1
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Moretti-Horten DN, Peselj C, Taskin AA, Myketin L, Schulte U, Einsle O, Drepper F, Luzarowski M, Vögtle FN. Synchronized assembly of the oxidative phosphorylation system controls mitochondrial respiration in yeast. Dev Cell 2024; 59:1043-1057.e8. [PMID: 38508182 DOI: 10.1016/j.devcel.2024.02.011] [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: 11/22/2023] [Revised: 01/19/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
Control of protein stoichiometry is essential for cell function. Mitochondrial oxidative phosphorylation (OXPHOS) presents a complex stoichiometric challenge as the ratio of the electron transport chain (ETC) and ATP synthase must be tightly controlled, and assembly requires coordinated integration of proteins encoded in the nuclear and mitochondrial genome. How correct OXPHOS stoichiometry is achieved is unknown. We identify the Mitochondrial Regulatory hub for respiratory Assembly (MiRA) platform, which synchronizes ETC and ATP synthase biogenesis in yeast. Molecularly, this is achieved by a stop-and-go mechanism: the uncharacterized protein Mra1 stalls complex IV assembly. Two "Go" signals are required for assembly progression: binding of the complex IV assembly factor Rcf2 and Mra1 interaction with an Atp9-translating mitoribosome induce Mra1 degradation, allowing synchronized maturation of complex IV and the ATP synthase. Failure of the stop-and-go mechanism results in cell death. MiRA controls OXPHOS assembly, ensuring correct stoichiometry of protein machineries encoded by two different genomes.
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Affiliation(s)
- Daiana N Moretti-Horten
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Carlotta Peselj
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Asli Aras Taskin
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Lisa Myketin
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Uwe Schulte
- Institute of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Oliver Einsle
- Institut für Biochemie, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Friedel Drepper
- CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; Biochemistry & Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Marcin Luzarowski
- Core Facility for Mass Spectrometry and Proteomics, Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - F-Nora Vögtle
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; Network Aging Research, Heidelberg University, 69120 Heidelberg, Germany.
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2
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Eldeeb MH, Camacho Lopez LJ, Fontanesi F. Mitochondrial respiratory supercomplexes of the yeast Saccharomyces cerevisiae. IUBMB Life 2024. [PMID: 38529880 DOI: 10.1002/iub.2817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/28/2024] [Indexed: 03/27/2024]
Abstract
The functional and structural relationship among the individual components of the mitochondrial respiratory chain constitutes a central aspect of our understanding of aerobic catabolism. This interplay has been a subject of intense debate for over 50 years. It is well established that individual respiratory enzymes associate into higher-order structures known as respiratory supercomplexes, which represent the evolutionarily conserved organizing principle of the mitochondrial respiratory chain. In the yeast Saccharomyces cerevisiae, supercomplexes are formed by a complex III homodimer flanked by one or two complex IV monomers, and their high-resolution structures have been recently elucidated. Despite the wealth of structural information, several proposed supercomplex functions remain speculative and our understanding of their physiological relevance is still limited. Recent advances in the field were made possible by the construction of yeast strains where the association of complex III and IV into supercomplexes is impeded, leading to diminished respiratory capacity and compromised cellular competitive fitness. Here, we discuss the experimental evidence and hypotheses relative to the functional roles of yeast respiratory supercomplexes. Moreover, we review the current models of yeast complex III and IV assembly in the context of supercomplex formation and highlight the data scattered throughout the literature suggesting the existence of cross talk between their biogenetic processes.
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Affiliation(s)
- Mazzen H Eldeeb
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Lizeth J Camacho Lopez
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Flavia Fontanesi
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, Florida, USA
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3
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Horten P, Song K, Garlich J, Hardt R, Colina-Tenorio L, Horvath SE, Schulte U, Fakler B, van der Laan M, Becker T, Stuart RA, Pfanner N, Rampelt H. Identification of MIMAS, a multifunctional mega-assembly integrating metabolic and respiratory biogenesis factors of mitochondria. Cell Rep 2024; 43:113772. [PMID: 38393949 PMCID: PMC11010658 DOI: 10.1016/j.celrep.2024.113772] [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: 11/07/2023] [Revised: 01/03/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The mitochondrial inner membrane plays central roles in bioenergetics and metabolism and contains several established membrane protein complexes. Here, we report the identification of a mega-complex of the inner membrane, termed mitochondrial multifunctional assembly (MIMAS). Its large size of 3 MDa explains why MIMAS has escaped detection in the analysis of mitochondria so far. MIMAS combines proteins of diverse functions from respiratory chain assembly to metabolite transport, dehydrogenases, and lipid biosynthesis but not the large established supercomplexes of the respiratory chain, ATP synthase, or prohibitin scaffold. MIMAS integrity depends on the non-bilayer phospholipid phosphatidylethanolamine, in contrast to respiratory supercomplexes whose stability depends on cardiolipin. Our findings suggest that MIMAS forms a protein-lipid mega-assembly in the mitochondrial inner membrane that integrates respiratory biogenesis and metabolic processes in a multifunctional platform.
