidative energy metabolism through altered expression of OXPHOS subunits in 26 ER/PR(+) breast tumors. We observed a significant correlation between the changes in the expression of mitochondrial translation-related proteins and OXPHOS subunits in the majority of the ER/PR(+) breast tumors and breast cancer cell lines. The reduced expression of OXPHOS and mitochondrial translation components also correlated well with the changes in epithelial-mesenchymal transition (EMT) markers, E-cadherin (CHD1), and vimentin (VIM) in the ER/PR(+) tumor biopsies. Data mining analysis of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) breast cancer proteome further supported the correlation between the reduced OXPHOS subunit expression and increased EMT and metastatic marker expression in the majority of the ER/PR(+) tumors. Therefore, understanding the role of MRPs in the remodeling of energy metabolism will be essential in the characterization of heterogeneity at the molecular level and serve as diagnostic and prognostic markers in breast cancer.
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Affiliation(s)
- Emine C. Koc
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, United States
- *Correspondence: Emine C. Koc, ; Hasan Koc,
| | - Fatih C. Koc
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, United States
| | - Funda Kartal
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, United States
| | - Maria Tirona
- Department of Medical Oncology, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, United States
| | - Hasan Koc
- Department of Pharmaceutical Science, School of Pharmacy, Marshall University, Huntington, WV, United States
- *Correspondence: Emine C. Koc, ; Hasan Koc,
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Liang C, Zhang S, Robinson D, Ploeg MV, Wilson R, Nah J, Taylor D, Beh S, Lim R, Sun L, Muoio DM, Stroud DA, Ho L. Mitochondrial microproteins link metabolic cues to respiratory chain biogenesis. Cell Rep 2022; 40:111204. [PMID: 35977508 DOI: 10.1016/j.celrep.2022.111204] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 05/25/2022] [Accepted: 07/21/2022] [Indexed: 11/28/2022] Open
Abstract
Electron transport chain (ETC) biogenesis is tightly coupled to energy levels and availability of ETC subunits. Complex III (CIII), controlling ubiquinol:ubiquinone ratio in ETC, is an attractive node for modulating ETC levels during metabolic stress. Here, we report the discovery of mammalian Co-ordinator of mitochondrial CYTB (COM) complexes that regulate the stepwise CIII biogenesis in response to nutrient and nuclear-encoded ETC subunit availability. The COMA complex, consisting of UQCC1/2 and membrane anchor C16ORF91, facilitates translation of CIII enzymatic core subunit CYTB. Subsequently, microproteins SMIM4 and BRAWNIN together with COMA subunits form the COMB complex to stabilize nascent CYTB. Finally, UQCC3-containing COMC facilitates CYTB hemylation and association with downstream CIII subunits. Furthermore, when nuclear CIII subunits are limiting, COMB is required to chaperone nascent CYTB to prevent OXPHOS collapse. Our studies highlight CYTB synthesis as a key regulatory node of ETC biogenesis and uncover the roles of microproteins in maintaining mitochondrial homeostasis.
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Affiliation(s)
- Chao Liang
- Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, 169857 Singapore, Singapore
| | - Shan Zhang
- Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, 169857 Singapore, Singapore; Department of Biochemistry, Department of Cardiology of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - David Robinson
- Department of Biochemistry and Pharmacology, the Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, VIC 3052, Australia
| | - Matthew Vander Ploeg
- Departments of Medicine and Pharmacology and Cancer Biology, Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute, Duke University, Durham, NC 27701, USA
| | - Rebecca Wilson
- Departments of Medicine and Pharmacology and Cancer Biology, Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute, Duke University, Durham, NC 27701, USA
| | - Jiemin Nah
- Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, 169857 Singapore, Singapore
| | - Dale Taylor
- Department of Biochemistry and Pharmacology, the Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, VIC 3052, Australia
| | - Sheryl Beh
- Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, 169857 Singapore, Singapore
| | - Radiance Lim
- Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, 169857 Singapore, Singapore
| | - Lei Sun
- Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, 169857 Singapore, Singapore
| | - Deborah M Muoio
- Departments of Medicine and Pharmacology and Cancer Biology, Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute, Duke University, Durham, NC 27701, USA
| | - David A Stroud
- Department of Biochemistry and Pharmacology, the Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, VIC 3052, Australia; Murdoch Children's Research Institute, the Royal Children's Hospital, 50 Flemington Road, Parkville, VIC 3052, Australia
| | - Lena Ho
- Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, 169857 Singapore, Singapore; Institute of Molecular and Cell Biology, A(∗)STAR, 61 Biopolis Dr, 138673 Singapore, Singapore.
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Harbauer AB, Schneider A, Wohlleber D. Analysis of Mitochondria by Single-Organelle Resolution. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2022; 15:1-16. [PMID: 35303775 DOI: 10.1146/annurev-anchem-061020-111722] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cellular organelles are highly specialized compartments with distinct functions. With the increasing resolution of detection methods, it is becoming clearer that same organelles may have different functions or properties not only within different cell populations of a tissue but also within the same cell. Dysfunction or altered function affects the organelle itself and may also lead to malignancies or undesirable cell death. To understand cellular function or dysfunction, it is therefore necessary to analyze cellular components at the single-organelle level. Here, we review the recent advances in analyzing cellular function at single-organelle resolution using high-parameter flow cytometry or multicolor confocal microscopy. We focus on the analysis of mitochondria, as they are organelles at the crossroads of various cellular signaling pathways and functions. However, most of the applied methods/technologies are transferable to any other organelle, such as the endoplasmic reticulum, lysosomes, or peroxisomes.
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Affiliation(s)
- Angelika B Harbauer
- Max Planck Institute of Neurobiology, Martinsried, Germany;
- Institute of Neuronal Cell Biology, TUM School of Medicine, Technical University of Munich, Munich, Germany
- Munich Cluster for Systems Neurology, Munich, Germany
| | - Annika Schneider
- Institute of Molecular Immunology and Experimental Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany; ,
| | - Dirk Wohlleber
- Institute of Molecular Immunology and Experimental Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany; ,
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9
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Apostolopoulos A, Iwasaki S. Into the matrix: current methods for mitochondrial translation studies. J Biochem 2022; 171:379-387. [PMID: 35080613 DOI: 10.1093/jb/mvac005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 01/18/2022] [Indexed: 11/12/2022] Open
Abstract
In addition to the cytoplasmic translation system, eukaryotic cells house additional protein synthesis machinery in mitochondria. The importance of this in organello translation is exemplified by clinical pathologies associated with mutations in mitochondrial translation factors. Although a detailed understanding of mitochondrial translation has long been awaited, quantitative, comprehensive, and spatiotemporal measurements have posed analytic challenges. The recent development of novel approaches for studying mitochondrial protein synthesis has overcome these issues and expands our understanding of the unique translation system. Here, we review the current technologies for the investigation of mitochondrial translation and the insights provided by their application.
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Affiliation(s)
- Antonios Apostolopoulos
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan.,RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Shintaro Iwasaki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan.,RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
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10
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Mennuni M, Filograna R, Felser A, Bonekamp NA, Giavalisco P, Lytovchenko O, Larsson N. Metabolic resistance to the inhibition of mitochondrial transcription revealed by CRISPR-Cas9 screen. EMBO Rep 2022; 23:e53054. [PMID: 34779571 PMCID: PMC8728608 DOI: 10.15252/embr.202153054] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 10/12/2021] [Accepted: 10/19/2021] [Indexed: 12/20/2022] Open
Abstract
Cancer cells depend on mitochondria to sustain their increased metabolic need and mitochondria therefore constitute possible targets for cancer treatment. We recently developed small-molecule inhibitors of mitochondrial transcription (IMTs) that selectively impair mitochondrial gene expression. IMTs have potent antitumor properties in vitro and in vivo, without affecting normal tissues. Because therapy-induced resistance is a major constraint to successful cancer therapy, we investigated mechanisms conferring resistance to IMTs. We employed a CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats)-(CRISP-associated protein 9) whole-genome screen to determine pathways conferring resistance to acute IMT1 treatment. Loss of genes belonging to von Hippel-Lindau (VHL) and mammalian target of rapamycin complex 1 (mTORC1) pathways caused resistance to acute IMT1 treatment and the relevance of these pathways was confirmed by chemical modulation. We also generated cells resistant to chronic IMT treatment to understand responses to persistent mitochondrial gene expression impairment. We report that IMT1-acquired resistance occurs through a compensatory increase of mitochondrial DNA (mtDNA) expression and cellular metabolites. We found that mitochondrial transcription factor A (TFAM) downregulation and inhibition of mitochondrial translation impaired survival of resistant cells. The identified susceptibility and resistance mechanisms to IMTs may be relevant for different types of mitochondria-targeted therapies.
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Affiliation(s)
- Mara Mennuni
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
| | - Roberta Filograna
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
| | - Andrea Felser
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
- University Institute of Clinical ChemistryBern University HospitalBernSwitzerland
| | - Nina A Bonekamp
- Mitochondrial Biology GroupMax Planck Institute for Biology of AgeingCologneGermany
- Department of NeuroanatomyMannheim Center for Translational Neuroscience (MCTN)Medical Faculty MannheimHeidelberg UniversityMannheimGermany
| | - Patrick Giavalisco
- Metabolomics Core FacilityMax Planck Institute for Biology of AgeingCologneGermany
| | - Oleksandr Lytovchenko
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
| | - Nils‐Göran Larsson
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
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11
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High-resolution imaging reveals compartmentalization of mitochondrial protein synthesis in cultured human cells. Proc Natl Acad Sci U S A 2021; 118:2008778118. [PMID: 33526660 PMCID: PMC8017971 DOI: 10.1073/pnas.2008778118] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In mitochondria from various species, the OXPHOS complexes reside mainly in the invaginated cristae membranes, as opposed to the inner boundary membrane (IBM) that parallels the mitochondrial outer membrane. However, the IBM contains dynamic contact sites enriched for translocases that import proteins from the cytosol. As the majority of OXPHOS components are imported and need to be integrated in assembly with the mtDNA-encoded components, where does intramitochondrial translation occur? Here we report: 1) a method for visualizing protein synthesis in human mitochondria at super resolution; 2) that synthesis is enriched at cristae membranes, in preference to the IBM; and 3) that sites of translation are spatially separated from RNA granules where RNA processing, maturation, and mitoribosomal assembly occur. Human mitochondria contain their own genome, mitochondrial DNA, that is expressed in the mitochondrial matrix. This genome encodes 13 vital polypeptides that are components of the multisubunit complexes that couple oxidative phosphorylation (OXPHOS). The inner mitochondrial membrane that houses these complexes comprises the inner boundary membrane that runs parallel to the outer membrane, infoldings that form the cristae membranes, and the cristae junctions that separate the two. It is in these cristae membranes that the OXPHOS complexes have been shown to reside in various species. The majority of the OXPHOS subunits are nuclear-encoded and must therefore be imported from the cytosol through the outer membrane at contact sites with the inner boundary membrane. As the mitochondrially encoded components are also integral members of these complexes, where does protein synthesis occur? As transcription, mRNA processing, maturation, and at least part of the mitoribosome assembly process occur at the nucleoid and the spatially juxtaposed mitochondrial RNA granules, is protein synthesis also performed at the RNA granules close to these entities, or does it occur distal to these sites? We have adapted a click chemistry-based method coupled with stimulated emission depletion nanoscopy to address these questions. We report that, in human cells in culture, within the limits of our methodology, the majority of mitochondrial protein synthesis is detected at the cristae membranes and is spatially separated from the sites of RNA processing and maturation.
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12
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Yousefi R, Fornasiero EF, Cyganek L, Montoya J, Jakobs S, Rizzoli SO, Rehling P, Pacheu‐Grau D. Monitoring mitochondrial translation in living cells. EMBO Rep 2021; 22:e51635. [PMID: 33586863 PMCID: PMC8024989 DOI: 10.15252/embr.202051635] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 01/05/2021] [Accepted: 01/13/2021] [Indexed: 12/20/2022] Open
Abstract
Mitochondria possess a small genome that codes for core subunits of the oxidative phosphorylation system and whose expression is essential for energy production. Information on the regulation and spatial organization of mitochondrial gene expression in the cellular context has been difficult to obtain. Here we devise an imaging approach to analyze mitochondrial translation within the context of single cells, by following the incorporation of clickable non-canonical amino acids. We apply this method to multiple cell types, including specialized cells such as cardiomyocytes and neurons, and monitor with spatial resolution mitochondrial translation in axons and dendrites. We also show that translation imaging allows to monitor mitochondrial protein expression in patient fibroblasts. Approaching mitochondrial translation with click chemistry opens new avenues to understand how mitochondrial biogenesis is integrated into the cellular context and can be used to assess mitochondrial gene expression in mitochondrial diseases.
