151
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Kahlhöfer F, Kmita K, Wittig I, Zwicker K, Zickermann V. Accessory subunit NUYM (NDUFS4) is required for stability of the electron input module and activity of mitochondrial complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1858:175-181. [PMID: 27871794 DOI: 10.1016/j.bbabio.2016.11.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 11/15/2016] [Accepted: 11/17/2016] [Indexed: 11/18/2022]
Abstract
Mitochondrial complex I is an intricate 1MDa membrane protein complex with a central role in aerobic energy metabolism. The minimal form of complex I consists of fourteen central subunits that are conserved from bacteria to man. In addition, eukaryotic complex I comprises some 30 accessory subunits of largely unknown function. The gene for the accessory NDUFS4 subunit of human complex I is a hot spot for fatal pathogenic mutations in humans. We have deleted the gene for the orthologous NUYM subunit in the aerobic yeast Yarrowia lipolytica, an established model system to study eukaryotic complex I and complex I linked diseases. We observed assembly of complex I which lacked only subunit NUYM and retained weak interaction with assembly factor N7BML (human NDUFAF2). Absence of NUYM caused distortion of iron sulfur clusters of the electron input domain leading to decreased complex I activity and increased release of reactive oxygen species. We conclude that NUYM has an important stabilizing function for the electron input module of complex I and is essential for proper complex I function.
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Affiliation(s)
- Flora Kahlhöfer
- Structural Bioenergetics Group, Institute of Biochemistry II, Medical School, Goethe-University Frankfurt am Main, Germany
| | - Katarzyna Kmita
- Structural Bioenergetics Group, Institute of Biochemistry II, Medical School, Goethe-University Frankfurt am Main, Germany
| | - Ilka Wittig
- Functional Proteomics, Institute of Biochemistry I, Medical School, Goethe-University Frankfurt am Main, Germany; Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University Frankfurt am Main, Germany
| | - Klaus Zwicker
- Institute of Biochemistry I, Medical School, Goethe University Frankfurt am Main, Germany
| | - Volker Zickermann
- Structural Bioenergetics Group, Institute of Biochemistry II, Medical School, Goethe-University Frankfurt am Main, Germany; Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University Frankfurt am Main, Germany.
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152
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Alston CL, Rocha MC, Lax NZ, Turnbull DM, Taylor RW. The genetics and pathology of mitochondrial disease. J Pathol 2016; 241:236-250. [PMID: 27659608 PMCID: PMC5215404 DOI: 10.1002/path.4809] [Citation(s) in RCA: 263] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 09/15/2016] [Accepted: 09/16/2016] [Indexed: 12/30/2022]
Abstract
Mitochondria are double-membrane-bound organelles that are present in all nucleated eukaryotic cells and are responsible for the production of cellular energy in the form of ATP. Mitochondrial function is under dual genetic control - the 16.6-kb mitochondrial genome, with only 37 genes, and the nuclear genome, which encodes the remaining ∼1300 proteins of the mitoproteome. Mitochondrial dysfunction can arise because of defects in either mitochondrial DNA or nuclear mitochondrial genes, and can present in childhood or adulthood in association with vast clinical heterogeneity, with symptoms affecting a single organ or tissue, or multisystem involvement. There is no cure for mitochondrial disease for the vast majority of mitochondrial disease patients, and a genetic diagnosis is therefore crucial for genetic counselling and recurrence risk calculation, and can impact on the clinical management of affected patients. Next-generation sequencing strategies are proving pivotal in the discovery of new disease genes and the diagnosis of clinically affected patients; mutations in >250 genes have now been shown to cause mitochondrial disease, and the biochemical, histochemical, immunocytochemical and neuropathological characterization of these patients has led to improved diagnostic testing strategies and novel diagnostic techniques. This review focuses on the current genetic landscape associated with mitochondrial disease, before focusing on advances in studying associated mitochondrial pathology in two, clinically relevant organs - skeletal muscle and brain. © 2016 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Charlotte L Alston
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Mariana C Rocha
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Nichola Z Lax
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Doug M Turnbull
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Robert W Taylor
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, UK
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153
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Wai T, Saita S, Nolte H, Müller S, König T, Richter-Dennerlein R, Sprenger HG, Madrenas J, Mühlmeister M, Brandt U, Krüger M, Langer T. The membrane scaffold SLP2 anchors a proteolytic hub in mitochondria containing PARL and the i-AAA protease YME1L. EMBO Rep 2016; 17:1844-1856. [PMID: 27737933 DOI: 10.15252/embr.201642698] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 09/13/2016] [Accepted: 09/15/2016] [Indexed: 02/05/2023] Open
Abstract
The SPFH (stomatin, prohibitin, flotillin, HflC/K) superfamily is composed of scaffold proteins that form ring-like structures and locally specify the protein-lipid composition in a variety of cellular membranes. Stomatin-like protein 2 (SLP2) is a member of this superfamily that localizes to the mitochondrial inner membrane (IM) where it acts as a membrane organizer. Here, we report that SLP2 anchors a large protease complex composed of the rhomboid protease PARL and the i-AAA protease YME1L, which we term the SPY complex (for SLP2-PARL-YME1L). Association with SLP2 in the SPY complex regulates PARL-mediated processing of PTEN-induced kinase PINK1 and the phosphatase PGAM5 in mitochondria. Moreover, SLP2 inhibits the stress-activated peptidase OMA1, which can bind to SLP2 and cleaves PGAM5 in depolarized mitochondria. SLP2 restricts OMA1-mediated processing of the dynamin-like GTPase OPA1 allowing stress-induced mitochondrial hyperfusion under starvation conditions. Together, our results reveal an important role of SLP2 membrane scaffolds for the spatial organization of IM proteases regulating mitochondrial dynamics, quality control, and cell survival.
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Affiliation(s)
- Timothy Wai
- Institute for Genetics Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and University of Cologne, Cologne, Germany
| | - Shotaro Saita
- Institute for Genetics Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and University of Cologne, Cologne, Germany
| | - Hendrik Nolte
- Institute for Genetics Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and University of Cologne, Cologne, Germany
| | - Sebastian Müller
- Institute for Genetics Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and University of Cologne, Cologne, Germany
| | - Tim König
- Institute for Genetics Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and University of Cologne, Cologne, Germany
| | - Ricarda Richter-Dennerlein
- Institute for Genetics Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and University of Cologne, Cologne, Germany
| | - Hans-Georg Sprenger
- Institute for Genetics Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and University of Cologne, Cologne, Germany
| | - Joaquin Madrenas
- Microbiome and Disease Tolerance Centre, Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Mareike Mühlmeister
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ulrich Brandt
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marcus Krüger
- Institute for Genetics Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and University of Cologne, Cologne, Germany
| | - Thomas Langer
- Institute for Genetics Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and University of Cologne, Cologne, Germany .,Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
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154
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Membrane-bound electron transport systems of an anammox bacterium: A complexome analysis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1694-704. [DOI: 10.1016/j.bbabio.2016.07.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/14/2016] [Accepted: 07/19/2016] [Indexed: 11/24/2022]
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155
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The m -AAA Protease Associated with Neurodegeneration Limits MCU Activity in Mitochondria. Mol Cell 2016; 64:148-162. [DOI: 10.1016/j.molcel.2016.08.020] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 06/16/2016] [Accepted: 08/12/2016] [Indexed: 11/23/2022]
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156
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Rudashevskaya EL, Sickmann A, Markoutsa S. Global profiling of protein complexes: current approaches and their perspective in biomedical research. Expert Rev Proteomics 2016; 13:951-964. [PMID: 27602509 DOI: 10.1080/14789450.2016.1233064] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Despite the rapid evolution of proteomic methods, protein interactions and their participation in protein complexes - an important aspect of their function - has rarely been investigated on the proteome-wide level. Disease states, such as muscular dystrophy or viral infection, are induced by interference in protein-protein interactions within complexes. The purpose of this review is to describe the current methods for global complexome analysis and to critically discuss the challenges and opportunities for the application of these methods in biomedical research. Areas covered: We discuss advancements in experimental techniques and computational tools that facilitate profiling of the complexome. The main focus is on the separation of native protein complexes via size exclusion chromatography and gel electrophoresis, which has recently been combined with quantitative mass spectrometry, for a global protein-complex profiling. The development of this approach has been supported by advanced bioinformatics strategies and fast and sensitive mass spectrometers that have allowed the analysis of whole cell lysates. The application of this technique to biomedical research is assessed, and future directions are anticipated. Expert commentary: The methodology is quite new, and has already shown great potential when combined with complementary methods for detection of protein complexes.
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Affiliation(s)
- Elena L Rudashevskaya
- a Department of Bioanalytics , Leibniz-Institut für Analytische Wissenschaften - ISAS eV , Dortmund , Germany
| | - Albert Sickmann
- a Department of Bioanalytics , Leibniz-Institut für Analytische Wissenschaften - ISAS eV , Dortmund , Germany.,b Medizinisches Proteom-Center , Ruhr-Universität Bochum , Bochum , Germany.,c School of Natural & Computing Sciences, Department of Chemistry , University of Aberdeen , Aberdeen , UK
| | - Stavroula Markoutsa
- a Department of Bioanalytics , Leibniz-Institut für Analytische Wissenschaften - ISAS eV , Dortmund , Germany
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157
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Stroud DA, Surgenor EE, Formosa LE, Reljic B, Frazier AE, Dibley MG, Osellame LD, Stait T, Beilharz TH, Thorburn DR, Salim A, Ryan MT. Accessory subunits are integral for assembly and function of human mitochondrial complex I. Nature 2016; 538:123-126. [PMID: 27626371 DOI: 10.1038/nature19754] [Citation(s) in RCA: 354] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 08/22/2016] [Indexed: 01/02/2023]
Abstract
Complex I (NADH:ubiquinone oxidoreductase) is the first enzyme of the mitochondrial respiratory chain and is composed of 45 subunits in humans, making it one of the largest known multi-subunit membrane protein complexes. Complex I exists in supercomplex forms with respiratory chain complexes III and IV, which are together required for the generation of a transmembrane proton gradient used for the synthesis of ATP. Complex I is also a major source of damaging reactive oxygen species and its dysfunction is associated with mitochondrial disease, Parkinson's disease and ageing. Bacterial and human complex I share 14 core subunits that are essential for enzymatic function; however, the role and necessity of the remaining 31 human accessory subunits is unclear. The incorporation of accessory subunits into the complex increases the cellular energetic cost and has necessitated the involvement of numerous assembly factors for complex I biogenesis. Here we use gene editing to generate human knockout cell lines for each accessory subunit. We show that 25 subunits are strictly required for assembly of a functional complex and 1 subunit is essential for cell viability. Quantitative proteomic analysis of cell lines revealed that loss of each subunit affects the stability of other subunits residing in the same structural module. Analysis of proteomic changes after the loss of specific modules revealed that ATP5SL and DMAC1 are required for assembly of the distal portion of the complex I membrane arm. Our results demonstrate the broad importance of accessory subunits in the structure and function of human complex I. Coupling gene-editing technology with proteomics represents a powerful tool for dissecting large multi-subunit complexes and enables the study of complex dysfunction at a cellular level.
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Affiliation(s)
- David A Stroud
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
| | - Elliot E Surgenor
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
| | - Luke E Formosa
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University 3086, Melbourne, Australia
| | - Boris Reljic
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University 3086, Melbourne, Australia
| | - Ann E Frazier
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne 3052, Australia.,Department of Pediatrics, University of Melbourne, Melbourne 3052, Australia
| | - Marris G Dibley
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
| | - Laura D Osellame
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
| | - Tegan Stait
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne 3052, Australia
| | - Traude H Beilharz
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
| | - David R Thorburn
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne 3052, Australia.,Department of Pediatrics, University of Melbourne, Melbourne 3052, Australia.,Victorian Clinical Genetics Services, Royal Children's Hospital 3052, Melbourne, Australia
| | - Agus Salim
- Department of Mathematics and Statistics, La Trobe University 3086, Melbourne Australia
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
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158
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Giachin G, Bouverot R, Acajjaoui S, Pantalone S, Soler-López M. Dynamics of Human Mitochondrial Complex I Assembly: Implications for Neurodegenerative Diseases. Front Mol Biosci 2016; 3:43. [PMID: 27597947 PMCID: PMC4992684 DOI: 10.3389/fmolb.2016.00043] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 08/02/2016] [Indexed: 12/14/2022] Open
Abstract
Neurons are extremely energy demanding cells and highly dependent on the mitochondrial oxidative phosphorylation (OXPHOS) system. Mitochondria generate the energetic potential via the respiratory complexes I to IV, which constitute the electron transport chain (ETC), together with complex V. These redox reactions release energy in the form of ATP and also generate reactive oxygen species (ROS) that are involved in cell signaling but can eventually lead to oxidative stress. Complex I (CI or NADH:ubiquinone oxidoreductase) is the largest ETC enzyme, containing 44 subunits and the main contributor to ROS production. In recent years, the structure of the CI has become available and has provided new insights into CI assembly. A number of chaperones have been identified in the assembly and stability of the mature holo-CI, although they are not part of its final structure. Interestingly, CI dysfunction is the most common OXPHOS disorder in humans and defects in the CI assembly process are often observed. However, the dynamics of the events leading to CI biogenesis remain elusive, which precludes our understanding of how ETC malfunctioning affects neuronal integrity. Here, we review the current knowledge of the structural features of CI and its assembly factors and the potential role of CI misassembly in human disorders such as Complex I Deficiencies or Alzheimer's and Parkinson's diseases.
