1
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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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2
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Burgin H, Sharpe AJ, Nie S, Ziemann M, Crameri JJ, Stojanovski D, Pitt J, Ohtake A, Murayama K, McKenzie M. Loss of mitochondrial fatty acid β-oxidation protein short-chain Enoyl-CoA hydratase disrupts oxidative phosphorylation protein complex stability and function. FEBS J 2023; 290:225-246. [PMID: 35962613 PMCID: PMC10087869 DOI: 10.1111/febs.16595] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/24/2022] [Accepted: 08/11/2022] [Indexed: 01/14/2023]
Abstract
Short-chain enoyl-CoA hydratase 1 (ECHS1) is involved in the second step of mitochondrial fatty acid β-oxidation (FAO), catalysing the hydration of short-chain enoyl-CoA esters to short-chain 3-hyroxyl-CoA esters. Genetic deficiency in ECHS1 (ECHS1D) is associated with a specific subset of Leigh Syndrome, a disease typically caused by defects in oxidative phosphorylation (OXPHOS). Here, we examined the molecular pathogenesis of ECHS1D using a CRISPR/Cas9 edited human cell 'knockout' model and fibroblasts from ECHS1D patients. Transcriptome analysis of ECHS1 'knockout' cells showed reductions in key mitochondrial pathways, including the tricarboxylic acid cycle, receptor-mediated mitophagy and nucleotide biosynthesis. Subsequent proteomic analyses confirmed these reductions and revealed additional defects in mitochondrial oxidoreductase activity and fatty acid β-oxidation. Functional analysis of ECHS1 'knockout' cells showed reduced mitochondrial oxygen consumption rates when metabolising glucose or OXPHOS complex I-linked substrates, as well as decreased complex I and complex IV enzyme activities. ECHS1 'knockout' cells also exhibited decreased OXPHOS protein complex steady-state levels (complex I, complex III2 , complex IV, complex V and supercomplexes CIII2 /CIV and CI/CIII2 /CIV), which were associated with a defect in complex I assembly. Patient fibroblasts exhibit varied reduction of mature OXPHOS complex steady-state levels, with defects detected in CIII2 , CIV, CV and the CI/CIII2 /CIV supercomplex. Overall, these findings highlight the contribution of defective OXPHOS function, in particular complex I deficiency, to the molecular pathogenesis of ECHS1D.
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Affiliation(s)
- Harrison Burgin
- School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Geelong, Australia
| | - Alice J Sharpe
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Australia
| | - Mark Ziemann
- School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Geelong, Australia
| | - Jordan J Crameri
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Australia
| | - Diana Stojanovski
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Australia
| | - James Pitt
- Department of Paediatrics, Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, The University of Melbourne, Australia
| | - Akira Ohtake
- Department of Pediatrics & Clinical Genomics, Faculty of Medicine, Saitama Medical University, Japan.,Centre for Intractable Diseases, Saitama Medical University Hospital, Japan
| | - Kei Murayama
- Department of Metabolism, Chiba Children's Hospital, Japan
| | - Matthew McKenzie
- School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Geelong, Australia.,Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, Australia.,Department of Molecular and Translational Science, Monash University, Melbourne, Australia
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3
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Yoval-Sánchez B, Ansari F, James J, Niatsetskaya Z, Sosunov S, Filipenko P, Tikhonova IG, Ten V, Wittig I, Rafikov R, Galkin A. Redox-dependent loss of flavin by mitochondria complex I is different in brain and heart. Redox Biol 2022; 51:102258. [PMID: 35189550 PMCID: PMC8861397 DOI: 10.1016/j.redox.2022.102258] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/26/2022] [Accepted: 01/31/2022] [Indexed: 12/14/2022] Open
Abstract
Pathologies associated with tissue ischemia/reperfusion (I/R) in highly metabolizing organs such as the brain and heart are leading causes of death and disability in humans. Molecular mechanisms underlying mitochondrial dysfunction during acute injury in I/R are tissue-specific, but their details are not completely understood. A metabolic shift and accumulation of substrates of reverse electron transfer (RET) such as succinate are observed in tissue ischemia, making mitochondrial complex I of the respiratory chain (NADH:ubiquinone oxidoreductase) the most vulnerable enzyme to the following reperfusion. It has been shown that brain complex I is predisposed to losing its flavin mononucleotide (FMN) cofactor when maintained in the reduced state in conditions of RET both in vitro and in vivo. Here we investigated the process of redox-dependent dissociation of FMN from mitochondrial complex I in brain and heart mitochondria. In contrast to the brain enzyme, cardiac complex I does not lose FMN when reduced in RET conditions. We proposed that the different kinetics of FMN loss during RET is due to the presence of brain-specific long 50 kDa isoform of the NDUFV3 subunit of complex I, which is absent in the heart where only the canonical 10 kDa short isoform is found. Our simulation studies suggest that the long NDUFV3 isoform can reach toward the FMN binding pocket and affect the nucleotide affinity to the apoenzyme. For the first time, we demonstrated a potential functional role of tissue-specific isoforms of complex I, providing the distinct molecular mechanism of I/R-induced mitochondrial impairment in cardiac and cerebral tissues. By combining functional studies of intact complex I and molecular structure simulations, we defined the critical difference between the brain and heart enzyme and suggested insights into the redox-dependent inactivation mechanisms of complex I during I/R injury in both tissues.