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Affiliation(s)
- Roya Yousefi
- Department of Cellular BiochemistryUniversity Medical Center GöttingenGöttingenGermany
| | - Eugenio F Fornasiero
- Department of Neuro‐ and Sensory PhysiologyUniversity Medical Center GöttingenGöttingenGermany
| | - Lukas Cyganek
- Clinic for Cardiology and PneumologyUniversity Medical Center GöttingenGöttingenGermany
- German Center for Cardiovascular Research (DZHK)GöttingenGermany
| | - Julio Montoya
- Departamento de BioquímicaBiología Molecular y CelularUniversidad de ZaragozaZaragozaSpain
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER)MadridSpain
- Instituto de Investigación Sanitaria de Aragón (IIS Aragón)Universidad de ZaragozaZaragozaSpain
| | - Stefan Jakobs
- Department of NanoBiophotonicsMax Planck Institute for Biophysical ChemistryGöttingenGermany
- Clinic of NeurologyUniversity Medical Center GöttingenGöttingenGermany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC)University of GoettingenGöttingenGermany
| | - Silvio O Rizzoli
- Department of Neuro‐ and Sensory PhysiologyUniversity Medical Center GöttingenGöttingenGermany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC)University of GoettingenGöttingenGermany
| | - Peter Rehling
- Department of Cellular BiochemistryUniversity Medical Center GöttingenGöttingenGermany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC)University of GoettingenGöttingenGermany
- Max‐Planck Institute for Biophysical ChemistryGöttingenGermany
| | - David Pacheu‐Grau
- Department of Cellular BiochemistryUniversity Medical Center GöttingenGöttingenGermany
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13
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Meng F, Zhou M, Xiao Y, Mao X, Zheng J, Lin J, Lin T, Ye Z, Cang X, Fu Y, Wang M, Guan MX. A deafness-associated tRNA mutation caused pleiotropic effects on the m1G37 modification, processing, stability and aminoacylation of tRNAIle and mitochondrial translation. Nucleic Acids Res 2021; 49:1075-1093. [PMID: 33398350 PMCID: PMC7826259 DOI: 10.1093/nar/gkaa1225] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 11/29/2020] [Accepted: 12/03/2020] [Indexed: 01/16/2023] Open
Abstract
Defects in the posttranscriptional modifications of mitochondrial tRNAs have been linked to human diseases, but their pathophysiology remains elusive. In this report, we investigated the molecular mechanism underlying a deafness-associated tRNAIle 4295A>G mutation affecting a highly conserved adenosine at position 37, 3′ adjacent to the tRNA’s anticodon. Primer extension and methylation activity assays revealed that the m.4295A>G mutation introduced a tRNA methyltransferase 5 (TRMT5)-catalyzed m1G37 modification of tRNAIle. Molecular dynamics simulations suggested that the m.4295A>G mutation affected tRNAIle structure and function, supported by increased melting temperature, conformational changes and instability of mutated tRNA. An in vitro processing experiment revealed that the m.4295A>G mutation reduced the 5′ end processing efficiency of tRNAIle precursors, catalyzed by RNase P. We demonstrated that cybrid cell lines carrying the m.4295A>G mutation exhibited significant alterations in aminoacylation and steady-state levels of tRNAIle. The aberrant tRNA metabolism resulted in the impairment of mitochondrial translation, respiratory deficiency, decreasing membrane potentials and ATP production, increasing production of reactive oxygen species and promoting autophagy. These demonstrated the pleiotropic effects of m.4295A>G mutation on tRNAIle and mitochondrial functions. Our findings highlighted the essential role of deficient posttranscriptional modifications in the structure and function of tRNA and their pathogenic consequence of deafness.
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Affiliation(s)
- Feilong Meng
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Mi Zhou
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Yun Xiao
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Xiaoting Mao
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jing Zheng
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310058, China
| | - Jiaxi Lin
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Tianxiang Lin
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Zhenzhen Ye
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Xiaohui Cang
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Yong Fu
- Division of Otolaryngology-Head and Neck Surgery, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Meng Wang
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Min-Xin Guan
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Zhejiang Provincial Key Lab of Genetic and Developmental Disorder, Hangzhou, Zhejiang 310058, China.,Joint Institute of Genetics and Genome Medicine between Zhejiang University and University of Toronto, Hangzhou, Zhejiang 310058, China
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14
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Lavdovskaia E, Denks K, Nadler F, Steube E, Linden A, Urlaub H, Rodnina MV, Richter-Dennerlein R. Dual function of GTPBP6 in biogenesis and recycling of human mitochondrial ribosomes. Nucleic Acids Res 2021; 48:12929-12942. [PMID: 33264405 PMCID: PMC7736812 DOI: 10.1093/nar/gkaa1132] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/19/2020] [Accepted: 11/09/2020] [Indexed: 01/01/2023] Open
Abstract
Translation and ribosome biogenesis in mitochondria require auxiliary factors that ensure rapid and accurate synthesis of mitochondrial proteins. Defects in translation are associated with oxidative phosphorylation deficiency and cause severe human diseases, but the exact roles of mitochondrial translation-associated factors are not known. Here we identify the functions of GTPBP6, a homolog of the bacterial ribosome-recycling factor HflX, in human mitochondria. Similarly to HflX, GTPBP6 facilitates the dissociation of ribosomes in vitro and in vivo. In contrast to HflX, GTPBP6 is also required for the assembly of mitochondrial ribosomes. GTPBP6 ablation leads to accumulation of late assembly intermediate(s) of the large ribosomal subunit containing ribosome biogenesis factors MTERF4, NSUN4, MALSU1 and the GTPases GTPBP5, GTPBP7 and GTPBP10. Our data show that GTPBP6 has a dual function acting in ribosome recycling and biogenesis. These findings contribute to our understanding of large ribosomal subunit assembly as well as ribosome recycling pathway in mitochondria.
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Affiliation(s)
- Elena Lavdovskaia
- Department of Cellular Biochemistry, University Medical Center Goettingen, D-37073 Goettingen, Germany.,Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Goettingen, Goettingen, Germany
| | - Kärt Denks
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Goettingen, Goettingen, Germany.,Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Goettingen, Germany
| | - Franziska Nadler
- Department of Cellular Biochemistry, University Medical Center Goettingen, D-37073 Goettingen, Germany
| | - Emely Steube
- Department of Cellular Biochemistry, University Medical Center Goettingen, D-37073 Goettingen, Germany
| | - Andreas Linden
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, D-37077 Goettingen, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Goettingen, D-37073 Goettingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, D-37077 Goettingen, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Goettingen, D-37073 Goettingen, Germany
| | - Marina V Rodnina
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Goettingen, Goettingen, Germany.,Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Goettingen, Germany
| | - Ricarda Richter-Dennerlein
- Department of Cellular Biochemistry, University Medical Center Goettingen, D-37073 Goettingen, Germany.,Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Goettingen, Goettingen, Germany
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15
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Zorkau M, Proctor-Kent Y, Berlinguer-Palmini R, Hamilton A, Chrzanowska-Lightowlers ZM, Lightowlers RN. Visualizing Mitochondrial Ribosomal RNA and Mitochondrial Protein Synthesis in Human Cell Lines. Methods Mol Biol 2021; 2192:159-181. [PMID: 33230773 DOI: 10.1007/978-1-0716-0834-0_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Human mitochondria contain their own DNA (mtDNA) that encodes 13 proteins all of which are core subunits of oxidative phosphorylation (OXPHOS) complexes. To form functional complexes, these 13 components need to be correctly assembled with approximately 70 nuclear-encoded subunits that are imported following synthesis in the cytosol. How this complicated coordinated translation and assembly is choreographed is still not clear. Methods are being developed to determine whether all members of a particular complex are translated in close proximity, whether protein synthesis is clustered in submitochondrial factories, whether these align with incoming polypeptides, and if there is evidence for co-translational translation that is regulated and limited by the interaction of the incoming proteins with synthesis of their mtDNA-encoded partners. Two methods are described in this chapter to visualize the distribution of mitochondrial ribosomal RNAs in conjunction with newly synthesized mitochondrial proteins. The first combines RNA Fluorescent In Situ Hybridization (FISH) and super-resolution immunocytochemistry to pinpoint mitochondrial ribosomal RNA. The second localizes nascent translation within the mitochondrial network through non-canonical amino acid labeling, click chemistry and fluorescent microscopy.
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Affiliation(s)
- Matthew Zorkau
- Wellcome Centre for Mitochondrial Research, Newcastle University Biosciences Institute, Newcastle University, Medical School, Newcastle Upon Tyne, UK
| | - Yasmin Proctor-Kent
- Wellcome Centre for Mitochondrial Research, Newcastle University Biosciences Institute, Newcastle University, Medical School, Newcastle Upon Tyne, UK
| | | | - Andrew Hamilton
- School of Medicine, Dentistry and Nursing, Glasgow University, Glasgow, UK
| | - Zofia M Chrzanowska-Lightowlers
- Wellcome Centre for Mitochondrial Research, Newcastle University Biosciences Institute, Newcastle University, Medical School, Newcastle Upon Tyne, UK.
| | - Robert N Lightowlers
- Wellcome Centre for Mitochondrial Research, Newcastle University Biosciences Institute, Newcastle University, Medical School, Newcastle Upon Tyne, UK.
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16
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Reyes A, Favia P, Vidoni S, Petruzzella V, Zeviani M. RCC1L (WBSCR16) isoforms coordinate mitochondrial ribosome assembly through their interaction with GTPases. PLoS Genet 2020; 16:e1008923. [PMID: 32735630 PMCID: PMC7423155 DOI: 10.1371/journal.pgen.1008923] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 08/12/2020] [Accepted: 06/10/2020] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial translation defects can be due to mutations affecting mitochondrial- or nuclear-encoded components. The number of known nuclear genes involved in mitochondrial translation has significantly increased in the past years. RCC1L (WBSCR16), a putative GDP/GTP exchange factor, has recently been described to interact with the mitochondrial large ribosomal subunit. In humans, three different RCC1L isoforms have been identified that originate from alternative splicing but share the same N-terminus, RCC1LV1, RCC1LV2 and RCC1LV3. All three isoforms were exclusively localized to mitochondria, interacted with its inner membrane and could associate with homopolymeric oligos to different extent. Mitochondrial immunoprecipitation experiments showed that RCC1LV1 and RCC1LV3 associated with the mitochondrial large and small ribosomal subunit, respectively, while no significant association was observed for RCC1LV2. Overexpression and silencing of RCC1LV1 or RCC1LV3 led to mitoribosome biogenesis defects that resulted in decreased translation. Indeed, significant changes in steady-state levels and distribution on isokinetic sucrose gradients were detected not only for mitoribosome proteins but also for GTPases, (GTPBP10, ERAL1 and C4orf14), and pseudouridylation proteins, (TRUB2, RPUSD3 and RPUSD4). All in all, our data suggest that RCC1L is essential for mitochondrial function and that the coordination of at least two isoforms is essential for proper ribosomal assembly.
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Affiliation(s)
- Aurelio Reyes
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
| | - Paola Favia
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
- Dipartimento di Scienze Mediche di Base, Neuroscienze e Organi di Senso - Università degli Studi Aldo Moro, Piazza G. Cesare, Bari, Italy
| | - Sara Vidoni
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Vittoria Petruzzella
- Dipartimento di Scienze Mediche di Base, Neuroscienze e Organi di Senso - Università degli Studi Aldo Moro, Piazza G. Cesare, Bari, Italy
| | - Massimo Zeviani
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
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17
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Di Nottia M, Marchese M, Verrigni D, Mutti CD, Torraco A, Oliva R, Fernandez-Vizarra E, Morani F, Trani G, Rizza T, Ghezzi D, Ardissone A, Nesti C, Vasco G, Zeviani M, Minczuk M, Bertini E, Santorelli FM, Carrozzo R. A homozygous MRPL24 mutation causes a complex movement disorder and affects the mitoribosome assembly. Neurobiol Dis 2020; 141:104880. [PMID: 32344152 DOI: 10.1016/j.nbd.2020.104880] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 03/04/2020] [Accepted: 04/23/2020] [Indexed: 01/31/2023] Open
Abstract
Mitochondrial ribosomal protein large 24 (MRPL24) is 1 of the 82 protein components of mitochondrial ribosomes, playing an essential role in the mitochondrial translation process. We report here on a baby girl with cerebellar atrophy, choreoathetosis of limbs and face, intellectual disability and a combined defect of complexes I and IV in muscle biopsy, caused by a homozygous missense mutation identified in MRPL24. The variant predicts a Leu91Pro substitution at an evolutionarily conserved site. Using human mutant cells and the zebrafish model, we demonstrated the pathological role of the identified variant. In fact, in fibroblasts we observed a significant reduction of MRPL24 protein and of mitochondrial respiratory chain complex I and IV subunits, as well a markedly reduced synthesis of the mtDNA-encoded peptides. In zebrafish we demonstrated that the orthologue gene is expressed in metabolically active tissues, and that gene knockdown induced locomotion impairment, structural defects and low ATP production. The motor phenotype was complemented by human WT but not mutant cRNA. Moreover, sucrose density gradient fractionation showed perturbed assembly of large subunit mitoribosomal proteins, suggesting that the mutation leads to a conformational change in MRPL24, which is expected to cause an aberrant interaction of the protein with other components of the 39S mitoribosomal subunit.