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Affiliation(s)
- Gabriele Giachin
- Structural Biology Group, European Synchrotron Radiation Facility Grenoble, France
| | - Romain Bouverot
- Structural Biology Group, European Synchrotron Radiation Facility Grenoble, France
| | - Samira Acajjaoui
- Structural Biology Group, European Synchrotron Radiation Facility Grenoble, France
| | - Serena Pantalone
- Structural Biology Group, European Synchrotron Radiation Facility Grenoble, France
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159
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Zurita Rendón O, Antonicka H, Horvath R, Shoubridge EA. A Mutation in the Flavin Adenine Dinucleotide-Dependent Oxidoreductase FOXRED1 Results in Cell-Type-Specific Assembly Defects in Oxidative Phosphorylation Complexes I and II. Mol Cell Biol 2016; 36:2132-40. [PMID: 27215383 PMCID: PMC4968213 DOI: 10.1128/mcb.00066-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 02/14/2016] [Accepted: 05/16/2016] [Indexed: 11/20/2022] Open
Abstract
Complex I (NADH ubiquinone oxidoreductase) is a large multisubunit enzyme that catalyzes the first step in oxidative phosphorylation (OXPHOS). In mammals, complex I biogenesis occurs in a stepwise manner, a process that requires the participation of several nucleus-encoded accessory proteins. The FAD-dependent oxidoreductase-containing domain 1 (FOXRED1) protein is a complex I assembly factor; however, its specific role in the assembly pathway remains poorly understood. We identified a homozygous missense mutation, c.1308 G→A (p.V421M) in FOXRED1 in a patient who presented with epilepsy and severe psychomotor retardation. A patient myoblast line showed a severe reduction in complex I, associated with the accumulation of subassemblies centered around ∼340 kDa, and a milder decrease in complex II, all of which were rescued by retroviral expression of wild-type FOXRED1. Two additional assembly factors, AIFM1 and ACAD9, coimmunoprecipitated with FOXRED1, and all were associated with a 370-kDa complex I subassembly that, together with a 315-kDa subassembly, forms the 550-kDa subcomplex. Loss of FOXRED1 function prevents efficient formation of this midassembly subcomplex. Although we could not identify subassemblies of complex II, our results establish that FOXRED1 function is both broader than expected, involving the assembly of two flavoprotein-containing OXPHOS complexes, and cell type specific.
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Affiliation(s)
- Olga Zurita Rendón
- Montreal Neurological Institute and Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Hana Antonicka
- Montreal Neurological Institute and Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Rita Horvath
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Eric A Shoubridge
- Montreal Neurological Institute and Department of Human Genetics, McGill University, Montreal, Quebec, Canada
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160
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Anand R, Strecker V, Urbach J, Wittig I, Reichert AS. Mic13 Is Essential for Formation of Crista Junctions in Mammalian Cells. PLoS One 2016; 11:e0160258. [PMID: 27479602 PMCID: PMC4968808 DOI: 10.1371/journal.pone.0160258] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 07/15/2016] [Indexed: 12/11/2022] Open
Abstract
Mitochondrial cristae are connected to the inner boundary membrane via crista junctions which are implicated in the regulation of oxidative phosphorylation, apoptosis, and import of lipids and proteins. The MICOS complex determines formation of crista junctions. We performed complexome profiling and identified Mic13, also termed Qil1, as a subunit of the MICOS complex. We show that MIC13 is an inner membrane protein physically interacting with MIC60, a central subunit of the MICOS complex. Using the CRISPR/Cas method we generated the first cell line deleted for MIC13. These knockout cells show a complete loss of crista junctions demonstrating that MIC13 is strictly required for the formation of crista junctions. MIC13 is required for the assembly of MIC10, MIC26, and MIC27 into the MICOS complex. However, it is not needed for the formation of the MIC60/MIC19/MIC25 subcomplex suggesting that the latter is not sufficient for crista junction formation. MIC13 is also dispensable for assembly of respiratory chain complexes and for maintaining mitochondrial network morphology. Still, lack of MIC13 resulted in a moderate reduction of mitochondrial respiration. In summary, we show that MIC13 has a fundamental role in crista junction formation and that assembly of respiratory chain supercomplexes is independent of mitochondrial cristae shape.
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Affiliation(s)
- Ruchika Anand
- Institute of Biochemistry and Molecular Biology I, Heinrich Heine University, Medical Faculty, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Valentina Strecker
- Functional Proteomics, SFB 815 Core Unit, Faculty of Medicine, Goethe-University, Frankfurt am Main, Germany
| | - Jennifer Urbach
- Institute of Biochemistry and Molecular Biology I, Heinrich Heine University, Medical Faculty, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Ilka Wittig
- Functional Proteomics, SFB 815 Core Unit, Faculty of Medicine, Goethe-University, Frankfurt am Main, Germany
- Cluster of Excellence “Macromolecular Complexes”, Goethe University, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Andreas S. Reichert
- Institute of Biochemistry and Molecular Biology I, Heinrich Heine University, Medical Faculty, Universitätsstr. 1, 40225, Düsseldorf, Germany
- * E-mail:
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161
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Rhein VF, Carroll J, Ding S, Fearnley IM, Walker JE. NDUFAF5 Hydroxylates NDUFS7 at an Early Stage in the Assembly of Human Complex I. J Biol Chem 2016; 291:14851-60. [PMID: 27226634 PMCID: PMC4938201 DOI: 10.1074/jbc.m116.734970] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Indexed: 02/02/2023] Open
Abstract
Complex I (NADH ubiquinone oxidoreductase) in mammalian mitochondria is an L-shaped assembly of 45 proteins. One arm lies in the inner membrane, and the other extends about 100 Å into the matrix of the organelle. The extrinsic arm contains binding sites for NADH, the primary electron acceptor FMN, and seven iron-sulfur clusters that form a pathway for electrons linking FMN to the terminal electron acceptor, ubiquinone, which is bound in a tunnel in the region of the junction between the arms. The membrane arm contains four antiporter-like domains, energetically coupled to the quinone site and involved in pumping protons from the matrix into the intermembrane space contributing to the proton motive force. Seven of the subunits, forming the core of the membrane arm, are translated from mitochondrial genes, and the remaining subunits, the products of nuclear genes, are imported from the cytosol. Their assembly is coordinated by at least thirteen extrinsic assembly factor proteins that are not part of the fully assembled complex. They assist in insertion of co-factors and in building up the complex from smaller sub-assemblies. One such factor, NDUFAF5, belongs to the family of seven-β-strand S-adenosylmethionine-dependent methyltransferases. However, similar to another family member, RdmB, it catalyzes the introduction of a hydroxyl group, in the case of NDUFAF5, into Arg-73 in the NDUFS7 subunit of human complex I. This modification occurs early in the pathway of assembly of complex I, before the formation of the juncture between peripheral and membrane arms.
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Affiliation(s)
- Virginie F. Rhein
- From the Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom
| | - Joe Carroll
- From the Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom
| | - Shujing Ding
- From the Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom
| | - Ian M. Fearnley
- From the Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom
| | - John E. Walker
- From the Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom, To whom correspondence should be addressed. E-mail:
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162
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Alston C, Compton A, Formosa L, Strecker V, Oláhová M, Haack T, Smet J, Stouffs K, Diakumis P, Ciara E, Cassiman D, Romain N, Yarham J, He L, De Paepe B, Vanlander A, Seneca S, Feichtinger R, Płoski R, Rokicki D, Pronicka E, Haller R, Van Hove J, Bahlo M, Mayr J, Van Coster R, Prokisch H, Wittig I, Ryan M, Thorburn D, Taylor R. Biallelic Mutations in TMEM126B Cause Severe Complex I Deficiency with a Variable Clinical Phenotype. Am J Hum Genet 2016; 99:217-27. [PMID: 27374774 PMCID: PMC5005451 DOI: 10.1016/j.ajhg.2016.05.021] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 05/18/2016] [Indexed: 11/22/2022] Open
Abstract
Complex I deficiency is the most common biochemical phenotype observed in individuals with mitochondrial disease. With 44 structural subunits and over 10 assembly factors, it is unsurprising that complex I deficiency is associated with clinical and genetic heterogeneity. Massively parallel sequencing (MPS) technologies including custom, targeted gene panels or unbiased whole-exome sequencing (WES) are hugely powerful in identifying the underlying genetic defect in a clinical diagnostic setting, yet many individuals remain without a genetic diagnosis. These individuals might harbor mutations in poorly understood or uncharacterized genes, and their diagnosis relies upon characterization of these orphan genes. Complexome profiling recently identified TMEM126B as a component of the mitochondrial complex I assembly complex alongside proteins ACAD9, ECSIT, NDUFAF1, and TIMMDC1. Here, we describe the clinical, biochemical, and molecular findings in six cases of mitochondrial disease from four unrelated families affected by biallelic (c.635G>T [p.Gly212Val] and/or c.401delA [p.Asn134Ilefs∗2]) TMEM126B variants. We provide functional evidence to support the pathogenicity of these TMEM126B variants, including evidence of founder effects for both variants, and establish defects within this gene as a cause of complex I deficiency in association with either pure myopathy in adulthood or, in one individual, a severe multisystem presentation (chronic renal failure and cardiomyopathy) in infancy. Functional experimentation including viral rescue and complexome profiling of subject cell lines has confirmed TMEM126B as the tenth complex I assembly factor associated with human disease and validates the importance of both genome-wide sequencing and proteomic approaches in characterizing disease-associated genes whose physiological roles have been previously undetermined.
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163
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Sánchez-Caballero L, Ruzzenente B, Bianchi L, Assouline Z, Barcia G, Metodiev M, Rio M, Funalot B, van den Brand M, Guerrero-Castillo S, Molenaar J, Koolen D, Brandt U, Rodenburg R, Nijtmans L, Rötig A. Mutations in Complex I Assembly Factor TMEM126B Result in Muscle Weakness and Isolated Complex I Deficiency. Am J Hum Genet 2016; 99:208-16. [PMID: 27374773 DOI: 10.1016/j.ajhg.2016.05.022] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 05/17/2016] [Indexed: 11/26/2022] Open
Abstract
Mitochondrial complex I deficiency results in a plethora of often severe clinical phenotypes manifesting in early childhood. Here, we report on three complex-I-deficient adult subjects with relatively mild clinical symptoms, including isolated, progressive exercise-induced myalgia and exercise intolerance but with normal later development. Exome sequencing and targeted exome sequencing revealed compound-heterozygous mutations in TMEM126B, encoding a complex I assembly factor. Further biochemical analysis of subject fibroblasts revealed a severe complex I deficiency caused by defective assembly. Lentiviral complementation with the wild-type cDNA restored the complex I deficiency, demonstrating the pathogenic nature of these mutations. Further complexome analysis of one subject indicated that the complex I assembly defect occurred during assembly of its membrane module. Our results show that TMEM126B defects can lead to complex I deficiencies and, interestingly, that symptoms can occur only after exercise.
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Strecker V, Kadeer Z, Heidler J, Cruciat CM, Angerer H, Giese H, Pfeiffer K, Stuart RA, Wittig I. Supercomplex-associated Cox26 protein binds to cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1863:1643-52. [PMID: 27091403 PMCID: PMC7140176 DOI: 10.1016/j.bbamcr.2016.04.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 04/12/2016] [Accepted: 04/14/2016] [Indexed: 10/21/2022]
Abstract
Here we identified a hydrophobic 6.4kDa protein, Cox26, as a novel component of yeast mitochondrial supercomplex comprising respiratory complexes III and IV. Multi-dimensional native and denaturing electrophoretic techniques were used to identify proteins interacting with Cox26. The majority of the Cox26 protein was found non-covalently bound to the complex IV moiety of the III-IV supercomplexes. A population of Cox26 was observed to exist in a disulfide bond partnership with the Cox2 subunit of complex IV. No pronounced growth phenotype for Cox26 deficiency was observed, indicating that Cox26 may not play a critical role in the COX enzymology, and we speculate that Cox26 may serve to regulate or support the Cox2 protein. Respiratory supercomplexes are assembled in the absence of the Cox26 protein, however their pattern slightly differs to the wild type III-IV supercomplex appearance. The catalytic activities of complexes III and IV were observed to be normal and respiration was comparable to wild type as long as cells were cultivated under normal growth conditions. Stress conditions, such as elevated temperatures resulted in mild decrease of respiration in non-fermentative media when the Cox26 protein was absent.
