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Othonicar MF, Garcia GS, Oliveira MT. The alternative enzymes-bearing tunicates lack multiple widely distributed genes coding for peripheral OXPHOS subunits. Biochim Biophys Acta Bioenerg 2024; 1865:149046. [PMID: 38642871 DOI: 10.1016/j.bbabio.2024.149046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 04/01/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
The respiratory chain alternative enzymes (AEs) NDX and AOX from the tunicate Ciona intestinalis (Ascidiacea) have been xenotopically expressed and characterized in human cells in culture and in the model organisms Drosophila melanogaster and mouse, with the purpose of developing bypass therapies to combat mitochondrial diseases in human patients with defective complexes I and III/IV, respectively. The fact that the genes coding for NDX and AOX have been lost from genomes of evolutionarily successful animal groups, such as vertebrates and insects, led us to investigate if the composition of the respiratory chain of Ciona and other tunicates differs significantly from that of humans and Drosophila, to accommodate the natural presence of AEs. We have failed to identify in tunicate genomes fifteen orthologous genes that code for subunits of the respiratory chain complexes; all of these putatively missing subunits are peripheral to complexes I, III and IV in mammals, and many are important for complex-complex interaction in supercomplexes (SCs), such as NDUFA11, UQCR11 and COX7A. Modeling of all respiratory chain subunit polypeptides of Ciona indicates significant structural divergence that is consistent with the lack of these fifteen clear orthologous subunits. We also provide evidence using Ciona AOX expressed in Drosophila that this AE cannot access the coenzyme Q pool reduced by complex I, but it is readily available to oxidize coenzyme Q molecules reduced by glycerophosphate oxidase, a mitochondrial inner membrane-bound dehydrogenase that is not involved in SCs. Altogether, our results suggest that Ciona AEs might have evolved in a mitochondrial inner membrane environment much different from that of mammals and insects, possibly without SCs; this correlates with the preferential functional interaction between these AEs and non-SC dehydrogenases in heterologous mammalian and insect systems. We discuss the implications of these findings for the applicability of Ciona AEs in human bypass therapies and for our understanding of the evolution of animal respiratory chain.
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Affiliation(s)
- Murilo F Othonicar
- Departamento de Biotecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil
| | - Geovana S Garcia
- Departamento de Biotecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil
| | - Marcos T Oliveira
- Departamento de Biotecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil.
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2
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van der Ven AT, Cabrera-Orefice A, Wente I, Feichtinger RG, Tsiakas K, Weiss D, Bierhals T, Scholle L, Prokisch H, Kopajtich R, Santer R, Mayr JA, Hempel M, Wittig I. Expanding the phenotypic and biochemical spectrum of NDUFAF3-related mitochondrial disease. Mol Genet Metab 2023; 140:107675. [PMID: 37572574 DOI: 10.1016/j.ymgme.2023.107675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/27/2023] [Accepted: 07/30/2023] [Indexed: 08/14/2023]
Abstract
Recessive variants in NDUFAF3 are a known cause of complex I (CI)-related mitochondrial disorders (MDs). The seven patients reported to date exhibited severe neurologic symptoms and lactic acidosis, followed by a fatal course and death during infancy in most cases. We present a 10-year-old patient with a neurodevelopmental disorder, progressive exercise intolerance, dystonia, basal ganglia abnormalities, and elevated lactate concentration in blood. Trio-exome sequencing revealed compound-heterozygosity for a pathogenic splice-site and a likely pathogenic missense variant in NDUFAF3. Spectrophotometric analysis of fibroblast-derived mitochondria demonstrated a relatively mild reduction of CI activity. Complexome analyses revealed severely reduced NDUFAF3 as well as CI in patient fibroblasts. Accumulation of early sub-assemblies of the membrane arm of CI associated with mitochondrial complex I intermediate assembly (MCIA) complex was observed. The most striking additional findings were both the unusual occurrence of free monomeric CI holding MCIA and other assembly factors. Here we discuss our patient in context of genotype, phenotype and metabolite data from previously reported NDUFAF3 cases. With the atypical presentation of our patient, we provide further insight into the phenotypic spectrum of NDUFAF3-related MDs. Complexome analysis in our patient confirms the previously defined role of NDUFAF3 within CI biogenesis, yet adds new aspects regarding the correct timing of both the association of soluble and membrane arm modules and CI-maturation as well as respiratory supercomplex formation.