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Affiliation(s)
- Michela Di Nottia
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maria Marchese
- Molecular Medicine & Neurogenetics, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - Daniela Verrigni
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Alessandra Torraco
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Naples, Italy
| | | | - Federica Morani
- Molecular Medicine & Neurogenetics, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - Giulia Trani
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Teresa Rizza
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy; Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Anna Ardissone
- Child Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy; Department of Molecular and Translational Medicine DIMET, University of Milan-Bicocca, Milan, Italy
| | - Claudia Nesti
- Molecular Medicine & Neurogenetics, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - Gessica Vasco
- Department of Neurosciences, IRCCS Bambino Gesù Children Hospital, Rome, Italy
| | - Massimo Zeviani
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Enrico Bertini
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Rosalba Carrozzo
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
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18
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Alsina D, Lytovchenko O, Schab A, Atanassov I, Schober FA, Jiang M, Koolmeister C, Wedell A, Taylor RW, Wredenberg A, Larsson NG. FBXL4 deficiency increases mitochondrial removal by autophagy. EMBO Mol Med 2020; 12:e11659. [PMID: 32525278 PMCID: PMC7338799 DOI: 10.15252/emmm.201911659] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 01/29/2023] Open
Abstract
Pathogenic variants in FBXL4 cause a severe encephalopathic syndrome associated with mtDNA depletion and deficient oxidative phosphorylation. To gain further insight into the enigmatic pathophysiology caused by FBXL4 deficiency, we generated homozygous Fbxl4 knockout mice and found that they display a predominant perinatal lethality. Surprisingly, the few surviving animals are apparently normal until the age of 8–12 months when they gradually develop signs of mitochondrial dysfunction and weight loss. One‐year‐old Fbxl4 knockouts show a global reduction in a variety of mitochondrial proteins and mtDNA depletion, whereas lysosomal proteins are upregulated. Fibroblasts from patients with FBXL4 deficiency and human FBXL4 knockout cells also have reduced steady‐state levels of mitochondrial proteins that can be attributed to increased mitochondrial turnover. Inhibition of lysosomal function in these cells reverses the mitochondrial phenotype, whereas proteasomal inhibition has no effect. Taken together, the results we present here show that FBXL4 prevents mitochondrial removal via autophagy and that loss of FBXL4 leads to decreased mitochondrial content and mitochondrial disease.
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Affiliation(s)
- David Alsina
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Oleksandr Lytovchenko
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Aleksandra Schab
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ilian Atanassov
- Proteomics Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germnay
| | - Florian A Schober
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Min Jiang
- Key Laboratory of Growth Regulation and Translation Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Camilla Koolmeister
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Anna Wedell
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Anna Wredenberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden.,Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Nils-Göran Larsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden.,Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
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19
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Bruni F, Proctor-Kent Y, Lightowlers RN, Chrzanowska-Lightowlers ZM. Messenger RNA delivery to mitoribosomes - hints from a bacterial toxin. FEBS J 2020; 288:437-451. [PMID: 32329962 PMCID: PMC7891357 DOI: 10.1111/febs.15342] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 04/06/2020] [Accepted: 04/21/2020] [Indexed: 11/28/2022]
Abstract
In mammalian mitochondria, messenger RNA is processed and matured from large primary transcripts in structures known as RNA granules. The identity of the factors and process transferring the matured mRNA to the mitoribosome for translation is unclear. Nascent mature transcripts are believed to associate initially with the small mitoribosomal subunit prior to recruitment of the large subunit to form the translationally active monosome. When the small subunit fails to assemble, however, the stability of mt‐mRNA is only marginally affected, and under these conditions, the LRPPRC/SLIRP RNA‐binding complex has been implicated in maintaining mt‐mRNA stability. Here, we exploit the activity of a bacterial ribotoxin, VapC20, to show that in the absence of the large mitoribosomal subunit, mt‐mRNA species are selectively lost. Further, if the small subunit is also depleted, the mt‐mRNA levels are recovered. As a consequence of these data, we suggest a natural pathway for loading processed mt‐mRNA onto the mitoribosome.
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Affiliation(s)
- Francesco Bruni
- The Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, UK.,Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, Italy
| | - Yasmin Proctor-Kent
- The Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, UK
| | - Robert N Lightowlers
- The Wellcome Centre for Mitochondrial Research, Institute for Cell and Molecular Biosciences, Newcastle University, UK
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20
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Initiation Factor 3 is Dispensable For Mitochondrial Translation in Cultured Human Cells. Sci Rep 2020; 10:7110. [PMID: 32346061 PMCID: PMC7188818 DOI: 10.1038/s41598-020-64139-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 04/13/2020] [Indexed: 11/08/2022] Open
Abstract
The initiation of protein synthesis in bacteria is ruled by three canonical factors: IF1, IF2, and IF3. This system persists in human mitochondria; however, it functions in a rather different way due to specialization and adaptation to the organellar micro-environment. We focused on human mitochondrial IF3, which was earlier studied in vitro, but no knock-out cellular models have been published up to date. In this work, we generated human HeLa cell lines deficient in the MTIF3 gene and analyzed their mitochondrial function. Despite the lack of IF3mt in these cells, they preserved functional mitochondria capable of oxygen consumption and protein synthesis; however, the translation of ATP6 mRNA was selectively decreased which compromised the assembly of ATP synthase. Together with the analogous results obtained earlier for baker's yeast mitochondrial IF3, our findings point to a functional divergence of mitochondrial initiation factors from their bacterial ancestors.
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Bergman O, Karry R, Milhem J, Ben-Shachar D. NDUFV2 pseudogene (NDUFV2P1) contributes to mitochondrial complex I deficits in schizophrenia. Mol Psychiatry 2020; 25:805-820. [PMID: 30531937 DOI: 10.1038/s41380-018-0309-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 11/06/2018] [Accepted: 11/14/2018] [Indexed: 12/18/2022]
Abstract
Mitochondria together with other cellular components maintain a constant crosstalk, modulating transcriptional and posttranslational processes. We and others demonstrated mitochondrial multifaceted dysfunction in schizophrenia, with aberrant complex I (CoI) as a major cause. Here we show deficits in CoI activity and homeostasis in schizophrenia-derived cell lines. Focusing on a core CoI subunit, NDUFV2, one of the most severely affected subunits in schizophrenia, we observed reduced protein level and functioning, with no change in mRNA transcripts. We further show that NDUFV2 pseudogene (NDUFV2P1) expression is increased in schizophrenia-derived cells and in postmortem brain specimens. In schizophrenia and controls pooled samples, NDUFV2P1 level demonstrated a significant inverse correlation with NDUFV2 pre- and matured protein level and with CoI-driven cellular respiration. Our data suggest a role for a pseudogene in its parent-gene regulation and possibly in CoI dysfunction in schizophrenia. The abnormal expression of the pseudogene may be one element of a vicious circle in which CoI deficits lead to mitochondrial dysfunction potentially affecting genome-wide regulation of gene expression, including the expression of pseudogenes.
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Affiliation(s)
- Oded Bergman
- Laboratory of Psychobiology, Department of Psychiatry, Rambam Health Care Campus, B. Rappaport Faculty of Medicine and Rappaport Family Institute for Research in Medical Sciences, Technion-Israel Institute of Technology, Haifa, Israel
| | - Rachel Karry
- Laboratory of Psychobiology, Department of Psychiatry, Rambam Health Care Campus, B. Rappaport Faculty of Medicine and Rappaport Family Institute for Research in Medical Sciences, Technion-Israel Institute of Technology, Haifa, Israel
| | - Jumana Milhem
- Laboratory of Psychobiology, Department of Psychiatry, Rambam Health Care Campus, B. Rappaport Faculty of Medicine and Rappaport Family Institute for Research in Medical Sciences, Technion-Israel Institute of Technology, Haifa, Israel
| | - Dorit Ben-Shachar
- Laboratory of Psychobiology, Department of Psychiatry, Rambam Health Care Campus, B. Rappaport Faculty of Medicine and Rappaport Family Institute for Research in Medical Sciences, Technion-Israel Institute of Technology, Haifa, Israel.
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22
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Protasoni M, Pérez‐Pérez R, Lobo‐Jarne T, Harbour ME, Ding S, Peñas A, Diaz F, Moraes CT, Fearnley IM, Zeviani M, Ugalde C, Fernández‐Vizarra E. Respiratory supercomplexes act as a platform for complex III-mediated maturation of human mitochondrial complexes I and IV. EMBO J 2020; 39:e102817. [PMID: 31912925 PMCID: PMC6996572 DOI: 10.15252/embj.2019102817] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 11/02/2019] [Accepted: 11/26/2019] [Indexed: 02/02/2023] Open
Abstract
Mitochondrial respiratory chain (MRC) enzymes associate in supercomplexes (SCs) that are structurally interdependent. This may explain why defects in a single component often produce combined enzyme deficiencies in patients. A case in point is the alleged destabilization of complex I in the absence of complex III. To clarify the structural and functional relationships between complexes, we have used comprehensive proteomic, functional, and biogenetical approaches to analyze a MT-CYB-deficient human cell line. We show that the absence of complex III blocks complex I biogenesis by preventing the incorporation of the NADH module rather than decreasing its stability. In addition, complex IV subunits appeared sequestered within complex III subassemblies, leading to defective complex IV assembly as well. Therefore, we propose that complex III is central for MRC maturation and SC formation. Our results challenge the notion that SC biogenesis requires the pre-formation of fully assembled individual complexes. In contrast, they support a cooperative-assembly model in which the main role of complex III in SCs is to provide a structural and functional platform for the completion of overall MRC biogenesis.
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Affiliation(s)
- Margherita Protasoni
- Medical Research Council‐Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | | | | | - Michael E Harbour
- Medical Research Council‐Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | - Shujing Ding
- Medical Research Council‐Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | - Ana Peñas
- Instituto de Investigación Hospital 12 de Octubre (i+12)MadridSpain
| | - Francisca Diaz
- Department of NeurologyMiller School of MedicineUniversity of MiamiMiamiFLUSA
| | - Carlos T Moraes
- Department of NeurologyMiller School of MedicineUniversity of MiamiMiamiFLUSA
| | - Ian M Fearnley
- Medical Research Council‐Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | - Massimo Zeviani
- Medical Research Council‐Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
- Department of NeurosciencesUniversity of PadovaPadovaItaly
| | - Cristina Ugalde
- Instituto de Investigación Hospital 12 de Octubre (i+12)MadridSpain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723MadridSpain
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23
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Reyes A, Rusecka J, Tońska K, Zeviani M. RNase H1 Regulates Mitochondrial Transcription and Translation via the Degradation of 7S RNA. Front Genet 2020; 10:1393. [PMID: 32082360 PMCID: PMC7006045 DOI: 10.3389/fgene.2019.01393] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/19/2019] [Indexed: 02/02/2023] Open
Abstract
RNase H1 is able to recognize DNA/RNA heteroduplexes and to degrade their RNA component. As a consequence, it has been implicated in different aspects of mtDNA replication such as primer formation, primer removal, and replication termination, and significant differences have been reported between control and mutant RNASEH1 skin fibroblasts from patients. However, neither mtDNA depletion nor the presence of deletions have been described in skin fibroblasts while still presenting signs of mitochondrial dysfunction (lower mitochondrial membrane potential, reduced oxygen consumption, slow growth in galactose). Here, we show that RNase H1 has an effect on mtDNA transcripts, most likely through the regulation of 7S RNA and other R-loops. The observed effect on both mitochondrial mRNAs and 16S rRNA results in decreased mitochondrial translation and subsequently mitochondrial dysfunction in cells carrying mutations in RNASEH1.
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Affiliation(s)
- Aurelio Reyes
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom,*Correspondence: Aurelio Reyes, ; Massimo Zeviani,
| | - Joanna Rusecka
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Katarzyna Tońska
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Massimo Zeviani
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom,*Correspondence: Aurelio Reyes, ; Massimo Zeviani,
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24
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Lavdovskaia E, Kolander E, Steube E, Mai MMQ, Urlaub H, Richter-Dennerlein R. The human Obg protein GTPBP10 is involved in mitoribosomal biogenesis. Nucleic Acids Res 2019; 46:8471-8482. [PMID: 30085210 PMCID: PMC6144781 DOI: 10.1093/nar/gky701] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/23/2018] [Indexed: 12/29/2022] Open
Abstract
The human mitochondrial translation apparatus, which synthesizes the core subunits of the oxidative phosphorylation system, is of central interest as mutations in several genes encoding for mitoribosomal proteins or translation factors cause severe human diseases. Little is known, how this complex machinery assembles from nuclear-encoded protein components and mitochondrial-encoded RNAs, and which ancillary factors are required to form a functional mitoribosome. We have characterized the human Obg protein GTPBP10, which associates specifically with the mitoribosomal large subunit at a late maturation state. Defining its interactome, we have shown that GTPBP10 is in a complex with other mtLSU biogenesis factors including mitochondrial RNA granule components, the 16S rRNA module and late mtLSU assembly factors such as MALSU1, SMCR7L, MTERF4 and NSUN4. GTPBP10 deficiency leads to a drastic reduction in 55S monosome formation resulting in defective mtDNA-expression and in a decrease in cell growth. Our results suggest that GTPBP10 is a ribosome biogenesis factor of the mtLSU required for late stages of maturation.