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Affiliation(s)
- Belem Yoval-Sánchez
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, 407 East 61st Street, New York, NY, 10065, USA
| | - Fariha Ansari
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, 407 East 61st Street, New York, NY, 10065, USA
| | - Joel James
- Division of Endocrinology, Department of Medicine, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Zoya Niatsetskaya
- Department of Pediatrics, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ, 08901, USA
| | - Sergey Sosunov
- Department of Pediatrics, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ, 08901, USA
| | - Peter Filipenko
- Department of Biochemistry, Weill Cornell Medical College, Cornell University, New York, NY, 10021, USA
| | - Irina G. Tikhonova
- School of Pharmacy, Medical Biology, Centre, Queen's University Belfast, Belfast, BT9 7BL, United Kingdom
| | - Vadim Ten
- Department of Pediatrics, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ, 08901, USA
| | - Ilka Wittig
- Functional Proteomics, Cardiovascular Physiology, Goethe University, 60590, Frankfurt am Main, Germany,German Center for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Ruslan Rafikov
- Division of Endocrinology, Department of Medicine, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Alexander Galkin
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, 407 East 61st Street, New York, NY, 10065, USA,Corresponding author.
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4
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Padavannil A, Ayala-Hernandez MG, Castellanos-Silva EA, Letts JA. The Mysterious Multitude: Structural Perspective on the Accessory Subunits of Respiratory Complex I. Front Mol Biosci 2022; 8:798353. [PMID: 35047558 PMCID: PMC8762328 DOI: 10.3389/fmolb.2021.798353] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/25/2021] [Indexed: 01/10/2023] Open
Abstract
Complex I (CI) is the largest protein complex in the mitochondrial oxidative phosphorylation electron transport chain of the inner mitochondrial membrane and plays a key role in the transport of electrons from reduced substrates to molecular oxygen. CI is composed of 14 core subunits that are conserved across species and an increasing number of accessory subunits from bacteria to mammals. The fact that adding accessory subunits incurs costs of protein production and import suggests that these subunits play important physiological roles. Accordingly, knockout studies have demonstrated that accessory subunits are essential for CI assembly and function. Furthermore, clinical studies have shown that amino acid substitutions in accessory subunits lead to several debilitating and fatal CI deficiencies. Nevertheless, the specific roles of CI’s accessory subunits have remained mysterious. In this review, we explore the possible roles of each of mammalian CI’s 31 accessory subunits by integrating recent high-resolution CI structures with knockout, assembly, and clinical studies. Thus, we develop a framework of experimentally testable hypotheses for the function of the accessory subunits. We believe that this framework will provide inroads towards the complete understanding of mitochondrial CI physiology and help to develop strategies for the treatment of CI deficiencies.