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Affiliation(s)
- Amelie T van der Ven
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Alfredo Cabrera-Orefice
- Functional Proteomics, Institute of Cardiovascular Physiology, Goethe University, Frankfurt am Main, Germany
| | - Isabell Wente
- Functional Proteomics, Institute of Cardiovascular Physiology, Goethe University, Frankfurt am Main, Germany
| | - René G Feichtinger
- University Children's Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), Salzburg, Austria
| | - Konstantinos Tsiakas
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Deike Weiss
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Leila Scholle
- Department of Neurology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Holger Prokisch
- Institute of Human Genetics, Klinikum Rechts der Isar, TUM, Munich, Germany.; Institute of Neurogenomics, Helmholtz Center Munich, Neuherberg, Germany
| | - Robert Kopajtich
- Institute of Human Genetics, Klinikum Rechts der Isar, TUM, Munich, Germany.; Institute of Neurogenomics, Helmholtz Center Munich, Neuherberg, Germany
| | - René Santer
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Johannes A Mayr
- University Children's Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), Salzburg, Austria
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Ilka Wittig
- Functional Proteomics, Institute of Cardiovascular Physiology, Goethe University, Frankfurt am Main, Germany
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3
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Nasca A, Mencacci NE, Invernizzi F, Zech M, Keller Sarmiento IJ, Legati A, Frascarelli C, Bustos BI, Romito LM, Krainc D, Winkelmann J, Carecchio M, Nardocci N, Zorzi G, Prokisch H, Lubbe SJ, Garavaglia B, Ghezzi D. Variants in ATP5F1B are associated with dominantly inherited dystonia. Brain 2023; 146:2730-2738. [PMID: 36860166 PMCID: PMC10316767 DOI: 10.1093/brain/awad068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 12/31/2022] [Accepted: 02/05/2023] [Indexed: 03/03/2023] Open
Abstract
ATP5F1B is a subunit of the mitochondrial ATP synthase or complex V of the mitochondrial respiratory chain. Pathogenic variants in nuclear genes encoding assembly factors or structural subunits are associated with complex V deficiency, typically characterized by autosomal recessive inheritance and multisystem phenotypes. Movement disorders have been described in a subset of cases carrying autosomal dominant variants in structural subunits genes ATP5F1A and ATP5MC3. Here, we report the identification of two different ATP5F1B missense variants (c.1000A>C; p.Thr334Pro and c.1445T>C; p.Val482Ala) segregating with early-onset isolated dystonia in two families, both with autosomal dominant mode of inheritance and incomplete penetrance. Functional studies in mutant fibroblasts revealed no decrease of ATP5F1B protein amount but severe reduction of complex V activity and impaired mitochondrial membrane potential, suggesting a dominant-negative effect. In conclusion, our study describes a new candidate gene associated with isolated dystonia and confirms that heterozygous variants in genes encoding subunits of the mitochondrial ATP synthase may cause autosomal dominant isolated dystonia with incomplete penetrance, likely through a dominant-negative mechanism.