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Affiliation(s)
- Elena Lavdovskaia
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Elisa Kolander
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Emely Steube
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Mandy Mong-Quyen Mai
- 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.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
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25
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Thompson K, Mai N, Oláhová M, Scialó F, Formosa LE, Stroud DA, Garrett M, Lax NZ, Robertson FM, Jou C, Nascimento A, Ortez C, Jimenez-Mallebrera C, Hardy SA, He L, Brown GK, Marttinen P, McFarland R, Sanz A, Battersby BJ, Bonnen PE, Ryan MT, Chrzanowska-Lightowlers ZM, Lightowlers RN, Taylor RW. OXA1L mutations cause mitochondrial encephalopathy and a combined oxidative phosphorylation defect. EMBO Mol Med 2019; 10:emmm.201809060. [PMID: 30201738 PMCID: PMC6220311 DOI: 10.15252/emmm.201809060] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
OXA1, the mitochondrial member of the YidC/Alb3/Oxa1 membrane protein insertase family, is required for the assembly of oxidative phosphorylation complexes IV and V in yeast. However, depletion of human OXA1 (OXA1L) was previously reported to impair assembly of complexes I and V only. We report a patient presenting with severe encephalopathy, hypotonia and developmental delay who died at 5 years showing complex IV deficiency in skeletal muscle. Whole exome sequencing identified biallelic OXA1L variants (c.500_507dup, p.(Ser170Glnfs*18) and c.620G>T, p.(Cys207Phe)) that segregated with disease. Patient muscle and fibroblasts showed decreased OXA1L and subunits of complexes IV and V. Crucially, expression of wild‐type human OXA1L in patient fibroblasts rescued the complex IV and V defects. Targeted depletion of OXA1L in human cells or Drosophila melanogaster caused defects in the assembly of complexes I, IV and V, consistent with patient data. Immunoprecipitation of OXA1L revealed the enrichment of mtDNA‐encoded subunits of complexes I, IV and V. Our data verify the pathogenicity of these OXA1L variants and demonstrate that OXA1L is required for the assembly of multiple respiratory chain complexes.
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Affiliation(s)
- Kyle Thompson
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Nicole Mai
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Monika Oláhová
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Filippo Scialó
- Institute for Cell and Molecular Biosciences, Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, UK
| | - Luke E Formosa
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Vic., Australia
| | - David A Stroud
- Department of Biochemistry and Molecular Biology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Vic., Australia
| | - Madeleine Garrett
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Vic., Australia
| | - Nichola Z Lax
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Fiona M Robertson
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Cristina Jou
- Pathology Department, Hospital Sant Joan de Déu, CIBERER, Barcelona, Spain
| | - Andres Nascimento
- Neuromuscular Unit, Neuropaediatrics Department, Hospital Sant Joan de Déu, CIBERER - ISCIII, Barcelona, Spain
| | - Carlos Ortez
- Neuromuscular Unit, Neuropaediatrics Department, Hospital Sant Joan de Déu, CIBERER - ISCIII, Barcelona, Spain
| | - Cecilia Jimenez-Mallebrera
- Neuromuscular Unit, Neuropaediatrics Department, Hospital Sant Joan de Déu, CIBERER - ISCIII, Barcelona, Spain
| | - Steven A Hardy
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Langping He
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Garry K Brown
- Oxford Medical Genetics Laboratories, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Paula Marttinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Alberto Sanz
- Institute for Cell and Molecular Biosciences, Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, UK
| | | | - Penelope E Bonnen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Vic., Australia
| | | | - Robert N Lightowlers
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
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26
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Ren H, Yang H, Xie M, Wen Y, Liu Q, Li X, Liu J, Xu H, Tang W, Wang M. Chondrocyte apoptosis in rat mandibular condyles induced by dental occlusion due to mitochondrial damage caused by nitric oxide. Arch Oral Biol 2019; 101:108-121. [DOI: 10.1016/j.archoralbio.2019.03.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/03/2019] [Accepted: 03/09/2019] [Indexed: 01/21/2023]
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27
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Pacheu-Grau D, Callegari S, Emperador S, Thompson K, Aich A, Topol SE, Spencer EG, McFarland R, Ruiz-Pesini E, Torkamani A, Taylor RW, Montoya J, Rehling P. Mutations of the mitochondrial carrier translocase channel subunit TIM22 cause early-onset mitochondrial myopathy. Hum Mol Genet 2018; 27:4135-4144. [PMID: 30452684 PMCID: PMC6240735 DOI: 10.1093/hmg/ddy305] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/10/2018] [Accepted: 08/10/2018] [Indexed: 11/13/2022] Open
Abstract
Protein import into mitochondria is facilitated by translocases within the outer and the inner mitochondrial membranes that are dedicated to a highly specific subset of client proteins. The mitochondrial carrier translocase (TIM22 complex) inserts multispanning proteins, such as mitochondrial metabolite carriers and translocase subunits (TIM23, TIM17A/B and TIM22), into the inner mitochondrial membrane. Both types of substrates are essential for mitochondrial metabolic function and biogenesis. Here, we report on a subject, diagnosed at 1.5 years, with a neuromuscular presentation, comprising hypotonia, gastroesophageal reflux disease and persistently elevated serum and Cerebrospinal fluid lactate (CSF). Patient fibroblasts displayed reduced oxidative capacity and altered mitochondrial morphology. Using trans-mitochondrial cybrid cell lines, we excluded a candidate variant in mitochondrial DNA as causative of these effects. Whole-exome sequencing identified compound heterozygous variants in the TIM22 gene (NM_013337), resulting in premature truncation in one allele (p.Tyr25Ter) and a point mutation in a conserved residue (p.Val33Leu), within the intermembrane space region, of the TIM22 protein in the second allele. Although mRNA transcripts of TIM22 were elevated, biochemical analyses revealed lower levels of TIM22 protein and an even greater deficiency of TIM22 complex formation. In agreement with a defect in carrier translocase function, carrier protein amounts in the inner membrane were found to be reduced. This is the first report of pathogenic variants in the TIM22 pore-forming subunit of the carrier translocase affecting the biogenesis of inner mitochondrial membrane proteins critical for metabolite exchange.
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Affiliation(s)
- David Pacheu-Grau
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, D-37073, Germany
| | - Sylvie Callegari
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, D-37073, Germany
| | - Sonia Emperador
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza-CIBER de Enfermedades Raras (CIBERER)-Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, 50013, Spain
| | - Kyle Thompson
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Abhishek Aich
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, D-37073, Germany
| | - Sarah E Topol
- The Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Emily G Spencer
- The Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Eduardo Ruiz-Pesini
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza-CIBER de Enfermedades Raras (CIBERER)-Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, 50013, Spain
| | - Ali Torkamani
- The Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, United States
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Julio Montoya
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza-CIBER de Enfermedades Raras (CIBERER)-Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, 50013, Spain
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, D-37073, Germany
- Max-Planck Institute for Biophysical Chemistry, D-37077, Göttingen, Germany
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28
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Wilkening A, Rüb C, Sylvester M, Voos W. Analysis of heat-induced protein aggregation in human mitochondria. J Biol Chem 2018; 293:11537-11552. [PMID: 29895621 DOI: 10.1074/jbc.ra118.002122] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 06/01/2018] [Indexed: 12/30/2022] Open
Abstract
Proteins in mammalian cells exhibit optimal stability at physiological temperatures, and even small temperature variations may cause unfolding and nonspecific aggregation. Because this process leads to a loss of function of the affected polypeptides and to cytotoxic stress, formation of protein aggregates has been recognized as a major pathogenic factor in human diseases. In this study, we determined the impact of physiological heat stress on mitochondria isolated from HeLa cells. We found that the heat-stressed mitochondria had lower membrane potential and ATP level and exhibited a decreased production of reactive oxygen species. An analysis of the mitochondrial proteome by 2D PAGE showed that the overall solubility of endogenous proteins was only marginally affected by elevated temperatures. However, a small subset of polypeptides exhibited an high sensitivity to heat stress. The mitochondrial translation elongation factor Tu (Tufm), a protein essential for organellar protein biosynthesis, was highly aggregation-prone and lost its solubility already under mild heat-stress conditions. Moreover, mitochondrial translation and the import of cytosolic proteins were defective in the heat-stressed mitochondria. Both types of nascent polypeptides, produced by translation or imported into the mitochondria, exhibited a strong tendency to aggregate in the heat-exposed mitochondria. We propose that a fast and specific inactivation of elongation factors may prevent the accumulation of misfolded nascent polypeptides and may thereby attenuate proteotoxicity under heat stress.
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Affiliation(s)
- Anne Wilkening
- Institute for Biochemistry and Molecular Biology, Friedrich Wilhelm University, 53115 Bonn, Germany
| | - Cornelia Rüb
- Institute for Biochemistry and Molecular Biology, Friedrich Wilhelm University, 53115 Bonn, Germany
| | - Marc Sylvester
- Institute for Biochemistry and Molecular Biology, Friedrich Wilhelm University, 53115 Bonn, Germany
| | - Wolfgang Voos
- Institute for Biochemistry and Molecular Biology, Friedrich Wilhelm University, 53115 Bonn, Germany.
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Lorenzi I, Oeljeklaus S, Aich A, Ronsör C, Callegari S, Dudek J, Warscheid B, Dennerlein S, Rehling P. The mitochondrial TMEM177 associates with COX20 during COX2 biogenesis. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2018; 1865:323-333. [PMID: 29154948 PMCID: PMC5764226 DOI: 10.1016/j.bbamcr.2017.11.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/10/2017] [Accepted: 11/14/2017] [Indexed: 12/17/2022]
Abstract
The three mitochondrial-encoded proteins, COX1, COX2, and COX3, form the core of the cytochrome c oxidase. Upon synthesis, COX2 engages with COX20 in the inner mitochondrial membrane, a scaffold protein that recruits metallochaperones for copper delivery to the CuA-Site of COX2. Here we identified the human protein, TMEM177 as a constituent of the COX20 interaction network. Loss or increase in the amount of TMEM177 affects COX20 abundance leading to reduced or increased COX20 levels respectively. TMEM177 associates with newly synthesized COX2 and SCO2 in a COX20-dependent manner. Our data shows that by unbalancing the amount of TMEM177, newly synthesized COX2 accumulates in a COX20-associated state. We conclude that TMEM177 promotes assembly of COX2 at the level of CuA-site formation.
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Affiliation(s)
- Isotta Lorenzi
- Department of Cellular Biochemistry, University Medical Centre Göttingen, GZMB, D-37073 Göttingen, Germany
| | - Silke Oeljeklaus
- Faculty of Biology, Department of Biochemistry and Functional Proteomics, University Freiburg, D-79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, D-79104 Freiburg, Germany
| | - Abhishek Aich
- Department of Cellular Biochemistry, University Medical Centre Göttingen, GZMB, D-37073 Göttingen, Germany
| | - Christin Ronsör
- Department of Cellular Biochemistry, University Medical Centre Göttingen, GZMB, D-37073 Göttingen, Germany
| | - Sylvie Callegari
- Department of Cellular Biochemistry, University Medical Centre Göttingen, GZMB, D-37073 Göttingen, Germany
| | - Jan Dudek
- Department of Cellular Biochemistry, University Medical Centre Göttingen, GZMB, D-37073 Göttingen, Germany
| | - Bettina Warscheid
- Faculty of Biology, Department of Biochemistry and Functional Proteomics, University Freiburg, D-79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, D-79104 Freiburg, Germany
| | - Sven Dennerlein
- Department of Cellular Biochemistry, University Medical Centre Göttingen, GZMB, D-37073 Göttingen, Germany.
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Centre Göttingen, GZMB, D-37073 Göttingen, Germany; Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany.
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30
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Aich A, Wang C, Chowdhury A, Ronsör C, Pacheu-Grau D, Richter-Dennerlein R, Dennerlein S, Rehling P. COX16 promotes COX2 metallation and assembly during respiratory complex IV biogenesis. eLife 2018; 7:32572. [PMID: 29381136 PMCID: PMC5809144 DOI: 10.7554/elife.32572] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 01/14/2018] [Indexed: 12/25/2022] Open
Abstract
Cytochrome c oxidase of the mitochondrial oxidative phosphorylation system reduces molecular oxygen with redox equivalent-derived electrons. The conserved mitochondrial-encoded COX1- and COX2-subunits are the heme- and copper-center containing core subunits that catalyze water formation. COX1 and COX2 initially follow independent biogenesis pathways creating assembly modules with subunit-specific, chaperone-like assembly factors that assist in redox centers formation. Here, we find that COX16, a protein required for cytochrome c oxidase assembly, interacts specifically with newly synthesized COX2 and its copper center-forming metallochaperones SCO1, SCO2, and COA6. The recruitment of SCO1 to the COX2-module is COX16- dependent and patient-mimicking mutations in SCO1 affect interaction with COX16. These findings implicate COX16 in CuA-site formation. Surprisingly, COX16 is also found in COX1-containing assembly intermediates and COX2 recruitment to COX1. We conclude that COX16 participates in merging the COX1 and COX2 assembly lines.
