1
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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. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 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] [Abstract] [Key Words] [MESH Headings] [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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Vercellino I, Sazanov LA. SCAF1 drives the compositional diversity of mammalian respirasomes. Nat Struct Mol Biol 2024:10.1038/s41594-024-01255-0. [PMID: 38575788 DOI: 10.1038/s41594-024-01255-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 02/16/2024] [Indexed: 04/06/2024]
Abstract
Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies have shown that different tissues/organs are equipped with specific sets of supercomplexes, depending on their metabolic needs, the notion that supercomplexes have a role in the regulation of metabolism has been challenged. However, irrespective of the mechanistic conclusions, the composition of various high molecular weight supercomplexes remains uncertain. Here, using cryogenic electron microscopy, we demonstrate that mammalian (mouse) tissues contain three defined types of 'respirasome', supercomplexes made of CI, CIII2 and CIV. The stoichiometry and position of CIV differs in the three respirasomes, of which only one contains the supercomplex-associated factor SCAF1, whose involvement in respirasome formation has long been contended. Our structures confirm that the 'canonical' respirasome (the C-respirasome, CICIII2CIV) does not contain SCAF1, which is instead associated to a different respirasome (the CS-respirasome), containing a second copy of CIV. We also identify an alternative respirasome (A-respirasome), with CIV bound to the 'back' of CI, instead of the 'toe'. This structural characterization of mouse mitochondrial supercomplexes allows us to hypothesize a mechanistic basis for their specific role in different metabolic conditions.
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Affiliation(s)
- Irene Vercellino
- Institute of Science and Technology Austria, Klosterneuburg, Austria
- Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Leonid A Sazanov
- Institute of Science and Technology Austria, Klosterneuburg, Austria.
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3
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Key J, Gispert S, Koepf G, Steinhoff-Wagner J, Reichlmeir M, Auburger G. Translation Fidelity and Respiration Deficits in CLPP-Deficient Tissues: Mechanistic Insights from Mitochondrial Complexome Profiling. Int J Mol Sci 2023; 24:17503. [PMID: 38139332 PMCID: PMC10743472 DOI: 10.3390/ijms242417503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
The mitochondrial matrix peptidase CLPP is crucial during cell stress. Its loss causes Perrault syndrome type 3 (PRLTS3) with infertility, neurodegeneration, and a growth deficit. Its target proteins are disaggregated by CLPX, which also regulates heme biosynthesis via unfolding ALAS enzymes, providing access for pyridoxal-5'-phosphate (PLP). Despite efforts in diverse organisms with multiple techniques, CLPXP substrates remain controversial. Here, avoiding recombinant overexpression, we employed complexomics in mitochondria from three mouse tissues to identify endogenous targets. A CLPP absence caused the accumulation and dispersion of CLPX-VWA8 as AAA+ unfoldases, and of PLPBP. Similar changes and CLPX-VWA8 co-migration were evident for mitoribosomal central protuberance clusters, translation factors like GFM1-HARS2, the RNA granule components LRPPRC-SLIRP, and enzymes OAT-ALDH18A1. Mitochondrially translated proteins in testes showed reductions to <30% for MTCO1-3, the mis-assembly of the complex IV supercomplex, and accumulated metal-binding assembly factors COX15-SFXN4. Indeed, heavy metal levels were increased for iron, molybdenum, cobalt, and manganese. RT-qPCR showed compensatory downregulation only for Clpx mRNA; most accumulated proteins appeared transcriptionally upregulated. Immunoblots validated VWA8, MRPL38, MRPL18, GFM1, and OAT accumulation. Co-immunoprecipitation confirmed CLPX binding to MRPL38, GFM1, and OAT, so excess CLPX and PLP may affect their activity. Our data mechanistically elucidate the mitochondrial translation fidelity deficits which underlie progressive hearing impairment in PRLTS3.
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Affiliation(s)
- Jana Key
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Suzana Gispert
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Gabriele Koepf
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Julia Steinhoff-Wagner
- TUM School of Life Sciences, Animal Nutrition and Metabolism, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising-Weihenstephan, Germany;
| | - Marina Reichlmeir
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Georg Auburger
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
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4
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Kohler A, Barrientos A, Fontanesi F, Ott M. The functional significance of mitochondrial respiratory chain supercomplexes. EMBO Rep 2023; 24:e57092. [PMID: 37828827 PMCID: PMC10626428 DOI: 10.15252/embr.202357092] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/10/2023] [Accepted: 09/14/2023] [Indexed: 10/14/2023] Open
Abstract
The mitochondrial respiratory chain (MRC) is a key energy transducer in eukaryotic cells. Four respiratory chain complexes cooperate in the transfer of electrons derived from various metabolic pathways to molecular oxygen, thereby establishing an electrochemical gradient over the inner mitochondrial membrane that powers ATP synthesis. This electron transport relies on mobile electron carries that functionally connect the complexes. While the individual complexes can operate independently, they are in situ organized into large assemblies termed respiratory supercomplexes. Recent structural and functional studies have provided some answers to the question of whether the supercomplex organization confers an advantage for cellular energy conversion. However, the jury is still out, regarding the universality of these claims. In this review, we discuss the current knowledge on the functional significance of MRC supercomplexes, highlight experimental limitations, and suggest potential new strategies to overcome these obstacles.
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Affiliation(s)
- Andreas Kohler
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
- Institute of Molecular BiosciencesUniversity of GrazGrazAustria
| | - Antoni Barrientos
- Department of Neurology, Miller School of MedicineUniversity of MiamiMiamiFLUSA
- Department of Biochemistry and Molecular Biology, Miller School of MedicineUniversity of MiamiMiamiFLUSA
| | - Flavia Fontanesi
- Department of Biochemistry and Molecular Biology, Miller School of MedicineUniversity of MiamiMiamiFLUSA
| | - Martin Ott
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
- Department of Medical Biochemistry and Cell BiologyUniversity of GothenburgGothenburgSweden
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5
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Kaw A, Wu T, Starosolski Z, Zhou Z, Pedroza AJ, Majumder S, Duan X, Kaw K, Pinelo JEE, Fischbein MP, Lorenzi PL, Tan L, Martinez SA, Mahmud I, Devkota L, Taegtmeyer H, Ghaghada KB, Marrelli SP, Kwartler CS, Milewicz DM. Augmenting Mitochondrial Respiration in Immature Smooth Muscle Cells with an ACTA2 Pathogenic Variant Mitigates Moyamoya-like Cerebrovascular Disease. RESEARCH SQUARE 2023:rs.3.rs-3304679. [PMID: 37886459 PMCID: PMC10602100 DOI: 10.21203/rs.3.rs-3304679/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
ACTA2 pathogenic variants altering arginine 179 cause childhood-onset strokes due to moyamoya disease (MMD)-like occlusion of the distal internal carotid arteries. A smooth muscle cell (SMC)-specific knock-in mouse model (Acta2SMC-R179C/+) inserted the mutation into 67% of aortic SMCs, whereas explanted SMCs were uniformly heterozygous. Acta2R179C/+ SMCs fail to fully differentiate and maintain stem cell-like features, including high glycolytic flux, and increasing oxidative respiration (OXPHOS) with nicotinamide riboside (NR) drives the mutant SMCs to differentiate and decreases migration. Acta2SMC-R179C/+ mice have intraluminal MMD-like occlusive lesions and strokes after carotid artery injury, whereas the similarly treated WT mice have no strokes and patent lumens. Treatment with NR prior to the carotid artery injury attenuates the strokes, MMD-like lumen occlusions, and aberrant vascular remodeling in the Acta2SMC-R179C/+ mice. These data highlight the role of immature SMCs in MMD-associated occlusive disease and demonstrate that altering SMC metabolism to drive quiescence of Acta2R179C/+ SMCs attenuates strokes and aberrant vascular remodeling in the Acta2SMC-R179C/+ mice.
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Affiliation(s)
- Anita Kaw
- Division of Medical Genetics, Department of Internal Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, TX 77030, USA
| | - Ting Wu
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, McGovern Medical School, 6431 Fannin Street, Houston, TX 77030, USA
| | - Zbigniew Starosolski
- Department of Radiology, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Zhen Zhou
- Division of Medical Genetics, Department of Internal Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, TX 77030, USA
| | - Albert J. Pedroza
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Suravi Majumder
- Division of Medical Genetics, Department of Internal Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, TX 77030, USA
| | - Xueyan Duan
- Division of Medical Genetics, Department of Internal Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, TX 77030, USA
| | - Kaveeta Kaw
- Division of Medical Genetics, Department of Internal Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, TX 77030, USA
| | - Jose E. E. Pinelo
- Division of Medical Genetics, Department of Internal Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, TX 77030, USA
| | - Michael P. Fischbein
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Philip L. Lorenzi
- Metabolomics Core Facility, Department of Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lin Tan
- Metabolomics Core Facility, Department of Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sara A. Martinez
- Metabolomics Core Facility, Department of Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Iqbal Mahmud
- Metabolomics Core Facility, Department of Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Laxman Devkota
- Department of Radiology, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Heinrich Taegtmeyer
- Division of Cardiovascular Medicine, Department of Internal Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, TX 77030, USA
| | - Ketan B. Ghaghada
- Department of Radiology, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Sean P. Marrelli
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, McGovern Medical School, 6431 Fannin Street, Houston, TX 77030, USA
| | - Callie S. Kwartler
- Division of Medical Genetics, Department of Internal Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, TX 77030, USA
| | - Dianna M. Milewicz
- Division of Medical Genetics, Department of Internal Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, TX 77030, USA
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6
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Anderson AJ, Crameri JJ, Ang C, Malcolm TR, Kang Y, Baker MJ, Palmer CS, Sharpe AJ, Formosa LE, Ganio K, Baker MJ, McDevitt CA, Ryan MT, Maher MJ, Stojanovski D. Human Tim8a, Tim8b and Tim13 are auxiliary assembly factors of mature Complex IV. EMBO Rep 2023; 24:e56430. [PMID: 37272231 PMCID: PMC10398661 DOI: 10.15252/embr.202256430] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 05/11/2023] [Accepted: 05/16/2023] [Indexed: 06/06/2023] Open
Abstract
Human Tim8a and Tim8b are paralogous intermembrane space proteins of the small TIM chaperone family. Yeast small TIMs function in the trafficking of proteins to the outer and inner mitochondrial membranes. This putative import function for hTim8a and hTim8b has been challenged in human models, but their precise molecular function(s) remains undefined. Likewise, the necessity for human cells to encode two Tim8 proteins and whether any potential redundancy exists is unclear. We demonstrate that hTim8a and hTim8b function in the assembly of cytochrome c oxidase (Complex IV). Using affinity enrichment mass spectrometry, we define the interaction network of hTim8a, hTim8b and hTim13, identifying subunits and assembly factors of the Complex IV COX2 module. hTim8-deficient cells have a COX2 and COX3 module defect and exhibit an accumulation of the Complex IV S2 subcomplex. These data suggest that hTim8a and hTim8b function in assembly of Complex IV via interactions with intermediate-assembly subcomplexes. We propose that hTim8-hTim13 complexes are auxiliary assembly factors involved in the formation of the Complex IV S3 subcomplex during assembly of mature Complex IV.