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Affiliation(s)
- Alessia Nasca
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
| | - Niccolò E Mencacci
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago 60611, IL, USA
| | - Federica Invernizzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
| | - Michael Zech
- Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, 85764 Munich, Germany
| | - Ignacio J Keller Sarmiento
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago 60611, IL, USA
| | - Andrea Legati
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
| | - Chiara Frascarelli
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
| | - Bernabe I Bustos
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago 60611, IL, USA
| | - Luigi M Romito
- Parkinson and Movement Disorders Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Dimitri Krainc
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago 60611, IL, USA
| | - Juliane Winkelmann
- Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, 85764 Munich, Germany
- Lehrstuhl für Neurogenetik, Technische Universität München, 81675 Munich, Germany
- Munich Cluster for Systems Neurology, SyNergy, 81377 Munich, Germany
| | - Miryam Carecchio
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
- Department Neuroscience, University of Padua, 35128 Padua, Italy
- Department of Pediatric Neuroscience, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Nardo Nardocci
- Department of Pediatric Neuroscience, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Giovanna Zorzi
- Department of Pediatric Neuroscience, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Holger Prokisch
- Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, 85764 Munich, Germany
| | - Steven J Lubbe
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago 60611, IL, USA
| | - Barbara Garavaglia
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
- Department of Pathophysiology and Transplantation (DEPT), University of Milan, 20122 Milan, Italy
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4
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Thompson K, Stroud DA, Thorburn DR, Taylor RW. Investigation of oxidative phosphorylation activity and complex composition in mitochondrial disease. Handb Clin Neurol 2023; 194:127-139. [PMID: 36813309 DOI: 10.1016/b978-0-12-821751-1.00008-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
A multidisciplinary approach to the laboratory diagnosis of mitochondrial disease has long been applied, with crucial information provided by deep clinical phenotyping, blood investigations, and biomarker screening as well as histopathological and biochemical testing of biopsy material to support molecular genetic screening. In an era of second and third generation sequencing technologies, traditional diagnostic algorithms for mitochondrial disease have been replaced by gene agnostic, genomic strategies including whole-exome sequencing (WES) and whole-genome sequencing (WGS), increasingly supported by other 'omics technologies (Alston et al., 2021). Whether a primary testing strategy, or one used to validate and interpret candidate genetic variants, the availability of a range of tests aimed at determining mitochondrial function (i.e., the assessment of individual respiratory chain enzyme activities in a tissue biopsy or cellular respiration in a patient cell line) remains an important part of the diagnostic armory. In this chapter, we summarize several disciplines used in the laboratory investigation of suspected mitochondrial disease, including the histopathological and biochemical assessment of mitochondrial function, as well as protein-based techniques to assess the steady-state levels of oxidative phosphorylation (OXPHOS) subunits and assembly of OXPHOS complexes via traditional (immunoblotting) and cutting-edge (quantitative proteomic) approaches.
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Affiliation(s)
- Kyle Thompson
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - David A Stroud
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, Australia; Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - David R Thorburn
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia; Mitochondrial Laboratory, Victorian Clinical Genetic Services, Melbourne, VIC, Australia
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom; NHS Highly Specialised Services for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom.
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5
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Cabrera-Orefice A, Potter A, Evers F, Hevler JF, Guerrero-Castillo S. Complexome Profiling-Exploring Mitochondrial Protein Complexes in Health and Disease. Front Cell Dev Biol 2022; 9:796128. [PMID: 35096826 PMCID: PMC8790184 DOI: 10.3389/fcell.2021.796128] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/08/2021] [Indexed: 12/14/2022] Open
Abstract
Complexome profiling (CP) is a state-of-the-art approach that combines separation of native proteins by electrophoresis, size exclusion chromatography or density gradient centrifugation with tandem mass spectrometry identification and quantification. Resulting data are computationally clustered to visualize the inventory, abundance and arrangement of multiprotein complexes in a biological sample. Since its formal introduction a decade ago, this method has been mostly applied to explore not only the composition and abundance of mitochondrial oxidative phosphorylation (OXPHOS) complexes in several species but also to identify novel protein interactors involved in their assembly, maintenance and functions. Besides, complexome profiling has been utilized to study the dynamics of OXPHOS complexes, as well as the impact of an increasing number of mutations leading to mitochondrial disorders or rearrangements of the whole mitochondrial complexome. Here, we summarize the major findings obtained by this approach; emphasize its advantages and current limitations; discuss multiple examples on how this tool could be applied to further investigate pathophysiological mechanisms and comment on the latest advances and opportunity areas to keep developing this methodology.