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Affiliation(s)
- Abhishek Aich
- Department of Cellular Biochemistry, University Medical Centre Göttingen, Göttingen, Germany
| | - Cong Wang
- Department of Cellular Biochemistry, University Medical Centre Göttingen, Göttingen, Germany
| | - Arpita Chowdhury
- Department of Cellular Biochemistry, University Medical Centre Göttingen, Göttingen, Germany
| | - Christin Ronsör
- Department of Cellular Biochemistry, University Medical Centre Göttingen, Göttingen, Germany
| | - David Pacheu-Grau
- Department of Cellular Biochemistry, University Medical Centre Göttingen, Göttingen, Germany
| | | | - Sven Dennerlein
- Department of Cellular Biochemistry, University Medical Centre Göttingen, Göttingen, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Centre Göttingen, Göttingen, Germany.,Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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31
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Glasgow RIC, Thompson K, Barbosa IA, He L, Alston CL, Deshpande C, Simpson MA, Morris AAM, Neu A, Löbel U, Hall J, Prokisch H, Haack TB, Hempel M, McFarland R, Taylor RW. Novel GFM2 variants associated with early-onset neurological presentations of mitochondrial disease and impaired expression of OXPHOS subunits. Neurogenetics 2017; 18:227-235. [PMID: 29075935 PMCID: PMC5705740 DOI: 10.1007/s10048-017-0526-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 10/03/2017] [Indexed: 11/29/2022]
Abstract
Mitochondrial diseases are characterised by clinical, molecular and functional heterogeneity, reflecting their bi-genomic control. The nuclear gene GFM2 encodes mtEFG2, a protein with an essential role during the termination stage of mitochondrial translation. We present here two unrelated patients harbouring different and previously unreported compound heterozygous (c.569G>A, p.(Arg190Gln); c.636delA, p.(Glu213Argfs*3)) and homozygous (c.275A>C, p.(Tyr92Ser)) recessive variants in GFM2 identified by whole exome sequencing (WES) together with histochemical and biochemical findings to support the diagnoses of pathological GFM2 variants in each case. Both patients presented similarly in early childhood with global developmental delay, raised CSF lactate and abnormalities on cranial MRI. Sanger sequencing of familial samples confirmed the segregation of bi-allelic GFM2 variants with disease, while investigations into steady-state mitochondrial protein levels revealed respiratory chain subunit defects and loss of mtEFG2 protein in muscle. These data demonstrate the effects of defective mtEFG2 function, caused by previously unreported variants, confirming pathogenicity and expanding the clinical phenotypes associated with GFM2 variants.
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Affiliation(s)
- Ruth I C Glasgow
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Kyle Thompson
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Inês A Barbosa
- Department of Medical and Molecular Genetics, King's College London School of Medicine, London, UK
| | - Langping He
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Charlotte L Alston
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Charu Deshpande
- Department of Medical and Molecular Genetics, King's College London School of Medicine, London, UK
| | - Michael A Simpson
- Department of Medical and Molecular Genetics, King's College London School of Medicine, London, UK
| | - Andrew A M Morris
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
- Alder Hey Children's Hospital NHS Foundation Trust, Liverpool, UK
| | - Axel Neu
- University Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrike Löbel
- Department of Diagnostic and Interventional Neuroradiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julie Hall
- Department of Neuroradiology, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Zentrum München, Oberschleißheim, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Tobias B Haack
- Institute of Human Genetics, Technische Universität München, Munich, Germany
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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The human RNA-binding protein RBFA promotes the maturation of the mitochondrial ribosome. Biochem J 2017; 474:2145-2158. [PMID: 28512204 PMCID: PMC5468982 DOI: 10.1042/bcj20170256] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 05/09/2017] [Accepted: 05/15/2017] [Indexed: 11/17/2022]
Abstract
Accurate assembly and maturation of human mitochondrial ribosomes is essential for synthesis of the 13 polypeptides encoded by the mitochondrial genome. This process requires the correct integration of 80 proteins, 1 mt (mitochondrial)-tRNA and 2 mt-rRNA species, the latter being post-transcriptionally modified at many sites. Here, we report that human ribosome-binding factor A (RBFA) is a mitochondrial RNA-binding protein that exerts crucial roles in mitoribosome biogenesis. Unlike its bacterial orthologue, RBFA associates mainly with helices 44 and 45 of the 12S rRNA in the mitoribosomal small subunit to promote dimethylation of two highly conserved consecutive adenines. Characterization of RBFA-depleted cells indicates that this dimethylation is not a prerequisite for assembly of the small ribosomal subunit. However, the RBFA-facilitated modification is necessary for completing mt-rRNA maturation and regulating association of the small and large subunits to form a functional monosome implicating RBFA in the quality control of mitoribosome formation.
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Li H, Shen L, Hu P, Huang R, Cao Y, Deng J, Yuan W, Liu D, Yang J, Gu H, Bai Y. Aging-associated mitochondrial DNA mutations alter oxidative phosphorylation machinery and cause mitochondrial dysfunctions. Biochim Biophys Acta Mol Basis Dis 2017; 1863:2266-2273. [PMID: 28559044 DOI: 10.1016/j.bbadis.2017.05.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/22/2017] [Accepted: 05/25/2017] [Indexed: 12/14/2022]
Abstract
Our previous study generated a series of cybrids containing mitochondria of synaptosomes from mice at different ages. The following functional analysis on these cybrids revealed an age-dependent decline of mitochondrial function. To understand the underlying mechanisms that contribute to the age-related mitochondrial dysfunction, we focused on three cybrids carrying mitochondria derived from synaptosomes of the old mice that exhibited severe respiratory deficiencies. In particular, we started with a comprehensive analysis of mitochondrial genome by high resolution, high sensitive deep sequencing method. Compared with young control, we detected a significant accumulation of heteroplasmic mtDNA mutations. These mutations included six alterations in main control region that has been shown to regulate overall gene-expression, and four alterations in protein coding region, two of which led to significant changes in complex I subunit ND5 and complex III subunit CytB. Interestingly, a reduced mtDNA-encoded protein synthesis was associated with the changes in the main control region. Likewise, mutations in ND5 and CytB were associated with defects in assembly of respiratory complexes. Altogether, the identified age-dependent accumulation of mtDNA mutations in mouse brain likely contributes to the decline in mitochondrial function.
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Affiliation(s)
- Hongzhi Li
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
| | - Luxi Shen
- Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Peiqing Hu
- Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Rong Huang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Ying Cao
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Janice Deng
- Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Weihua Yuan
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Danhui Liu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Jifeng Yang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Haihua Gu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
| | - Yidong Bai
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China; Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
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Wakim J, Goudenege D, Perrot R, Gueguen N, Desquiret-Dumas V, Chao de la Barca JM, Dalla Rosa I, Manero F, Le Mao M, Chupin S, Chevrollier A, Procaccio V, Bonneau D, Logan DC, Reynier P, Lenaers G, Khiati S. CLUH couples mitochondrial distribution to the energetic and metabolic status. J Cell Sci 2017; 130:1940-1951. [PMID: 28424233 DOI: 10.1242/jcs.201616] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 04/12/2017] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial dynamics and distribution are critical for supplying ATP in response to energy demand. CLUH is a protein involved in mitochondrial distribution whose dysfunction leads to mitochondrial clustering, the metabolic consequences of which remain unknown. To gain insight into the role of CLUH on mitochondrial energy production and cellular metabolism, we have generated CLUH-knockout cells using CRISPR/Cas9. Mitochondrial clustering was associated with a smaller cell size and with decreased abundance of respiratory complexes, resulting in oxidative phosphorylation (OXPHOS) defects. This energetic impairment was found to be due to the alteration of mitochondrial translation and to a metabolic shift towards glucose dependency. Metabolomic profiling by mass spectroscopy revealed an increase in the concentration of some amino acids, indicating a dysfunctional Krebs cycle, and increased palmitoylcarnitine concentration, indicating an alteration of fatty acid oxidation, and a dramatic decrease in the concentrations of phosphatidylcholine and sphingomyeline, consistent with the decreased cell size. Taken together, our study establishes a clear function for CLUH in coupling mitochondrial distribution to the control of cell energetic and metabolic status.
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Affiliation(s)
- Jamal Wakim
- Equipe MitoLab, Institut MitoVasc, Université d'Angers, UMR CNRS 6015, INSERM U1083, Angers, 49933 France
| | - David Goudenege
- Equipe MitoLab, Institut MitoVasc, Université d'Angers, UMR CNRS 6015, INSERM U1083, Angers, 49933 France
| | - Rodolphe Perrot
- SCIAM, Institut de Biologie en Sante, Université d'Angers, Angers 49933, France
| | - Naig Gueguen
- Equipe MitoLab, Institut MitoVasc, Université d'Angers, UMR CNRS 6015, INSERM U1083, Angers, 49933 France
| | - Valerie Desquiret-Dumas
- Equipe MitoLab, Institut MitoVasc, Université d'Angers, UMR CNRS 6015, INSERM U1083, Angers, 49933 France
| | | | | | - Florence Manero
- SCIAM, Institut de Biologie en Sante, Université d'Angers, Angers 49933, France
| | - Morgane Le Mao
- Equipe MitoLab, Institut MitoVasc, Université d'Angers, UMR CNRS 6015, INSERM U1083, Angers, 49933 France
| | - Stephanie Chupin
- Equipe MitoLab, Institut MitoVasc, Université d'Angers, UMR CNRS 6015, INSERM U1083, Angers, 49933 France
| | - Arnaud Chevrollier
- Equipe MitoLab, Institut MitoVasc, Université d'Angers, UMR CNRS 6015, INSERM U1083, Angers, 49933 France
| | - Vincent Procaccio
- Equipe MitoLab, Institut MitoVasc, Université d'Angers, UMR CNRS 6015, INSERM U1083, Angers, 49933 France
| | - Dominique Bonneau
- Equipe MitoLab, Institut MitoVasc, Université d'Angers, UMR CNRS 6015, INSERM U1083, Angers, 49933 France
| | - David C Logan
- MitoStress team, IRHS, Université d'Angers, Agrocampus-Ouest, INRA, SFR QuaSaV, Beaucouzé 49071, France
| | - Pascal Reynier
- Equipe MitoLab, Institut MitoVasc, Université d'Angers, UMR CNRS 6015, INSERM U1083, Angers, 49933 France
| | - Guy Lenaers
- Equipe MitoLab, Institut MitoVasc, Université d'Angers, UMR CNRS 6015, INSERM U1083, Angers, 49933 France
| | - Salim Khiati
- Equipe MitoLab, Institut MitoVasc, Université d'Angers, UMR CNRS 6015, INSERM U1083, Angers, 49933 France
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35
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Connor TM, Hoer S, Mallett A, Gale DP, Gomez-Duran A, Posse V, Antrobus R, Moreno P, Sciacovelli M, Frezza C, Duff J, Sheerin NS, Sayer JA, Ashcroft M, Wiesener MS, Hudson G, Gustafsson CM, Chinnery PF, Maxwell PH. Mutations in mitochondrial DNA causing tubulointerstitial kidney disease. PLoS Genet 2017; 13:e1006620. [PMID: 28267784 PMCID: PMC5360345 DOI: 10.1371/journal.pgen.1006620] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 03/21/2017] [Accepted: 02/07/2017] [Indexed: 11/19/2022] Open
Abstract
Tubulointerstitial kidney disease is an important cause of progressive renal failure whose aetiology is incompletely understood. We analysed a large pedigree with maternally inherited tubulointerstitial kidney disease and identified a homoplasmic substitution in the control region of the mitochondrial genome (m.547A>T). While mutations in mtDNA coding sequence are a well recognised cause of disease affecting multiple organs, mutations in the control region have never been shown to cause disease. Strikingly, our patients did not have classical features of mitochondrial disease. Patient fibroblasts showed reduced levels of mitochondrial tRNAPhe, tRNALeu1 and reduced mitochondrial protein translation and respiration. Mitochondrial transfer demonstrated mitochondrial transmission of the defect and in vitro assays showed reduced activity of the heavy strand promoter. We also identified further kindreds with the same phenotype carrying a homoplasmic mutation in mitochondrial tRNAPhe (m.616T>C). Thus mutations in mitochondrial DNA can cause maternally inherited renal disease, likely mediated through reduced function of mitochondrial tRNAPhe.