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Affiliation(s)
- Abhilash Padavannil
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
| | - Maria G Ayala-Hernandez
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
| | - Eimy A Castellanos-Silva
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
| | - James A Letts
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
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5
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Clinical Relevance and Tumor Growth Suppression of Mitochondrial ROS Regulators along NADH:Ubiquinone Oxidoreductase Subunit B3 in Thyroid Cancer. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:8038857. [PMID: 35087620 PMCID: PMC8787455 DOI: 10.1155/2022/8038857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/24/2021] [Accepted: 12/06/2021] [Indexed: 02/05/2023]
Abstract
Mitochondrial reactive oxygen species (mitoROS) are a double-edged sword in cancer progression, connoting the ROS-dependent malignant transformation and the oxidative stress-induced cell death. However, the underlying role of mitoROS in thyroid cancer remains unclear. Here, we collected 35 prominent mitoROS regulators to stratify 510 thyroid cancer patients in TCGA cohort through consensus clustering. Three molecular subtypes (cluster 1/2/3) were identified, among which cluster 1 (mitoROSlow) was preferentially associated with unfavorable prognosis. Individually, there were 12 regulators with a high expression that predicted a significantly favorable progression-free survival. The NADH:Ubiquinone Oxidoreductase Subunit B3 (NDUFB3) had a highest impact. NDUFB3 knockdown significantly reduced mitoROS levels in BCPAP and C643 cells. Bioinformatically, the consistency between NDUFB3 expression and cluster 1/2/3 was confirmed; lower expression of NUDFB3 was associated with a poor clinical outcome. Pathway analysis of differentially expressed genes in the NDUFB3low and NDUFB3high cohorts revealed a predominance of oxidative phosphorylation pathway changes. Consistently, mitochondrial functions, including oxygen consumption rate, ATP levels, complex I activity, mitoROS levels, and the expression of mitochondrially encoded NADH:Ubiquinone oxidoreductase core subunit 5, were significantly increased in NDUFB3-overexpressed BCPAP cells or C643 cells. The in vivo NDUFB3 overexpression and sideroxylin treatment significantly suppressed tumor growth and prolonged survival, concurrently elevating mitoROS levels ex vivo in mouse xenograft models. Conversely, NDUFB3 knockdown had the opposite effect. Together, these findings implicated the importance of mitoROS regulators in predicting clinical outcomes of patients with thyroid cancer. Our findings may pave the way for developing a mitoROS-based treatment for thyroid cancer patients.
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6
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Abstract
Oxygen (O2) is essential for life and therefore the supply of sufficient O2 to the tissues is a major physiological challenge. In mammals, a deficit of O2 (hypoxia) triggers rapid cardiorespiratory reflexes (e.g. hyperventilation and increased heart output) that within a few seconds increase the uptake of O2 by the lungs and its distribution throughout the body. The prototypical acute O2-sensing organ is the carotid body (CB), which contains sensory glomus cells expressing O2-regulated ion channels. In response to hypoxia, glomus cells depolarize and release transmitters which activate afferent fibers terminating at the brainstem respiratory and autonomic centers. In this review, we summarize the basic properties of CB chemoreceptor cells and the essential role played by their specialized mitochondria in acute O2 sensing and signaling. We focus on recent data supporting a "mitochondria-to-membrane signaling" model of CB chemosensory transduction. The possibility that the differential expression of specific subunit isoforms and enzymes could allow mitochondria to play a generalized adaptive O2-sensing and signaling role in a wide variety of cells is also discussed.
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Affiliation(s)
- José López-Barneo
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain.,Departamento de Fisiología Médica y Biofísica, Facultad de Medicina, Universidad de Sevilla, Seville, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Patricia Ortega-Sáenz
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain.,Departamento de Fisiología Médica y Biofísica, Facultad de Medicina, Universidad de Sevilla, Seville, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
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7
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Alvarez-Rodriguez M, Martinez CA, Roca J, Rodriguez-Martinez H. mRNA expression of oxidative-reductive proteins in boars with documented different fertility can identify relevant prognostic biomarkers. Res Vet Sci 2021; 141:195-202. [PMID: 34763256 DOI: 10.1016/j.rvsc.2021.10.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/27/2021] [Accepted: 10/28/2021] [Indexed: 11/20/2022]
Abstract
Oxidative stress unbalance is a major factor causing impairment of sperm function and, ultimately, sperm death. In this study, we identified transcriptomic and proteomic markers for oxidative-related protectors from the generation of reactive oxygen species (ROS) in spermatozoa from breeding boars with documented high- or low-fertility. Particular attention was paid to glutathione peroxidases, and to transcripts related to DNA stabilization and compaction, as protamine and transition proteins. mRNA cargo analysis was performed using porcine-specific micro-arrays (GeneChip® miRNA 4.0 and GeneChip® Porcine Gene 1.0 ST) and qPCR validation. Differences between fertility-classed boars were ample among biomarkers; some upregulated only at protein level (catalase (CAT), superoxide dismutase 1 (SOD1) and glutathione proteins), or only at the mRNA level (ATOX1, Antioxidant Protein 1). In addition, protamines 2 and 3, essential for sperm DNA condensation and also transition proteins 1 and 2 (TNP1 and TNP2), required during histone-to-protamine replacement, were overexpressed in spermatozoa from high-fertile boars. This up-regulation seems concerted to reduce DNA accessibility to ROS attack, protecting the DNA. The upregulated intracellular phospholipid hydroperoxide glutathione peroxidase (GPx4), in high-fertile boars at mRNA level, can be considered a most relevant biomarker for fertility disclosure during sperm evaluation.