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Affiliation(s)
- Alfredo Cabrera-Orefice
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Alisa Potter
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Felix Evers
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Johannes F Hevler
- Biomolecular Mass Spectrometry and Proteomics, University of Utrecht, Utrecht, Netherlands.,Bijvoet Center for Biomolecular Research, University of Utrecht, Utrecht, Netherlands.,Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, Netherlands.,Netherlands Proteomics Center, Utrecht, Netherlands
| | - Sergio Guerrero-Castillo
- University Children's Research@Kinder-UKE, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Marra F, Lunetti P, Curcio R, Lasorsa FM, Capobianco L, Porcelli V, Dolce V, Fiermonte G, Scarcia P. An Overview of Mitochondrial Protein Defects in Neuromuscular Diseases. Biomolecules 2021; 11:1633. [PMID: 34827632 PMCID: PMC8615828 DOI: 10.3390/biom11111633] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 11/18/2022] Open
Abstract
Neuromuscular diseases (NMDs) are dysfunctions that involve skeletal muscle and cause incorrect communication between the nerves and muscles. The specific causes of NMDs are not well known, but most of them are caused by genetic mutations. NMDs are generally progressive and entail muscle weakness and fatigue. Muscular impairments can differ in onset, severity, prognosis, and phenotype. A multitude of possible injury sites can make diagnosis of NMDs difficult. Mitochondria are crucial for cellular homeostasis and are involved in various metabolic pathways; for this reason, their dysfunction can lead to the development of different pathologies, including NMDs. Most NMDs due to mitochondrial dysfunction have been associated with mutations of genes involved in mitochondrial biogenesis and metabolism. This review is focused on some mitochondrial routes such as the TCA cycle, OXPHOS, and β-oxidation, recently found to be altered in NMDs. Particular attention is given to the alterations found in some genes encoding mitochondrial carriers, proteins of the inner mitochondrial membrane able to exchange metabolites between mitochondria and the cytosol. Briefly, we discuss possible strategies used to diagnose NMDs and therapies able to promote patient outcome.
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Affiliation(s)
- Federica Marra
- Department of Pharmacy, Health, and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy; (F.M.); (R.C.); (V.D.)
| | - Paola Lunetti
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (P.L.); (L.C.)
| | - Rosita Curcio
- Department of Pharmacy, Health, and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy; (F.M.); (R.C.); (V.D.)
| | - Francesco Massimo Lasorsa
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy; (F.M.L.); (V.P.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, 00155 Rome, Italy
| | - Loredana Capobianco
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (P.L.); (L.C.)
| | - Vito Porcelli
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy; (F.M.L.); (V.P.)
| | - Vincenza Dolce
- Department of Pharmacy, Health, and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy; (F.M.); (R.C.); (V.D.)
| | - Giuseppe Fiermonte
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy; (F.M.L.); (V.P.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, 00155 Rome, Italy
| | - Pasquale Scarcia
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy; (F.M.L.); (V.P.)
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Zanfardino P, Doccini S, Santorelli FM, Petruzzella V. Tackling Dysfunction of Mitochondrial Bioenergetics in the Brain. Int J Mol Sci 2021; 22:8325. [PMID: 34361091 PMCID: PMC8348117 DOI: 10.3390/ijms22158325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 12/15/2022] Open
Abstract
Oxidative phosphorylation (OxPhos) is the basic function of mitochondria, although the landscape of mitochondrial functions is continuously growing to include more aspects of cellular homeostasis. Thanks to the application of -omics technologies to the study of the OxPhos system, novel features emerge from the cataloging of novel proteins as mitochondrial thus adding details to the mitochondrial proteome and defining novel metabolic cellular interrelations, especially in the human brain. We focussed on the diversity of bioenergetics demand and different aspects of mitochondrial structure, functions, and dysfunction in the brain. Definition such as 'mitoexome', 'mitoproteome' and 'mitointeractome' have entered the field of 'mitochondrial medicine'. In this context, we reviewed several genetic defects that hamper the last step of aerobic metabolism, mostly involving the nervous tissue as one of the most prominent energy-dependent tissues and, as consequence, as a primary target of mitochondrial dysfunction. The dual genetic origin of the OxPhos complexes is one of the reasons for the complexity of the genotype-phenotype correlation when facing human diseases associated with mitochondrial defects. Such complexity clinically manifests with extremely heterogeneous symptoms, ranging from organ-specific to multisystemic dysfunction with different clinical courses. Finally, we briefly discuss the future directions of the multi-omics study of human brain disorders.