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Affiliation(s)
- Alexander J Anderson
- Department of Biochemistry and PharmacologyThe University of MelbourneParkvilleVicAustralia
- The Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneParkvilleVicAustralia
| | - Jordan J Crameri
- Department of Biochemistry and PharmacologyThe University of MelbourneParkvilleVicAustralia
- The Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneParkvilleVicAustralia
| | - Ching‐Seng Ang
- The Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneParkvilleVicAustralia
| | - Tess R Malcolm
- The Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneParkvilleVicAustralia
- School of ChemistryThe University of MelbourneParkvilleVicAustralia
| | - Yilin Kang
- Department of Biochemistry and PharmacologyThe University of MelbourneParkvilleVicAustralia
- The Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneParkvilleVicAustralia
| | - Megan J Baker
- Department of Biochemistry and PharmacologyThe University of MelbourneParkvilleVicAustralia
- The Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneParkvilleVicAustralia
| | - Catherine S Palmer
- Department of Biochemistry and PharmacologyThe University of MelbourneParkvilleVicAustralia
- The Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneParkvilleVicAustralia
| | - Alice J Sharpe
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery InstituteMonash UniversityClaytonVicAustralia
| | - Luke E Formosa
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery InstituteMonash UniversityClaytonVicAustralia
| | - Katherine Ganio
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and ImmunityThe University of MelbourneParkvilleVicAustralia
| | - Michael J Baker
- Department of Biochemistry and PharmacologyThe University of MelbourneParkvilleVicAustralia
- The Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneParkvilleVicAustralia
| | - Christopher A McDevitt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and ImmunityThe University of MelbourneParkvilleVicAustralia
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery InstituteMonash UniversityClaytonVicAustralia
| | - Megan J Maher
- The Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneParkvilleVicAustralia
- School of ChemistryThe University of MelbourneParkvilleVicAustralia
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVicAustralia
| | - Diana Stojanovski
- Department of Biochemistry and PharmacologyThe University of MelbourneParkvilleVicAustralia
- The Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneParkvilleVicAustralia
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7
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Carvalho D, Diaz-Amarilla P, Dapueto R, Santi MD, Duarte P, Savio E, Engler H, Abin-Carriquiry JA, Arredondo F. Transcriptomic Analyses of Neurotoxic Astrocytes Derived from Adult Triple Transgenic Alzheimer's Disease Mice. J Mol Neurosci 2023; 73:487-515. [PMID: 37318736 DOI: 10.1007/s12031-023-02105-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/03/2023] [Indexed: 06/16/2023]
Abstract
Neurodegenerative diseases such as Alzheimer's disease have been classically studied from a purely neuronocentric point of view. More recent evidences support the notion that other cell populations are involved in disease progression. In this sense, the possible pathogenic role of glial cells like astrocytes is increasingly being recognized. Once faced with tissue damage signals and other stimuli present in disease environments, astrocytes suffer many morphological and functional changes, a process referred as reactive astrogliosis. Studies from murine models and humans suggest that these complex and heterogeneous responses could manifest as disease-specific astrocyte phenotypes. Clear understanding of disease-associated astrocytes is a necessary step to fully disclose neurodegenerative processes, aiding in the design of new therapeutic and diagnostic strategies. In this work, we present the transcriptomics characterization of neurotoxic astrocytic cultures isolated from adult symptomatic animals of the triple transgenic mouse model of Alzheimer's disease (3xTg-AD). According to the observed profile, 3xTg-AD neurotoxic astrocytes show various reactivity features including alteration of the extracellular matrix and release of pro-inflammatory and proliferative factors that could result in harmful effects to neurons. Moreover, these alterations could be a consequence of stress responses at the endoplasmic reticulum and mitochondria as well as of concomitant metabolic adaptations. Present results support the hypothesis that adaptive changes of astrocytic function induced by a stressed microenvironment could later promote harmful astrocyte phenotypes and further accelerate or induce neurodegenerative processes.
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Affiliation(s)
- Diego Carvalho
- Departamento de Neuroquímica, Instituto de Investigaciones Biológicas Clemente Estable, 11600, Montevideo, Uruguay
| | - Pablo Diaz-Amarilla
- Área I+D Biomédica, Centro Uruguayo de Imagenología Molecular, 11600, Montevideo, Uruguay
| | - Rosina Dapueto
- Área I+D Biomédica, Centro Uruguayo de Imagenología Molecular, 11600, Montevideo, Uruguay
| | - María Daniela Santi
- Área I+D Biomédica, Centro Uruguayo de Imagenología Molecular, 11600, Montevideo, Uruguay
- College of Dentistry, Bluestone Center for Clinical Research, New York University, New York, 10010, USA
| | - Pablo Duarte
- Área I+D Biomédica, Centro Uruguayo de Imagenología Molecular, 11600, Montevideo, Uruguay
| | - Eduardo Savio
- Área I+D Biomédica, Centro Uruguayo de Imagenología Molecular, 11600, Montevideo, Uruguay
| | - Henry Engler
- Área I+D Biomédica, Centro Uruguayo de Imagenología Molecular, 11600, Montevideo, Uruguay
- Facultad de Medicina, Universidad de la República, 1800, Montevideo, Uruguay
| | - Juan A Abin-Carriquiry
- Departamento de Neuroquímica, Instituto de Investigaciones Biológicas Clemente Estable, 11600, Montevideo, Uruguay.
- Laboratorio de Biofármacos, Institut Pasteur de Montevideo, 11600, Montevideo, Uruguay.
| | - Florencia Arredondo
- Departamento de Neuroquímica, Instituto de Investigaciones Biológicas Clemente Estable, 11600, Montevideo, Uruguay.
- Área I+D Biomédica, Centro Uruguayo de Imagenología Molecular, 11600, Montevideo, Uruguay.
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8
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van Strien J, Evers F, Lutikurti M, Berendsen SL, Garanto A, van Gemert GJ, Cabrera-Orefice A, Rodenburg RJ, Brandt U, Kooij TWA, Huynen MA. Comparative Clustering (CompaCt) of eukaryote complexomes identifies novel interactions and sheds light on protein complex evolution. PLoS Comput Biol 2023; 19:e1011090. [PMID: 37549177 PMCID: PMC10434966 DOI: 10.1371/journal.pcbi.1011090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 08/17/2023] [Accepted: 07/10/2023] [Indexed: 08/09/2023] Open
Abstract
Complexome profiling allows large-scale, untargeted, and comprehensive characterization of protein complexes in a biological sample using a combined approach of separating intact protein complexes e.g., by native gel electrophoresis, followed by mass spectrometric analysis of the proteins in the resulting fractions. Over the last decade, its application has resulted in a large collection of complexome profiling datasets. While computational methods have been developed for the analysis of individual datasets, methods for large-scale comparative analysis of complexomes from multiple species are lacking. Here, we present Comparative Clustering (CompaCt), that performs fully automated integrative analysis of complexome profiling data from multiple species, enabling systematic characterization and comparison of complexomes. CompaCt implements a novel method for leveraging orthology in comparative analysis to allow systematic identification of conserved as well as taxon-specific elements of the analyzed complexomes. We applied this method to a collection of 53 complexome profiles spanning the major branches of the eukaryotes. We demonstrate the ability of CompaCt to robustly identify the composition of protein complexes, and show that integrated analysis of multiple datasets improves characterization of complexes from specific complexome profiles when compared to separate analyses. We identified novel candidate interactors and complexes in a number of species from previously analyzed datasets, like the emp24, the V-ATPase and mitochondrial ATP synthase complexes. Lastly, we demonstrate the utility of CompaCt for the automated large-scale characterization of the complexome of the mosquito Anopheles stephensi shedding light on the evolution of metazoan protein complexes. CompaCt is available from https://github.com/cmbi/compact-bio.
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Affiliation(s)
- Joeri van Strien
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Felix Evers
- Medical Microbiology, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Madhurya Lutikurti
- Department of Pediatrics, Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Stijn L. Berendsen
- Department of Pediatrics, Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Alejandro Garanto
- Department of Pediatrics, Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Geert-Jan van Gemert
- Medical Microbiology, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alfredo Cabrera-Orefice
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Richard J. Rodenburg
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Pediatrics, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ulrich Brandt
- Department of Pediatrics, Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, the Netherlands
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Taco W. A. Kooij
- Medical Microbiology, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Martijn A. Huynen
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
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9
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Nadler F, Richter-Dennerlein R. Translation termination in human mitochondria - substrate specificity of mitochondrial release factors. Biol Chem 2023; 404:769-779. [PMID: 37377370 DOI: 10.1515/hsz-2023-0127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 06/19/2023] [Indexed: 06/29/2023]
Abstract
Mitochondria are the essential players in eukaryotic ATP production by oxidative phosphorylation, which relies on the maintenance and accurate expression of the mitochondrial genome. Even though the basic principles of translation are conserved due to the descendance from a bacterial ancestor, some deviations regarding translation factors as well as mRNA characteristics and the applied genetic code are present in human mitochondria. Together, these features are certain challenges during translation the mitochondrion has to handle. Here, we discuss the current knowledge regarding mitochondrial translation focusing on the termination process and the associated quality control mechanisms. We describe how mtRF1a resembles bacterial RF1 mechanistically and summarize in vitro and recent in vivo data leading to the conclusion of mtRF1a being the major mitochondrial release factor. On the other hand, we discuss the ongoing debate about the function of the second codon-dependent mitochondrial release factor mtRF1 regarding its role as a specialized termination factor. Finally, we link defects in mitochondrial translation termination to the activation of mitochondrial rescue mechanisms highlighting the importance of ribosome-associated quality control for sufficient respiratory function and therefore for human health.
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Affiliation(s)
- Franziska Nadler
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Ricarda Richter-Dennerlein
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, D-37075 Göttingen, Germany
- Goettingen Center for Molecular Biosciences, University of Göttingen, D-37077 Göttingen, Germany
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10
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Li BY, Peng WQ, Liu Y, Guo L, Tang QQ. HIGD1A links SIRT1 activity to adipose browning by inhibiting the ROS/DNA damage pathway. Cell Rep 2023; 42:112731. [PMID: 37393616 DOI: 10.1016/j.celrep.2023.112731] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/28/2023] [Accepted: 06/16/2023] [Indexed: 07/04/2023] Open
Abstract
Energy-dissipating adipocytes have the potential to improve metabolic health. Here, we identify hypoxia-induced gene domain protein-1a (HIGD1A), a mitochondrial inner membrane protein, as a positive regulator of adipose browning. HIGD1A is induced in thermogenic fats by cold exposure. Peroxisome proliferator-activated receptor gamma (PPARγ) transactivates HIGD1A expression synergistically with peroxisome proliferators-activated receptor γ coactivator α (PGC1α). HIGD1A knockdown inhibits adipocyte browning, whereas HIGD1A upregulation promotes the browning process. Mechanistically, HIGD1A deficiency impairs mitochondrial respiration to increase reactive oxygen species (ROS) level. This increases NAD+ consumption for DNA damage repair and curtails the NAD+/NADH ratio, which inhibits sirtuin1 (SIRT1) activity, thereby compromising adipocyte browning. Conversely, overexpression of HIGD1A blunts the above process to promote adaptive thermogenesis. Furthermore, mice with HIGD1A knockdown in inguinal and brown fat have impaired thermogenesis and are prone to diet-induced obesity (DIO). Overexpression of HIGD1A favors adipose tissue browning, ultimately preventing DIO and metabolic disorders. Thus, the mitochondrial protein HIGD1A links SIRT1 activity to adipocyte browning by inhibiting ROS levels.
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Affiliation(s)
- Bai-Yu Li
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences and Department of Endocrinology and Metabolism of Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Wan-Qiu Peng
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences and Department of Endocrinology and Metabolism of Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yang Liu
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences and Department of Endocrinology and Metabolism of Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Liang Guo
- School of Exercise and Health and Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, Shanghai University of Sport, Shanghai 200438, China.
| | - Qi-Qun Tang
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences and Department of Endocrinology and Metabolism of Zhongshan Hospital, Fudan University, Shanghai 200032, China.
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11
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Ghifari AS, Saha S, Murcha MW. The biogenesis and regulation of the plant oxidative phosphorylation system. PLANT PHYSIOLOGY 2023; 192:728-747. [PMID: 36806687 DOI: 10.1093/plphys/kiad108] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/19/2023] [Accepted: 01/22/2023] [Indexed: 06/01/2023]
Abstract
Mitochondria are central organelles for respiration in plants. At the heart of this process is oxidative phosphorylation (OXPHOS) system, which generates ATP required for cellular energetic needs. OXPHOS complexes comprise of multiple subunits that originated from both mitochondrial and nuclear genome, which requires careful orchestration of expression, translation, import, and assembly. Constant exposure to reactive oxygen species due to redox activity also renders OXPHOS subunits to be more prone to oxidative damage, which requires coordination of disassembly and degradation. In this review, we highlight the composition, assembly, and activity of OXPHOS complexes in plants based on recent biochemical and structural studies. We also discuss how plants regulate the biogenesis and turnover of OXPHOS subunits and the importance of OXPHOS in overall plant respiration. Further studies in determining the regulation of biogenesis and activity of OXPHOS will advances the field, especially in understanding plant respiration and its role to plant growth and development.