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Affiliation(s)
- Manuel Alvarez-Rodriguez
- Department of Biomedical & Clinical Sciences (BKV), BKH/Obstetrics & Gynecology, Faculty of Medicine and Health Sciences, Linköping University, SE-58185 Linköping, Sweden; Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, 08193, Bellaterra, (Cerdanyola del Vallès), Barcelona, Spain.
| | - Cristina A Martinez
- Department of Biomedical & Clinical Sciences (BKV), BKH/Obstetrics & Gynecology, Faculty of Medicine and Health Sciences, Linköping University, SE-58185 Linköping, Sweden
| | - Jordi Roca
- Department of Medicine and Animal Surgery, Faculty of Veterinary Medicine, International Campus for Higher Education and Research "Campus Mare Nostrum", University of Murcia, 30100 Murcia, Spain
| | - Heriberto Rodriguez-Martinez
- Department of Biomedical & Clinical Sciences (BKV), BKH/Obstetrics & Gynecology, Faculty of Medicine and Health Sciences, Linköping University, SE-58185 Linköping, Sweden
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8
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Accessory Subunits of the Matrix Arm of Mitochondrial Complex I with a Focus on Subunit NDUFS4 and Its Role in Complex I Function and Assembly. Life (Basel) 2021; 11:life11050455. [PMID: 34069703 PMCID: PMC8161149 DOI: 10.3390/life11050455] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 12/19/2022] Open
Abstract
NADH:ubiquinone-oxidoreductase (complex I) is the largest membrane protein complex of the respiratory chain. Complex I couples electron transfer to vectorial proton translocation across the inner mitochondrial membrane. The L shaped structure of complex I is divided into a membrane arm and a matrix arm. Fourteen central subunits are conserved throughout species, while some 30 accessory subunits are typically found in eukaryotes. Complex I dysfunction is associated with mutations in the nuclear and mitochondrial genome, resulting in a broad spectrum of neuromuscular and neurodegenerative diseases. Accessory subunit NDUFS4 in the matrix arm is a hot spot for mutations causing Leigh or Leigh-like syndrome. In this review, we focus on accessory subunits of the matrix arm and discuss recent reports on the function of accessory subunit NDUFS4 and its interplay with NDUFS6, NDUFA12, and assembly factor NDUFAF2 in complex I assembly.
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9
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The road to the structure of the mitochondrial respiratory chain supercomplex. Biochem Soc Trans 2021; 48:621-629. [PMID: 32311046 PMCID: PMC7200630 DOI: 10.1042/bst20190930] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 03/30/2020] [Accepted: 03/31/2020] [Indexed: 01/04/2023]
Abstract
The four complexes of the mitochondrial respiratory chain are critical for ATP production in most eukaryotic cells. Structural characterisation of these complexes has been critical for understanding the mechanisms underpinning their function. The three proton-pumping complexes, Complexes I, III and IV associate to form stable supercomplexes or respirasomes, the most abundant form containing 80 subunits in mammals. Multiple functions have been proposed for the supercomplexes, including enhancing the diffusion of electron carriers, providing stability for the complexes and protection against reactive oxygen species. Although high-resolution structures for Complexes III and IV were determined by X-ray crystallography in the 1990s, the size of Complex I and the supercomplexes necessitated advances in sample preparation and the development of cryo-electron microscopy techniques. We now enjoy structures for these beautiful complexes isolated from multiple organisms and in multiple states and together they provide important insights into respiratory chain function and the role of the supercomplex. While we as non-structural biologists use these structures for interpreting our own functional data, we need to remind ourselves that they stand on the shoulders of a large body of previous structural studies, many of which are still appropriate for use in understanding our results. In this mini-review, we discuss the history of respiratory chain structural biology studies leading to the structures of the mammalian supercomplexes and beyond.