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Affiliation(s)
- Valentina Strecker
- Molekulare Bioenergetik, Zentrum der Biologischen Chemie, Cluster of Excellence Frankfurt Macromolecular Complexes Goethe-Universität Frankfurt, D-60590 Frankfurt, Germany; Functional Proteomics, Institute of Biochemistry I, Faculty of Medicine, Goethe-University of Frankfurt, D-60590 Frankfurt, Germany
| | - Zibirnisa Kadeer
- Molekulare Bioenergetik, Zentrum der Biologischen Chemie, Cluster of Excellence Frankfurt Macromolecular Complexes Goethe-Universität Frankfurt, D-60590 Frankfurt, Germany
| | - Juliana Heidler
- Functional Proteomics, Institute of Biochemistry I, Faculty of Medicine, Goethe-University of Frankfurt, D-60590 Frankfurt, Germany
| | - Cristina-Maria Cruciat
- Fakultät Angewandte Naturwissenschaften, Hochschule Esslingen, University of Applied Sciences, D-73728 Esslingen, Germany
| | - Heike Angerer
- Molekulare Bioenergetik, Zentrum der Biologischen Chemie, Cluster of Excellence Frankfurt Macromolecular Complexes Goethe-Universität Frankfurt, D-60590 Frankfurt, Germany; Structural Bioenergetics Group, Institute of Biochemistry II, Medical School, Goethe University of Frankfurt, Germany
| | - Heiko Giese
- Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University, D-60325 Frankfurt am Main, Germany
| | - Kathy Pfeiffer
- Department of Functional Proteomics, Medizinisches Proteom-Center, Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - Rosemary A Stuart
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Ilka Wittig
- Molekulare Bioenergetik, Zentrum der Biologischen Chemie, Cluster of Excellence Frankfurt Macromolecular Complexes Goethe-Universität Frankfurt, D-60590 Frankfurt, Germany; Functional Proteomics, Institute of Biochemistry I, Faculty of Medicine, Goethe-University of Frankfurt, D-60590 Frankfurt, Germany.
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165
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Cell Type-Specific Modulation of Respiratory Chain Supercomplex Organization. Int J Mol Sci 2016; 17:ijms17060926. [PMID: 27338358 PMCID: PMC4926459 DOI: 10.3390/ijms17060926] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 05/31/2016] [Accepted: 06/06/2016] [Indexed: 02/02/2023] Open
Abstract
Respiratory chain complexes are organized into large supercomplexes among which supercomplex In + IIIn + IVn is the only one that can directly transfer electrons from NADH to oxygen. Recently, it was reported that the formation of supercomplex In + IIIn + IVn in mice largely depends on their genetic background. However, in this study, we showed that the composition of supercomplex In + IIIn + IVn is well conserved in various mouse and human cell lines. Strikingly, we found that a minimal supercomplex In + IIIn, termed “lowest supercomplex” (LSC) in this study because of its migration at the lowest position close to complex V dimers in blue native polyacrylamide gel electrophoresis, was associated with complex IV to form a supercomplex In + IIIn + IVn in some, but not all of the human and mouse cells. In addition, we observed that the 3697G>A mutation in mitochondrial-encoded NADH dehydrogenase 1 (ND1) in one patient with Leigh’s disease specifically affected the assembly of supercomplex In + IIIn + IVn containing LSC, leading to decreased cellular respiration and ATP generation. In conclusion, we showed the existence of LSC In + IIIn + IVn and impairment of this supercomplex causes disease.
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Pronicka E, Piekutowska-Abramczuk D, Ciara E, Trubicka J, Rokicki D, Karkucińska-Więckowska A, Pajdowska M, Jurkiewicz E, Halat P, Kosińska J, Pollak A, Rydzanicz M, Stawinski P, Pronicki M, Krajewska-Walasek M, Płoski R. New perspective in diagnostics of mitochondrial disorders: two years' experience with whole-exome sequencing at a national paediatric centre. J Transl Med 2016; 14:174. [PMID: 27290639 PMCID: PMC4903158 DOI: 10.1186/s12967-016-0930-9] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/31/2016] [Indexed: 12/30/2022] Open
Abstract
Background Whole-exome sequencing (WES) has led to an exponential increase in identification of causative variants in mitochondrial disorders (MD). Methods We performed WES in 113 MD suspected patients from Polish paediatric reference centre, in whom routine testing failed to identify a molecular defect. WES was performed using TruSeqExome enrichment, followed by variant prioritization, validation by Sanger sequencing, and segregation with the disease phenotype in the family. Results Likely causative mutations were identified in 67 (59.3 %) patients; these included variants in mtDNA (6 patients) and nDNA: X-linked (9 patients), autosomal dominant (5 patients), and autosomal recessive (47 patients, 11 homozygotes). Novel variants accounted for 50.5 % (50/99) of all detected changes. In 47 patients, changes in 31 MD-related genes (ACAD9, ADCK3, AIFM1, CLPB, COX10, DLD, EARS2, FBXL4, MTATP6, MTFMT, MTND1, MTND3, MTND5, NAXE, NDUFS6, NDUFS7, NDUFV1, OPA1, PARS2, PC, PDHA1, POLG, RARS2, RRM2B, SCO2, SERAC1, SLC19A3, SLC25A12, TAZ, TMEM126B, VARS2) were identified. The ACAD9, CLPB, FBXL4, PDHA1 genes recurred more than twice suggesting higher general/ethnic prevalence. In 19 cases, variants in 18 non-MD related genes (ADAR, CACNA1A, CDKL5, CLN3, CPS1, DMD, DYSF, GBE1, GFAP, HSD17B4, MECP2, MYBPC3, PEX5, PGAP2, PIGN, PRF1, SBDS, SCN2A) were found. The percentage of positive WES results rose gradually with increasing probability of MD according to the Mitochondrial Disease Criteria (MDC) scale (from 36 to 90 % for low and high probability, respectively). The percentage of detected MD-related genes compared with non MD-related genes also grew with the increasing MD likelihood (from 20 to 97 %). Molecular diagnosis was established in 30/47 (63.8 %) neonates and in 17/28 (60.7 %) patients with basal ganglia involvement. Mutations in CLPB, SERAC1, TAZ genes were identified in neonates with 3-methylglutaconic aciduria (3-MGA) as a discriminative feature. New MD-related candidate gene (NDUFB8) is under verification. Conclusions We suggest WES rather than targeted NGS as the method of choice in diagnostics of MD in children, including neonates with 3-MGA aciduria, who died without determination of disease cause and with limited availability of laboratory data. There is a strong correlation between the degree of MD diagnosis by WES and MD likelihood expressed by the MDC scale. Electronic supplementary material The online version of this article (doi:10.1186/s12967-016-0930-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ewa Pronicka
- Department of Medical Genetics, The Children's Memorial Health Institute, 04-730, Warsaw, Poland. .,Department of Paediatrics, Nutrition and Metabolic Diseases,, The Children's Memorial Health Institute, Warsaw, Poland.
| | | | - Elżbieta Ciara
- Department of Medical Genetics, The Children's Memorial Health Institute, 04-730, Warsaw, Poland
| | - Joanna Trubicka
- Department of Medical Genetics, The Children's Memorial Health Institute, 04-730, Warsaw, Poland
| | - Dariusz Rokicki
- Department of Paediatrics, Nutrition and Metabolic Diseases,, The Children's Memorial Health Institute, Warsaw, Poland
| | | | - Magdalena Pajdowska
- Department of Biochemistry and Experimental Medicine, The Children's Memorial Health Institute, Warsaw, Poland
| | - Elżbieta Jurkiewicz
- Department of Radiology, The Children's Memorial Health Institute, Warsaw, Poland
| | - Paulina Halat
- Department of Medical Genetics, The Children's Memorial Health Institute, 04-730, Warsaw, Poland
| | - Joanna Kosińska
- Department of Medical Genetics, Warsaw Medical University, Pawińskiego str, 02-106, Warsaw, Poland
| | - Agnieszka Pollak
- Department of Genetics, Institute of Physiology and Pathology of Hearing, Nadarzyn, Poland
| | - Małgorzata Rydzanicz
- Department of Medical Genetics, Warsaw Medical University, Pawińskiego str, 02-106, Warsaw, Poland
| | - Piotr Stawinski
- Department of Genetics, Institute of Physiology and Pathology of Hearing, Nadarzyn, Poland
| | - Maciej Pronicki
- Department of Pathology, The Children's Memorial Health Institute, Warsaw, Poland
| | | | - Rafał Płoski
- Department of Medical Genetics, Warsaw Medical University, Pawińskiego str, 02-106, Warsaw, Poland.
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Shatsky M, Dong M, Liu H, Yang LL, Choi M, Singer ME, Geller JT, Fisher SJ, Hall SC, Hazen TC, Brenner SE, Butland G, Jin J, Witkowska HE, Chandonia JM, Biggin MD. Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions. Mol Cell Proteomics 2016; 15:2186-202. [PMID: 27099342 PMCID: PMC5083090 DOI: 10.1074/mcp.m115.057117] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Indexed: 01/18/2023] Open
Abstract
Identifying protein-protein interactions (PPIs) at an acceptable false discovery rate (FDR) is challenging. Previously we identified several hundred PPIs from affinity purification - mass spectrometry (AP-MS) data for the bacteria Escherichia coli and Desulfovibrio vulgaris. These two interactomes have lower FDRs than any of the nine interactomes proposed previously for bacteria and are more enriched in PPIs validated by other data than the nine earlier interactomes. To more thoroughly determine the accuracy of ours or other interactomes and to discover further PPIs de novo, here we present a quantitative tagless method that employs iTRAQ MS to measure the copurification of endogenous proteins through orthogonal chromatography steps. 5273 fractions from a four-step fractionation of a D. vulgaris protein extract were assayed, resulting in the detection of 1242 proteins. Protein partners from our D. vulgaris and E. coli AP-MS interactomes copurify as frequently as pairs belonging to three benchmark data sets of well-characterized PPIs. In contrast, the protein pairs from the nine other bacterial interactomes copurify two- to 20-fold less often. We also identify 200 high confidence D. vulgaris PPIs based on tagless copurification and colocalization in the genome. These PPIs are as strongly validated by other data as our AP-MS interactomes and overlap with our AP-MS interactome for D.vulgaris within 3% of expectation, once FDRs and false negative rates are taken into account. Finally, we reanalyzed data from two quantitative tagless screens of human cell extracts. We estimate that the novel PPIs reported in these studies have an FDR of at least 85% and find that less than 7% of the novel PPIs identified in each screen overlap. Our results establish that a quantitative tagless method can be used to validate and identify PPIs, but that such data must be analyzed carefully to minimize the FDR.
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Affiliation(s)
- Maxim Shatsky
- From the ‡Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Ming Dong
- §Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Haichuan Liu
- ¶OB/GYN Department, University of California San Francisco-Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, California 94143
| | - Lee Lisheng Yang
- ‖Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Megan Choi
- §Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Mary E Singer
- **Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Jil T Geller
- **Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Susan J Fisher
- ¶OB/GYN Department, University of California San Francisco-Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, California 94143
| | - Steven C Hall
- ¶OB/GYN Department, University of California San Francisco-Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, California 94143
| | - Terry C Hazen
- ‡‡Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996; §§Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Steven E Brenner
- From the ‡Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720; ¶¶Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Gareth Butland
- ‖‖Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Jian Jin
- ‖Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - H Ewa Witkowska
- ¶OB/GYN Department, University of California San Francisco-Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, California 94143
| | - John-Marc Chandonia
- From the ‡Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720;
| | - Mark D Biggin
- §Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720;
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168
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The origin of the supernumerary subunits and assembly factors of complex I: A treasure trove of pathway evolution. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:971-9. [PMID: 27048931 DOI: 10.1016/j.bbabio.2016.03.027] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 03/16/2016] [Accepted: 03/18/2016] [Indexed: 11/20/2022]
Abstract
We review and document the evolutionary origin of all complex I assembly factors and nine supernumerary subunits from protein families. Based on experimental data and the conservation of critical residues we identify a spectrum of protein function conservation between the complex I representatives and their non-complex I homologs. This spectrum ranges from proteins that have retained their molecular function but in which the substrate specificity may have changed or have become more specific, like NDUFAF5, to proteins that have lost their original molecular function and critical catalytic residues like NDUFAF6. In between are proteins that have retained their molecular function, which however appears unrelated to complex I, like ACAD9, or proteins in which amino acids of the active site are conserved but for which no enzymatic activity has been reported, like NDUFA10. We interpret complex I evolution against the background of molecular evolution theory. Complex I supernumerary subunits and assembly factors appear to have been recruited from proteins that are mitochondrial and/or that are expressed when complex I is active. Within the evolution of complex I and its assembly there are many cases of neofunctionalization after gene duplication, like ACAD9 and TMEM126B, one case of subfunctionalization: ACPM1 and ACPM2 in Yarrowia lipolytica, and one case in which a complex I protein itself appears to have been the source of a new protein from another complex: NDUFS6 gave rise to cytochrome c oxidase subunit COX4/COX5b. Complex I and its assembly can therewith be regarded as a treasure trove for pathway evolution. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
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169
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Sánchez-Caballero L, Guerrero-Castillo S, Nijtmans L. Unraveling the complexity of mitochondrial complex I assembly: A dynamic process. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:980-90. [PMID: 27040506 DOI: 10.1016/j.bbabio.2016.03.031] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/17/2016] [Accepted: 03/29/2016] [Indexed: 11/17/2022]
Abstract
Mammalian complex I is composed of 44 different subunits and its assembly requires at least 13 specific assembly factors. Proper function of the mitochondrial respiratory chain enzyme is of crucial importance for cell survival due to its major participation in energy production and cell signaling. Complex I assembly depends on the coordination of several crucial processes that need to be tightly interconnected and orchestrated by a number of assembly factors. The understanding of complex I assembly evolved from simple sequential concept to the more sophisticated modular assembly model describing a convoluted process. According to this model, the different modules assemble independently and associate afterwards with each other to form the final enzyme. In this review, we aim to unravel the complexity of complex I assembly and provide the latest insights in this fundamental and fascinating process. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
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Affiliation(s)
- Laura Sánchez-Caballero
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Sergio Guerrero-Castillo
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Leo Nijtmans
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
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170
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Wessels HJCT, de Almeida NM, Kartal B, Keltjens JT. Bacterial Electron Transfer Chains Primed by Proteomics. Adv Microb Physiol 2016; 68:219-352. [PMID: 27134025 DOI: 10.1016/bs.ampbs.2016.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Electron transport phosphorylation is the central mechanism for most prokaryotic species to harvest energy released in the respiration of their substrates as ATP. Microorganisms have evolved incredible variations on this principle, most of these we perhaps do not know, considering that only a fraction of the microbial richness is known. Besides these variations, microbial species may show substantial versatility in using respiratory systems. In connection herewith, regulatory mechanisms control the expression of these respiratory enzyme systems and their assembly at the translational and posttranslational levels, to optimally accommodate changes in the supply of their energy substrates. Here, we present an overview of methods and techniques from the field of proteomics to explore bacterial electron transfer chains and their regulation at levels ranging from the whole organism down to the Ångstrom scales of protein structures. From the survey of the literature on this subject, it is concluded that proteomics, indeed, has substantially contributed to our comprehending of bacterial respiratory mechanisms, often in elegant combinations with genetic and biochemical approaches. However, we also note that advanced proteomics offers a wealth of opportunities, which have not been exploited at all, or at best underexploited in hypothesis-driving and hypothesis-driven research on bacterial bioenergetics. Examples obtained from the related area of mitochondrial oxidative phosphorylation research, where the application of advanced proteomics is more common, may illustrate these opportunities.