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Affiliation(s)
- Paola Zanfardino
- Department of Medical Basic Sciences, Neurosciences and Sense Organs, University of Bari Aldo Moro, 70124 Bari, Italy;
| | - Stefano Doccini
- IRCCS Fondazione Stella Maris, Calambrone, 56128 Pisa, Italy;
| | | | - Vittoria Petruzzella
- Department of Medical Basic Sciences, Neurosciences and Sense Organs, University of Bari Aldo Moro, 70124 Bari, Italy;
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Wittig I, Malacarne PF. Complexome Profiling: Assembly and Remodeling of Protein Complexes. Int J Mol Sci 2021; 22:7809. [PMID: 34360575 DOI: 10.3390/ijms22157809] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/13/2021] [Accepted: 07/19/2021] [Indexed: 02/06/2023] Open
Abstract
Many proteins have been found to operate in a complex with various biomolecules such as proteins, nucleic acids, carbohydrates, or lipids. Protein complexes can be transient, stable or dynamic and their association is controlled under variable cellular conditions. Complexome profiling is a recently developed mass spectrometry-based method that combines mild separation techniques, native gel electrophoresis, and density gradient centrifugation with quantitative mass spectrometry to generate inventories of protein assemblies within a cell or subcellular fraction. This review summarizes applications of complexome profiling with respect to assembly ranging from single subunits to large macromolecular complexes, as well as their stability, and remodeling in health and disease.
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9
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Páleníková P, Harbour ME, Prodi F, Minczuk M, Zeviani M, Ghelli A, Fernández-Vizarra E. Duplexing complexome profiling with SILAC to study human respiratory chain assembly defects. Biochim Biophys Acta Bioenerg 2021; 1862:148395. [PMID: 33600785 DOI: 10.1016/j.bbabio.2021.148395] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 12/19/2022]
Abstract
Complexome Profiling (CP) combines size separation, by electrophoresis or other means, of native multimeric complexes with protein identification by mass spectrometry (MS). Peptide MS analysis of the multiple fractions in which the sample is separated, results in the creation of protein abundance profiles in function of molecular size, providing a visual output of the assembly status of a group of proteins of interest. Stable isotope labeling by amino acids in cell culture (SILAC) is an established quantitative proteomics technique that allows duplexing in the MS analysis as well as the comparison of relative protein abundances between the samples, which are processed and analyzed together. Combining SILAC and CP permitted the direct comparison of migration and abundance of the proteins present in the mitochondrial respiratory chain complexes in two different samples. This analysis, however, introduced a level of complexity in data processing for which bioinformatic tools had to be developed in order to generate the normalized protein abundance profiles. The advantages and challenges of using of this type of analysis for the characterization of two cell lines carrying pathological variants in MT-CO3 and MT-CYB is reviewed. An additional unpublished example of SILAC-CP of a cell line with an in-frame 18-bp deletion in MT-CYB is presented. In these cells, in contrast to other MT-CYB deficient models, a small proportion of complex III2 is formed and it is found associated with fully assembled complex I. This analysis also revealed a profuse accumulation of assembly intermediates containing complex III subunits UQCR10 and CYC1, as well as a profound early-stage complex IV assembly defect.