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10
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Medini H, Cohen T, Mishmar D. Mitochondria Are Fundamental for the Emergence of Metazoans: On Metabolism, Genomic Regulation, and the Birth of Complex Organisms. Annu Rev Genet 2020; 54:151-166. [PMID: 32857636 DOI: 10.1146/annurev-genet-021920-105545] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Out of many intracellular bacteria, only the mitochondria and chloroplasts abandoned their independence billions of years ago and became endosymbionts within the host eukaryotic cell. Consequently, one cannot grow eukaryotic cells without their mitochondria, and the mitochondria cannot divide outside of the cell, thus reflecting interdependence. Here, we argue that such interdependence underlies the fundamental role of mitochondrial activities in the emergence of metazoans. Several lines of evidence support our hypothesis: (a) Differentiation and embryogenesis rely on mitochondrial function; (b) mitochondrial metabolites are primary precursors for epigenetic modifications (such as methyl and acetyl), which are critical for chromatin remodeling and gene expression, particularly during differentiation and embryogenesis; and (c) mitonuclear coregulation adapted to accommodate both housekeeping and tissue-dependent metabolic needs. We discuss the evolution of the unique mitochondrial genetic system, mitochondrial metabolites, mitonuclear coregulation, and their critical roles in the emergence of metazoans and in human disorders.
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Affiliation(s)
- Hadar Medini
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501 Israel;
| | - Tal Cohen
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501 Israel;
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501 Israel;
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11
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Adjobo-Hermans MJW, de Haas R, Willems PHGM, Wojtala A, van Emst-de Vries SE, Wagenaars JA, van den Brand M, Rodenburg RJ, Smeitink JAM, Nijtmans LG, Sazanov LA, Wieckowski MR, Koopman WJH. NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4 -/- mice and Leigh syndrome patients: A stabilizing role for NDUFAF2. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148213. [PMID: 32335026 DOI: 10.1016/j.bbabio.2020.148213] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 01/07/2023]
Abstract
Mutations in NDUFS4, which encodes an accessory subunit of mitochondrial oxidative phosphorylation (OXPHOS) complex I (CI), induce Leigh syndrome (LS). LS is a poorly understood pediatric disorder featuring brain-specific anomalies and early death. To study the LS pathomechanism, we here compared OXPHOS proteomes between various Ndufs4-/- mouse tissues. Ndufs4-/- animals displayed significantly lower CI subunit levels in brain/diaphragm relative to other tissues (liver/heart/kidney/skeletal muscle), whereas other OXPHOS subunit levels were not reduced. Absence of NDUFS4 induced near complete absence of the NDUFA12 accessory subunit, a 50% reduction in other CI subunit levels, and an increase in specific CI assembly factors. Among the latter, NDUFAF2 was most highly increased. Regarding NDUFS4, NDUFA12 and NDUFAF2, identical results were obtained in Ndufs4-/- mouse embryonic fibroblasts (MEFs) and NDUFS4-mutated LS patient cells. Ndufs4-/- MEFs contained active CI in situ but blue-native-PAGE highlighted that NDUFAF2 attached to an inactive CI subcomplex (CI-830) and inactive assemblies of higher MW. In NDUFA12-mutated LS patient cells, NDUFA12 absence did not reduce NDUFS4 levels but triggered NDUFAF2 association to active CI. BN-PAGE revealed no such association in LS patient fibroblasts with mutations in other CI subunit-encoding genes where NDUFAF2 was attached to CI-830 (NDUFS1, NDUFV1 mutation) or not detected (NDUFS7 mutation). Supported by enzymological and CI in silico structural analysis, we conclude that absence of NDUFS4 induces near complete absence of NDUFA12 but not vice versa, and that NDUFAF2 stabilizes active CI in Ndufs4-/- mice and LS patient cells, perhaps in concert with mitochondrial inner membrane lipids.