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Affiliation(s)
- H J C T Wessels
- Nijmegen Center for Mitochondrial Disorders, Radboud Proteomics Centre, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - N M de Almeida
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - B Kartal
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands; Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | - J T Keltjens
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands.
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171
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Lim SC, Hroudová J, Van Bergen NJ, Lopez Sanchez MIG, Trounce IA, McKenzie M. Loss of mitochondrial DNA-encoded protein ND1 results in disruption of complex I biogenesis during early stages of assembly. FASEB J 2016; 30:2236-48. [PMID: 26929434 DOI: 10.1096/fj.201500137r] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 02/12/2016] [Indexed: 12/20/2022]
Abstract
Mitochondrial complex I (NADH:ubiquinone oxidoreductase) must be assembled precisely from 45 protein subunits for it to function correctly. One of its mitochondrial DNA (mtDNA) encoded subunits, ND1, is incorporated during the early stages of complex I assembly. However, little is known about how mutations in ND1 affect this assembly process. We found that in human 143B cybrid cells carrying a homoplasmic MT-ND1 mutation, ND1 protein could not be translated. As a result, the early stages of complex I assembly were disrupted, with mature complex I undetectable and complex I-linked respiration severely reduced to 2.0% of control levels. Interestingly, complex IV (ferrocytochrome c:oxygen oxidoreductase) steady-state levels were also reduced to 40.3%, possibly due to its diminished stability in the absence of respiratory supercomplex formation. This was in comparison with 143B cybrid controls (that contained wild-type mtDNA on the same nuclear background), which exhibited normal complex I, complex IV, and supercomplex assembly. We conclude that the loss of ND1 stalls complex I assembly during the early stages of its biogenesis, which not only results in the loss of mature complex I but also disrupts the stability of complex IV and the respiratory supercomplex to cause mitochondrial dysfunction.-Lim, S. C., Hroudová, J., Van Bergen, N. J., Lopez Sanchez, M. I. G., Trounce, I. A., McKenzie, M. Loss of mitochondrial DNA-encoded protein ND1 results in disruption of complex I biogenesis during early stages of assembly.
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Affiliation(s)
- Sze Chern Lim
- Centre for Genetic Diseases, Hudson Institute of Medical Research, Clayton, Melbourne, Victoria, Australia
| | - Jana Hroudová
- Department of Psychiatry, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Nicole J Van Bergen
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia; and
| | - M Isabel G Lopez Sanchez
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia; and
| | - Ian A Trounce
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia; and
| | - Matthew McKenzie
- Centre for Genetic Diseases, Hudson Institute of Medical Research, Clayton, Melbourne, Victoria, Australia; Monash University, Clayton, Melbourne, Victoria, Australia
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172
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Ke M, Zhang Y, Xiong Y, Saeed Y, Deng Y. Identification of protein complexes of microsomes in rat adipocytes by native gel coupled with LC-ESI-QTOF. MOLECULAR BIOSYSTEMS 2016; 12:1313-23. [PMID: 26886786 DOI: 10.1039/c5mb00707k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The study of the composition of microsome proteins/complexes/interactions in adipocytes provides useful information for researchers related to energy metabolism disorders. The native gel coupled with LC-ESI-QTOF approach was employed here for separating protein complexes. We found a series of proteins functionally clustered in biological processes of protein metabolism, cellular carbohydrate catabolism, response to stimulus and wounding, macromolecular complex subunit organization, positive regulation of molecular function, regulation of programmed cell death and biomolecule transport. According to clustering of proteins' electrophoresis profiles across native gel fractions and bioinformatics data retrieval, protein complexes/interactions involved in protein metabolism, cellular carbohydrate catabolism, macromolecular complex subunit organization and biomolecule transport were identified. Besides, the results also revealed some functional linkages, which may provide useful information for discovering previously unknown interactions. The interaction between SSAO and ALDH2 was verified by co-immunoprecipitation. The native gel combining mass spectrometry approach appeared to be a useful tool for investigating microsome proteins and complexes to complement the traditional electrophoresis approaches. The native gel strategy together with our findings should facilitate future studies of the composition of rat adipocyte microsome protein complexes under different conditions.
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Affiliation(s)
- Ming Ke
- School of Life Science, Beijing Institute of Technology, Beijing 100081, P. R. China.
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Prior KK, Wittig I, Leisegang MS, Groenendyk J, Weissmann N, Michalak M, Jansen-Dürr P, Shah AM, Brandes RP. The Endoplasmic Reticulum Chaperone Calnexin Is a NADPH Oxidase NOX4 Interacting Protein. J Biol Chem 2016; 291:7045-59. [PMID: 26861875 PMCID: PMC4807287 DOI: 10.1074/jbc.m115.710772] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Indexed: 11/24/2022] Open
Abstract
Within the family of NADPH oxidases, NOX4 is unique as it is predominantly localized in the endoplasmic reticulum, has constitutive activity, and generates hydrogen peroxide (H2O2). We hypothesize that these features are consequences of a so far unidentified NOX4-interacting protein. Two-dimensional blue native (BN) electrophorese combined with SDS-PAGE yielded NOX4 to reside in macromolecular complexes. Interacting proteins were screened by quantitative SILAC (stable isotope labeling of amino acids in cell culture) co-immunoprecipitation (Co-IP) in HEK293 cells stably overexpressing NOX4. By this technique, several interacting proteins were identified with calnexin showing the most robust interaction. Calnexin also resided in NOX4-containing complexes as demonstrated by complexome profiling from BN-PAGE. The calnexin NOX4 interaction could be confirmed by reverse Co-IP and proximity ligation assay, whereas NOX1, NOX2, or NOX5 did not interact with calnexin. Calnexin deficiency as studied in mouse embryonic fibroblasts from calnexin−/− mice or in response to calnexin shRNA reduced cellular NOX4 protein expression and reactive oxygen species formation. Our results suggest that endogenous NOX4 forms macromolecular complexes with calnexin, which are needed for the proper maturation, processing, and function of NOX4 in the endoplasmic reticulum.
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Affiliation(s)
- Kim-Kristin Prior
- From the Institut für Kardiovaskuläre Physiologie, Goethe-Universität, Frankfurt am Main, 60590 Germany, the German Center for Cardiovascular Research (DZHK), Partner site RheinMain, 60590 Frankfurt am Main, Germany
| | - Ilka Wittig
- the German Center for Cardiovascular Research (DZHK), Partner site RheinMain, 60590 Frankfurt am Main, Germany the Functional Proteomics, SFB 815 Core Unit, Goethe-Universität, 60590 Frankfurt am Main, Germany, the Cluster of Excellence "Macromolecular Complexes," Goethe-Universität, 60590 Frankfurt am Main, Germany
| | - Matthias S Leisegang
- From the Institut für Kardiovaskuläre Physiologie, Goethe-Universität, Frankfurt am Main, 60590 Germany, the German Center for Cardiovascular Research (DZHK), Partner site RheinMain, 60590 Frankfurt am Main, Germany
| | - Jody Groenendyk
- the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Norbert Weissmann
- the Excellence Cluster Cardio-Pulmonary System, Justus-Liebig-University Member of the German Center for Lung Research (DZL), 60590 Giessen, Germany
| | - Marek Michalak
- the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Pidder Jansen-Dürr
- the Institute for Biomedical Ageing Research and Center for Molecular Biosciences Innsbruck (CMBI), Universität Innsbruck, 6020 Insbruk, Austria
| | - Ajay M Shah
- the King's College London British Heart Foundation Centre, Cardiovascular Division, London WC2R 2LS, United Kingdom, and
| | - Ralf P Brandes
- From the Institut für Kardiovaskuläre Physiologie, Goethe-Universität, Frankfurt am Main, 60590 Germany, the German Center for Cardiovascular Research (DZHK), Partner site RheinMain, 60590 Frankfurt am Main, Germany
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174
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Subrahmanian N, Remacle C, Hamel PP. Plant mitochondrial Complex I composition and assembly: A review. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1001-14. [PMID: 26801215 DOI: 10.1016/j.bbabio.2016.01.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/18/2016] [Accepted: 01/18/2016] [Indexed: 12/31/2022]
Abstract
In the mitochondrial inner membrane, oxidative phosphorylation generates ATP via the operation of several multimeric enzymes. The proton-pumping Complex I (NADH:ubiquinone oxidoreductase) is the first and most complicated enzyme required in this process. Complex I is an L-shaped enzyme consisting of more than 40 subunits, one FMN molecule and eight Fe-S clusters. In recent years, genetic and proteomic analyses of Complex I mutants in various model systems, including plants, have provided valuable insights into the assembly of this multimeric enzyme. Assisted by a number of key players, referred to as "assembly factors", the assembly of Complex I takes place in a sequential and modular manner. Although a number of factors have been identified, their precise function in mediating Complex I assembly still remains to be elucidated. This review summarizes our current knowledge of plant Complex I composition and assembly derived from studies in plant model systems such as Arabidopsis thaliana and Chlamydomonas reinhardtii. Plant Complex I is highly conserved and comprises a significant number of subunits also present in mammalian and fungal Complexes I. Plant Complex I also contains additional subunits absent from the mammalian and fungal counterpart, whose function in enzyme activity and assembly is not clearly understood. While 14 assembly factors have been identified for human Complex I, only two proteins, namely GLDH and INDH, have been established as bona fide assembly factors for plant Complex I. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
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Affiliation(s)
- Nitya Subrahmanian
- The Ohio State University, Department of Molecular Genetics, 500 Aronoff Laboratory, 318 W. 12th Avenue, Columbus, OH 43210, USA
| | - Claire Remacle
- Institute of Botany, Department of Life Sciences, University of Liège, 4000 Liège, Belgium
| | - Patrice Paul Hamel
- The Ohio State University, Department of Molecular Genetics, 500 Aronoff Laboratory, 318 W. 12th Avenue, Columbus, OH 43210, USA; The Ohio State University, Department of Biological Chemistry and Pharmacology, 500 Aronoff Laboratory, 318 W. 12th Avenue, Columbus, OH 43210, USA.