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Affiliation(s)
- Abi S Ghifari
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia
| | - Saurabh Saha
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia
| | - Monika W Murcha
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia
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12
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Wall SW, Sanchez L, Tuttle KS, Pearson SJ, Soma S, Wyatt GL, Carter HN, Jenschke RM, Tan L, Martinez SA, Lorenzi PL, Gohil VM, Rijnkels M, Porter WW. Noncanonical role of singleminded-2s in mitochondrial respiratory chain formation in breast cancer. Exp Mol Med 2023; 55:1046-1063. [PMID: 37121978 PMCID: PMC10238511 DOI: 10.1038/s12276-023-00996-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 05/02/2023] Open
Abstract
Dysregulation of cellular metabolism is a hallmark of breast cancer progression and is associated with metastasis and therapeutic resistance. Here, we show that the breast tumor suppressor gene SIM2 promotes mitochondrial oxidative phosphorylation (OXPHOS) using breast cancer cell line models. Mechanistically, we found that SIM2s functions not as a transcription factor but localizes to mitochondria and directly interacts with the mitochondrial respiratory chain (MRC) to facilitate functional supercomplex (SC) formation. Loss of SIM2s expression disrupts SC formation through destabilization of MRC Complex III, leading to inhibition of electron transport, although Complex I (CI) activity is retained. A metabolomic analysis showed that knockout of SIM2s leads to a compensatory increase in ATP production through glycolysis and accelerated glutamine-driven TCA cycle production of NADH, creating a favorable environment for high cell proliferation. Our findings indicate that SIM2s is a novel stabilizing factor required for SC assembly, providing insight into the impact of the MRC on metabolic adaptation and breast cancer progression.
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Affiliation(s)
- Steven W Wall
- Department of Veterinary Physiology and Pharmacology, School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Lilia Sanchez
- Department of Veterinary Physiology and Pharmacology, School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | | | - Scott J Pearson
- Department of Veterinary Physiology and Pharmacology, School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Shivatheja Soma
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Garhett L Wyatt
- Department of Veterinary Physiology and Pharmacology, School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Hannah N Carter
- Department of Veterinary Physiology and Pharmacology, School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Ramsey M Jenschke
- Department of Veterinary Physiology and Pharmacology, School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Lin Tan
- Metabolomics Core Facility, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Sara A Martinez
- Metabolomics Core Facility, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Philip L Lorenzi
- Metabolomics Core Facility, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Vishal M Gohil
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Monique Rijnkels
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Weston W Porter
- Department of Veterinary Physiology and Pharmacology, School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA.
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13
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Baden P, Perez MJ, Raji H, Bertoli F, Kalb S, Illescas M, Spanos F, Giuliano C, Calogero AM, Oldrati M, Hebestreit H, Cappelletti G, Brockmann K, Gasser T, Schapira AHV, Ugalde C, Deleidi M. Glucocerebrosidase is imported into mitochondria and preserves complex I integrity and energy metabolism. Nat Commun 2023; 14:1930. [PMID: 37024507 PMCID: PMC10079970 DOI: 10.1038/s41467-023-37454-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 03/17/2023] [Indexed: 04/08/2023] Open
Abstract
Mutations in GBA1, the gene encoding the lysosomal enzyme β-glucocerebrosidase (GCase), which cause Gaucher's disease, are the most frequent genetic risk factor for Parkinson's disease (PD). Here, we employ global proteomic and single-cell genomic approaches in stable cell lines as well as induced pluripotent stem cell (iPSC)-derived neurons and midbrain organoids to dissect the mechanisms underlying GCase-related neurodegeneration. We demonstrate that GCase can be imported from the cytosol into the mitochondria via recognition of internal mitochondrial targeting sequence-like signals. In mitochondria, GCase promotes the maintenance of mitochondrial complex I (CI) integrity and function. Furthermore, GCase interacts with the mitochondrial quality control proteins HSP60 and LONP1. Disease-associated mutations impair CI stability and function and enhance the interaction with the mitochondrial quality control machinery. These findings reveal a mitochondrial role of GCase and suggest that defective CI activity and energy metabolism may drive the pathogenesis of GCase-linked neurodegeneration.
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Affiliation(s)
- Pascale Baden
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Department of Neurodegenerative Diseases, Center of Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Maria Jose Perez
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Department of Neurodegenerative Diseases, Center of Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Hariam Raji
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Department of Neurodegenerative Diseases, Center of Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Federico Bertoli
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Department of Neurodegenerative Diseases, Center of Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Stefanie Kalb
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Department of Neurodegenerative Diseases, Center of Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - María Illescas
- Instituto de Investigación Hospital 12 de Octubre (i + 12), Madrid, 28041, Spain
| | - Fokion Spanos
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Department of Neurodegenerative Diseases, Center of Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Claudio Giuliano
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Department of Neurodegenerative Diseases, Center of Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Unit of Cellular and Molecular Neurobiology, IRCCS Mondino Foundation, 27100, Pavia, Italy
| | - Alessandra Maria Calogero
- Department of Biosciences, Center of Excellence on Neurodegenerative Diseases, Università degli Studi di Milano, Milan, Italy
| | - Marvin Oldrati
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Department of Neurodegenerative Diseases, Center of Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Hannah Hebestreit
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Department of Neurodegenerative Diseases, Center of Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Graziella Cappelletti
- Department of Biosciences, Center of Excellence on Neurodegenerative Diseases, Università degli Studi di Milano, Milan, Italy
| | - Kathrin Brockmann
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Department of Neurodegenerative Diseases, Center of Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Thomas Gasser
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Department of Neurodegenerative Diseases, Center of Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Anthony H V Schapira
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, Royal Free Campus, London, NW3 2PF, UK
| | - Cristina Ugalde
- Instituto de Investigación Hospital 12 de Octubre (i + 12), Madrid, 28041, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723, Madrid, Spain
| | - Michela Deleidi
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany.
- Department of Neurodegenerative Diseases, Center of Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA.
- Institut Imagine, INSERM UMR1163 Paris Cite' University, 24 boulevard du Montparnasse, 75015, Paris, France.
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14
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Krüger A, Remes C, Shiriaev DI, Liu Y, Spåhr H, Wibom R, Atanassov I, Nguyen MD, Cooperman BS, Rorbach J. Human mitochondria require mtRF1 for translation termination at non-canonical stop codons. Nat Commun 2023; 14:30. [PMID: 36596788 PMCID: PMC9810596 DOI: 10.1038/s41467-022-35684-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/19/2022] [Indexed: 01/04/2023] Open
Abstract
The mitochondrial translation machinery highly diverged from its bacterial counterpart. This includes deviation from the universal genetic code, with AGA and AGG codons lacking cognate tRNAs in human mitochondria. The locations of these codons at the end of COX1 and ND6 open reading frames, respectively, suggest they might function as stop codons. However, while the canonical stop codons UAA and UAG are known to be recognized by mtRF1a, the release mechanism at AGA and AGG codons remains a debated issue. Here, we show that upon the loss of another member of the mitochondrial release factor family, mtRF1, mitoribosomes accumulate specifically at AGA and AGG codons. Stalling of mitoribosomes alters COX1 transcript and protein levels, but not ND6 synthesis. In addition, using an in vitro reconstituted mitochondrial translation system, we demonstrate the specific peptide release activity of mtRF1 at the AGA and AGG codons. Together, our results reveal the role of mtRF1 in translation termination at non-canonical stop codons in mitochondria.
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Affiliation(s)
- Annika Krüger
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65, Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Cristina Remes
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Dmitrii Igorevich Shiriaev
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65, Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Yong Liu
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65, Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Spåhr
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65, Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Rolf Wibom
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ilian Atanassov
- Proteomics Core Facility, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931, Cologne, Germany
| | - Minh Duc Nguyen
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65, Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Barry S Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65, Solna, Sweden. .,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden. .,S.T.I.A.S: Stellenbosch Institute for Advanced Study, Marais Rd, Mostertsdrift, Stellenbosch, 7600, South Africa.
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15
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Fernández-Vizarra E, Ugalde C. Cooperative assembly of the mitochondrial respiratory chain. Trends Biochem Sci 2022; 47:999-1008. [PMID: 35961810 DOI: 10.1016/j.tibs.2022.07.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/30/2022] [Accepted: 07/18/2022] [Indexed: 12/24/2022]
Abstract
Deep understanding of the pathophysiological role of the mitochondrial respiratory chain (MRC) relies on a well-grounded model explaining how its biogenesis is regulated. The lack of a consistent framework to clarify the modes and mechanisms governing the assembly of the MRC complexes and supercomplexes (SCs) works against progress in the field. The plasticity model was postulated as an attempt to explain the coexistence of mammalian MRC complexes as individual entities and associated in SC species. However, mounting data accumulated throughout the years question the universal validity of the plasticity model as originally proposed. Instead, as we argue here, a cooperative assembly model provides a much better explanation to the phenomena observed when studying MRC biogenesis in physiological and pathological settings.
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Affiliation(s)
- Erika Fernández-Vizarra
- Veneto Institute of Molecular Medicine, 35129 Padova, Italy; Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy.
| | - Cristina Ugalde
- Instituto de Investigación Hospital 12 de Octubre, Madrid 28041, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723, Madrid, Spain.
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16
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Fernández-Vizarra E, López-Calcerrada S, Sierra-Magro A, Pérez-Pérez R, Formosa LE, Hock DH, Illescas M, Peñas A, Brischigliaro M, Ding S, Fearnley IM, Tzoulis C, Pitceathly RDS, Arenas J, Martín MA, Stroud DA, Zeviani M, Ryan MT, Ugalde C. Two independent respiratory chains adapt OXPHOS performance to glycolytic switch. Cell Metab 2022; 34:1792-1808.e6. [PMID: 36198313 DOI: 10.1016/j.cmet.2022.09.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/21/2022] [Accepted: 09/08/2022] [Indexed: 01/11/2023]
Abstract
The structural and functional organization of the mitochondrial respiratory chain (MRC) remains intensely debated. Here, we show the co-existence of two separate MRC organizations in human cells and postmitotic tissues, C-MRC and S-MRC, defined by the preferential expression of three COX7A subunit isoforms, COX7A1/2 and SCAFI (COX7A2L). COX7A isoforms promote the functional reorganization of distinct co-existing MRC structures to prevent metabolic exhaustion and MRC deficiency. Notably, prevalence of each MRC organization is reversibly regulated by the activation state of the pyruvate dehydrogenase complex (PDC). Under oxidative conditions, the C-MRC is bioenergetically more efficient, whereas the S-MRC preferentially maintains oxidative phosphorylation (OXPHOS) upon metabolic rewiring toward glycolysis. We show a link between the metabolic signatures converging at the PDC and the structural and functional organization of the MRC, challenging the widespread notion of the MRC as a single functional unit and concluding that its structural heterogeneity warrants optimal adaptation to metabolic function.
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Affiliation(s)
- Erika Fernández-Vizarra
- Medical Research Council, Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; Veneto Institute of Molecular Medicine, 35129 Padova, Italy; Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy.
| | | | - Ana Sierra-Magro
- Instituto de Investigación Hospital 12 de Octubre, Madrid 28041, Spain
| | | | - Luke E Formosa
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800 Melbourne, Australia
| | - Daniella H Hock
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 3052 Melbourne, Australia
| | - María Illescas
- Instituto de Investigación Hospital 12 de Octubre, Madrid 28041, Spain
| | - Ana Peñas
- Instituto de Investigación Hospital 12 de Octubre, Madrid 28041, Spain
| | | | - Shujing Ding
- Medical Research Council, Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Ian M Fearnley
- Medical Research Council, Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Charalampos Tzoulis
- Neuro-SysMed Center of Excellence for Clinical Research in Neurological Diseases, Department of Neurology, Haukeland University Hospital and Department of Clinical Medicine, University of Bergen, Pb 7804, 5020 Bergen, Norway
| | - Robert D S Pitceathly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Joaquín Arenas
- Instituto de Investigación Hospital 12 de Octubre, Madrid 28041, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723 Madrid, Spain
| | - Miguel A Martín
- Instituto de Investigación Hospital 12 de Octubre, Madrid 28041, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723 Madrid, Spain
| | - David A Stroud
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 3052 Melbourne, Australia
| | - Massimo Zeviani
- Medical Research Council, Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; Veneto Institute of Molecular Medicine, 35129 Padova, Italy; Department of Neurosciences, University of Padova, 35128 Padova, Italy
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800 Melbourne, Australia
| | - Cristina Ugalde
- Instituto de Investigación Hospital 12 de Octubre, Madrid 28041, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723 Madrid, Spain.