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Affiliation(s)
| | - Simon Hoer
- Cambridge Institute for Medical Research, University of Cambridge, United Kingdom
| | - Andrew Mallett
- Kidney Health Service, Royal Brisbane and Women’s Hospital, School of Medicine, The University of Queensland, Australia
| | - Daniel P. Gale
- UCL Centre for Nephrology, Royal Free Hospital, London, United Kingdom
| | | | - Viktor Posse
- Institute of Biomedicine, University of Gothenburg, Sweden
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, United Kingdom
| | - Pablo Moreno
- Cambridge Institute for Medical Research, University of Cambridge, United Kingdom
| | | | | | - Jennifer Duff
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Neil S. Sheerin
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - John A. Sayer
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Michael S. Wiesener
- Department of Nephrology and Hypertension, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Gavin Hudson
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | | | - Patrick H. Maxwell
- School of Clinical Medicine, Cambridge University, Cambridge, United Kingdom
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36
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Di Nottia M, Montanari A, Verrigni D, Oliva R, Torraco A, Fernandez-Vizarra E, Diodato D, Rizza T, Bianchi M, Catteruccia M, Zeviani M, Dionisi-Vici C, Francisci S, Bertini E, Carrozzo R. Novel mutation in mitochondrial Elongation Factor EF-Tu associated to dysplastic leukoencephalopathy and defective mitochondrial DNA translation. Biochim Biophys Acta Mol Basis Dis 2017; 1863:961-967. [PMID: 28132884 PMCID: PMC5335904 DOI: 10.1016/j.bbadis.2017.01.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 12/20/2016] [Accepted: 01/25/2017] [Indexed: 12/27/2022]
Abstract
The mitochondrial Elongation Factor Tu (EF-Tu), encoded by the TUFM gene, is a highly conserved GTPase, which is part of the mitochondrial protein translation machinery. In its activated form it delivers the aminoacyl-tRNAs to the A site of the mitochondrial ribosome. We report here on a baby girl with severe infantile macrocystic leukodystrophy with micropolygyria and a combined defect of complexes I and IV in muscle biopsy, caused by a novel mutation identified in TUFM. Using human mutant cells and the yeast model, we demonstrate the pathological role of the novel variant. Moreover, results of a molecular modeling study suggest that the mutant is inactive in mitochondrial polypeptide chain elongation, probably as a consequence of its reduced ability to bind mitochondrial aa-tRNAs. Four patients have so far been described with mutations in TUFM, and, following the first description of the disease in a single patient, we describe similar clinical and neuroradiological features in an additional patient.
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Affiliation(s)
- Michela Di Nottia
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Arianna Montanari
- Pasteur Institute Italy - Cenci Bolognetti Foundation, Italy; Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Daniela Verrigni
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143 Naples, Italy
| | - Alessandra Torraco
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Daria Diodato
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Teresa Rizza
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Marzia Bianchi
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Michela Catteruccia
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Massimo Zeviani
- Mitochondrial Biology Unit, Medical Research Council, Cambridge, UK
| | - Carlo Dionisi-Vici
- Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Silvia Francisci
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Enrico Bertini
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rosalba Carrozzo
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
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37
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Fyn kinase regulates translation in mammalian mitochondria. Biochim Biophys Acta Gen Subj 2016; 1861:533-540. [PMID: 27940153 DOI: 10.1016/j.bbagen.2016.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 11/22/2016] [Accepted: 12/05/2016] [Indexed: 11/24/2022]
Abstract
BACKGROUND Mitochondrial translation machinery solely exists for the synthesis of 13 mitochondrially-encoded subunits of the oxidative phosphorylation (OXPHOS) complexes in mammals. Therefore, it plays a critical role in mitochondrial energy production. However, regulation of the mitochondrial translation machinery is still poorly understood. In comprehensive proteomics studies with normal and diseased tissues and cell lines, we and others have found the majority of mitochondrial ribosomal proteins (MRPs) to be phosphorylated. Neither the kinases for these phosphorylation events nor their specific roles in mitochondrial translation are known. METHODS Mitochondrial kinases are responsible for phosphorylation of MRPs enriched from bovine mitoplasts by strong cation-exchange chromatography and identified by mass spectrometry-based proteomics analyses of kinase rich fractions. Phosphorylation of recombinant MRPs and 55S ribosomes was assessed by in vitro phosphorylation assays using the kinase-rich fractions. The effect of identified kinase on OXPHOS and mitochondrial translation was assessed by various cell biological and immunoblotting approaches. RESULTS Here, we provide the first evidence for the association of Fyn kinase, a Src family kinase, with mitochondrial translation components and its involvement in phosphorylation of 55S ribosomal proteins in vitro. Modulation of Fyn expression in human cell lines has provided a link between mitochondrial translation and energy metabolism, which was evident by the changes in 13 mitochondrially encoded subunits of OXPHOS complexes. CONCLUSIONS AND GENERAL SIGNIFICANCE Our findings suggest that Fyn kinase is part of a complex mechanism that regulates protein synthesis and OXPHOS possibly by tyrosine phosphorylation of translation components in mammalian mitochondria.
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38
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Etzler JC, Bollo M, Holstein D, Deng JJ, Perez V, Lin DT, Richardson A, Bai Y, Lechleiter JD. Cyclophilin D over-expression increases mitochondrial complex III activity and accelerates supercomplex formation. Arch Biochem Biophys 2016; 613:61-68. [PMID: 27916505 DOI: 10.1016/j.abb.2016.11.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/27/2016] [Accepted: 11/23/2016] [Indexed: 12/15/2022]
Abstract
Cyclophilin D (CyPD), a mitochondrial matrix protein, has been widely studied for its role in mitochondrial-mediated cell death. Unexpectedly, we previously discovered that overexpression of CyPD in a stable cell line, increased mitochondrial membrane potentials and enhanced cell survival under conditions of oxidative stress. Here, we investigated the underlying mechanisms responsible for these findings. Spectrophotometric measurements in isolated mitochondria revealed that overexpression of CyPD in HEK293 cells increased respiratory chain activity, but only for Complex III (CIII). Acute treatment of mitochondria with the immumosupressant cyclosporine A did not affect CIII activity. Expression levels of the CIII subunits cytochrome b and Rieske-FeS were elevated in HEK293 cells overexpressing CyPD. However, CIII activity was still significantly higher compared to control mitochondria, even when normalized by protein expression. Blue native gel electrophoresis and Western blot assays revealed a molecular interaction of CyPD with CIII and increased levels of supercomplexes in mitochondrial protein extracts. Radiolabeled protein synthesis in mitochondria showed that CIII assembly and formation of supercomplexes containing CIII were significantly faster when CyPD was overexpressed. Taken together, these data indicate that CyPD regulates mitochondrial metabolism, and likely cell survival, by promoting more efficient electrons flow through the respiratory chain via increased supercomplex formation.
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Affiliation(s)
- Julie C Etzler
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Mariana Bollo
- Instituto de Investigación Médica M y M Ferreyra, INIMEC-CONICET, Universidad Nacional de Córdoba, 5016, Argentina
| | - Deborah Holstein
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Janice Jianhong Deng
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Viviana Perez
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 73104, USA
| | - Da-Ting Lin
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Arlan Richardson
- Department of Geriatrics, University of Oklahoma Health Science Center, Oklahoma City, OK, 73104, USA
| | - Yidong Bai
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - James D Lechleiter
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
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39
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Richter-Dennerlein R, Oeljeklaus S, Lorenzi I, Ronsör C, Bareth B, Schendzielorz AB, Wang C, Warscheid B, Rehling P, Dennerlein S. Mitochondrial Protein Synthesis Adapts to Influx of Nuclear-Encoded Protein. Cell 2016; 167:471-483.e10. [PMID: 27693358 PMCID: PMC5055049 DOI: 10.1016/j.cell.2016.09.003] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 08/01/2016] [Accepted: 08/30/2016] [Indexed: 12/11/2022]
Abstract
Mitochondrial ribosomes translate membrane integral core subunits of the oxidative phosphorylation system encoded by mtDNA. These translation products associate with nuclear-encoded, imported proteins to form enzyme complexes that produce ATP. Here, we show that human mitochondrial ribosomes display translational plasticity to cope with the supply of imported nuclear-encoded subunits. Ribosomes expressing mitochondrial-encoded COX1 mRNA selectively engage with cytochrome c oxidase assembly factors in the inner membrane. Assembly defects of the cytochrome c oxidase arrest mitochondrial translation in a ribosome nascent chain complex with a partially membrane-inserted COX1 translation product. This complex represents a primed state of the translation product that can be retrieved for assembly. These findings establish a mammalian translational plasticity pathway in mitochondria that enables adaptation of mitochondrial protein synthesis to the influx of nuclear-encoded subunits. Mitochondrial ribosomes display translational plasticity COX1 translation in mitochondria is stalled in the absence of nuclear-encoded COX4 A ribosome nascent chain complex of COX1 is a primed state for complex IV assembly MITRAC regulates translation via COX1 ribosome nascent chain complexes interaction
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Affiliation(s)
- Ricarda Richter-Dennerlein
- Department of Cellular Biochemistry, University Medical Centre Göttingen, GZMB, 37073 Göttingen, Germany
| | - Silke Oeljeklaus
- Department of Biochemistry and Functional Proteomics, Faculty of Biology, University Freiburg, 79104 Freiburg, Germany
| | - Isotta Lorenzi
- Department of Cellular Biochemistry, University Medical Centre Göttingen, GZMB, 37073 Göttingen, Germany
| | - Christin Ronsör
- Department of Cellular Biochemistry, University Medical Centre Göttingen, GZMB, 37073 Göttingen, Germany
| | - Bettina Bareth
- Department of Cellular Biochemistry, University Medical Centre Göttingen, GZMB, 37073 Göttingen, Germany
| | | | - Cong Wang
- Department of Cellular Biochemistry, University Medical Centre Göttingen, GZMB, 37073 Göttingen, Germany
| | - Bettina Warscheid
- Department of Biochemistry and Functional Proteomics, Faculty of Biology, University Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Centre Göttingen, GZMB, 37073 Göttingen, Germany; Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
| | - Sven Dennerlein
- Department of Cellular Biochemistry, University Medical Centre Göttingen, GZMB, 37073 Göttingen, Germany
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40
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Formosa LE, Hofer A, Tischner C, Wenz T, Ryan MT. Translation and Assembly of Radiolabeled Mitochondrial DNA-Encoded Protein Subunits from Cultured Cells and Isolated Mitochondria. Methods Mol Biol 2016; 1351:115-29. [PMID: 26530678 DOI: 10.1007/978-1-4939-3040-1_9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
In higher eukaryotes, the mitochondrial electron transport chain consists of five multi-subunit membrane complexes responsible for the generation of cellular ATP. Of these, four complexes are under dual genetic control as they contain subunits encoded by both the mitochondrial and nuclear genomes, thereby adding another layer of complexity to the puzzle of respiratory complex biogenesis. These subunits must be synthesized and assembled in a coordinated manner in order to ensure correct biogenesis of different respiratory complexes. Here, we describe techniques to (1) specifically radiolabel proteins encoded by mtDNA to monitor the rate of synthesis using pulse labeling methods, and (2) analyze the stability, assembly, and turnover of subunits using pulse-chase methods in cultured cells and isolated mitochondria.
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Affiliation(s)
- Luke E Formosa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Building 77, Level 2, Clayton Campus, Melbourne, VIC, 3800, Australia
| | - Annette Hofer
- Institute for Genetics and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Zülpicher Str. 47A, Cologne, 50674, Germany
| | - Christin Tischner
- Institute for Genetics and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Zülpicher Str. 47A, Cologne, 50674, Germany
| | - Tina Wenz
- Institute for Genetics and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Zülpicher Str. 47A, Cologne, 50674, Germany
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash University, Building 77, Level 2, Clayton Campus, Melbourne, VIC, 3800, Australia.
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Haag S, Sloan KE, Ranjan N, Warda AS, Kretschmer J, Blessing C, Hübner B, Seikowski J, Dennerlein S, Rehling P, Rodnina MV, Höbartner C, Bohnsack MT. NSUN3 and ABH1 modify the wobble position of mt-tRNAMet to expand codon recognition in mitochondrial translation. EMBO J 2016; 35:2104-2119. [PMID: 27497299 PMCID: PMC5048346 DOI: 10.15252/embj.201694885] [Citation(s) in RCA: 184] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/20/2016] [Indexed: 12/22/2022] Open
Abstract
Mitochondrial gene expression uses a non‐universal genetic code in mammals. Besides reading the conventional AUG codon, mitochondrial (mt‐)tRNAMet mediates incorporation of methionine on AUA and AUU codons during translation initiation and on AUA codons during elongation. We show that the RNA methyltransferase NSUN3 localises to mitochondria and interacts with mt‐tRNAMet to methylate cytosine 34 (C34) at the wobble position. NSUN3 specifically recognises the anticodon stem loop (ASL) of the tRNA, explaining why a mutation that compromises ASL basepairing leads to disease. We further identify ALKBH1/ABH1 as the dioxygenase responsible for oxidising m5C34 of mt‐tRNAMet to generate an f5C34 modification. In vitro codon recognition studies with mitochondrial translation factors reveal preferential utilisation of m5C34 mt‐tRNAMet in initiation. Depletion of either NSUN3 or ABH1 strongly affects mitochondrial translation in human cells, implying that modifications generated by both enzymes are necessary for mt‐tRNAMet function. Together, our data reveal how modifications in mt‐tRNAMet are generated by the sequential action of NSUN3 and ABH1, allowing the single mitochondrial tRNAMet to recognise the different codons encoding methionine.