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175
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Birkenmeier K, Dröse S, Wittig I, Winkelmann R, Käfer V, Döring C, Hartmann S, Wenz T, Reichert AS, Brandt U, Hansmann ML. Hodgkin and Reed-Sternberg cells of classical Hodgkin lymphoma are highly dependent on oxidative phosphorylation. Int J Cancer 2016; 138:2231-46. [DOI: 10.1002/ijc.29934] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 10/30/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Katrin Birkenmeier
- Dr. Senckenberg Institute of Pathology, Goethe-University Hospital; Theodor-Stern-Kai 7 Frankfurt Am Main 60596 Germany
| | - Stefan Dröse
- Clinic of Anesthesiology, Intensive-Care Medicine and Pain Therapy; Goethe-University Hospital; Theodor-Stern Kai 7 Frankfurt Am Main 60596 Germany
- Centre of Biological Chemistry, and Centre for Membrane Proteomics, Molecular Bioenergetics Group; Medical School, Goethe-University; Theodor-Stern-Kai 7 Frankfurt Am Main 60596 Germany
| | - Ilka Wittig
- Centre of Biological Chemistry, and Centre for Membrane Proteomics, Molecular Bioenergetics Group; Medical School, Goethe-University; Theodor-Stern-Kai 7 Frankfurt Am Main 60596 Germany
| | - Ria Winkelmann
- Dr. Senckenberg Institute of Pathology, Goethe-University Hospital; Theodor-Stern-Kai 7 Frankfurt Am Main 60596 Germany
| | - Viktoria Käfer
- Dr. Senckenberg Institute of Pathology, Goethe-University Hospital; Theodor-Stern-Kai 7 Frankfurt Am Main 60596 Germany
| | - Claudia Döring
- Dr. Senckenberg Institute of Pathology, Goethe-University Hospital; Theodor-Stern-Kai 7 Frankfurt Am Main 60596 Germany
| | - Sylvia Hartmann
- Dr. Senckenberg Institute of Pathology, Goethe-University Hospital; Theodor-Stern-Kai 7 Frankfurt Am Main 60596 Germany
| | - Tina Wenz
- Institute for Genetics, University of Cologne; Zülpicher Str. 47A Cologne 50674 Germany
| | - Andreas S. Reichert
- Institute of Biochemistry and Molecular Biology I, Medical Faculty, Heinrich-Heine-University; Düsseldorf Germany
| | - Ulrich Brandt
- Department of Pediatrics, Radboud University Medical Center; Nijmegen Center for Mitochondrial Disorders (NCMD); The Netherlands
- Cluster of Excellence Frankfurt “Macromolecular Complexes”, Goethe-University; Frankfurt Am Main Germany
| | - Martin-Leo Hansmann
- Dr. Senckenberg Institute of Pathology, Goethe-University Hospital; Theodor-Stern-Kai 7 Frankfurt Am Main 60596 Germany
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176
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Huynen MA, Mühlmeister M, Gotthardt K, Guerrero-Castillo S, Brandt U. Evolution and structural organization of the mitochondrial contact site (MICOS) complex and the mitochondrial intermembrane space bridging (MIB) complex. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:91-101. [DOI: 10.1016/j.bbamcr.2015.10.009] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/25/2015] [Accepted: 10/14/2015] [Indexed: 02/03/2023]
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177
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Bode D, Yu L, Tate P, Pardo M, Choudhary J. Characterization of Two Distinct Nucleosome Remodeling and Deacetylase (NuRD) Complex Assemblies in Embryonic Stem Cells. Mol Cell Proteomics 2015; 15:878-91. [PMID: 26714524 PMCID: PMC4813707 DOI: 10.1074/mcp.m115.053207] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Indexed: 11/26/2022] Open
Abstract
Pluripotency and self-renewal, the defining properties of embryonic stem cells, are brought about by transcriptional programs involving an intricate network of transcription factors and chromatin remodeling complexes. The Nucleosome Remodeling and Deacetylase (NuRD) complex plays a crucial and dynamic role in the regulation of stemness and differentiation. Several NuRD-associated factors have been reported but how they are organized has not been investigated in detail. Here, we have combined affinity purification and blue native polyacrylamide gel electrophoresis followed by protein identification by mass spectrometry and protein correlation profiling to characterize the topology of the NuRD complex. Our data show that in mouse embryonic stem cells the NuRD complex is present as two distinct assemblies of differing topology with different binding partners. Cell cycle regulator Cdk2ap1 and transcription factor Sall4 associate only with the higher mass NuRD assembly. We further establish that only isoform Sall4a, and not Sall4b, associates with NuRD. By contrast, Suz12, a component of the PRC2 Polycomb repressor complex, associates with the lower mass entity. In addition, we identify and validate a novel NuRD-associated protein, Wdr5, a regulatory subunit of the MLL histone methyltransferase complex, which associates with both NuRD entities. Bioinformatic analyses of published target gene sets of these chromatin binding proteins are in agreement with these structural observations. In summary, this study provides an interesting insight into mechanistic aspects of NuRD function in stem cell biology. The relevance of our work has broader implications because of the ubiquitous nature of the NuRD complex. The strategy described here can be more broadly applicable to investigate the topology of the multiple complexes an individual protein can participate in.
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Affiliation(s)
- Daniel Bode
- From the ‡Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Lu Yu
- From the ‡Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Peri Tate
- §Stem Cell Engineering, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Mercedes Pardo
- From the ‡Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK;
| | - Jyoti Choudhary
- From the ‡Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
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178
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Wang Y, Javed I, Liu Y, Lu S, Peng G, Zhang Y, Qing H, Deng Y. Effect of Prolonged Simulated Microgravity on Metabolic Proteins in Rat Hippocampus: Steps toward Safe Space Travel. J Proteome Res 2015; 15:29-37. [PMID: 26523826 DOI: 10.1021/acs.jproteome.5b00777] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mitochondria are not only the main source of energy in cells but also produce reactive oxygen species (ROS), which result in oxidative stress when in space. This oxidative stress is responsible for energy imbalances and cellular damage. In this study, a rat tail suspension model was used in individual experiments for 7 and 21 days to explore the effect of simulated microgravity (SM) on metabolic proteins in the hippocampus, a vital brain region involved in learning, memory, and navigation. A comparative (18)O-labeled quantitative proteomic strategy was used to observe the differential expression of metabolic proteins. Forty-two and sixty-seven mitochondrial metabolic proteins were differentially expressed after 21 and 7 days of SM, respectively. Mitochondrial Complex I, III, and IV, isocitrate dehydrogenase and malate dehydrogenase were down-regulated. Moreover, DJ-1 and peroxiredoxin 6, which defend against oxidative damage, were up-regulated in the hippocampus. Western blot analysis of proteins DJ-1 and COX 5A confirmed the mass spectrometry results. Despite these changes in mitochondrial protein expression, no obvious cell apoptosis was observed after 21 days of SM. The results of this study indicate that the oxidative stress induced by SM has profound effects on metabolic proteins.
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Affiliation(s)
- Yun Wang
- School of Life Sciences, Beijing Institute of Technology , No. 5 Zhongguancun South Street, Beijing 100081, P.R. China
| | - Iqbal Javed
- School of Life Sciences, Beijing Institute of Technology , No. 5 Zhongguancun South Street, Beijing 100081, P.R. China
| | - Yahui Liu
- School of Life Sciences, Beijing Institute of Technology , No. 5 Zhongguancun South Street, Beijing 100081, P.R. China
| | - Song Lu
- School of Life Sciences, Beijing Institute of Technology , No. 5 Zhongguancun South Street, Beijing 100081, P.R. China
| | - Guang Peng
- School of Life Sciences, Beijing Institute of Technology , No. 5 Zhongguancun South Street, Beijing 100081, P.R. China
| | - Yongqian Zhang
- School of Life Sciences, Beijing Institute of Technology , No. 5 Zhongguancun South Street, Beijing 100081, P.R. China
| | - Hong Qing
- School of Life Sciences, Beijing Institute of Technology , No. 5 Zhongguancun South Street, Beijing 100081, P.R. China
| | - Yulin Deng
- School of Life Sciences, Beijing Institute of Technology , No. 5 Zhongguancun South Street, Beijing 100081, P.R. China
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179
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Müller CS, Bildl W, Haupt A, Ellenrieder L, Becker T, Hunte C, Fakler B, Schulte U. Cryo-slicing Blue Native-Mass Spectrometry (csBN-MS), a Novel Technology for High Resolution Complexome Profiling. Mol Cell Proteomics 2015; 15:669-81. [PMID: 26598645 DOI: 10.1074/mcp.m115.054080] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Indexed: 11/06/2022] Open
Abstract
Blue native (BN) gel electrophoresis is a powerful method for protein separation. Combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS), it enables large scale identification of protein complexes and their subunits. Current BN-MS approaches, however, are limited in size resolution, comprehensiveness, and quantification. Here, we present a new methodology combining defined sub-millimeter slicing of BN gels by a cryo-microtome with high performance LC-MS/MS and label-free quantification of protein amounts. Application of this cryo-slicing BN-MS approach to mitochondria from rat brain demonstrated a high degree of comprehensiveness, accuracy, and size resolution. The technique provided abundance-mass profiles for 774 mitochondrial proteins, including all canonical subunits of the oxidative respiratory chain assembled into 13 distinct (super-)complexes. Moreover, the data revealed COX7R as a constitutive subunit of distinct super-complexes and identified novel assemblies of voltage-dependent anion channels/porins and TOM proteins. Together, cryo-slicing BN-MS enables quantitative profiling of complexomes with resolution close to the limits of native gel electrophoresis.
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Affiliation(s)
- Catrin S Müller
- From the ‡Institute of Physiology, University of Freiburg, Hermann-Herder-Strasse 7, 79104 Freiburg
| | - Wolfgang Bildl
- From the ‡Institute of Physiology, University of Freiburg, Hermann-Herder-Strasse 7, 79104 Freiburg
| | - Alexander Haupt
- From the ‡Institute of Physiology, University of Freiburg, Hermann-Herder-Strasse 7, 79104 Freiburg
| | - Lars Ellenrieder
- §Institute for Biochemistry and Molecular Biology, Stefan-Meier-Strasse 17, 79104 Freiburg
| | - Thomas Becker
- §Institute for Biochemistry and Molecular Biology, Stefan-Meier-Strasse 17, 79104 Freiburg; ¶Center for Biological Signaling Studies (BIOSS), Schänzlestrasse 18, 79104 Freiburg
| | - Carola Hunte
- §Institute for Biochemistry and Molecular Biology, Stefan-Meier-Strasse 17, 79104 Freiburg; ¶Center for Biological Signaling Studies (BIOSS), Schänzlestrasse 18, 79104 Freiburg
| | - Bernd Fakler
- From the ‡Institute of Physiology, University of Freiburg, Hermann-Herder-Strasse 7, 79104 Freiburg; ¶Center for Biological Signaling Studies (BIOSS), Schänzlestrasse 18, 79104 Freiburg
| | - Uwe Schulte
- From the ‡Institute of Physiology, University of Freiburg, Hermann-Herder-Strasse 7, 79104 Freiburg; ¶Center for Biological Signaling Studies (BIOSS), Schänzlestrasse 18, 79104 Freiburg; ‖Logopharm GmbH, Schlossstrasse 14, 79232 March-Buchheim, Germany
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180
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Wang Y, Iqbal J, Liu Y, Su R, Lu S, Peng G, Zhang Y, Qing H, Deng Y. Effects of simulated microgravity on the expression of presynaptic proteins distorting the GABA/glutamate equilibrium - A proteomics approach. Proteomics 2015; 15:3883-91. [DOI: 10.1002/pmic.201500302] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 08/28/2015] [Accepted: 09/07/2015] [Indexed: 01/03/2023]
Affiliation(s)
- Yun Wang
- School of Life Sciences; Beijing Institute of Technology; Beijing P.R. China
| | - Javed Iqbal
- School of Life Sciences; Beijing Institute of Technology; Beijing P.R. China
| | - Yahui Liu
- School of Life Sciences; Beijing Institute of Technology; Beijing P.R. China
| | - Rui Su
- School of Life Sciences; Beijing Institute of Technology; Beijing P.R. China
| | - Song Lu
- School of Life Sciences; Beijing Institute of Technology; Beijing P.R. China
| | - Guang Peng
- School of Life Sciences; Beijing Institute of Technology; Beijing P.R. China
| | - Yongqian Zhang
- School of Life Sciences; Beijing Institute of Technology; Beijing P.R. China
| | - Hong Qing
- School of Life Sciences; Beijing Institute of Technology; Beijing P.R. China
| | - Yulin Deng
- School of Life Sciences; Beijing Institute of Technology; Beijing P.R. China
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181
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Sakai C, Yamaguchi S, Sasaki M, Miyamoto Y, Matsushima Y, Goto YI. ECHS1 mutations cause combined respiratory chain deficiency resulting in Leigh syndrome. Hum Mutat 2015; 36:232-9. [PMID: 25393721 DOI: 10.1002/humu.22730] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 11/05/2014] [Indexed: 12/31/2022]
Abstract
The human ECHS1 gene encodes the short-chain enoyl coenzyme A hydratase, the enzyme that catalyzes the second step of β-oxidation of fatty acids in the mitochondrial matrix. We report on a boy with ECHS1 deficiency who was diagnosed with Leigh syndrome at 21 months of age. The patient presented with hypotonia, metabolic acidosis, and developmental delay. A combined respiratory chain deficiency was also observed. Targeted exome sequencing of 776 mitochondria-associated genes encoded by nuclear DNA identified compound heterozygous mutations in ECHS1. ECHS1 protein expression was severely depleted in the patient's skeletal muscle and patient-derived myoblasts; a marked decrease in enzyme activity was also evident in patient-derived myoblasts. Immortalized patient-derived myoblasts that expressed exogenous wild-type ECHS1 exhibited the recovery of the ECHS1 activity, indicating that the gene defect was pathogenic. Mitochondrial respiratory complex activity was also mostly restored in these cells, suggesting that there was an unidentified link between deficiency of ECHS1 and respiratory chain. Here, we describe the patient with ECHS1 deficiency; these findings will advance our understanding not only the pathology of mitochondrial fatty acid β-oxidation disorders, but also the regulation of mitochondrial metabolism.