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17
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cAMP/PKA Signaling Modulates Mitochondrial Supercomplex Organization. Int J Mol Sci 2022; 23:ijms23179655. [PMID: 36077053 PMCID: PMC9455794 DOI: 10.3390/ijms23179655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
The oxidative phosphorylation (OXPHOS) system couples the transfer of electrons to oxygen with pumping of protons across the inner mitochondrial membrane, ensuring the ATP production. Evidence suggests that respiratory chain complexes may also assemble into supramolecular structures, called supercomplexes (SCs). The SCs appear to increase the efficiency/capacity of OXPHOS and reduce the reactive oxygen species (ROS) production, especially that which is produced by complex I. Studies suggest a mutual regulation between complex I and SCs, while SCs organization is important for complex I assembly/stability, complex I is involved in the supercomplex formation. Complex I is a pacemaker of the OXPHOS system, and it has been shown that the PKA-dependent phosphorylation of some of its subunits increases the activity of the complex, reducing the ROS production. In this work, using in ex vivo and in vitro models, we show that the activation of cAMP/PKA cascade resulted in an increase in SCs formation associated with an enhanced capacity of electron flux and ATP production rate. This is also associated with the phosphorylation of the NDUFS4 subunit of complex I. This aspect highlights the key role of complex I in cellular energy production.
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18
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Yin Y, Shen H. Common methods in mitochondrial research (Review). Int J Mol Med 2022; 50:126. [PMID: 36004457 PMCID: PMC9448300 DOI: 10.3892/ijmm.2022.5182] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/09/2022] [Indexed: 01/18/2023] Open
Affiliation(s)
- Yiyuan Yin
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Haitao Shen
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
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19
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Hutchinson AJ, Duffy BM, Staples JF. Hibernation is super complex: distribution, dynamics, and stability of electron transport system supercomplexes in Ictidomys tridecemlineatus. Am J Physiol Regul Integr Comp Physiol 2022; 323:R28-R42. [PMID: 35470710 DOI: 10.1152/ajpregu.00008.2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Complexes of the electron transport system can associate with each other to form supercomplexes (SCs) within mitochondrial membranes, perhaps increasing respiratory capacity or reducing reactive oxygen species production. In this study, we determined the abundance, composition, and stability of SCs in a mammalian hibernator, in which both whole-animal and mitochondria metabolism change greatly throughout winter. We isolated mitochondria from thirteen-lined ground squirrels (Ictidomys tridecemlineatus) in different hibernation states, as well as from rats (Rattus norvegicus). We extracted mitochondrial proteins using two non-ionic detergents of different strengths, and quantified SC abundance using two-dimensional gel electrophoresis and immunoblotting. Rat heart and liver had fewer SCs than ground squirrels. Within ground squirrels, SCs are dynamic, changing among hibernation states within a matter of hours. In brown adipose tissue, Complex III composition in different SCs differed between the torpid and interbout euthermic phase of a hibernation bout. In heart and liver, complex III composition changed between winter and summer. We also evaluated the stability of liver SCs using a stronger detergent and found that the stability of SCs differed: torpor SCs were more stable than the SCs of ground squirrels in other states and rats. This study is the first report of SC changes during hibernation, and the first to demonstrate their dynamics on a short timescale.
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Affiliation(s)
| | - Brynne Morgan Duffy
- Department of biology, the University of Western Ontario, London, Ontario, Canada
| | - James F Staples
- Department of biology, the University of Western Ontario, London, Ontario, Canada
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20
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Therapeutic Targets for Regulating Oxidative Damage Induced by Ischemia-Reperfusion Injury: A Study from a Pharmacological Perspective. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:8624318. [PMID: 35450409 PMCID: PMC9017553 DOI: 10.1155/2022/8624318] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/28/2022] [Accepted: 03/15/2022] [Indexed: 12/22/2022]
Abstract
Ischemia-reperfusion (I-R) injury is damage caused by restoring blood flow into ischemic tissues or organs. This complex and characteristic lesion accelerates cell death induced by signaling pathways such as apoptosis, necrosis, and even ferroptosis. In addition to the direct association between I-R and the release of reactive oxygen species and reactive nitrogen species, it is involved in developing mitochondrial oxidative damage. Thus, its mechanism plays a critical role via reactive species scavenging, calcium overload modulation, electron transport chain blocking, mitochondrial permeability transition pore activation, or noncoding RNA transcription. Other receptors and molecules reduce tissue and organ damage caused by this pathology and other related diseases. These molecular targets have been gradually discovered and have essential roles in I-R resolution. Therefore, the current study is aimed at highlighting the importance of these discoveries. In this review, we inquire about the oxidative damage receptors that are relevant to reducing the damage induced by oxidative stress associated with I-R. Several complications on surgical techniques and pathology interventions do not mitigate the damage caused by I-R. Nevertheless, these therapies developed using alternative targets could work as coadjuvants in tissue transplants or I-R-related pathologies
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21
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van de Wal MAE, Adjobo-Hermans MJW, Keijer J, Schirris TJJ, Homberg JR, Wieckowski MR, Grefte S, van Schothorst EM, van Karnebeek C, Quintana A, Koopman WJH. Ndufs4 knockout mouse models of Leigh syndrome: pathophysiology and intervention. Brain 2022. [PMID: 34849584 DOI: 10.1093/brain/awab426%jbrain] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Mitochondria are small cellular constituents that generate cellular energy (ATP) by oxidative phosphorylation (OXPHOS). Dysfunction of these organelles is linked to a heterogeneous group of multisystemic disorders, including diabetes, cancer, ageing-related pathologies and rare mitochondrial diseases. With respect to the latter, mutations in subunit-encoding genes and assembly factors of the first OXPHOS complex (complex I) induce isolated complex I deficiency and Leigh syndrome. This syndrome is an early-onset, often fatal, encephalopathy with a variable clinical presentation and poor prognosis due to the lack of effective intervention strategies. Mutations in the nuclear DNA-encoded NDUFS4 gene, encoding the NADH:ubiquinone oxidoreductase subunit S4 (NDUFS4) of complex I, induce 'mitochondrial complex I deficiency, nuclear type 1' (MC1DN1) and Leigh syndrome in paediatric patients. A variety of (tissue-specific) Ndufs4 knockout mouse models were developed to study the Leigh syndrome pathomechanism and intervention testing. Here, we review and discuss the role of complex I and NDUFS4 mutations in human mitochondrial disease, and review how the analysis of Ndufs4 knockout mouse models has generated new insights into the MC1ND1/Leigh syndrome pathomechanism and its therapeutic targeting.
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Affiliation(s)
- Melissa A E van de Wal
- Department of Pediatrics, Amalia Children's Hospital, RIMLS, RCMM, Radboudumc, Nijmegen, The Netherlands
| | | | - Jaap Keijer
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | - Tom J J Schirris
- Department of Pharmacology and Toxicology, RIMLS, RCMM, Radboudumc, Nijmegen, The Netherlands
| | - Judith R Homberg
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - Mariusz R Wieckowski
- Laboratory of Mitochondrial Biology and Metabolism, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Sander Grefte
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | | | - Clara van Karnebeek
- Department of Pediatrics, Amalia Children's Hospital, RIMLS, RCMM, Radboudumc, Nijmegen, The Netherlands
- Department of Pediatrics, Emma Personalized Medicine Center, Emma Children's Hospital, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Department of Human Genetics, Emma Personalized Medicine Center, Emma Children's Hospital, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Albert Quintana
- Mitochondrial Neuropathology Laboratory, Institut de Neurociències and Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Werner J H Koopman
- Department of Pediatrics, Amalia Children's Hospital, RIMLS, RCMM, Radboudumc, Nijmegen, The Netherlands
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
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22
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Torraco A, Morlino S, Rizza T, Nottia MD, Bottaro G, Bisceglia L, Montanari A, Cappa M, Castori M, Bertini E, Carrozzo R. A novel homozygous variant in COX5A causes an attenuated phenotype with failure to thrive, lactic acidosis, hypoglycemia and short stature. Clin Genet 2022; 102:56-60. [PMID: 35246835 DOI: 10.1111/cge.14127] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 11/29/2022]
Abstract
Genetic defect in the nuclear encoded subunits of cytochrome c oxidase are very rare. To date, most deleterious variants affect the mitochondrially encoded subunits of complex IV and the nuclear genes encoded for assembly factors. A biallelic pathogenic variant in the mitochondrial complex IV subunit COX5A was previously reported in a couple of sibs with failure to thrive, lactic acidosis and pulmonary hypertension and a lethal phenotype. Here, we describe a second family with a 11-year-old girl presenting with failure to thrive, lactic acidosis, hypoglycemia and short stature. Clinical exome revealed the homozygous missense variant c.266T>G in COX5A, which produces a drop of the corresponding protein and a reduction of the COX activity. Compared to the previous observation, this girl showed an attenuated metabolic derangement without involvement of the cardiovascular system and neurodevelopment. Our observation confirms that COX5A recessive variants may cause mitochondrial disease and expands the associated phenotype to less severe presentations. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Alessandra Torraco
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Silvia Morlino
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Teresa Rizza
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Michela Di Nottia
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Giorgia Bottaro
- Endocrinology Unit, Pediatric University Department, Bambino Gesù Children's Hospital, Rome, Italy
| | - Luigi Bisceglia
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Arianna Montanari
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Marco Cappa
- Endocrinology Unit, Pediatric University Department, Bambino Gesù Children's Hospital, Rome, Italy
| | - Marco Castori
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Enrico Bertini
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rosalba Carrozzo
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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23
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Mitochondrial COA7 is a heme-binding protein with disulfide reductase activity, which acts in the early stages of complex IV assembly. Proc Natl Acad Sci U S A 2022; 119:2110357119. [PMID: 35210360 PMCID: PMC8892353 DOI: 10.1073/pnas.2110357119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2022] [Indexed: 12/12/2022] Open
Abstract
Assembly factors play key roles in the biogenesis of mitochondrial protein complexes, regulating their stabilities, activities, and incorporation of essential cofactors. Cytochrome c oxidase assembly factor 7 (COA7) is a metazoan-specific assembly factor, the absence or mutation of which in humans accompanies complex IV assembly defects and neurological conditions. Here, we report the crystal structure of COA7 to 2.4 Å resolution, revealing a banana-shaped molecule composed of five helix-turn-helix (α/α) repeats. COA7 binds heme with micromolar affinity, even though the protein structure does not resemble previously characterized heme-binding proteins. The heme-bound COA7 can redox cycle between oxidation states Fe(II) and Fe(III) and shows disulfide reductase activity toward copper binding assembly factors. We propose that COA7 functions to facilitate the biogenesis of the binuclear copper site (CuA) of complex IV. Cytochrome c oxidase (COX) assembly factor 7 (COA7) is a metazoan-specific assembly factor, critical for the biogenesis of mitochondrial complex IV (cytochrome c oxidase). Although mutations in COA7 have been linked to complex IV assembly defects and neurological conditions such as peripheral neuropathy, ataxia, and leukoencephalopathy, the precise role COA7 plays in the biogenesis of complex IV is not known. Here, we show that loss of COA7 blocks complex IV assembly after the initial step where the COX1 module is built, progression from which requires the incorporation of copper and addition of the COX2 and COX3 modules. The crystal structure of COA7, determined to 2.4 Å resolution, reveals a banana-shaped molecule composed of five helix-turn-helix (α/α) repeats, tethered by disulfide bonds. COA7 interacts transiently with the copper metallochaperones SCO1 and SCO2 and catalyzes the reduction of disulfide bonds within these proteins, which are crucial for copper relay to COX2. COA7 binds heme with micromolar affinity, through axial ligation to the central iron atom by histidine and methionine residues. We therefore propose that COA7 is a heme-binding disulfide reductase for regenerating the copper relay system that underpins complex IV assembly.