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Affiliation(s)
- Petra Páleníková
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Michael E Harbour
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Federica Prodi
- Dipartimento di Farmacia e Biotecnologie (FABIT), Università di Bologna, Bologna, Italy
| | - Michal Minczuk
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Massimo Zeviani
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Anna Ghelli
- Dipartimento di Farmacia e Biotecnologie (FABIT), Università di Bologna, Bologna, Italy
| | - Erika Fernández-Vizarra
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
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Guerrero-Castillo S, Krisp C, Küchler K, Arnold S, Schlüter H, Gersting SW. Multiplexed complexome profiling using tandem mass tags. Biochim Biophys Acta Bioenerg 2021; 1862:148448. [PMID: 34015258 DOI: 10.1016/j.bbabio.2021.148448] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 05/05/2021] [Accepted: 05/13/2021] [Indexed: 12/28/2022]
Abstract
Complexome profiling is a rapidly spreading, powerful technique to gain insight into the nature of protein complexes. It identifies and quantifies protein complexes separated into multiple fractions of increasing molecular mass using mass spectrometry-based, label-free bottom-up proteomics. Complexome profiling enables a sophisticated and thorough characterization of the composition, molecular mass, assembly, and interactions of protein complexes. However, in practice, its application is limited by the large number of samples it generates and the related time of mass spectrometry analyses. Here, we report an improved process workflow that implements tandem mass tags for multiplexing complexome profiling. This workflow substantially reduces the number of samples and measuring time without compromising protein identification or quantification reliability. In profiles from mitochondrial fractions of cells recovering from chloramphenicol treatment, tandem mass tags-multiplexed complexome profiling exhibited migration patterns of mature ATP synthase (complex V) and assembly intermediates that were consistent in composition and abundance with profiles obtained by the label-free approach. Reporter ion quantifications of proteins and complexes unaffected by the chloramphenicol treatment presented less variation in comparison to the label-free method. Incorporation of tandem mass tags enabled an efficient and robust complexome profiling analysis and may foster broader application for protein complex profiling in biomedical research and diagnostics.
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11
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Alston CL, Stenton SL, Hudson G, Prokisch H, Taylor RW. The genetics of mitochondrial disease: dissecting mitochondrial pathology using multi-omic pipelines. J Pathol 2021; 254:430-442. [PMID: 33586140 PMCID: PMC8600955 DOI: 10.1002/path.5641] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 12/12/2022]
Abstract
Mitochondria play essential roles in numerous metabolic pathways including the synthesis of adenosine triphosphate through oxidative phosphorylation. Clinically, mitochondrial diseases occur when there is mitochondrial dysfunction – manifesting at any age and affecting any organ system; tissues with high energy requirements, such as muscle and the brain, are often affected. The clinical heterogeneity is parallel to the degree of genetic heterogeneity associated with mitochondrial dysfunction. Around 10% of human genes are predicted to have a mitochondrial function, and defects in over 300 genes are reported to cause mitochondrial disease. Some involve the mitochondrial genome (mtDNA), but the vast majority occur within the nuclear genome. Except for a few specific genetic defects, there remains no cure for mitochondrial diseases, which means that a genetic diagnosis is imperative for genetic counselling and the provision of reproductive options for at‐risk families. Next‐generation sequencing strategies, particularly exome and whole‐genome sequencing, have revolutionised mitochondrial diagnostics such that the traditional muscle biopsy has largely been replaced with a minimally‐invasive blood sample for an unbiased approach to genetic diagnosis. Where these genomic approaches have not identified a causative defect, or where there is insufficient support for pathogenicity, additional functional investigations are required. The application of supplementary ‘omics’ technologies, including transcriptomics, proteomics, and metabolomics, has the potential to greatly improve diagnostic strategies. This review aims to demonstrate that whilst a molecular diagnosis can be achieved for many cases through next‐generation sequencing of blood DNA, the use of patient tissues and an integrated, multidisciplinary multi‐omics approach is pivotal for the diagnosis of more challenging cases. Moreover, the analysis of clinically relevant tissues from affected individuals remains crucial for understanding the molecular mechanisms underlying mitochondrial pathology. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Charlotte L Alston
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,NHS Highly Specialised Services for Rare Mitochondrial Disorders, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Sarah L Stenton
- Institute of Human Genetics, Technische Universität München, München, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Gavin Hudson
- Wellcome Centre for Mitochondrial Research, Bioscience Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Holger Prokisch
- Institute of Human Genetics, Technische Universität München, München, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,NHS Highly Specialised Services for Rare Mitochondrial Disorders, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
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12
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Protasoni M, Zeviani M. Mitochondrial Structure and Bioenergetics in Normal and Disease Conditions. Int J Mol Sci 2021; 22:E586. [PMID: 33435522 DOI: 10.3390/ijms22020586] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/03/2021] [Accepted: 01/04/2021] [Indexed: 02/06/2023] Open
Abstract
Mitochondria are ubiquitous intracellular organelles found in almost all eukaryotes and involved in various aspects of cellular life, with a primary role in energy production. The interest in this organelle has grown stronger with the discovery of their link to various pathologies, including cancer, aging and neurodegenerative diseases. Indeed, dysfunctional mitochondria cannot provide the required energy to tissues with a high-energy demand, such as heart, brain and muscles, leading to a large spectrum of clinical phenotypes. Mitochondrial defects are at the origin of a group of clinically heterogeneous pathologies, called mitochondrial diseases, with an incidence of 1 in 5000 live births. Primary mitochondrial diseases are associated with genetic mutations both in nuclear and mitochondrial DNA (mtDNA), affecting genes involved in every aspect of the organelle function. As a consequence, it is difficult to find a common cause for mitochondrial diseases and, subsequently, to offer a precise clinical definition of the pathology. Moreover, the complexity of this condition makes it challenging to identify possible therapies or drug targets.