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Affiliation(s)
- Chika Sakai
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
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182
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van der Lee R, Szklarczyk R, Smeitink J, Smeets HJM, Huynen MA, Vogel R. Transcriptome analysis of complex I-deficient patients reveals distinct expression programs for subunits and assembly factors of the oxidative phosphorylation system. BMC Genomics 2015; 16:691. [PMID: 26369791 PMCID: PMC4570683 DOI: 10.1186/s12864-015-1883-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 08/27/2015] [Indexed: 12/17/2022] Open
Abstract
Background Transcriptional control of mitochondrial metabolism is essential for cellular function. A better understanding of this process will aid the elucidation of mitochondrial disorders, in particular of the many genetically unsolved cases of oxidative phosphorylation (OXPHOS) deficiency. Yet, to date only few studies have investigated nuclear gene regulation in the context of OXPHOS deficiency. In this study we performed RNA sequencing of two control and two complex I-deficient patient cell lines cultured in the presence of compounds that perturb mitochondrial metabolism: chloramphenicol, AICAR, or resveratrol. We combined this with a comprehensive analysis of mitochondrial and nuclear gene expression patterns, co-expression calculations and transcription factor binding sites. Results Our analyses show that subsets of mitochondrial OXPHOS genes respond opposingly to chloramphenicol and AICAR, whereas the response of nuclear OXPHOS genes is less consistent between cell lines and treatments. Across all samples nuclear OXPHOS genes have a significantly higher co-expression with each other than with other genes, including those encoding mitochondrial proteins. We found no evidence for complex-specific mRNA expression regulation: subunits of different OXPHOS complexes are similarly (co-)expressed and regulated by a common set of transcription factors. However, we did observe significant differences between the expression of nuclear genes for OXPHOS subunits versus assembly factors, suggesting divergent transcription programs. Furthermore, complex I co-expression calculations identified 684 genes with a likely role in OXPHOS biogenesis and function. Analysis of evolutionarily conserved transcription factor binding sites in the promoters of these genes revealed almost all known OXPHOS regulators (including GABP, NRF1/2, SP1, YY1, E-box factors) and a set of novel candidates (ELK1, KLF7, SP4, EHF, ZNF143, and TEL2). Conclusions OXPHOS genes share an expression program distinct from other genes encoding mitochondrial proteins, indicative of targeted nuclear regulation of a mitochondrial sub-process. Within the subset of OXPHOS genes we established a difference in expression between mitochondrial and nuclear genes, and between nuclear genes encoding subunits and assembly factors. Most transcription regulators of genes that co-express with complex I are well-established factors for OXPHOS biogenesis. For the remaining six factors we here suggest for the first time a link with transcription regulation in OXPHOS deficiency. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1883-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Robin van der Lee
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO BOX 9101, 6500 HB, Nijmegen, The Netherlands.
| | - Radek Szklarczyk
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO BOX 9101, 6500 HB, Nijmegen, The Netherlands. .,Department of Clinical Genetics, Unit Clinical Genomics, Maastricht University Medical Centre, 6200 MD, Maastricht, The Netherlands.
| | - Jan Smeitink
- Nijmegen Center for Mitochondrial Disorders, Department of Pediatrics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO BOX 9101, 6500 HB, Nijmegen, The Netherlands.
| | - Hubert J M Smeets
- Unit Clinical Genomics, Department of Genetics and Cell Biology, School for Growth and Development and for Cardiovascular Research, Maastricht University Medical Centre, Maastricht, The Netherlands.
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO BOX 9101, 6500 HB, Nijmegen, The Netherlands.
| | - Rutger Vogel
- Nijmegen Center for Mitochondrial Disorders, Department of Pediatrics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO BOX 9101, 6500 HB, Nijmegen, The Netherlands.
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183
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Cameron JM, MacKay N, Feigenbaum A, Tarnopolsky M, Blaser S, Robinson BH, Schulze A. Exome sequencing identifies complex I NDUFV2 mutations as a novel cause of Leigh syndrome. Eur J Paediatr Neurol 2015; 19:525-32. [PMID: 26008862 DOI: 10.1016/j.ejpn.2015.05.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 02/12/2015] [Accepted: 05/05/2015] [Indexed: 12/30/2022]
Abstract
BACKGROUND Two siblings with hypertrophic cardiomyopathy and brain atrophy were diagnosed with Complex I deficiency based on low enzyme activity in muscle and high lactate/pyruvate ratio in fibroblasts. METHODS Whole exome sequencing results of fibroblast gDNA from one sibling was narrowed down to 190 SNPs or In/Dels in 185 candidate genes by selecting non-synonymous coding sequence base pair changes that were not present in the SNP database. RESULTS Two compound heterozygous mutations were identified in both siblings in NDUFV2, encoding the 24 kDa subunit of Complex I. The intronic mutation (c.IVS2 + 1delGTAA) is disease causing and has been reported before. The other mutation is novel (c.669_670insG, p.Ser224Valfs*3) and predicted to cause a pathogenic frameshift in the protein. Subsequent investigation of 10 probands with complex I deficiency from different families revealed homozygosity for the intronic c.IVS2 + 1delGTAA mutation in a second, consanguineous family. In this family three of five siblings were affected. Interestingly, they presented with Leigh syndrome but no cardiac involvement. The same genotype had been reported previously in a two families but presenting with hypertrophic cardiomyopathy, trunk hypotonia and encephalopathy. CONCLUSION We have identified NDUFV2 mutations in two families with Complex I deficiency, including a novel mutation. The diagnosis of Leigh syndrome expands the clinical phenotypes associated with the c.IVS2 + 1delGTAA mutation in this gene.
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Affiliation(s)
- Jessie M Cameron
- Genetics & Genome Biology Program, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, ON M5G 0A4, Canada.
| | - Nevena MacKay
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada
| | - Annette Feigenbaum
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, ON M5G 1X8, Canada.
| | - Mark Tarnopolsky
- Department of Pediatrics, McMaster University Medical Center, Hamilton, ON L8N 3Z5, Canada.
| | - Susan Blaser
- Department of Radiology, The Hospital for Sick Children and University of Toronto, ON M5G 1X8, Canada.
| | - Brian H Robinson
- Genetics & Genome Biology Program, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Andreas Schulze
- Genetics & Genome Biology Program, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, ON M5G 1X8, Canada.
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184
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Munawar N, Olivero G, Jerman E, Doyle B, Streubel G, Wynne K, Bracken A, Cagney G. Native gel analysis of macromolecular protein complexes in cultured mammalian cells. Proteomics 2015. [PMID: 26223664 DOI: 10.1002/pmic.201500045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Native gel electrophoresis enables separation of cellular proteins in their non-denatured state. In experiments aimed at analysing proteins in higher order or multimeric assemblies (i.e. protein complexes) it offers some advantages over rival approaches, particularly as an interface technology with mass spectrometry. Here we separated fractions from HEK293 cells by native electrophoresis in order to survey protein complexes in the cytoplasmic, nuclear and chromatin environments, finding 689 proteins distributed among 217 previously described complexes. As expected, different fractions contained distinct combinations of macromolecular complexes, with subunits of the same complex tending to co-migrate. Exceptions to this observation could often be explained by the presence of subunits shared among different complexes. We investigated one identified complex, the Polycomb Repressor Complex 2 (PRC2), in more detail following affinity purification of the EZH2 subunit. This approach resulted in the identification of all previously reported members of PRC2. Overall, this work demonstrates that the use of native gel electrophoresis as an upstream separating step is an effective approach for analysis of the components and cellular distribution of protein complexes.
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Affiliation(s)
- Nayla Munawar
- School of Biomolecular and Biomedical Research, University College Dublin, Belfield, Ireland
| | - Giorgio Olivero
- School of Biomolecular and Biomedical Research, University College Dublin, Belfield, Ireland
| | - Emilia Jerman
- Smurfit Institute of Genetics, Trinity College, Dublin, Ireland
| | - Benjamin Doyle
- School of Biomolecular and Biomedical Research, University College Dublin, Belfield, Ireland
| | | | - Kieran Wynne
- School of Biomolecular and Biomedical Research, University College Dublin, Belfield, Ireland
| | - Adrian Bracken
- Smurfit Institute of Genetics, Trinity College, Dublin, Ireland
| | - Gerard Cagney
- School of Biomolecular and Biomedical Research, University College Dublin, Belfield, Ireland
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185
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Munawar N, Olivero G, Jerman E, Doyle B, Streubel G, Wynne K, Bracken A, Cagney G. Native gel analysis of macromolecular protein complexes in cultured mammalian cells. Proteomics 2015. [DOI: https://doi.org/10.1002/pmic.201500045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Nayla Munawar
- School of Biomolecular and Biomedical Research; University College Dublin; Belfield Ireland
| | - Giorgio Olivero
- School of Biomolecular and Biomedical Research; University College Dublin; Belfield Ireland
| | - Emilia Jerman
- Smurfit Institute of Genetics; Trinity College; Dublin Ireland
| | - Benjamin Doyle
- School of Biomolecular and Biomedical Research; University College Dublin; Belfield Ireland
| | | | - Kieran Wynne
- School of Biomolecular and Biomedical Research; University College Dublin; Belfield Ireland
| | - Adrian Bracken
- Smurfit Institute of Genetics; Trinity College; Dublin Ireland
| | - Gerard Cagney
- School of Biomolecular and Biomedical Research; University College Dublin; Belfield Ireland
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186
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Mitochondrial ATP synthasome: Expression and structural interaction of its components. Biochem Biophys Res Commun 2015; 464:787-93. [PMID: 26168732 DOI: 10.1016/j.bbrc.2015.07.034] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 07/07/2015] [Indexed: 11/20/2022]
Abstract
Mitochondrial ATP synthase, ADP/ATP translocase (ANT), and inorganic phosphate carrier (PiC) are supposed to form a supercomplex called ATP synthasome. Our protein and transcript analysis of rat tissues indicates that the expression of ANT and PiC is transcriptionally controlled in accordance with the biogenesis of ATP synthase. In contrast, the content of ANT and PiC is increased in ATP synthase deficient patients' fibroblasts, likely due to a post-transcriptional adaptive mechanism. A structural analysis of rat heart mitochondria by immunoprecipitation, blue native/SDS electrophoresis, immunodetection and MS analysis revealed the presence of ATP synthasome. However, the majority of PiC and especially ANT did not associate with ATP synthase, suggesting that most of PiC, ANT and ATP synthase exist as separate entities.
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187
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Randriamboavonjy V, Mann WA, Elgheznawy A, Popp R, Rogowski P, Dornauf I, Dröse S, Fleming I. Metformin reduces hyper-reactivity of platelets from patients with polycystic ovary syndrome by improving mitochondrial integrity. Thromb Haemost 2015; 114:569-78. [PMID: 25993908 DOI: 10.1160/th14-09-0797] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 04/11/2015] [Indexed: 12/22/2022]
Abstract
Polycystic ovary syndrome (PCOS) is associated with decreased fertility, insulin resistance and an increased risk of developing cardiovascular disease. Treating PCOS patients with metformin improves fertility and decreases cardiovascular complications. Given that platelet activation contributes to both infertility and cardiovascular disease development, we assessed platelet reactivity in PCOS patients and the consequences of metformin treatment. Compared to washed platelets from healthy donors, platelets from PCOS patients demonstrated enhanced reactivity and impaired activation of the AMP-activated kinase (AMPK). PCOS platelets also demonstrated enhanced expression of mitochondrial proteins such as the cytochrome c reductase, ATP synthase and the voltage-dependent anion channel-1. However, mitochondrial function was impaired as demonstrated by a decreased respiration rate. In parallel, the phosphorylation of dynamin-related protein-1 (Drp-1) on Ser616 was increased while that on Ser637 decreased. The latter changes were accompanied by decreased mitochondrial size. In insulin-resistant PCOS patients (HOMA-IR> 2) metformin treatment (1.7 g per day for 4 weeks to 6 months) improved insulin sensitivity, restored mitochondrial integrity and function and normalised platelet aggregation. Treatment was without effect in PCOS patients with HOMA-IR< 2. Moreover, treatment of megakaryocytes with metformin enhanced mitochondrial content and in the same cells metformin enhanced the phosphorylation of the Drp-1 on Ser637 via an AMPKα1-dependent mechanism. In conclusion, the improvement of mitochondrial integrity and platelet reactivity may contribute to the beneficial effects of metformin on cardiovascular disease.
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Affiliation(s)
- Voahanginirina Randriamboavonjy
- Voahanginirina Randriamboavonjy PhD, Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe-University, Theodor-Stern-Kai 7, D-60596 Frankfurt am Main, Germany, Tel.: +49 69 6301 6973, Fax: +49 69 6301 86880,
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188
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Scheffler IE. Mitochondrial disease associated with complex I (NADH-CoQ oxidoreductase) deficiency. J Inherit Metab Dis 2015; 38:405-15. [PMID: 25224827 DOI: 10.1007/s10545-014-9768-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/27/2014] [Accepted: 09/02/2014] [Indexed: 01/09/2023]
Abstract
Mitochondrial diseases due to a reduced capacity for oxidative phosphorylation were first identified more than 20 years ago, and their incidence is now recognized to be quite significant. In a large proportion of cases the problem can be traced to a complex I (NADH-CoQ oxidoreductase) deficiency (Phenotype MIM #252010). Because the complex consists of 44 subunits, there are many potential targets for pathogenic mutations, both on the nuclear and mitochondrial genomes. Surprisingly, however, almost half of the complex I deficiencies are due to defects in as yet unidentified genes that encode proteins other than the structural proteins of the complex. This review attempts to summarize what we know about the molecular basis of complex I deficiencies: mutations in the known structural genes, and mutations in an increasing number of genes encoding "assembly factors", that is, proteins required for the biogenesis of a functional complex I that are not found in the final complex I. More such genes must be identified before definitive genetic counselling can be applied in all cases of affected families.