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24
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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] [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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25
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Vercellino I, Sazanov LA. The assembly, regulation and function of the mitochondrial respiratory chain. Nat Rev Mol Cell Biol 2022; 23:141-161. [PMID: 34621061 DOI: 10.1038/s41580-021-00415-0] [Citation(s) in RCA: 268] [Impact Index Per Article: 134.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2021] [Indexed: 02/08/2023]
Abstract
The mitochondrial oxidative phosphorylation system is central to cellular metabolism. It comprises five enzymatic complexes and two mobile electron carriers that work in a mitochondrial respiratory chain. By coupling the oxidation of reducing equivalents coming into mitochondria to the generation and subsequent dissipation of a proton gradient across the inner mitochondrial membrane, this electron transport chain drives the production of ATP, which is then used as a primary energy carrier in virtually all cellular processes. Minimal perturbations of the respiratory chain activity are linked to diseases; therefore, it is necessary to understand how these complexes are assembled and regulated and how they function. In this Review, we outline the latest assembly models for each individual complex, and we also highlight the recent discoveries indicating that the formation of larger assemblies, known as respiratory supercomplexes, originates from the association of the intermediates of individual complexes. We then discuss how recent cryo-electron microscopy structures have been key to answering open questions on the function of the electron transport chain in mitochondrial respiration and how supercomplexes and other factors, including metabolites, can regulate the activity of the single complexes. When relevant, we discuss how these mechanisms contribute to physiology and outline their deregulation in human diseases.
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Affiliation(s)
- Irene Vercellino
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Leonid A Sazanov
- Institute of Science and Technology Austria, Klosterneuburg, Austria.
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26
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Chojnacka KJ, Elancheliyan P, Mussulini BHM, Mohanraj K, Callegari S, Gosk A, Banach T, Góral T, Szczepanowska K, Rehling P, Serwa RA, Chacińska A. Ovarian carcinoma immunoreactive antigen-like protein 2 (OCIAD2) is a novel complex III specific assembly factor in mitochondria. Mol Biol Cell 2022; 33:ar29. [PMID: 35080992 PMCID: PMC9250361 DOI: 10.1091/mbc.e21-03-0143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Assembly of the dimeric complex III (CIII2) in the mitochondrial inner membrane is an intricate process in which several accessory proteins are involved as assembly factors. Despite numerous studies, this process has yet to be fully understood. Here we report the identification of human OCIAD2 (ovarian carcinoma immunoreactive antigen–like protein 2) as an assembly factor for CIII2. OCIAD2 was found to be deregulated in several carcinomas and also in some neurogenerative disorders; however, its nonpathological role had not been elucidated. We have shown that OCIAD2 localizes to mitochondria and interacts with electron transport chain (ETC) proteins. Complete loss of OCIAD2 using gene editing in HEK293 cells resulted in abnormal mitochondrial morphology, a substantial decrease of both CIII2 and supercomplex III2+IV, and a reduction in CIII enzymatic activity. Identification of OCIAD2 as a protein required for assembly of functional CIII2 provides a new insight into the biogenesis and architecture of the ETC. Elucidating the mechanism of OCIAD2 action is important both for the understanding of cellular metabolism and for an understanding of its role in malignant transformation.
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Affiliation(s)
| | | | | | - Karthik Mohanraj
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw, Poland
| | - Sylvie Callegari
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Cellular Biochemistry, University Medical Center Göttingen, 37073, Göttingen, Germany
| | - Aleksandra Gosk
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Tomasz Banach
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw, Poland
| | - Tomasz Góral
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Karolina Szczepanowska
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw, Poland
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, 37073, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Germany.,Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Remigiusz Adam Serwa
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw, Poland
| | - Agnieszka Chacińska
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw, Poland
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27
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van de Wal M, Adjobo-Hermans M, Keijer J, Schirris T, Homberg J, Wieckowski MR, Grefte S, van Schothorst EM, van Karnebeek C, Quintana A, Koopman WJH. Ndufs4 knockout mouse models of Leigh syndrome: pathophysiology and intervention. Brain 2021; 145:45-63. [PMID: 34849584 PMCID: PMC8967107 DOI: 10.1093/brain/awab426] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/25/2021] [Accepted: 11/11/2021] [Indexed: 11/14/2022] Open
Abstract
Mitochondria are small cellular constituents that generate cellular energy (ATP) by oxidative phosphorylation (OXPHOS). Dysfunction of these organelles is linked to a heterogeneous group of multisystemic disorders, including diabetes, cancer, ageing-related pathologies and rare mitochondrial diseases. With respect to the latter, mutations in subunit-encoding genes and assembly factors of the first OXPHOS complex (complex I) induce isolated complex I deficiency and Leigh syndrome. This syndrome is an early-onset, often fatal, encephalopathy with a variable clinical presentation and poor prognosis due to the lack of effective intervention strategies. Mutations in the nuclear DNA-encoded NDUFS4 gene, encoding the NADH:ubiquinone oxidoreductase subunit S4 (NDUFS4) of complex I, induce ‘mitochondrial complex I deficiency, nuclear type 1’ (MC1DN1) and Leigh syndrome in paediatric patients. A variety of (tissue-specific) Ndufs4 knockout mouse models were developed to study the Leigh syndrome pathomechanism and intervention testing. Here, we review and discuss the role of complex I and NDUFS4 mutations in human mitochondrial disease, and review how the analysis of Ndufs4 knockout mouse models has generated new insights into the MC1ND1/Leigh syndrome pathomechanism and its therapeutic targeting.
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Affiliation(s)
- Melissa van de Wal
- Department of Pediatrics, Amalia Children's Hospital, RIMLS, RCMM, Radboudumc, Nijmegen, The Netherlands
| | - Merel Adjobo-Hermans
- Department of Biochemistry (286), RIMLS, RCMM, Radboudumc, Nijmegen, The Netherlands
| | - Jaap Keijer
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | - Tom Schirris
- Department of Pharmacology and Toxicology, RIMLS, RCMM, Radboudumc, Nijmegen, The Netherlands
| | - Judith Homberg
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - Mariusz R Wieckowski
- Laboratory of Mitochondrial Biology and Metabolism, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Sander Grefte
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | | | - Clara van Karnebeek
- Department of Pediatrics, Amalia Children's Hospital, RIMLS, RCMM, Radboudumc, Nijmegen, The Netherlands.,Department of Pediatrics, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Albert Quintana
- Mitochondrial Neuropathology Laboratory, Institut de Neurociències and Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Werner J H Koopman
- Department of Pediatrics, Amalia Children's Hospital, RIMLS, RCMM, Radboudumc, Nijmegen, The Netherlands.,Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
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28
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Regulation and functional role of the electron transport chain supercomplexes. Biochem Soc Trans 2021; 49:2655-2668. [PMID: 34747989 PMCID: PMC8786287 DOI: 10.1042/bst20210460] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/12/2021] [Accepted: 10/21/2021] [Indexed: 12/17/2022]
Abstract
Mitochondria are one of the most exhaustively investigated organelles in the cell and most attention has been paid to the components of the mitochondrial electron transport chain (ETC) in the last 100 years. The ETC collects electrons from NADH or FADH2 and transfers them through a series of electron carriers within multiprotein respiratory complexes (complex I to IV) to oxygen, therefore generating an electrochemical gradient that can be used by the F1-F0-ATP synthase (also named complex V) in the mitochondrial inner membrane to synthesize ATP. The organization and function of the ETC is a continuous source of surprises. One of the latest is the discovery that the respiratory complexes can assemble to form a variety of larger structures called super-complexes (SCs). This opened an unexpected level of complexity in this well-known and fundamental biological process. This review will focus on the current evidence for the formation of different SCs and will explore how they modulate the ETC organization according to the metabolic state. Since the field is rapidly growing, we also comment on the experimental techniques used to describe these SC and hope that this overview may inspire new technologies that will help to advance the field.
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29
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Guerrero-Castillo S, van Strien J, Brandt U, Arnold S. Ablation of mitochondrial DNA results in widespread remodeling of the mitochondrial complexome. EMBO J 2021; 40:e108648. [PMID: 34542926 PMCID: PMC8561636 DOI: 10.15252/embj.2021108648] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/26/2021] [Accepted: 09/01/2021] [Indexed: 11/16/2022] Open
Abstract
So‐called ρ0 cells lack mitochondrial DNA and are therefore incapable of aerobic ATP synthesis. How cells adapt to survive ablation of oxidative phosphorylation remains poorly understood. Complexome profiling analysis of ρ0 cells covered 1,002 mitochondrial proteins and revealed changes in abundance and organization of numerous multiprotein complexes including previously not described assemblies. Beyond multiple subassemblies of complexes that would normally contain components encoded by mitochondrial DNA, we observed widespread reorganization of the complexome. This included distinct changes in the expression pattern of adenine nucleotide carrier isoforms, other mitochondrial transporters, and components of the protein import machinery. Remarkably, ablation of mitochondrial DNA hardly affected the complexes organizing cristae junctions indicating that the altered cristae morphology in ρ0 mitochondria predominantly resulted from the loss of complex V dimers required to impose narrow curvatures to the inner membrane. Our data provide a comprehensive resource for in‐depth analysis of remodeling of the mitochondrial complexome in response to respiratory deficiency.
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Affiliation(s)
- Sergio Guerrero-Castillo
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.,University Children's Research@Kinder-UKE, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Joeri van Strien
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.,Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ulrich Brandt
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Susanne Arnold
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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30
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Brzezinski P, Moe A, Ädelroth P. Structure and Mechanism of Respiratory III-IV Supercomplexes in Bioenergetic Membranes. Chem Rev 2021; 121:9644-9673. [PMID: 34184881 PMCID: PMC8361435 DOI: 10.1021/acs.chemrev.1c00140] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Indexed: 12/12/2022]
Abstract
In the final steps of energy conservation in aerobic organisms, free energy from electron transfer through the respiratory chain is transduced into a proton electrochemical gradient across a membrane. In mitochondria and many bacteria, reduction of the dioxygen electron acceptor is catalyzed by cytochrome c oxidase (complex IV), which receives electrons from cytochrome bc1 (complex III), via membrane-bound or water-soluble cytochrome c. These complexes function independently, but in many organisms they associate to form supercomplexes. Here, we review the structural features and the functional significance of the nonobligate III2IV1/2 Saccharomyces cerevisiae mitochondrial supercomplex as well as the obligate III2IV2 supercomplex from actinobacteria. The analysis is centered around the Q-cycle of complex III, proton uptake by CytcO, as well as mechanistic and structural solutions to the electronic link between complexes III and IV.
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Affiliation(s)
- Peter Brzezinski
- Department of Biochemistry and Biophysics,
The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Agnes Moe
- Department of Biochemistry and Biophysics,
The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics,
The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
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31
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Complexome Profiling: Assembly and Remodeling of Protein Complexes. Int J Mol Sci 2021; 22:ijms22157809. [PMID: 34360575 PMCID: PMC8346016 DOI: 10.3390/ijms22157809] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [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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Fernández-Vizarra E, López-Calcerrada S, Formosa LE, Pérez-Pérez R, Ding S, Fearnley IM, Arenas J, Martín MA, Zeviani M, Ryan MT, Ugalde C. SILAC-based complexome profiling dissects the structural organization of the human respiratory supercomplexes in SCAFI KO cells. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2021; 1862:148414. [PMID: 33727070 DOI: 10.1016/j.bbabio.2021.148414] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 12/29/2022]
Abstract
The study of the mitochondrial respiratory chain (MRC) function in relation with its structural organization is of great interest due to the central role of this system in eukaryotic cell metabolism. The complexome profiling technique has provided invaluable information for our understanding of the composition and assembly of the individual MRC complexes, and also of their association into larger supercomplexes (SCs) and respirasomes. The formation of the SCs has been highly debated, and their assembly and regulation mechanisms are still unclear. Previous studies demonstrated a prominent role for COX7A2L (SCAFI) as a structural protein bridging the association of individual MRC complexes III and IV in the minor SC III2 + IV, although its relevance for respirasome formation and function remains controversial. In this work, we have used SILAC-based complexome profiling to dissect the structural organization of the human MRC in HEK293T cells depleted of SCAFI (SCAFIKO) by CRISPR-Cas9 genome editing. SCAFI ablation led to a preferential loss of SC III2 + IV and of a minor subset of respirasomes without affecting OXPHOS function. Our data suggest that the loss of SCAFI-dependent respirasomes in SCAFIKO cells is mainly due to alterations on early stages of CI assembly, without impacting the biogenesis of complexes III and IV. Contrary to the idea of SCAFI being the main player in respirasome formation, SILAC-complexome profiling showed that, in wild-type cells, the majority of respirasomes (ca. 70%) contained COX7A2 and that these species were present at roughly the same levels when SCAFI was knocked-out. We thus demonstrate the co-existence of structurally distinct respirasomes defined by the preferential binding of complex IV via COX7A2, rather than SCAFI, in human cultured cells.