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Affiliation(s)
- Merel J W Adjobo-Hermans
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud Center for Mitochondrial Medicine, Radboudumc, Nijmegen, the Netherlands
| | - Ria de Haas
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboudumc, Nijmegen, the Netherlands
| | - Peter H G M Willems
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud Center for Mitochondrial Medicine, Radboudumc, Nijmegen, the Netherlands
| | | | - Sjenet E van Emst-de Vries
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud Center for Mitochondrial Medicine, Radboudumc, Nijmegen, the Netherlands
| | - Jori A Wagenaars
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud Center for Mitochondrial Medicine, Radboudumc, Nijmegen, the Netherlands
| | - Mariel van den Brand
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboudumc, Nijmegen, the Netherlands
| | - Richard J Rodenburg
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboudumc, Nijmegen, the Netherlands
| | - Jan A M Smeitink
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboudumc, Nijmegen, the Netherlands
| | - Leo G Nijtmans
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboudumc, Nijmegen, the Netherlands
| | | | | | - Werner J H Koopman
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud Center for Mitochondrial Medicine, Radboudumc, Nijmegen, the Netherlands.
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12
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Formosa LE, Muellner-Wong L, Reljic B, Sharpe AJ, Jackson TD, Beilharz TH, Stojanovski D, Lazarou M, Stroud DA, Ryan MT. Dissecting the Roles of Mitochondrial Complex I Intermediate Assembly Complex Factors in the Biogenesis of Complex I. Cell Rep 2020; 31:107541. [DOI: 10.1016/j.celrep.2020.107541] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/17/2020] [Accepted: 03/27/2020] [Indexed: 10/24/2022] Open
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13
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Rhooms SK, Murari A, Goparaju NSV, Vilanueva M, Owusu-Ansah E. Insights from Drosophila on mitochondrial complex I. Cell Mol Life Sci 2020; 77:607-618. [PMID: 31485716 PMCID: PMC7289077 DOI: 10.1007/s00018-019-03293-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 08/08/2019] [Accepted: 08/28/2019] [Indexed: 12/26/2022]
Abstract
NADH:ubiquinone oxidoreductase, more commonly referred to as mitochondrial complex I (CI), is the largest discrete enzyme of the oxidative phosphorylation system (OXPHOS). It is localized to the mitochondrial inner membrane. CI oxidizes NADH generated from the tricarboxylic acid cycle to NAD+, in a series of redox reactions that culminates in the reduction of ubiquinone, and the transport of protons from the matrix across the inner membrane to the intermembrane space. The resulting proton-motive force is consumed by ATP synthase to generate ATP, or harnessed to transport ions, metabolites and proteins into the mitochondrion. CI is also a major source of reactive oxygen species. Accordingly, impaired CI function has been associated with a host of chronic metabolic and degenerative disorders such as diabetes, cardiomyopathy, Parkinson's disease (PD) and Leigh syndrome. Studies on Drosophila have contributed to our understanding of the multiple roles of CI in bioenergetics and organismal physiology. Here, we explore and discuss some of the studies on Drosophila that have informed our understanding of this complex and conclude with some of the open questions about CI that can be resolved by studies on Drosophila.
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Affiliation(s)
- Shauna-Kay Rhooms
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY, 10032, USA
| | - Anjaneyulu Murari
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY, 10032, USA
| | - Naga Sri Vidya Goparaju
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY, 10032, USA
| | - Maximino Vilanueva
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY, 10032, USA
| | - Edward Owusu-Ansah
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY, 10032, USA.
- The Robert N. Butler Columbia Aging Center, Columbia University Medical Center, New York, NY, 10032, USA.