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13
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Fernandez-Vizarra E, Zeviani M. Mitochondrial disorders of the OXPHOS system. FEBS Lett 2020; 595:1062-1106. [PMID: 33159691 DOI: 10.1002/1873-3468.13995] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/21/2020] [Accepted: 11/01/2020] [Indexed: 12/13/2022]
Abstract
Mitochondrial disorders are among the most frequent inborn errors of metabolism, their primary cause being the dysfunction of the oxidative phosphorylation system (OXPHOS). OXPHOS is composed of the electron transport chain (ETC), formed by four multimeric enzymes and two mobile electron carriers, plus an ATP synthase [also called complex V (cV)]. The ETC performs the redox reactions involved in cellular respiration while generating the proton motive force used by cV to synthesize ATP. OXPHOS biogenesis involves multiple steps, starting from the expression of genes encoded in physically separated genomes, namely the mitochondrial and nuclear DNA, to the coordinated assembly of components and cofactors building each individual complex and eventually the supercomplexes. The genetic cause underlying around half of the diagnosed mitochondrial disease cases is currently known. Many of these cases result from pathogenic variants in genes encoding structural subunits or additional factors directly involved in the assembly of the ETC complexes. Here, we review the historical and most recent findings concerning the clinical phenotypes and the molecular pathological mechanisms underlying this particular group of disorders.
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Affiliation(s)
- Erika Fernandez-Vizarra
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK
| | - Massimo Zeviani
- Venetian Institute of Molecular Medicine, Padova, Italy.,Department of Neurosciences, University of Padova, Italy
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14
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Dang QCL, Phan DH, Johnson AN, Pasapuleti M, Alkhaldi HA, Zhang F, Vik SB. Analysis of Human Mutations in the Supernumerary Subunits of Complex I. Life (Basel) 2020; 10:life10110296. [PMID: 33233646 PMCID: PMC7699753 DOI: 10.3390/life10110296] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/16/2020] [Accepted: 11/16/2020] [Indexed: 01/02/2023] Open
Abstract
Complex I is the largest member of the electron transport chain in human mitochondria. It comprises 45 subunits and requires at least 15 assembly factors. The subunits can be divided into 14 "core" subunits that carry out oxidation-reduction reactions and proton translocation, as well as 31 additional supernumerary (or accessory) subunits whose functions are less well known. Diminished levels of complex I activity are seen in many mitochondrial disease states. This review seeks to tabulate mutations in the supernumerary subunits of humans that appear to cause disease. Mutations in 20 of the supernumerary subunits have been identified. The mutations were analyzed in light of the tertiary and quaternary structure of human complex I (PDB id = 5xtd). Mutations were found that might disrupt the folding of that subunit or that would weaken binding to another subunit. In some cases, it appeared that no protein was made or, at least, could not be detected. A very common outcome is the lack of assembly of complex I when supernumerary subunits are mutated or missing. We suggest that poor assembly is the result of disrupting the large network of subunit interactions that the supernumerary subunits typically engage in.