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Affiliation(s)
- Erika Fernández-Vizarra
- Medical Research Council - Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow G12 8QQ, Scotland, UK
| | | | - Luke E Formosa
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800 Melbourne, Australia
| | - Rafael Pérez-Pérez
- Instituto de Investigación, Hospital Universitario, 12 de Octubre, Madrid 28041, Spain
| | - Shujing Ding
- Medical Research Council - Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Ian M Fearnley
- Medical Research Council - Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Joaquín Arenas
- Instituto de Investigación, Hospital Universitario, 12 de Octubre, Madrid 28041, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723 Madrid, Spain
| | - Miguel A Martín
- Instituto de Investigación, Hospital Universitario, 12 de Octubre, Madrid 28041, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723 Madrid, Spain
| | - Massimo Zeviani
- Medical Research Council - Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; Department of Neurosciences, University of Padova, Via Giustiniani, 2, 35128 Padova, Italy
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800 Melbourne, Australia
| | - Cristina Ugalde
- Instituto de Investigación, Hospital Universitario, 12 de Octubre, Madrid 28041, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723 Madrid, Spain.
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33
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van Strien J, Haupt A, Schulte U, Braun HP, Cabrera-Orefice A, Choudhary JS, Evers F, Fernandez-Vizarra E, Guerrero-Castillo S, Kooij TWA, Páleníková P, Pardo M, Ugalde C, Wittig I, Wöhlbrand L, Brandt U, Arnold S, Huynen MA. CEDAR, an online resource for the reporting and exploration of complexome profiling data. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2021; 1862:148411. [PMID: 33722514 DOI: 10.1016/j.bbabio.2021.148411] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/02/2021] [Accepted: 03/08/2021] [Indexed: 02/06/2023]
Abstract
Complexome profiling is an emerging 'omics' approach that systematically interrogates the composition of protein complexes (the complexome) of a sample, by combining biochemical separation of native protein complexes with mass-spectrometry based quantitation proteomics. The resulting fractionation profiles hold comprehensive information on the abundance and composition of the complexome, and have a high potential for reuse by experimental and computational researchers. However, the lack of a central resource that provides access to these data, reported with adequate descriptions and an analysis tool, has limited their reuse. Therefore, we established the ComplexomE profiling DAta Resource (CEDAR, www3.cmbi.umcn.nl/cedar/), an openly accessible database for depositing and exploring mass spectrometry data from complexome profiling studies. Compatibility and reusability of the data is ensured by a standardized data and reporting format containing the "minimum information required for a complexome profiling experiment" (MIACE). The data can be accessed through a user-friendly web interface, as well as programmatically using the REST API portal. Additionally, all complexome profiles available on CEDAR can be inspected directly on the website with the profile viewer tool that allows the detection of correlated profiles and inference of potential complexes. In conclusion, CEDAR is a unique, growing and invaluable resource for the study of protein complex composition and dynamics across biological systems.
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Affiliation(s)
- Joeri van Strien
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Alexander Haupt
- Institute of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Uwe Schulte
- Institute of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Center for Biological Signalling Studies (BIOSS) and Center for Integrative Signalling Studies (CIBSS), 79104 Freiburg, Germany
| | - Hans-Peter Braun
- Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Alfredo Cabrera-Orefice
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jyoti S Choudhary
- Functional Proteomics, The Institute of Cancer Research, London SW7 3RP, UK
| | - Felix Evers
- Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Sergio Guerrero-Castillo
- University Children's Research@Kinder-UKE, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Taco W A Kooij
- Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Mercedes Pardo
- Functional Proteomics, The Institute of Cancer Research, London SW7 3RP, UK
| | - Cristina Ugalde
- Hospital 12 de Octubre Research Institute, Madrid 28041, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723, Madrid, Spain
| | - Ilka Wittig
- Functional Proteomics, Medical School, Goethe-University, 60590 Frankfurt am Main, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Ulrich Brandt
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Susanne Arnold
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Martijn A Huynen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.
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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. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 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] [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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35
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Le Vasseur M, Friedman J, Jost M, Xu J, Yamada J, Kampmann M, Horlbeck MA, Salemi MR, Phinney BS, Weissman JS, Nunnari J. Genome-wide CRISPRi screening identifies OCIAD1 as a prohibitin client and regulatory determinant of mitochondrial Complex III assembly in human cells. eLife 2021; 10:67624. [PMID: 34034859 PMCID: PMC8154037 DOI: 10.7554/elife.67624] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/10/2021] [Indexed: 01/01/2023] Open
Abstract
Dysfunction of the mitochondrial electron transport chain (mETC) is a major cause of human mitochondrial diseases. To identify determinants of mETC function, we screened a genome-wide human CRISPRi library under oxidative metabolic conditions with selective inhibition of mitochondrial Complex III and identified ovarian carcinoma immunoreactive antigen (OCIA) domain-containing protein 1 (OCIAD1) as a Complex III assembly factor. We find that OCIAD1 is an inner mitochondrial membrane protein that forms a complex with supramolecular prohibitin assemblies. Our data indicate that OCIAD1 is required for maintenance of normal steady-state levels of Complex III and the proteolytic processing of the catalytic subunit cytochrome c1 (CYC1). In OCIAD1 depleted mitochondria, unprocessed CYC1 is hemylated and incorporated into Complex III. We propose that OCIAD1 acts as an adaptor within prohibitin assemblies to stabilize and/or chaperone CYC1 and to facilitate its proteolytic processing by the IMMP2L protease.
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Affiliation(s)
- Maxence Le Vasseur
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, Davis, United States
| | - Jonathan Friedman
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, Davis, United States.,Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Marco Jost
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, United States.,Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, United States
| | - Jiawei Xu
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, Davis, United States
| | - Justin Yamada
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, Davis, United States
| | - Martin Kampmann
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, United States.,Institute for Neurodegenerative Diseases and Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, United States.,Chan-Zuckerberg Biohub, San Francisco, United States
| | - Max A Horlbeck
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, United States
| | - Michelle R Salemi
- Proteomics Core Facility, University of California, Davis, Davis, United States
| | - Brett S Phinney
- Proteomics Core Facility, University of California, Davis, Davis, United States
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, United States.,Whitehead Institute, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Jodi Nunnari
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, Davis, United States
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36
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Bertan F, Wischhof L, Scifo E, Guranda M, Jackson J, Marsal-Cots A, Piazzesi A, Stork M, Peitz M, Prehn JHM, Ehninger D, Nicotera P, Bano D. Comparative analysis of CI- and CIV-containing respiratory supercomplexes at single-cell resolution. CELL REPORTS METHODS 2021; 1:100002. [PMID: 35474694 PMCID: PMC9017192 DOI: 10.1016/j.crmeth.2021.100002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 02/03/2021] [Accepted: 03/03/2021] [Indexed: 12/29/2022]
Abstract
Mitochondria sustain the energy demand of the cell. The composition and functional state of the mitochondrial oxidative phosphorylation system are informative indicators of organelle bioenergetic capacity. Here, we describe a highly sensitive and reproducible method for a single-cell quantification of mitochondrial CI- and CIV-containing respiratory supercomplexes (CI∗CIV-SCs) as an alternative means of assessing mitochondrial respiratory chain integrity. We apply a proximity ligation assay (PLA) and stain CI∗CIV-SCs in fixed human and mouse brains, tumorigenic cells, induced pluripotent stem cells (iPSCs) and iPSC-derived neural precursor cells (NPCs), and neurons. Spatial visualization of CI∗CIV-SCs enables the detection of mitochondrial lesions in various experimental models, including complex tissues undergoing degenerative processes. We report that comparative assessments of CI∗CIV-SCs facilitate the quantitative profiling of even subtle mitochondrial variations by overcoming the confounding effects that mixed cell populations have on other measurements. Together, our PLA-based analysis of CI∗CIV-SCs is a sensitive and complementary technique for detecting cell-type-specific mitochondrial perturbations in fixed materials.
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Affiliation(s)
- Fabio Bertan
- German Center for Neurodegenerative Diseases (DZNE), Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Venusberg-Campus 1, Gebäude 99, Bonn, North Rhine-Westphalia 53127, Germany
| | - Lena Wischhof
- German Center for Neurodegenerative Diseases (DZNE), Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Venusberg-Campus 1, Gebäude 99, Bonn, North Rhine-Westphalia 53127, Germany
| | - Enzo Scifo
- German Center for Neurodegenerative Diseases (DZNE), Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Venusberg-Campus 1, Gebäude 99, Bonn, North Rhine-Westphalia 53127, Germany
| | - Mihaela Guranda
- German Center for Neurodegenerative Diseases (DZNE), Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Venusberg-Campus 1, Gebäude 99, Bonn, North Rhine-Westphalia 53127, Germany
| | - Joshua Jackson
- German Center for Neurodegenerative Diseases (DZNE), Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Venusberg-Campus 1, Gebäude 99, Bonn, North Rhine-Westphalia 53127, Germany
| | - Anaïs Marsal-Cots
- German Center for Neurodegenerative Diseases (DZNE), Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Venusberg-Campus 1, Gebäude 99, Bonn, North Rhine-Westphalia 53127, Germany
| | - Antonia Piazzesi
- German Center for Neurodegenerative Diseases (DZNE), Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Venusberg-Campus 1, Gebäude 99, Bonn, North Rhine-Westphalia 53127, Germany
| | - Miriam Stork
- German Center for Neurodegenerative Diseases (DZNE), Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Venusberg-Campus 1, Gebäude 99, Bonn, North Rhine-Westphalia 53127, Germany
| | - Michael Peitz
- Institute of Reconstructive Neurobiology, University of Bonn Medical Faculty and University Hospital Bonn, Bonn, North Rhine-Westphalia 53127, Germany
- Cell Programming Core Facility, University of Bonn Medical Faculty, Bonn, North Rhine-Westphalia 53127, Germany
| | - Jochen Herbert Martin Prehn
- Royal College of Surgeons in Ireland, Department of Physiology and Medical Physics Department, D02 YN77 Dublin, Ireland
| | - Dan Ehninger
- German Center for Neurodegenerative Diseases (DZNE), Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Venusberg-Campus 1, Gebäude 99, Bonn, North Rhine-Westphalia 53127, Germany
| | - Pierluigi Nicotera
- German Center for Neurodegenerative Diseases (DZNE), Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Venusberg-Campus 1, Gebäude 99, Bonn, North Rhine-Westphalia 53127, Germany
| | - Daniele Bano
- German Center for Neurodegenerative Diseases (DZNE), Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Venusberg-Campus 1, Gebäude 99, Bonn, North Rhine-Westphalia 53127, Germany
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37
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Multiplexed complexome profiling using tandem mass tags. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 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] [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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Rotko D, Kudin AP, Zsurka G, Kulawiak B, Szewczyk A, Kunz WS. Molecular and Functional Effects of Loss of Cytochrome c Oxidase Subunit 8A. BIOCHEMISTRY (MOSCOW) 2021; 86:33-43. [PMID: 33705280 DOI: 10.1134/s0006297921010041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this work we studied molecular and functional effects of the loss of the smallest nuclear encoded subunit of cytochrome c oxidase COX8A in fibroblasts from a patient with a homozygous splice site mutation and in CRISPR/Cas9 genome-edited HEK293T cells. In both cellular model systems, between 20 to 30% of the residual enzymatic activity of cytochrome c oxidase (COX) was detectable. In immunoblots of BN-PAGE separated mitochondria from both cellular models almost no monomers and dimers of the fully assembled COX could be visualized. Interestingly, supercomplexes of COX formed with complex III and also with complexes I and III retained considerable immunoreactivity, while nearly no immunoreactivity attributable to subassemblies was found. That indicates that COX lacking subunit 8A is stabilized in supercomplexes, while monomers and dimers are rapidly degraded. With transcriptome analysis by 3'-RNA sequencing we failed to detect in our cellular models of COX8A deficiency transcriptional changes of genes involved in the mitochondrial unfolded protein response (mtUPR) and the integrated stress response (ISR). Thus, our data strongly suggest that the smallest subunit of cytochrome c oxidase COX8A is required for maintenance of the structural stability of COX monomers and dimers.