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14
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Dibley MG, Formosa LE, Lyu B, Reljic B, McGann D, Muellner-Wong L, Kraus F, Sharpe AJ, Stroud DA, Ryan MT. The Mitochondrial Acyl-carrier Protein Interaction Network Highlights Important Roles for LYRM Family Members in Complex I and Mitoribosome Assembly. Mol Cell Proteomics 2020; 19:65-77. [PMID: 31666358 PMCID: PMC6944232 DOI: 10.1074/mcp.ra119.001784] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Indexed: 01/25/2023] Open
Abstract
NDUFAB1 is the mitochondrial acyl carrier protein (ACP) essential for cell viability. Through its pantetheine-4'-phosphate post-translational modification, NDUFAB1 interacts with members of the leucine-tyrosine-arginine motif (LYRM) protein family. Although several LYRM proteins have been described to participate in a variety of defined processes, the functions of others remain either partially or entirely unknown. We profiled the interaction network of NDUFAB1 to reveal associations with 9 known LYRM proteins as well as more than 20 other proteins involved in mitochondrial respiratory chain complex and mitochondrial ribosome assembly. Subsequent knockout and interaction network studies in human cells revealed the LYRM member AltMiD51 to be important for optimal assembly of the large mitoribosome subunit, consistent with recent structural studies. In addition, we used proteomics coupled with topographical heat-mapping to reveal that knockout of LYRM2 impairs assembly of the NADH-dehydrogenase module of complex I, leading to defects in cellular respiration. Together, this work adds to the catalogue of functions executed by LYRM family of proteins in building mitochondrial complexes and emphasizes the common and essential role of NDUFAB1 as a protagonist in mitochondrial metabolism.
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Affiliation(s)
- Marris G Dibley
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Luke E Formosa
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Baobei Lyu
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Boris Reljic
- Department of Biochemistry and Molecular Biology, The Bio21 Molecular Science & Biotechnology Institute, University of Melbourne, Melbourne, Australia
| | - Dylan McGann
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Linden Muellner-Wong
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Felix Kraus
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Alice J Sharpe
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - David A Stroud
- Department of Biochemistry and Molecular Biology, The Bio21 Molecular Science & Biotechnology Institute, University of Melbourne, Melbourne, Australia
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia.
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15
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Lo S, MacMillan-Crow LA, Parajuli N. Renal cold storage followed by transplantation impairs proteasome function and mitochondrial protein homeostasis. Am J Physiol Renal Physiol 2018; 316:F42-F53. [PMID: 30303714 DOI: 10.1152/ajprenal.00316.2018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Identifying pathways related to renal cold storage (CS) that lead to renal damage after transplantation (Tx) will help us design novel pathway-specific therapies to improve graft outcome. Our recent report showed that mitochondrial function was compromised after CS alone, and this was exacerbated when CS was combined with Tx (CS/Tx). The goal of this study was to determine whether the proteasome exacerbates mitochondrial dysfunction after CS/Tx. We exposed the kidneys of male Lewis rats (in vivo) and rat renal proximal tubular (NRK) cells (in vitro) to CS/Tx or rewarming (CS/RW), respectively. To compare CS-induced effects, in vivo kidney Tx without CS exposure (autotransplantation; ATx) was also used. Our study provides the first evidence that the chymotrypsin-like (ChT-L) peptidase activity of the proteasome declined only after CS/Tx or CS/RW, but not after CS or ATx. Interestingly, key mitochondrial proteins involved with respiration [succinate dehydrogenase complex, subunit A (SDHA), a complex II subunit, and ATP5B, an ATP synthase/complex V subunit] were detected in the detergent-insoluble fraction after CS/Tx or CS/RW, with compromised complex V activity. Pharmacological inhibition of ChT-L activity in NRK cells decreased the activity of mitochondrial complexes I, II, and V and also increased the levels of SDHA and ATP5B in the insoluble fraction. On the other hand, inhibiting mitochondrial respiration in NRK cells with antimycin A compromised ChT-L function and increased the amounts of SDHA and ATP5B in the insoluble fraction. Our results suggest that mitochondrial respiratory dysfunction during CS precedes compromised ChT-L function after CS/Tx and proteasome dysfunction further alters mitochondrial protein homeostasis and decreases respiration in the kidneys after CS/Tx. Therefore, therapeutics that preserve mitochondrial and proteasome function during CS may provide beneficial outcomes following transplantation.