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Reinson K, Õunap K. Complex I deficiency and Leigh syndrome through the eyes of a clinician. EMBO Mol Med 2020; 12:e13187. [PMID: 33124751 PMCID: PMC7645367 DOI: 10.15252/emmm.202013187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Mitochondrial complex I deficiency is associated with a wide range of clinical presentations, including Leigh syndrome. Its genetic causes are heterogeneous, with poor genotype-phenotype correlation. It is impossible to identify the genetic defect of complex I deficiency using clinical observation and metabolic/imaging studies alone. As a result, whole-exome sequencing (WES) is increasingly used in clinical work to identify an underlying genetic defect causing the disease. The article in this issue of EMBO Molecular Medicine by Alahmad et al (2020) is timely and valuable, as it expands on the genotype of mitochondrial complex I deficiency by identifying and characterising pathogenic variants of the NDUFC2 gene in children with Leigh syndrome.
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Affiliation(s)
- Karit Reinson
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Katrin Õunap
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
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16
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Alahmad A, Nasca A, Heidler J, Thompson K, Oláhová M, Legati A, Lamantea E, Meisterknecht J, Spagnolo M, He L, Alameer S, Hakami F, Almehdar A, Ardissone A, Alston CL, McFarland R, Wittig I, Ghezzi D, Taylor RW. Bi-allelic pathogenic variants in NDUFC2 cause early-onset Leigh syndrome and stalled biogenesis of complex I. EMBO Mol Med 2020; 12:e12619. [PMID: 32969598 PMCID: PMC7645371 DOI: 10.15252/emmm.202012619] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/14/2020] [Accepted: 08/26/2020] [Indexed: 01/13/2023] Open
Abstract
Leigh syndrome is a progressive neurodegenerative disorder, most commonly observed in paediatric mitochondrial disease, and is often associated with pathogenic variants in complex I structural subunits or assembly factors resulting in isolated respiratory chain complex I deficiency. Clinical heterogeneity has been reported, but key diagnostic findings are developmental regression, elevated lactate and characteristic neuroimaging abnormalities. Here, we describe three affected children from two unrelated families who presented with Leigh syndrome due to homozygous variants (c.346_*7del and c.173A>T p.His58Leu) in NDUFC2, encoding a complex I subunit. Biochemical and functional investigation of subjects’ fibroblasts confirmed a severe defect in complex I activity, subunit expression and assembly. Lentiviral transduction of subjects’ fibroblasts with wild‐type NDUFC2 cDNA increased complex I assembly supporting the association of the identified NDUFC2 variants with mitochondrial pathology. Complexome profiling confirmed a loss of NDUFC2 and defective complex I assembly, revealing aberrant assembly intermediates suggestive of stalled biogenesis of the complex I holoenzyme and indicating a crucial role for NDUFC2 in the assembly of the membrane arm of complex I, particularly the ND2 module.
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Affiliation(s)
- Ahmad Alahmad
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK.,Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,Kuwait Medical Genetics Centre, Al-Sabah Medical Area, Kuwait
| | - Alessia Nasca
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Juliana Heidler
- SFB815 Core Unit, Functional Proteomics, Medical School, Goethe-Universität, Frankfurt am Main, Germany
| | - Kyle Thompson
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK.,Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Monika Oláhová
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK.,Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Andrea Legati
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Eleonora Lamantea
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Jana Meisterknecht
- SFB815 Core Unit, Functional Proteomics, Medical School, Goethe-Universität, Frankfurt am Main, Germany
| | - Manuela Spagnolo
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Langping He
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK.,NHS Highly Specialised Service for Rare Mitochondrial Disorders, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Seham Alameer
- Pediatric Department, Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia.,King Abdullah International Medical Research Center, Jeddah, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Fahad Hakami
- Section of Molecular Medicine, King Abdulaziz Medical City-WR, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Abeer Almehdar
- Department of Medical Imaging, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City-WR, National Guard Health Affairs, Jeddah, Saudi Arabia
| | - Anna Ardissone
- Child Neurology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Charlotte L Alston
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK.,Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,NHS Highly Specialised Service for Rare Mitochondrial Disorders, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK.,Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,NHS Highly Specialised Service for Rare Mitochondrial Disorders, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Ilka Wittig
- SFB815 Core Unit, Functional Proteomics, Medical School, Goethe-Universität, Frankfurt am Main, Germany.,German Center for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.,Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK.,Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,NHS Highly Specialised Service for Rare Mitochondrial Disorders, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
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