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Affiliation(s)
- Daria Rotko
- Institute of Experimental Epileptology and Cognition Research, Life & Brain Center, University of Bonn, Venusberg-Campus 1, Bonn, 53127, Germany. .,Laboratory of Intracellular Ion Channels, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, 02-093, Poland
| | - Alexei P Kudin
- Institute of Experimental Epileptology and Cognition Research, Life & Brain Center, University of Bonn, Venusberg-Campus 1, Bonn, 53127, Germany.
| | - Gábor Zsurka
- Institute of Experimental Epileptology and Cognition Research, Life & Brain Center, University of Bonn, Venusberg-Campus 1, Bonn, 53127, Germany. .,Department of Epileptology, University Bonn Medical Center, Venusberg-Campus 1, Bonn, 53127, Germany
| | - Bogusz Kulawiak
- Laboratory of Intracellular Ion Channels, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, 02-093, Poland.
| | - Adam Szewczyk
- Laboratory of Intracellular Ion Channels, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, 02-093, Poland.
| | - Wolfram S Kunz
- Institute of Experimental Epileptology and Cognition Research, Life & Brain Center, University of Bonn, Venusberg-Campus 1, Bonn, 53127, Germany. .,Department of Epileptology, University Bonn Medical Center, Venusberg-Campus 1, Bonn, 53127, Germany
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39
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D'Angelo L, Astro E, De Luise M, Kurelac I, Umesh-Ganesh N, Ding S, Fearnley IM, Gasparre G, Zeviani M, Porcelli AM, Fernandez-Vizarra E, Iommarini L. NDUFS3 depletion permits complex I maturation and reveals TMEM126A/OPA7 as an assembly factor binding the ND4-module intermediate. Cell Rep 2021; 35:109002. [PMID: 33882309 PMCID: PMC8076766 DOI: 10.1016/j.celrep.2021.109002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 02/25/2021] [Accepted: 03/25/2021] [Indexed: 11/25/2022] Open
Abstract
Complex I (CI) is the largest enzyme of the mitochondrial respiratory chain, and its defects are the main cause of mitochondrial disease. To understand the mechanisms regulating the extremely intricate biogenesis of this fundamental bioenergetic machine, we analyze the structural and functional consequences of the ablation of NDUFS3, a non-catalytic core subunit. We show that, in diverse mammalian cell types, a small amount of functional CI can still be detected in the complete absence of NDUFS3. In addition, we determine the dynamics of CI disassembly when the amount of NDUFS3 is gradually decreased. The process of degradation of the complex occurs in a hierarchical and modular fashion in which the ND4 module remains stable and bound to TMEM126A. We, thus, uncover the function of TMEM126A, the product of a disease gene causing recessive optic atrophy as a factor necessary for the correct assembly and function of CI.
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Affiliation(s)
- Luigi D'Angelo
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy
| | - Elisa Astro
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy
| | - Monica De Luise
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy
| | - Ivana Kurelac
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy
| | - Nikkitha Umesh-Ganesh
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy
| | - Shujing Ding
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY Cambridge, UK
| | - Ian M Fearnley
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY Cambridge, UK
| | - Giuseppe Gasparre
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy
| | - Massimo Zeviani
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY Cambridge, UK; Venetian Institute of Molecular Medicine, 35128 Padua, Italy; Department of Neurosciences, University of Padua, 35128 Padua, Italy
| | - Anna Maria Porcelli
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy; Interdepartmental Center of Industrial Research (CIRI) Life Science and Health Technologies, University of Bologna, 40064 Ozzano dell'Emilia, Italy
| | - Erika Fernandez-Vizarra
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY Cambridge, UK; Institute of Molecular, Cell and Systems Biology, University of Glasgow, G12 8QQ Glasgow, UK.
| | - Luisa Iommarini
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy.
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Organization of the Respiratory Supercomplexes in Cells with Defective Complex III: Structural Features and Metabolic Consequences. Life (Basel) 2021; 11:life11040351. [PMID: 33920624 PMCID: PMC8074069 DOI: 10.3390/life11040351] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/13/2022] Open
Abstract
The mitochondrial respiratory chain encompasses four oligomeric enzymatic complexes (complex I, II, III and IV) which, together with the redox carrier ubiquinone and cytochrome c, catalyze electron transport coupled to proton extrusion from the inner membrane. The protonmotive force is utilized by complex V for ATP synthesis in the process of oxidative phosphorylation. Respiratory complexes are known to coexist in the membrane as single functional entities and as supramolecular aggregates or supercomplexes (SCs). Understanding the assembly features of SCs has relevant biomedical implications because defects in a single protein can derange the overall SC organization and compromise the energetic function, causing severe mitochondrial disorders. Here we describe in detail the main types of SCs, all characterized by the presence of complex III. We show that the genetic alterations that hinder the assembly of Complex III, not just the activity, cause a rearrangement of the architecture of the SC that can help to preserve a minimal energetic function. Finally, the major metabolic disturbances associated with severe SCs perturbation due to defective complex III are discussed along with interventions that may circumvent these deficiencies.
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Čunátová K, Reguera DP, Vrbacký M, Fernández-Vizarra E, Ding S, Fearnley IM, Zeviani M, Houštěk J, Mráček T, Pecina P. Loss of COX4I1 Leads to Combined Respiratory Chain Deficiency and Impaired Mitochondrial Protein Synthesis. Cells 2021; 10:369. [PMID: 33578848 PMCID: PMC7916595 DOI: 10.3390/cells10020369] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 01/07/2023] Open
Abstract
The oxidative phosphorylation (OXPHOS) system localized in the inner mitochondrial membrane secures production of the majority of ATP in mammalian organisms. Individual OXPHOS complexes form supramolecular assemblies termed supercomplexes. The complexes are linked not only by their function but also by interdependency of individual complex biogenesis or maintenance. For instance, cytochrome c oxidase (cIV) or cytochrome bc1 complex (cIII) deficiencies affect the level of fully assembled NADH dehydrogenase (cI) in monomeric as well as supercomplex forms. It was hypothesized that cI is affected at the level of enzyme assembly as well as at the level of cI stability and maintenance. However, the true nature of interdependency between cI and cIV is not fully understood yet. We used a HEK293 cellular model where the COX4 subunit was completely knocked out, serving as an ideal system to study interdependency of cI and cIV, as early phases of cIV assembly process were disrupted. Total absence of cIV was accompanied by profound deficiency of cI, documented by decrease in the levels of cI subunits and significantly reduced amount of assembled cI. Supercomplexes assembled from cI, cIII, and cIV were missing in COX4I1 knock-out (KO) due to loss of cIV and decrease in cI amount. Pulse-chase metabolic labeling of mitochondrial DNA (mtDNA)-encoded proteins uncovered a decrease in the translation of cIV and cI subunits. Moreover, partial impairment of mitochondrial protein synthesis correlated with decreased content of mitochondrial ribosomal proteins. In addition, complexome profiling revealed accumulation of cI assembly intermediates, indicating that cI biogenesis, rather than stability, was affected. We propose that attenuation of mitochondrial protein synthesis caused by cIV deficiency represents one of the mechanisms, which may impair biogenesis of cI.
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Affiliation(s)
- Kristýna Čunátová
- Laboratory of Bioenergetics, Institute of Physiology, Czech Academy of Sciences, 142 00 Prague, Czech Republic; (K.Č.); (D.P.R.); (M.V.); (J.H.)
- Department of Cell Biology, Faculty of Science, Charles University, 128 00 Prague, Czech Republic
| | - David Pajuelo Reguera
- Laboratory of Bioenergetics, Institute of Physiology, Czech Academy of Sciences, 142 00 Prague, Czech Republic; (K.Č.); (D.P.R.); (M.V.); (J.H.)
| | - Marek Vrbacký
- Laboratory of Bioenergetics, Institute of Physiology, Czech Academy of Sciences, 142 00 Prague, Czech Republic; (K.Č.); (D.P.R.); (M.V.); (J.H.)
| | - Erika Fernández-Vizarra
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK; (E.F.-V.); (S.D.); (I.M.F.); (M.Z.)
| | - Shujing Ding
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK; (E.F.-V.); (S.D.); (I.M.F.); (M.Z.)
| | - Ian M. Fearnley
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK; (E.F.-V.); (S.D.); (I.M.F.); (M.Z.)
| | - Massimo Zeviani
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK; (E.F.-V.); (S.D.); (I.M.F.); (M.Z.)
| | - Josef Houštěk
- Laboratory of Bioenergetics, Institute of Physiology, Czech Academy of Sciences, 142 00 Prague, Czech Republic; (K.Č.); (D.P.R.); (M.V.); (J.H.)
| | - Tomáš Mráček
- Laboratory of Bioenergetics, Institute of Physiology, Czech Academy of Sciences, 142 00 Prague, Czech Republic; (K.Č.); (D.P.R.); (M.V.); (J.H.)
| | - Petr Pecina
- Laboratory of Bioenergetics, Institute of Physiology, Czech Academy of Sciences, 142 00 Prague, Czech Republic; (K.Č.); (D.P.R.); (M.V.); (J.H.)
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42
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Szczepanowska K, Trifunovic A. Tune instead of destroy: How proteolysis keeps OXPHOS in shape. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148365. [PMID: 33417924 DOI: 10.1016/j.bbabio.2020.148365] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/11/2020] [Accepted: 12/16/2020] [Indexed: 02/06/2023]
Abstract
Mitochondria are highly dynamic and stress-responsive organelles that are renewed, maintained and removed by a number of different mechanisms. Recent findings bring more evidence for the focused, defined, and regulatory function of the intramitochondrial proteases extending far beyond the traditional concepts of damage control and stress responses. Until recently, the macrodegradation processes, such as mitophagy, were promoted as the major regulator of OXPHOS remodelling and turnover. However, the spatiotemporal dynamics of the OXPHOS system can be greatly modulated by the intrinsic mitochondrial mechanisms acting apart from changes in the global mitochondrial dynamics. This, in turn, may substantially contribute to the shaping of the metabolic status of the cell.
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Affiliation(s)
- Karolina Szczepanowska
- Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), and Institute for Mitochondrial Diseases and Ageing, Medical Faculty, University of Cologne D-50931 Cologne, Germany; Institute for Mitochondrial Diseases and Ageing, Medical Faculty and Center for Molecular Medicine Cologne (CMMC), D-50931 Cologne, Germany.
| | - Aleksandra Trifunovic
- Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), and Institute for Mitochondrial Diseases and Ageing, Medical Faculty, University of Cologne D-50931 Cologne, Germany; Institute for Mitochondrial Diseases and Ageing, Medical Faculty and Center for Molecular Medicine Cologne (CMMC), D-50931 Cologne, Germany.