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Affiliation(s)
- Sara Haag
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Katherine E Sloan
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Namit Ranjan
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ahmed S Warda
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Jens Kretschmer
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Charlotte Blessing
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Benedikt Hübner
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Jan Seikowski
- Institute for Organic and Biomolecular Chemistry, Georg-August-University, Göttingen, Germany Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Sven Dennerlein
- Institute for Cellular Biochemistry, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Peter Rehling
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany Institute for Cellular Biochemistry, University Medical Center Göttingen Georg-August-University, Göttingen, Germany Göttingen Centre for Molecular Biosciences, Georg-August-University, Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Claudia Höbartner
- Institute for Organic and Biomolecular Chemistry, Georg-August-University, Göttingen, Germany
| | - Markus T Bohnsack
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany Göttingen Centre for Molecular Biosciences, Georg-August-University, Göttingen, Germany
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Porcelli AM, Calvaruso MA, Iommarini L, Kurelac I, Zuntini R, Ferrari S, Gasparre G. A unique combination of rare mitochondrial ribosomal RNA variants affects the kinetics of complex I assembly. Int J Biochem Cell Biol 2016; 75:117-22. [PMID: 27102412 DOI: 10.1016/j.biocel.2016.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 04/08/2016] [Accepted: 04/15/2016] [Indexed: 01/17/2023]
Abstract
Mitochondrial DNA (mtDNA) mutations in respiratory complexes subunits contribute to a large spectrum of human diseases. Nonetheless, ribosomal RNA variants remain largely under-investigated from a functional point of view. We here report a unique combination of two rare mitochondrial rRNA variants detected by serendipity in a subject with chronic granulomatous disease and never reported to co-occur within the same mitochondrial haplotype. In silico prediction of the mitochondrial ribosomal structure showed a dramatic rearrangement of the rRNA secondary structure. Functional investigation of cybrids carrying this unique haplotype demonstrated that the co-occurrence of the two rRNA variants determines a slow-down of the mitochondrial protein synthesis, especially in cells with an elevated metabolic rate, which impairs the assembly kinetics of Complex I, induces a bioenergetic defect and stimulates reactive oxygen species production. In conclusion, our results point to a sub-pathogenic role for these two rare mitochondrial rRNA variants, when found in the unique combination here reported in a single individual.
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Affiliation(s)
- Anna Maria Porcelli
- Dip. Farmacia e Biotecnologie (FABIT), Università di Bologna, via Irnerio 42, 40126 Bologna, Italy; Centro Interdipartimentale di Ricerca Industriale Scienze della Vita e Tecnologie per la Salute, Università di Bologna, 40100 Bologna, Italy
| | | | - Luisa Iommarini
- Dip. Farmacia e Biotecnologie (FABIT), Università di Bologna, via Irnerio 42, 40126 Bologna, Italy
| | - Ivana Kurelac
- Dip. Scienze Mediche e Chirurgiche (DIMEC), U.O. Genetica Medica, Pol. Universitario S. Orsola-Malpighi, Università di Bologna, via Massarenti 9, 40138 Bologna, Italy
| | - Roberta Zuntini
- Dip. Scienze Mediche e Chirurgiche (DIMEC), U.O. Genetica Medica, Pol. Universitario S. Orsola-Malpighi, Università di Bologna, via Massarenti 9, 40138 Bologna, Italy
| | - Simona Ferrari
- Dip. Scienze Mediche e Chirurgiche (DIMEC), U.O. Genetica Medica, Pol. Universitario S. Orsola-Malpighi, Università di Bologna, via Massarenti 9, 40138 Bologna, Italy
| | - Giuseppe Gasparre
- Dip. Scienze Mediche e Chirurgiche (DIMEC), U.O. Genetica Medica, Pol. Universitario S. Orsola-Malpighi, Università di Bologna, via Massarenti 9, 40138 Bologna, Italy.
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Guarás A, Perales-Clemente E, Calvo E, Acín-Pérez R, Loureiro-Lopez M, Pujol C, Martínez-Carrascoso I, Nuñez E, García-Marqués F, Rodríguez-Hernández MA, Cortés A, Diaz F, Pérez-Martos A, Moraes CT, Fernández-Silva P, Trifunovic A, Navas P, Vazquez J, Enríquez JA. The CoQH2/CoQ Ratio Serves as a Sensor of Respiratory Chain Efficiency. Cell Rep 2016; 15:197-209. [PMID: 27052170 DOI: 10.1016/j.celrep.2016.03.009] [Citation(s) in RCA: 189] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 02/03/2016] [Accepted: 02/27/2016] [Indexed: 02/01/2023] Open
Abstract
Electrons feed into the mitochondrial electron transport chain (mETC) from NAD- or FAD-dependent enzymes. A shift from glucose to fatty acids increases electron flux through FAD, which can saturate the oxidation capacity of the dedicated coenzyme Q (CoQ) pool and result in the generation of reactive oxygen species. To prevent this, the mETC superstructure can be reconfigured through the degradation of respiratory complex I, liberating associated complex III to increase electron flux via FAD at the expense of NAD. Here, we demonstrate that this adaptation is driven by the ratio of reduced to oxidized CoQ. Saturation of CoQ oxidation capacity induces reverse electron transport from reduced CoQ to complex I, and the resulting local generation of superoxide oxidizes specific complex I proteins, triggering their degradation and the disintegration of the complex. Thus, CoQ redox status acts as a metabolic sensor that fine-tunes mETC configuration in order to match the prevailing substrate profile.
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Affiliation(s)
- Adela Guarás
- Departamento de Desarrollo y Reparación Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid 28029, Spain
| | - Ester Perales-Clemente
- Departamento de Desarrollo y Reparación Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid 28029, Spain
| | - Enrique Calvo
- Laboratorio de Proteómica Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid 28029, Spain
| | - Rebeca Acín-Pérez
- Departamento de Desarrollo y Reparación Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid 28029, Spain
| | - Marta Loureiro-Lopez
- Laboratorio de Proteómica Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid 28029, Spain
| | - Claire Pujol
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany; Institute for Mitochondrial Diseases and Aging, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Isabel Martínez-Carrascoso
- Departamento de Desarrollo y Reparación Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid 28029, Spain
| | - Estefanía Nuñez
- Laboratorio de Proteómica Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid 28029, Spain
| | - Fernando García-Marqués
- Laboratorio de Proteómica Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid 28029, Spain
| | - María Angeles Rodríguez-Hernández
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC, Sevilla 41013, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Sevilla 41013, Spain
| | - Ana Cortés
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC, Sevilla 41013, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Sevilla 41013, Spain
| | - Francisca Diaz
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Acisclo Pérez-Martos
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza 50009, Spain
| | - Carlos T Moraes
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; Department of Cell Biology and Anatomy, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Patricio Fernández-Silva
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza 50009, Spain
| | - Aleksandra Trifunovic
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany; Institute for Mitochondrial Diseases and Aging, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Plácido Navas
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC, Sevilla 41013, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Sevilla 41013, Spain
| | - Jesús Vazquez
- Laboratorio de Proteómica Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid 28029, Spain
| | - Jose A Enríquez
- Departamento de Desarrollo y Reparación Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid 28029, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza 50009, Spain.
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Martínez-Zamora A, Meseguer S, Esteve JM, Villarroya M, Aguado C, Enríquez JA, Knecht E, Armengod ME. Defective Expression of the Mitochondrial-tRNA Modifying Enzyme GTPBP3 Triggers AMPK-Mediated Adaptive Responses Involving Complex I Assembly Factors, Uncoupling Protein 2, and the Mitochondrial Pyruvate Carrier. PLoS One 2015; 10:e0144273. [PMID: 26642043 PMCID: PMC4671719 DOI: 10.1371/journal.pone.0144273] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 11/16/2015] [Indexed: 12/22/2022] Open
Abstract
GTPBP3 is an evolutionary conserved protein presumably involved in mitochondrial tRNA (mt-tRNA) modification. In humans, GTPBP3 mutations cause hypertrophic cardiomyopathy with lactic acidosis, and have been associated with a defect in mitochondrial translation, yet the pathomechanism remains unclear. Here we use a GTPBP3 stable-silencing model (shGTPBP3 cells) for a further characterization of the phenotype conferred by the GTPBP3 defect. We experimentally show for the first time that GTPBP3 depletion is associated with an mt-tRNA hypomodification status, as mt-tRNAs from shGTPBP3 cells were more sensitive to digestion by angiogenin than tRNAs from control cells. Despite the effect of stable silencing of GTPBP3 on global mitochondrial translation being rather mild, the steady-state levels and activity of Complex I, and cellular ATP levels were 50% of those found in the controls. Notably, the ATPase activity of Complex V increased by about 40% in GTPBP3 depleted cells suggesting that mitochondria consume ATP to maintain the membrane potential. Moreover, shGTPBP3 cells exhibited enhanced antioxidant capacity and a nearly 2-fold increase in the uncoupling protein UCP2 levels. Our data indicate that stable silencing of GTPBP3 triggers an AMPK-dependent retrograde signaling pathway that down-regulates the expression of the NDUFAF3 and NDUFAF4 Complex I assembly factors and the mitochondrial pyruvate carrier (MPC), while up-regulating the expression of UCP2. We also found that genes involved in glycolysis and oxidation of fatty acids are up-regulated. These data are compatible with a model in which high UCP2 levels, together with a reduction in pyruvate transport due to the down-regulation of MPC, promote a shift from pyruvate to fatty acid oxidation, and to an uncoupling of glycolysis and oxidative phosphorylation. These metabolic alterations, and the low ATP levels, may negatively affect heart function.
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Affiliation(s)
- Ana Martínez-Zamora
- Laboratory of RNA Modification and Mitochondrial Diseases, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Salvador Meseguer
- Laboratory of RNA Modification and Mitochondrial Diseases, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Juan M. Esteve
- Laboratory of Intracellular Protein Degradation and Rare Diseases, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Magda Villarroya
- Laboratory of RNA Modification and Mitochondrial Diseases, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Carmen Aguado
- Laboratory of Intracellular Protein Degradation and Rare Diseases, Centro de Investigación Príncipe Felipe, Valencia, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Raras (CIBERER), node U721, Valencia, Spain
| | - J. Antonio Enríquez
- Departamento de Desarrollo y Reparación Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Erwin Knecht
- Laboratory of Intracellular Protein Degradation and Rare Diseases, Centro de Investigación Príncipe Felipe, Valencia, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Raras (CIBERER), node U721, Valencia, Spain
| | - M.-Eugenia Armengod
- Laboratory of RNA Modification and Mitochondrial Diseases, Centro de Investigación Príncipe Felipe, Valencia, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Raras (CIBERER), node U721, Valencia, Spain
- * E-mail:
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45
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Yang H, Zhang M, Wang X, Zhang H, Zhang J, Jing L, Liao L, Wang M. TNF Accelerates Death of Mandibular Condyle Chondrocytes in Rats with Biomechanical Stimulation-Induced Temporomandibular Joint Disease. PLoS One 2015; 10:e0141774. [PMID: 26529096 PMCID: PMC4631347 DOI: 10.1371/journal.pone.0141774] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/13/2015] [Indexed: 11/19/2022] Open
Abstract
Objective To determine if temporomandibular joint chondrocyte apoptosis is induced in rats with dental biomechanical stimulation and what a role TNF takes. Methods Thirty-two rats were divided into 4 groups (n = 8/group) and exposed to incisor mal-occlusion induced by unilateral anterior crossbite biomechanical stimulation. Two groups were sampled at 2 or 4 weeks. The other two groups were treated with local injections of a TNF inhibitor or PBS into the temporomandibular joints area at 2 weeks and then sampled at 4 weeks. Twenty-four rats either served as unilateral anterior crossbite mock operation controls (n = 8/group) with sampling at 2 or 4 weeks or received a local injection of the TNF inhibitor at 2 weeks with sampling at 4 weeks. Chondrocytes were isolated from the temporomandibular joints of 6 additional rats and treated with TNF in vitro. Joint samples were assessed using Hematoxylin&eosin, Safranin O, TUNEL and immunohistochemistry staining, real-time PCR, fluorogenic activity assays and Western blot analyses. The isolated chondrocytes were also analyzed by flow cytometry. Results Unilateral anterior crossbite stimulation led to temporomandibular joint cartilage degradation, associated with an increase in TUNEL-positive chondrocytes number, caspase-9 expression levels, and the release of cytochrome c from mitochondria at 2 weeks without changes in TNF and caspase-8 levels until after 4 weeks. TNF stimulated apoptosis of the isolated chondrocytes and up-regulated caspase-8 expression, but did not change caspase-9 expression levels. Local injection of TNF inhibitor down-regulated caspase-8 expression and reduced TUNEL-positive cell number, but did not reverse cartilage thickness reduction, caspase-9 up-regulation or cytochrome c release. Conclusions Unilateral anterior crossbite stimulation induces mitochondrion-mediated apoptosis of articular chondrocytes. TNF accelerated the unilateral anterior crossbite induced chondrocytes apoptosis via death-receptor pathway. However, anti-TNF therapy does not prevent cartilage loss in this model of temporomandibular joint.