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Affiliation(s)
- Sorena Lo
- Department of Pharmacology and Toxicology, University of Arkansas for Medical Sciences , Little Rock, Arkansas
| | - Lee Ann MacMillan-Crow
- Department of Pharmacology and Toxicology, University of Arkansas for Medical Sciences , Little Rock, Arkansas
| | - Nirmala Parajuli
- Department of Pharmacology and Toxicology, University of Arkansas for Medical Sciences , Little Rock, Arkansas.,Arkansas Children's Research Institute, Little Rock, Arkansas
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16
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Barshad G, Blumberg A, Cohen T, Mishmar D. Human primitive brain displays negative mitochondrial-nuclear expression correlation of respiratory genes. Genome Res 2018; 28:952-967. [PMID: 29903725 PMCID: PMC6028125 DOI: 10.1101/gr.226324.117] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 05/31/2018] [Indexed: 01/04/2023]
Abstract
Oxidative phosphorylation (OXPHOS), a fundamental energy source in all human tissues, requires interactions between mitochondrial (mtDNA)- and nuclear (nDNA)-encoded protein subunits. Although such interactions are fundamental to OXPHOS, bi-genomic coregulation is poorly understood. To address this question, we analyzed ∼8500 RNA-seq experiments from 48 human body sites. Despite well-known variation in mitochondrial activity, quantity, and morphology, we found overall positive mtDNA-nDNA OXPHOS genes' co-expression across human tissues. Nevertheless, negative mtDNA-nDNA gene expression correlation was identified in the hypothalamus, basal ganglia, and amygdala (subcortical brain regions, collectively termed the "primitive" brain). Single-cell RNA-seq analysis of mouse and human brains revealed that this phenomenon is evolutionarily conserved, and both are influenced by brain cell types (involving excitatory/inhibitory neurons and nonneuronal cells) and by their spatial brain location. As the "primitive" brain is highly oxidative, we hypothesized that such negative mtDNA-nDNA co-expression likely controls for the high mtDNA transcript levels, which enforce tight OXPHOS regulation, rather than rewiring toward glycolysis. Accordingly, we found "primitive" brain-specific up-regulation of lactate dehydrogenase B (LDHB), which associates with high OXPHOS activity, at the expense of LDHA, which promotes glycolysis. Analyses of co-expression, DNase-seq, and ChIP-seq experiments revealed candidate RNA-binding proteins and CEBPB as the best regulatory candidates to explain these phenomena. Finally, cross-tissue expression analysis unearthed tissue-dependent splice variants and OXPHOS subunit paralogs and allowed revising the list of canonical OXPHOS transcripts. Taken together, our analysis provides a comprehensive view of mito-nuclear gene co-expression across human tissues and provides overall insights into the bi-genomic regulation of mitochondrial activities.
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Affiliation(s)
- Gilad Barshad
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Amit Blumberg
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Tal Cohen
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
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17
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Gladyshev GV, Grivennikova VG, Vinogradov AD. FMN site-independent energy-linked reverse electron transfer in mitochondrial respiratory complex I. FEBS Lett 2018; 592:2213-2219. [PMID: 29851085 DOI: 10.1002/1873-3468.13117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 11/06/2022]
Abstract
A simple assay procedure for measuring ATP-dependent reverse electron transfer from ubiquinol to hexaammineruthenium (III) (HAR) catalyzed by mitochondrial respiratory complex I is introduced. The specific activity of the enzyme in this reaction and its sensitivity to the standard inhibitors and uncoupling are the same as with other well-known electron acceptors, NAD+ and ferricyanide. In contrast to the reactions with these acceptors, the energy-dependent HAR reduction is not inhibited by NADH-OH, the specific inhibitor of NADH-binding site. These results suggest that a catalytically competent electron connection exists between HAR and a redox component of complex I that is different from flavin mononucleotide bound at the substrate-binding site.
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Affiliation(s)
- Grigory V Gladyshev
- Department of Biochemistry, School of Biology, Moscow State University, Russia
| | - Vera G Grivennikova
- Department of Biochemistry, School of Biology, Moscow State University, Russia
| | - Andrei D Vinogradov
- Department of Biochemistry, School of Biology, Moscow State University, Russia
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18
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Formosa LE, Dibley MG, Stroud DA, Ryan MT. Building a complex complex: Assembly of mitochondrial respiratory chain complex I. Semin Cell Dev Biol 2018; 76:154-162. [DOI: 10.1016/j.semcdb.2017.08.011] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 07/26/2017] [Accepted: 08/04/2017] [Indexed: 10/19/2022]
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