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43
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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: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [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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44
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Timón-Gómez A, Bartley-Dier EL, Fontanesi F, Barrientos A. HIGD-Driven Regulation of Cytochrome c Oxidase Biogenesis and Function. Cells 2020; 9:cells9122620. [PMID: 33291261 PMCID: PMC7762129 DOI: 10.3390/cells9122620] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/02/2020] [Accepted: 12/04/2020] [Indexed: 12/24/2022] Open
Abstract
The biogenesis and function of eukaryotic cytochrome c oxidase or mitochondrial respiratory chain complex IV (CIV) undergo several levels of regulation to adapt to changing environmental conditions. Adaptation to hypoxia and oxidative stress involves CIV subunit isoform switch, changes in phosphorylation status, and modulation of CIV assembly and enzymatic activity by interacting factors. The latter include the Hypoxia Inducible Gene Domain (HIGD) family yeast respiratory supercomplex factors 1 and 2 (Rcf1 and Rcf2) and two mammalian homologs of Rcf1, the proteins HIGD1A and HIGD2A. Whereas Rcf1 and Rcf2 are expressed constitutively, expression of HIGD1A and HIGD2A is induced under stress conditions, such as hypoxia and/or low glucose levels. In both systems, the HIGD proteins localize in the mitochondrial inner membrane and play a role in the biogenesis of CIV as a free unit or as part as respiratory supercomplexes. Notably, they remain bound to assembled CIV and, by modulating its activity, regulate cellular respiration. Here, we will describe the current knowledge regarding the specific and overlapping roles of the several HIGD proteins in physiological and stress conditions.
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Affiliation(s)
- Alba Timón-Gómez
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA;
| | - Emma L. Bartley-Dier
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; (E.L.B.-D.); (F.F.)
| | - Flavia Fontanesi
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; (E.L.B.-D.); (F.F.)
| | - Antoni Barrientos
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA;
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; (E.L.B.-D.); (F.F.)
- Correspondence:
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45
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Berndtsson J, Kohler A, Rathore S, Marin‐Buera L, Dawitz H, Diessl J, Kohler V, Barrientos A, Büttner S, Fontanesi F, Ott M. Respiratory supercomplexes enhance electron transport by decreasing cytochrome c diffusion distance. EMBO Rep 2020; 21:e51015. [PMID: 33016568 PMCID: PMC7726804 DOI: 10.15252/embr.202051015] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/02/2020] [Accepted: 09/10/2020] [Indexed: 01/03/2023] Open
Abstract
Respiratory chains are crucial for cellular energy conversion and consist of multi-subunit complexes that can assemble into supercomplexes. These structures have been intensively characterized in various organisms, but their physiological roles remain unclear. Here, we elucidate their function by leveraging a high-resolution structural model of yeast respiratory supercomplexes that allowed us to inhibit supercomplex formation by mutation of key residues in the interaction interface. Analyses of a mutant defective in supercomplex formation, which still contains fully functional individual complexes, show that the lack of supercomplex assembly delays the diffusion of cytochrome c between the separated complexes, thus reducing electron transfer efficiency. Consequently, competitive cellular fitness is severely reduced in the absence of supercomplex formation and can be restored by overexpression of cytochrome c. In sum, our results establish how respiratory supercomplexes increase the efficiency of cellular energy conversion, thereby providing an evolutionary advantage for aerobic organisms.
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Affiliation(s)
- Jens Berndtsson
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
| | - Andreas Kohler
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
| | - Sorbhi Rathore
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
| | - Lorena Marin‐Buera
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
| | - Hannah Dawitz
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
| | - Jutta Diessl
- Department of Molecular BiosciencesThe Wenner‐Gren InstituteStockholm UniversityStockholmSweden
| | - Verena Kohler
- Department of Molecular BiosciencesThe Wenner‐Gren InstituteStockholm UniversityStockholmSweden
| | - Antoni Barrientos
- Department of NeurologyMiller School of MedicineUniversity of MiamiMiamiFLUSA
- Department of Biochemistry and Molecular BiologyMiller School of MedicineUniversity of MiamiMiamiFLUSA
| | - Sabrina Büttner
- Department of Molecular BiosciencesThe Wenner‐Gren InstituteStockholm UniversityStockholmSweden
- Institute of Molecular BiosciencesUniversity of GrazGrazAustria
| | - Flavia Fontanesi
- Department of Biochemistry and Molecular BiologyMiller School of MedicineUniversity of MiamiMiamiFLUSA
| | - Martin Ott
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
- Department of Medical Biochemistry and Cell BiologyUniversity of GothenburgGothenburgSweden
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46
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Mitochondrial respiratory supercomplexes in mammalian cells: structural versus functional role. J Mol Med (Berl) 2020; 99:57-73. [PMID: 33201259 DOI: 10.1007/s00109-020-02004-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/06/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023]
Abstract
Mitochondria are recognized as the main source of ATP to meet the energy demands of the cell. ATP production occurs by oxidative phosphorylation when electrons are transported through the electron transport chain (ETC) complexes and develop the proton motive force across the inner mitochondrial membrane that is used for ATP synthesis. Studies since the 1960s have been concentrated on the two models of structural organization of ETC complexes known as "solid-state" and "fluid-state" models. However, advanced new techniques such as blue-native gel electrophoresis, mass spectroscopy, and cryogenic electron microscopy for analysis of macromolecular protein complexes provided new data in favor of the solid-state model. According to this model, individual ETC complexes are assembled into macromolecular structures known as respiratory supercomplexes (SCs). A large number of studies over the last 20 years proposed the potential role of SCs to facilitate substrate channeling, maintain the integrity of individual ETC complexes, reduce electron leakage and production of reactive oxygen species, and prevent excessive and random aggregation of proteins in the inner mitochondrial membrane. However, many other studies have challenged the proposed functional role of SCs. Recently, a third model known as the "plasticity" model was proposed that partly reconciles both "solid-state" and "fluid-state" models. According to the "plasticity" model, respiratory SCs can co-exist with the individual ETC complexes. To date, the physiological role of SCs remains unknown, although several studies using tissue samples of patients or animal/cell models of human diseases revealed an associative link between functional changes and the disintegration of SC assembly. This review summarizes and discusses previous studies on the mechanisms and regulation of SC assembly under physiological and pathological conditions.
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47
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Kadenbach B. Complex IV - The regulatory center of mitochondrial oxidative phosphorylation. Mitochondrion 2020; 58:296-302. [PMID: 33069909 DOI: 10.1016/j.mito.2020.10.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 09/01/2020] [Accepted: 10/12/2020] [Indexed: 12/19/2022]
Abstract
ATP, the universal energy currency in all living cells, is mainly synthesized in mitochondria by oxidative phosphorylation (OXPHOS). The final and rate limiting step of the respiratory chain is cytochrome c oxidase (COX) which represents the regulatory center of OXPHOS. COX is regulated through binding of various effectors to its "supernumerary" subunits, by reversible phosphorylation, and by expression of subunit isoforms. Of particular interest is its feedback inhibition by ATP, the final product of OXPHOS. This "allosteric ATP-inhibition" of phosphorylated and dimeric COX maintains a low and healthy mitochondrial membrane potential (relaxed state), and prevents the formation of ROS (reactive oxygen species) which are known to cause numerous diseases. Excessive work and stress abolish this feedback inhibition of COX by Ca2+-activated dephosphorylation which leads to monomerization and movement of NDUFA4 from complex I to COX with higher rates of COX activity and ATP synthesis (active state) but increased ROS formation and decreased efficiency.
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48
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Altered Expression Ratio of Actin-Binding Gelsolin Isoforms Is a Novel Hallmark of Mitochondrial OXPHOS Dysfunction. Cells 2020; 9:cells9091922. [PMID: 32824961 PMCID: PMC7563380 DOI: 10.3390/cells9091922] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 08/07/2020] [Accepted: 08/15/2020] [Indexed: 12/30/2022] Open
Abstract
Mitochondrial oxidative phosphorylation (OXPHOS) defects are the primary cause of inborn errors of energy metabolism. Despite considerable progress on their genetic basis, their global pathophysiological consequences remain undefined. Previous studies reported that OXPHOS dysfunction associated with complex III deficiency exacerbated the expression and mitochondrial location of cytoskeletal gelsolin (GSN) to promote cell survival responses. In humans, besides the cytosolic isoform, GSN presents a plasma isoform secreted to extracellular environments. We analyzed the interplay between both GSN isoforms in human cellular and clinical models of OXPHOS dysfunction. Regardless of its pathogenic origin, OXPHOS dysfunction induced the physiological upregulation of cytosolic GSN in the mitochondria (mGSN), in parallel with a significant downregulation of plasma GSN (pGSN) levels. Consequently, significantly high mGSN-to-pGSN ratios were associated with OXPHOS deficiency both in human cells and blood. In contrast, control cells subjected to hydrogen peroxide or staurosporine treatments showed no correlation between oxidative stress or cell death induction and the altered levels and subcellular location of GSN isoforms, suggesting their specificity for OXPHOS dysfunction. In conclusion, a high mitochondrial-to-plasma GSN ratio represents a useful cellular indicator of OXPHOS defects, with potential use for future research of a wide range of clinical conditions with mitochondrial involvement.
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Age-Related Deterioration of Mitochondrial Function in the Intestine. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:4898217. [PMID: 32922652 PMCID: PMC7453234 DOI: 10.1155/2020/4898217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 07/22/2020] [Indexed: 12/29/2022]
Abstract
Aging is an important and inevitable biological process in human life, associated with the onset of chronic disease and death. The mechanisms behind aging remain unclear. However, changes in mitochondrial function and structure, including reduced activity of the mitochondrial respiratory chain and increased production of reactive oxygen species—thus oxidative damage—are believed to play a major role. Mitochondria are the main source of cellular energy, producing adenosine triphosphate (ATP) via oxidative phosphorylation. Accumulation of damaged cellular components reduces a body's capacity to preserve tissue homeostasis and affects biological aging and all age-related chronic conditions. This includes the onset and progression of classic degenerative diseases such as cardiovascular disease, kidney failure, neurodegenerative diseases, and cancer. Clinical manifestations of intestinal disorders, such as mucosal barrier dysfunction, intestinal dysmotility, and chronic obstipation, are highly prevalent in the elderly population and have been shown to be associated with an age-dependent decline of mitochondrial function. This review summarizes our current understanding of the role of mitochondrial dysfunction in intestinal aging.
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50
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Lobo-Jarne T, Pérez-Pérez R, Fontanesi F, Timón-Gómez A, Wittig I, Peñas A, Serrano-Lorenzo P, García-Consuegra I, Arenas J, Martín MA, Barrientos A, Ugalde C. Multiple pathways coordinate assembly of human mitochondrial complex IV and stabilization of respiratory supercomplexes. EMBO J 2020; 39:e103912. [PMID: 32511785 DOI: 10.15252/embj.2019103912] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 04/20/2020] [Accepted: 05/06/2020] [Indexed: 12/28/2022] Open
Abstract
Mitochondrial respiratory chain complexes I, III, and IV can associate into larger structures termed supercomplexes or respirasomes, thereby generating structural interdependences among the individual complexes yet to be understood. In patients, nonsense mutations in complex IV subunit genes cause severe encephalomyopathies randomly associated with pleiotropic complex I defects. Using complexome profiling and biochemical analyses, we have explored the structural rearrangements of the respiratory chain in human cell lines depleted of the catalytic complex IV subunit COX1 or COX2. In the absence of a functional complex IV holoenzyme, several supercomplex I+III2 species coexist, which differ in their content of COX subunits and COX7A2L/HIGD2A assembly factors. The incorporation of an atypical COX1-HIGD2A submodule attenuates supercomplex I+III2 turnover rate, indicating an unexpected molecular adaptation for supercomplexes stabilization that relies on the presence of COX1 independently of holo-complex IV formation. Our data set the basis for complex I structural dependence on complex IV, revealing the co-existence of alternative pathways for the biogenesis of "supercomplex-associated" versus individual complex IV, which could determine physiological adaptations under different stress and disease scenarios.
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Affiliation(s)
- Teresa Lobo-Jarne
- Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain
| | | | - Flavia Fontanesi
- Department of Biochemistry, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Alba Timón-Gómez
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Ilka Wittig
- SFB 815 Core Unit, Functional Proteomics, Goethe-Universität, Frankfurt am Main, Germany
| | - Ana Peñas
- Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain
| | | | - Inés García-Consuegra
- Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723, Madrid, Spain
| | - Joaquín Arenas
- Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723, Madrid, Spain
| | - Miguel A Martín
- Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723, Madrid, Spain
| | - Antoni Barrientos
- Department of Biochemistry, University of Miami Miller School of Medicine, Miami, FL, USA.,Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Cristina Ugalde
- Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723, Madrid, Spain
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