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Affiliation(s)
- Hongxu Yang
- State Key Laboratory of Military Stomatology, Department of Oral Anatomy and Physiology and TMD, School of Stomatology, the Fourth Military Medical University, 145 Changle West Road, Xi’an, China
| | - Mian Zhang
- State Key Laboratory of Military Stomatology, Department of Oral Anatomy and Physiology and TMD, School of Stomatology, the Fourth Military Medical University, 145 Changle West Road, Xi’an, China
| | - Xin Wang
- State Key Laboratory of Military Stomatology, Department of Oral Anatomy and Physiology and TMD, School of Stomatology, the Fourth Military Medical University, 145 Changle West Road, Xi’an, China
| | - Hongyun Zhang
- State Key Laboratory of Military Stomatology, Department of Oral Anatomy and Physiology and TMD, School of Stomatology, the Fourth Military Medical University, 145 Changle West Road, Xi’an, China
| | - Jing Zhang
- State Key Laboratory of Military Stomatology, Department of Oral Anatomy and Physiology and TMD, School of Stomatology, the Fourth Military Medical University, 145 Changle West Road, Xi’an, China
| | - Lei Jing
- State Key Laboratory of Military Stomatology, Department of Oral Anatomy and Physiology and TMD, School of Stomatology, the Fourth Military Medical University, 145 Changle West Road, Xi’an, China
| | - Lifan Liao
- State Key Laboratory of Military Stomatology, Department of Oral Anatomy and Physiology and TMD, School of Stomatology, the Fourth Military Medical University, 145 Changle West Road, Xi’an, China
| | - Meiqing Wang
- State Key Laboratory of Military Stomatology, Department of Oral Anatomy and Physiology and TMD, School of Stomatology, the Fourth Military Medical University, 145 Changle West Road, Xi’an, China
- * E-mail:
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Wesolowska M, Gorman GS, Alston CL, Pajak A, Pyle A, He L, Griffin H, Chinnery PF, Miller JAL, Schaefer AM, Taylor RW, Lightowlers RN, Chrzanowska-Lightowlers ZM. Adult Onset Leigh Syndrome in the Intensive Care Setting: A Novel Presentation of a C12orf65 Related Mitochondrial Disease. J Neuromuscul Dis 2015; 2:409-419. [PMID: 27858754 PMCID: PMC5240610 DOI: 10.3233/jnd-150121] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Background: Mitochondrial disease can present at any age, with dysfunction in almost any tissue making diagnosis a challenge. It can result from inherited or sporadic mutations in either the mitochondrial or the nuclear genome, many of which affect intraorganellar gene expression. The estimated prevalence of 1/4300 indicates these to be amongst the commonest inherited neuromuscular disorders, emphasising the importance of recognition of the diagnostic clinical features. Objective: Despite major advances in our understanding of the molecular basis of mitochondrial diseases, accurate and early diagnoses are critically dependent on the fastidious clinical and biochemical characterisation of patients. Here we describe a patient harbouring a previously reported homozygous mutation in C12orf65, a mitochondrial protein of unknown function, which does not adhere to the proposed distinct genotype-phenotype relationship. Methods: We performed clinical, biochemical and molecular analysis including whole exome sequencing on patient samples and cell lines. Results: We report an extremely rare case of an adult presenting with Leigh-like disease, in intensive care, in the 5th decade of life, harbouring a recessively inherited mutation previously reported in children. A global reduction in intra-mitochondrial protein synthesis was observed despite normal or elevated levels of mt-RNA, leading to an isolated complex IV deficiency. Conclusions: All the reported C12orf65 mutations have shown an autosomal recessive pattern of inheritance. Mitochondrial disease causing mutations inherited in this manner are usually of early onset and associated with a severe, often fatal clinical phenotype. Presentations in adulthood are usually less severe. This patient’s late adulthood presentation is in sharp contrast emphasising the clinical variability that is characteristic of mitochondrial disease and illustrates why making a definitive diagnosis remains a formidable challenge.
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Affiliation(s)
- Maria Wesolowska
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK.,Wellcome Trust Centre for Mitochondrial Research, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Grainne S Gorman
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK.,Movelab, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Charlotte L Alston
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Aleksandra Pajak
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK.,Department Laboratory Medicine, Karolinska Institutet, Division of metabolic diseases, Stockholm, Retziusväg 8, Sweden
| | - Angela Pyle
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Langping He
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Helen Griffin
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Patrick F Chinnery
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - James A L Miller
- Department of Neurology, Newcastle upon Tyne Hospitals NHS Foundation Trust Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - Andrew M Schaefer
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Robert W Taylor
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Robert N Lightowlers
- Wellcome Trust Centre for Mitochondrial Research, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
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Llobet L, Toivonen JM, Montoya J, Ruiz-Pesini E, López-Gallardo E. Xenobiotics that affect oxidative phosphorylation alter differentiation of human adipose-derived stem cells at concentrations that are found in human blood. Dis Model Mech 2015; 8:1441-55. [PMID: 26398948 PMCID: PMC4631789 DOI: 10.1242/dmm.021774] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 09/03/2015] [Indexed: 12/17/2022] Open
Abstract
Adipogenesis is accompanied by differentiation of adipose tissue-derived stem cells to adipocytes. As part of this differentiation, biogenesis of the oxidative phosphorylation system occurs. Many chemical compounds used in medicine, agriculture or other human activities affect oxidative phosphorylation function. Therefore, these xenobiotics could alter adipogenesis. We have analyzed the effects on adipocyte differentiation of some xenobiotics that act on the oxidative phosphorylation system. The tested concentrations have been previously reported in human blood. Our results show that pharmaceutical drugs that decrease mitochondrial DNA replication, such as nucleoside reverse transcriptase inhibitors, or inhibitors of mitochondrial protein synthesis, such as ribosomal antibiotics, diminish adipocyte differentiation and leptin secretion. By contrast, the environmental chemical pollutant tributyltin chloride, which inhibits the ATP synthase of the oxidative phosphorylation system, can promote adipocyte differentiation and leptin secretion, leading to obesity and metabolic syndrome as postulated by the obesogen hypothesis. Summary: Some medical drugs and environmental chemical pollutants acting on the oxidative phosphorylation system can alter adipocyte differentiation and adipogenesis and, thus, have important consequences for human health.
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Affiliation(s)
- Laura Llobet
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, 50013-Zaragoza, Spain Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza, 50013-Zaragoza, Spain CIBER de Enfermedades Raras (CIBERER), Universidad de Zaragoza, 50013-Zaragoza, Spain
| | - Janne M Toivonen
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, 50013-Zaragoza, Spain Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza, 50013-Zaragoza, Spain
| | - Julio Montoya
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, 50013-Zaragoza, Spain Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza, 50013-Zaragoza, Spain CIBER de Enfermedades Raras (CIBERER), Universidad de Zaragoza, 50013-Zaragoza, Spain
| | - Eduardo Ruiz-Pesini
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, 50013-Zaragoza, Spain Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza, 50013-Zaragoza, Spain CIBER de Enfermedades Raras (CIBERER), Universidad de Zaragoza, 50013-Zaragoza, Spain Fundación ARAID, Universidad de Zaragoza, 50013-Zaragoza, Spain
| | - Ester López-Gallardo
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, 50013-Zaragoza, Spain Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza, 50013-Zaragoza, Spain CIBER de Enfermedades Raras (CIBERER), Universidad de Zaragoza, 50013-Zaragoza, Spain
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48
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Dennerlein S, Oeljeklaus S, Jans D, Hellwig C, Bareth B, Jakobs S, Deckers M, Warscheid B, Rehling P. MITRAC7 Acts as a COX1-Specific Chaperone and Reveals a Checkpoint during Cytochrome c Oxidase Assembly. Cell Rep 2015; 12:1644-55. [PMID: 26321642 DOI: 10.1016/j.celrep.2015.08.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 07/16/2015] [Accepted: 08/03/2015] [Indexed: 11/29/2022] Open
Abstract
Cytochrome c oxidase, the terminal enzyme of the respiratory chain, is assembled from mitochondria- and nuclear-encoded subunits. The MITRAC complex represents the central assembly intermediate during this process as it receives imported subunits and regulates mitochondrial translation of COX1 mRNA. The molecular processes that promote and regulate the progression of assembly downstream of MITRAC are still unknown. Here, we identify MITRAC7 as a constituent of a late form of MITRAC and as a COX1-specific chaperone. MITRAC7 is required for cytochrome c oxidase biogenesis. Surprisingly, loss of MITRAC7 or an increase in its amount causes selective cytochrome c oxidase deficiency in human cells. We demonstrate that increased MITRAC7 levels stabilize and trap COX1 in MITRAC, blocking progression in the assembly process. In contrast, MITRAC7 deficiency leads to turnover of newly synthesized COX1. Accordingly, MITRAC7 affects the biogenesis pathway by stabilizing newly synthesized COX1 in assembly intermediates, concomitantly preventing turnover.
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Affiliation(s)
- Sven Dennerlein
- Department of Cellular Biochemistry, University of Göttingen, 37073 Göttingen, Germany
| | - Silke Oeljeklaus
- Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Daniel Jans
- Department of NanoBiophotonics, Mitochondrial Structure and Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Christin Hellwig
- Department of Cellular Biochemistry, University of Göttingen, 37073 Göttingen, Germany
| | - Bettina Bareth
- Department of Cellular Biochemistry, University of Göttingen, 37073 Göttingen, Germany
| | - Stefan Jakobs
- Department of NanoBiophotonics, Mitochondrial Structure and Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany; Department of Neurology, University of Göttingen, 37073 Göttingen, Germany
| | - Markus Deckers
- Department of Cellular Biochemistry, University of Göttingen, 37073 Göttingen, Germany
| | - Bettina Warscheid
- Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University of Göttingen, 37073 Göttingen, Germany; Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
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49
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Cooperation between COA6 and SCO2 in COX2 maturation during cytochrome c oxidase assembly links two mitochondrial cardiomyopathies. Cell Metab 2015; 21:823-33. [PMID: 25959673 DOI: 10.1016/j.cmet.2015.04.012] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/03/2015] [Accepted: 04/04/2015] [Indexed: 11/20/2022]
Abstract
Three mitochondria-encoded subunits form the catalytic core of cytochrome c oxidase, the terminal enzyme of the respiratory chain. COX1 and COX2 contain heme and copper redox centers, which are integrated during assembly of the enzyme. Defects in this process lead to an enzyme deficiency and manifest as mitochondrial disorders in humans. Here we demonstrate that COA6 is specifically required for COX2 biogenesis. Absence of COA6 leads to fast turnover of newly synthesized COX2 and a concomitant reduction in cytochrome c oxidase levels. COA6 interacts transiently with the copper-containing catalytic domain of newly synthesized COX2. Interestingly, similar to the copper metallochaperone SCO2, loss of COA6 causes cardiomyopathy in humans. We show that COA6 and SCO2 interact and that corresponding pathogenic mutations in each protein affect complex formation. Our analyses define COA6 as a constituent of the mitochondrial copper relay system, linking defects in COX2 metallation to cardiac cytochrome c oxidase deficiency.
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50
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Vartak R, Deng J, Fang H, Bai Y. Redefining the roles of mitochondrial DNA-encoded subunits in respiratory Complex I assembly. Biochim Biophys Acta Mol Basis Dis 2015; 1852:1531-9. [PMID: 25887158 DOI: 10.1016/j.bbadis.2015.04.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/01/2015] [Accepted: 04/07/2015] [Indexed: 02/03/2023]
Abstract
Respiratory Complex I deficiency is implicated in numerous degenerative and metabolic diseases. In particular, mutations in several mitochondrial DNA (mtDNA)-encoded Complex I subunits including ND4, ND5 and ND6 have been identified in several neurological diseases. We previously demonstrated that these subunits played essential roles in Complex I assembly which in turn affected mitochondrial function. Here, we carried out a comprehensive study of the Complex I assembly pathway. We identified a new Complex I intermediate containing both membrane and matrix arms at an early assembly stage. We find that lack of the ND6 subunit does not hinder membrane arm formation; instead it recruits ND1 and ND5 enters the intermediate. While ND4 is important for the formation of the newly identified intermediate, the addition of ND5 stabilizes the complex and is required for the critical transition from Complex I to supercomplex assembly. As a result, the Complex I assembly pathway has been redefined in this study.
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Affiliation(s)
- Rasika Vartak
- Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Janice Deng
- Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Hezhi Fang
- Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Yidong Bai
- Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
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