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Affiliation(s)
- Immo E Scheffler
- Division of Biology (Molecular Biology Section), University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093-0322, USA,
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189
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Accessory NUMM (NDUFS6) subunit harbors a Zn-binding site and is essential for biogenesis of mitochondrial complex I. Proc Natl Acad Sci U S A 2015; 112:5685-90. [PMID: 25902503 DOI: 10.1073/pnas.1424353112] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial proton-pumping NADH:ubiquinone oxidoreductase (respiratory complex I) comprises more than 40 polypeptides and contains eight canonical FeS clusters. The integration of subunits and insertion of cofactors into the nascent complex is a complicated multistep process that is aided by assembly factors. We show that the accessory NUMM subunit of complex I (human NDUFS6) harbors a Zn-binding site and resolve its position by X-ray crystallography. Chromosomal deletion of the NUMM gene or mutation of Zn-binding residues blocked a late step of complex I assembly. An accumulating assembly intermediate lacked accessory subunit N7BM (NDUFA12), whereas a paralog of this subunit, the assembly factor N7BML (NDUFAF2), was found firmly bound instead. EPR spectroscopic analysis and metal content determination after chromatographic purification of the assembly intermediate showed that NUMM is required for insertion or stabilization of FeS cluster N4.
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190
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Schiff M, Haberberger B, Xia C, Mohsen AW, Goetzman ES, Wang Y, Uppala R, Zhang Y, Karunanidhi A, Prabhu D, Alharbi H, Prochownik EV, Haack T, Häberle J, Munnich A, Rötig A, Taylor RW, Nicholls RD, Kim JJ, Prokisch H, Vockley J. Complex I assembly function and fatty acid oxidation enzyme activity of ACAD9 both contribute to disease severity in ACAD9 deficiency. Hum Mol Genet 2015; 24:3238-47. [PMID: 25721401 DOI: 10.1093/hmg/ddv074] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 02/23/2015] [Indexed: 01/05/2023] Open
Abstract
Acyl-CoA dehydrogenase 9 (ACAD9) is an assembly factor for mitochondrial respiratory chain Complex I (CI), and ACAD9 mutations are recognized as a frequent cause of CI deficiency. ACAD9 also retains enzyme ACAD activity for long-chain fatty acids in vitro, but the biological relevance of this function remains controversial partly because of the tissue specificity of ACAD9 expression: high in liver and neurons and minimal in skin fibroblasts. In this study, we hypothesized that this enzymatic ACAD activity is required for full fatty acid oxidation capacity in cells expressing high levels of ACAD9 and that loss of this function is important in determining phenotype in ACAD9-deficient patients. First, we confirmed that HEK293 cells express ACAD9 abundantly. Then, we showed that ACAD9 knockout in HEK293 cells affected long-chain fatty acid oxidation along with Cl, both of which were rescued by wild type ACAD9. Further, we evaluated whether the loss of ACAD9 enzymatic fatty acid oxidation affects clinical severity in patients with ACAD9 mutations. The effects on ACAD activity of 16 ACAD9 mutations identified in 24 patients were evaluated using a prokaryotic expression system. We showed that there was a significant inverse correlation between residual enzyme ACAD activity and phenotypic severity of ACAD9-deficient patients. These results provide evidence that in cells where it is strongly expressed, ACAD9 plays a physiological role in fatty acid oxidation, which contributes to the severity of the phenotype in ACAD9-deficient patients. Accordingly, treatment of ACAD9 patients should aim at counteracting both CI and fatty acid oxidation dysfunctions.
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Affiliation(s)
- Manuel Schiff
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA Reference Center for Inborn Errors of Metabolism, Hôpital Robert Debré, APHP, INSERM U1141 and Université Paris-Diderot, Sorbonne Paris Cité, Paris, France
| | - Birgit Haberberger
- Institute of Human Genetics, Technische Universität München, Munich, Germany Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Chuanwu Xia
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Al-Walid Mohsen
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA
| | - Eric S Goetzman
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA
| | - Yudong Wang
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA
| | - Radha Uppala
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA
| | - Yuxun Zhang
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA
| | - Anuradha Karunanidhi
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA
| | - Dolly Prabhu
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA
| | - Hana Alharbi
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA
| | - Edward V Prochownik
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA
| | - Tobias Haack
- Institute of Human Genetics, Technische Universität München, Munich, Germany Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Johannes Häberle
- Division of Metabolism, University Children's Hospital Zurich, Zurich, Switzerland
| | - Arnold Munnich
- Institut Imagine and INSERM U781, Sorbonne Paris Cité, Hôpital Necker-Enfants Malades, APHP, Université Paris-Descartes, Paris, France
| | - Agnes Rötig
- Institut Imagine and INSERM U781, Sorbonne Paris Cité, Hôpital Necker-Enfants Malades, APHP, Université Paris-Descartes, Paris, France
| | - Robert W Taylor
- Wellcome Trust Centre for Mitochondrial Research, The Medical School, Newcastle University, Newcastle upon Tyne, UK and
| | - Robert D Nicholls
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Jung-Ja Kim
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Holger Prokisch
- Institute of Human Genetics, Technische Universität München, Munich, Germany Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Jerry Vockley
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15224, USA
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191
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A mitochondria-specific isoform of FASTK is present in mitochondrial RNA granules and regulates gene expression and function. Cell Rep 2015; 10:1110-21. [PMID: 25704814 DOI: 10.1016/j.celrep.2015.01.063] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 12/10/2014] [Accepted: 01/29/2015] [Indexed: 11/21/2022] Open
Abstract
The mitochondrial genome relies heavily on post-transcriptional events for its proper expression, and misregulation of this process can cause mitochondrial genetic diseases in humans. Here, we report that a novel translational variant of Fas-activated serine/threonine kinase (FASTK) co-localizes with mitochondrial RNA granules and is required for the biogenesis of ND6 mRNA, a mitochondrial-encoded subunit of the NADH dehydrogenase complex (complex I). We show that ablating FASTK expression in cultured cells and mice results specifically in loss of ND6 mRNA and reduced complex I activity in vivo. FASTK binds at multiple sites along the ND6 mRNA and its precursors and cooperates with the mitochondrial degradosome to ensure regulated ND6 mRNA biogenesis. These data provide insights into the mechanism and control of mitochondrial RNA processing within mitochondrial RNA granules.
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192
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Formosa LE, Mimaki M, Frazier AE, McKenzie M, Stait TL, Thorburn DR, Stroud DA, Ryan MT. Characterization of mitochondrial FOXRED1 in the assembly of respiratory chain complex I. Hum Mol Genet 2015; 24:2952-65. [DOI: 10.1093/hmg/ddv058] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 02/09/2015] [Indexed: 11/12/2022] Open
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193
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Koob S, Reichert AS. Novel intracellular functions of apolipoproteins: the ApoO protein family as constituents of the Mitofilin/MINOS complex determines cristae morphology in mitochondria. Biol Chem 2015; 395:285-96. [PMID: 24391192 DOI: 10.1515/hsz-2013-0274] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 12/21/2013] [Indexed: 11/15/2022]
Abstract
Mitochondria exist in a highly dynamic network that is constantly altered by fusion and fission events depending on various factors such as cellular bioenergetic state and cell cycle. Next to this dynamic nature of the organelle, its cristae membrane also undergoes drastic morphological changes upon physiological or pathological alterations. The Mitofilin/mitochondrial inner membrane organizing system (MINOS) complex was recently reported to ensure mitochondrial architecture and crista junction integrity. Several subunits of this complex are linked to a diverse set of neurological human disorders. Recently, two apolipoproteins, ApoO (APOO) and ApoO-like (APOOL) were suggested to represent constituents of the mammalian Mitofilin/MINOS complex. APOOL was shown to bind the mitochondrial phospholipid cardiolipin (CL) and to interact physically with this complex. In this review we highlight the current view on the mammalian Mitofilin/MINOS complex and focus on APOOL and the role of CL in determining cristae morphology. We will discuss possible functions of the Mitofilin/MINOS complex on lipid transport, on assembly of respiratory supercomplexes, on F1FO-ATP synthase organization, on contact site formation, and on trapping CL within the cristae subcompartment.
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194
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Scott NE, Brown LM, Kristensen AR, Foster LJ. Development of a computational framework for the analysis of protein correlation profiling and spatial proteomics experiments. J Proteomics 2014; 118:112-29. [PMID: 25464368 DOI: 10.1016/j.jprot.2014.10.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 10/18/2014] [Accepted: 10/27/2014] [Indexed: 01/12/2023]
Abstract
UNLABELLED Standard approaches to studying an interactome do not easily allow conditional experiments but in recent years numerous groups have demonstrated the potential for co-fractionation/co-migration based approaches to assess an interactome at a similar sensitivity and specificity yet significantly lower cost and higher speed than traditional approaches. Unfortunately, there is as yet no implementation of the bioinformatics tools required to robustly analyze co-fractionation data in a way that can also integrate the valuable information contained in biological replicates. Here we have developed a freely available, integrated bioinformatics solution for the analysis of protein correlation profiling SILAC data. This modular solution allows the deconvolution of protein chromatograms into individual Gaussian curves enabling the use of these chromatography features to align replicates and assemble a consensus map of features observed across replicates; the chromatograms and individual curves are then used to quantify changes in protein interactions and construct the interactome. We have applied this workflow to the analysis of HeLa cells infected with a Salmonella enterica serovar Typhimurium infection model where we can identify specific interactions that are affected by the infection. These bioinformatics tools simplify the analysis of co-fractionation/co-migration data to the point where there is no specialized knowledge required to measure an interactome in this way. BIOLOGICAL SIGNIFICANCE We describe a set of software tools for the bioinformatics analysis of co-migration/co-fractionation data that integrates the results from multiple replicates to generate an interactome, including the impact on individual interactions of any external perturbation. This article is part of a Special Issue entitled: Protein dynamics in health and disease. Guest Editors: Pierre Thibault and Anne-Claude Gingras.
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Affiliation(s)
- Nichollas E Scott
- Centre for High-throughput Biology, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada.
| | - Lyda M Brown
- Centre for High-throughput Biology, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada
| | - Anders R Kristensen
- Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver V5Z 4S6, British Columbia, Canada
| | - Leonard J Foster
- Centre for High-throughput Biology, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada.
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195
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Wi SM, Moon G, Kim J, Kim ST, Shim JH, Chun E, Lee KY. TAK1-ECSIT-TRAF6 complex plays a key role in the TLR4 signal to activate NF-κB. J Biol Chem 2014; 289:35205-14. [PMID: 25371197 DOI: 10.1074/jbc.m114.597187] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
ECSIT (evolutionarily conserved signaling intermediate in Toll pathways) is known as a multifunctional regulator in different signals, including Toll-like receptors (TLRs), TGF-β, and BMP. Here, we report a new regulatory role of ECSIT in TLR4-mediated signal. By LPS stimulation, ECSIT formed a high molecular endogenous complex including TAK1 and TRAF6, in which ECSIT interacted with each protein and regulated TAK1 activity, leading to the activation of NF-κB. ECSIT-knockdown THP-1 (ECSIT(KD) THP-1) cells exhibited severe impairments in NF-κB activity, cytokine production, and NF-κB-dependent gene expression, whereas those were dramatically restored by reintroduction of wild type (WT) ECSIT gene. Interestingly, ECSIT mutants, which lack a specific interacting domain for either TAK1 or TRAF6, could not restore these activities. Moreover, no significant changes in both NF-κB activity and cytokine production induced by TLR4 could be seen in TAK1(KD) or TRAF6(KD) THP-1 cells transduced by WT ECSIT, strongly suggesting the essential requirement of TAK1-ECSIT-TRAF6 complex in TLR4 signaling. Taken together, our data demonstrate that the ECSIT complex, including TAK1 and TRAF6, plays a pivotal role in TLR4-mediated signals to activate NF-κB.
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Affiliation(s)
- Sae Mi Wi
- From the Department of Molecular Cell Biology and Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea
| | - Gyuyoung Moon
- From the Department of Molecular Cell Biology and Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea
| | - Juhong Kim
- From the Department of Molecular Cell Biology and Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea
| | - Seong-Tae Kim
- From the Department of Molecular Cell Biology and Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea
| | - Jae-Hyuck Shim
- the Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York 10065
| | - Eunyoung Chun
- the Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115, and the Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115
| | - Ki-Young Lee
- From the Department of Molecular Cell Biology and Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea,
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196
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Mi Wi S, Park J, Shim JH, Chun E, Lee KY. Ubiquitination of ECSIT is crucial for the activation of p65/p50 NF-κBs in Toll-like receptor 4 signaling. Mol Biol Cell 2014; 26:151-60. [PMID: 25355951 PMCID: PMC4279226 DOI: 10.1091/mbc.e14-08-1277] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The localization of ECSIT into the nucleus is specifically accompanied by p65/p50 NF-κB in a TLR4-dependent manner. p65 NF-κB specifically interacts with the ubiquitinated ECSIT on the Lys-372 residue, thereby regulating NF-κB activity, NF-κB–dependent gene expression, and production of proinflammatory cytokines. Recent evidence shows that evolutionarily conserved signaling intermediate in Toll pathways (ECSIT) interacts with tumor necrosis factor receptor–associated factor 6 (TRAF6), is ubiquitinated, and contributes to bactericidal activity during Toll-like receptor (TLR) signaling. Here we report a new regulatory role for ECSIT in TLR4 signaling. On TLR4 stimulation, endogenous ECSIT formed a molecular complex with p65/p50 NF-κB proteins. Our biochemical studies showed that ECSIT specifically interacted with p65/p50 NF-κB proteins, which colocalized in the nucleus. Of interest, these effects were critically dependent on ubiquitination of the ECSIT lysine (K) 372 residue. K372A mutant ECSIT did not interact with p65/p50 NF-κB proteins and markedly attenuated nuclear colocalization. In addition, ECSIT-knockdown THP-1 cells could not activate NF-κB DNA-binding activities of p65 and p50, production of proinflammatory cytokines, or NF-κB–dependent gene expression in response to TLR4 stimulation. However, these activities were markedly restored by expressing the wild-type ECSIT protein but not the K372A mutant ECSIT protein. These data strongly suggest that the ubiquitination of ECSIT might have a role in the regulation of NF-κB activity in TLR4 signaling.
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Affiliation(s)
- Sae Mi Wi
- Department of Molecular Cell Biology and Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Jeongho Park
- Department of Molecular Cell Biology and Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Jae-Hyuck Shim
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065
| | - Eunyoung Chun
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, and Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Ki-Young Lee
- Department of Molecular Cell Biology and Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
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197
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Giese H, Ackermann J, Heide H, Bleier L, Dröse S, Wittig I, Brandt U, Koch I. NOVA: a software to analyze complexome profiling data. Bioinformatics 2014; 31:440-1. [PMID: 25301849 DOI: 10.1093/bioinformatics/btu623] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
SUMMARY We introduce nova, a software for the analysis of complexome profiling data. nova supports the investigation of the composition of complexes, cluster analysis of the experimental data, visual inspection and comparison of experiments and many other features. AVAILABILITY AND IMPLEMENTATION nova is licensed under the Artistic License 2.0. It is freely available at http://www.bioinformatik.uni-frankfurt.de. nova requires at least Java 7 and runs under Linux, Microsoft Windows and Mac OS. CONTACT ina.koch@bioinformatik.uni-frankfurt.de.
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Affiliation(s)
- Heiko Giese
- Molecular Bioinformatics Group, Institute of Computer Science, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University, Robert-Mayer-Str. 11-15, 60325 Frankfurt am Main, Germany, Molecular Bioenergetics Group, Medical School, Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany, Functional Proteomics, SFB815 core unit, Medical School, Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany and Nijmegen Centre for Mitochondrial Disorders, Radboud University Medical Centre, 6525 GA, Nijmegen, The Netherlands
| | - Jörg Ackermann
- Molecular Bioinformatics Group, Institute of Computer Science, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University, Robert-Mayer-Str. 11-15, 60325 Frankfurt am Main, Germany, Molecular Bioenergetics Group, Medical School, Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany, Functional Proteomics, SFB815 core unit, Medical School, Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany and Nijmegen Centre for Mitochondrial Disorders, Radboud University Medical Centre, 6525 GA, Nijmegen, The Netherlands
| | - Heinrich Heide
- Molecular Bioinformatics Group, Institute of Computer Science, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University, Robert-Mayer-Str. 11-15, 60325 Frankfurt am Main, Germany, Molecular Bioenergetics Group, Medical School, Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany, Functional Proteomics, SFB815 core unit, Medical School, Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany and Nijmegen Centre for Mitochondrial Disorders, Radboud University Medical Centre, 6525 GA, Nijmegen, The Netherlands Molecular Bioinformatics Group, Institute of Computer Science, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University, Robert-Mayer-Str. 11-15, 60325 Frankfurt am Main, Germany, Molecular Bioenergetics Group, Medical School, Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany, Functional Proteomics, SFB815 core unit, Medical School, Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany and Nijmegen Centre for Mitochondrial Disorders, Radboud University Medical Centre, 6525 GA, Nijmegen, The Netherlands
| | - Lea Bleier
- Molecular Bioinformatics Group, Institute of Computer Science, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University, Robert-Mayer-Str. 11-15, 60325 Frankfurt am Main, Germany, Molecular Bioenergetics Group, Medical School, Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany, Functional Proteomics, SFB815 core unit, Medical School, Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany and Nijmegen Centre for Mitochondrial Disorders, Radboud University Medical Centre, 6525 GA, Nijmegen, The Netherlands
| | - Stefan Dröse
- Molecular Bioinformatics Group, Institute of Computer Science, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University, Robert-Mayer-Str. 11-15, 60325 Frankfurt am Main, Germany, Molecular Bioenergetics Group, Medical School, Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany, Functional Proteomics, SFB815 core unit, Medical School, Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany and Nijmegen Centre for Mitochondrial Disorders, Radboud University Medical Centre, 6525 GA, Nijmegen, The Netherlands
| | - Ilka Wittig
- Molecular Bioinformatics Group, Institute of Computer Science, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University, Robert-Mayer-Str. 11-15, 60325 Frankfurt am Main, Germany, Molecular Bioenergetics Group, Medical School, Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany, Functional Proteomics, SFB815 core unit, Medical School, Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany and Nijmegen Centre for Mitochondrial Disorders, Radboud University Medical Centre, 6525 GA, Nijmegen, The Netherlands Molecular Bioinformatics Group, Institute of Computer Science, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University, Robert-Mayer-Str. 11-15, 60325 Frankfurt am Main, Germany, Molecular Bioenergetics Group, Medical School, Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany, Functional Proteomics, SFB815 core unit, Medical School, Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany and Nijmegen Centre for Mitochondrial Disorders, Radboud University Medical Centre, 6525 GA, Nijmegen, The Netherlands
| | - Ulrich Brandt
- Molecular Bioinformatics Group, Institute of Computer Science, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University, Robert-Mayer-Str. 11-15, 60325 Frankfurt am Main, Germany, Molecular Bioenergetics Group, Medical School, Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany, Functional Proteomics, SFB815 core unit, Medical School, Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany and Nijmegen Centre for Mitochondrial Disorders, Radboud University Medical Centre, 6525 GA, Nijmegen, The Netherlands Molecular Bioinformatics Group, Institute of Computer Science, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University, Robert-Mayer-Str. 11-15, 60325 Frankfurt am Main, Germany, Molecular Bioenergetics Group, Medical School, Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany, Functional Proteomics, SFB815 core unit, Medical School, Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany and Nijmegen Centre for Mitochondrial Disorders, Radboud University Medical Centre, 6525 GA, Nijmegen, The Netherlands
| | - Ina Koch
- Molecular Bioinformatics Group, Institute of Computer Science, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University, Robert-Mayer-Str. 11-15, 60325 Frankfurt am Main, Germany, Molecular Bioenergetics Group, Medical School, Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany, Functional Proteomics, SFB815 core unit, Medical School, Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany and Nijmegen Centre for Mitochondrial Disorders, Radboud University Medical Centre, 6525 GA, Nijmegen, The Netherlands
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Vartak RS, Semwal MK, Bai Y. An update on complex I assembly: the assembly of players. J Bioenerg Biomembr 2014; 46:323-8. [PMID: 25030182 DOI: 10.1007/s10863-014-9564-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 07/02/2014] [Indexed: 12/19/2022]
Abstract
Defects in Complex I assembly is one of the emerging underlying causes of severe mitochondrial disorders. The assembly of Complex I has been difficult to understand due to its large size, dual genetic control and the number of proteins involved. Mutations in Complex I subunits as well as assembly factors have been reported to hinder its assembly and give rise to a range of mitochondria disorders. In this review, we summarize the recent progress made in understanding the Complex I assembly pathway. In particularly, we focus on the known as well as novel assembly factors and their role in assembly of Complex I and human disease.
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Affiliation(s)
- Rasika S Vartak
- Department of Cellular and Structural Biology, UT Health Science Center, San Antonio, TX, USA
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199
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Burkhart JM, Gambaryan S, Watson SP, Jurk K, Walter U, Sickmann A, Heemskerk JWM, Zahedi RP. What can proteomics tell us about platelets? Circ Res 2014; 114:1204-19. [PMID: 24677239 DOI: 10.1161/circresaha.114.301598] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
More than 130 years ago, it was recognized that platelets are key mediators of hemostasis. Nowadays, it is established that platelets participate in additional physiological processes and contribute to the genesis and progression of cardiovascular diseases. Recent data indicate that the platelet proteome, defined as the complete set of expressed proteins, comprises >5000 proteins and is highly similar between different healthy individuals. Owing to their anucleate nature, platelets have limited protein synthesis. By implication, in patients experiencing platelet disorders, platelet (dys)function is almost completely attributable to alterations in protein expression and dynamic differences in post-translational modifications. Modern platelet proteomics approaches can reveal (1) quantitative changes in the abundance of thousands of proteins, (2) post-translational modifications, (3) protein-protein interactions, and (4) protein localization, while requiring only small blood donations in the range of a few milliliters. Consequently, platelet proteomics will represent an invaluable tool for characterizing the fundamental processes that affect platelet homeostasis and thus determine the roles of platelets in health and disease. In this article we provide a critical overview on the achievements, the current possibilities, and the future perspectives of platelet proteomics to study patients experiencing cardiovascular, inflammatory, and bleeding disorders.
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Affiliation(s)
- Julia M Burkhart
- From the Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany (J.M.B., A.S., R.P.Z); Institut für Klinische Biochemie und Pathobiochemie, Universitätsklinikum Würzburg, Würzburg, Germany (S.G.); Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg, Russia (S.G.); Centre for Cardiovascular Sciences, Institute for Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom (S.P.W.); Center for Thrombosis and Hemostasis, Universitätsklinikum der Johannes Gutenberg-Universität Mainz, Mainz, Germany (K.J., U.W.); Medizinisches Proteom Center, Ruhr Universität Bochum, Bochum, Germany (A.S.); Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom (A.S.); and Department of Biochemistry, CARIM, Maastricht University, Maastricht, The Netherlands (J.W.M.H.)
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200
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Awwad K, Steinbrink SD, Frömel T, Lill N, Isaak J, Häfner AK, Roos J, Hofmann B, Heide H, Geisslinger G, Steinhilber D, Freeman BA, Maier TJ, Fleming I. Electrophilic fatty acid species inhibit 5-lipoxygenase and attenuate sepsis-induced pulmonary inflammation. Antioxid Redox Signal 2014; 20:2667-80. [PMID: 24206143 PMCID: PMC4026401 DOI: 10.1089/ars.2013.5473] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
AIMS The reaction of nitric oxide and nitrite-derived species with polyunsaturated fatty acids yields electrophilic fatty acid nitroalkene derivatives (NO2-FA), which display anti-inflammatory properties. Given that the 5-lipoxygenase (5-LO, ALOX5) possesses critical nucleophilic amino acids, which are potentially sensitive to electrophilic modifications, we determined the consequences of NO2-FA on 5-LO activity in vitro and on 5-LO-mediated inflammation in vivo. RESULTS Stimulation of human polymorphonuclear leukocytes (PMNL) with nitro-oleic (NO2-OA) or nitro-linoleic acid (NO2-LA) (but not the parent lipids) resulted in the concentration-dependent and irreversible inhibition of 5-LO activity. Similar effects were observed in cell lysates and using the recombinant human protein, indicating a direct reaction with 5-LO. NO2-FAs did not affect the activity of the platelet-type 12-LO (ALOX12) or 15-LO-1 (ALOX15) in intact cells or the recombinant protein. The NO2-FA-induced inhibition of 5-LO was attributed to the alkylation of Cys418, and the exchange of Cys418 to serine rendered 5-LO insensitive to NO2-FA. In vivo, the systemic administration of NO2-OA to mice decreased neutrophil and monocyte mobilization in response to lipopolysaccharide (LPS), attenuated the formation of the 5-LO product 5-hydroxyeicosatetraenoic acid (5-HETE), and inhibited lung injury. The administration of NO2-OA to 5-LO knockout mice had no effect on LPS-induced neutrophil or monocyte mobilization as well as on lung injury. INNOVATION Prophylactic administration of NO2-OA to septic mice inhibits inflammation and promotes its resolution by interfering in 5-LO-mediated inflammatory processes. CONCLUSION NO2-FAs directly and irreversibly inhibit 5-LO and attenuate downstream acute inflammatory responses.
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Affiliation(s)
- Khader Awwad
- 1 Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University , Frankfurt am Main, Germany
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