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Affiliation(s)
- Patrick Horten
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Kuo Song
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Joshua Garlich
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Robert Hardt
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany
| | - Lilia Colina-Tenorio
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Susanne E Horvath
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Uwe Schulte
- Institute of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Bernd Fakler
- Institute of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Martin van der Laan
- Medical Biochemistry and Molecular Biology, Center for Molecular Signaling, PZMS, Faculty of Medicine, Saarland University, 66421 Homburg, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany
| | - Rosemary A Stuart
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
| | - Heike Rampelt
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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4
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Parmar G, Fong-McMaster C, Pileggi CA, Patten DA, Cuillerier A, Myers S, Wang Y, Hekimi S, Cuperlovic-Culf M, Harper ME. Accessory subunit NDUFB4 participates in mitochondrial complex I supercomplex formation. J Biol Chem 2024; 300:105626. [PMID: 38211818 PMCID: PMC10862015 DOI: 10.1016/j.jbc.2024.105626] [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: 09/21/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 01/13/2024] Open
Abstract
Mitochondrial electron transport chain complexes organize into supramolecular structures called respiratory supercomplexes (SCs). The role of respiratory SCs remains largely unconfirmed despite evidence supporting their necessity for mitochondrial respiratory function. The mechanisms underlying the formation of the I1III2IV1 "respirasome" SC are also not fully understood, further limiting insights into these processes in physiology and diseases, including neurodegeneration and metabolic syndromes. NDUFB4 is a complex I accessory subunit that contains residues that interact with the subunit UQCRC1 from complex III, suggesting that NDUFB4 is integral for I1III2IV1 respirasome integrity. Here, we introduced specific point mutations to Asn24 (N24) and Arg30 (R30) residues on NDUFB4 to decipher the role of I1III2-containing respiratory SCs in cellular metabolism while minimizing the functional consequences to complex I assembly. Our results demonstrate that NDUFB4 point mutations N24A and R30A impair I1III2IV1 respirasome assembly and reduce mitochondrial respiratory flux. Steady-state metabolomics also revealed a global decrease in citric acid cycle metabolites, affecting NADH-generating substrates. Taken together, our findings highlight an integral role of NDUFB4 in respirasome assembly and demonstrate the functional significance of SCs in regulating mammalian cell bioenergetics.
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Affiliation(s)
- Gaganvir Parmar
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ontario, Canada
| | - Claire Fong-McMaster
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ontario, Canada
| | - Chantal A Pileggi
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ontario, Canada
| | - David A Patten
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ontario, Canada
| | - Alexanne Cuillerier
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Stephanie Myers
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ontario, Canada
| | - Ying Wang
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Siegfried Hekimi
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Miroslava Cuperlovic-Culf
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ontario, Canada; National Research Council of Canada, Digital Technologies Research Centre, Ottawa, Ontario, Canada
| | - Mary-Ellen Harper
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ontario, Canada.
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5
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Lenaz G, Nesci S, Genova ML. Understanding differential aspects of microdiffusion (channeling) in the Coenzyme Q and Cytochrome c regions of the mitochondrial respiratory system. Mitochondrion 2024; 74:101822. [PMID: 38040170 DOI: 10.1016/j.mito.2023.11.005] [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: 08/04/2023] [Revised: 11/18/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
Over the past decades, models of the organization of mitochondrial respiratory system have been controversial. The goal of this perspective is to assess this "conflict of models" by focusing on specific kinetic evidence in the two distinct segments of Coenzyme Q- and Cytochrome c-mediated electron transfer. Respiratory supercomplexes provide kinetic advantage by allowing a restricted diffusion of Coenzyme Q and Cytochrome c, and short-range interaction with their partner enzymes. In particular, electron transfer from NADH is compartmentalized by channeling of Coenzyme Q within supercomplexes, whereas succinate oxidation proceeds separately using the free Coenzyme Q pool. Previous evidence favoring Coenzyme Q random diffusion in the NADH-dependent electron transfer is due to downstream flux interference and misinterpretation of results. Indeed, electron transfer by complexes III and IV via Cytochrome c is less strictly dependent on substrate channeling in mammalian mitochondria. We briefly describe these differences and their physiological implications.
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Affiliation(s)
- Giorgio Lenaz
- University of Bologna, Via Zamboni 33, 40126 Bologna, Italy.
| | - Salvatore Nesci
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia, BO, Italy.
| | - Maria Luisa Genova
- Department of Biomedical and Neuromotor Sciences, O.U. Biochemistry, University of Bologna, Via Irnerio 48, 40126 Bologna, BO, Italy.
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6
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Moe A, Dimogkioka AR, Rapaport D, Öjemyr LN, Brzezinski P. Structure and function of the S. pombe III-IV-cyt c supercomplex. Proc Natl Acad Sci U S A 2023; 120:e2307697120. [PMID: 37939086 PMCID: PMC10655221 DOI: 10.1073/pnas.2307697120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/14/2023] [Indexed: 11/10/2023] Open
Abstract
The respiratory chain in aerobic organisms is composed of a number of membrane-bound protein complexes that link electron transfer to proton translocation across the membrane. In mitochondria, the final electron acceptor, complex IV (CIV), receives electrons from dimeric complex III (CIII2), via a mobile electron carrier, cytochrome c. In the present study, we isolated the CIII2CIV supercomplex from the fission yeast Schizosaccharomyces pombe and determined its structure with bound cyt. c using single-particle electron cryomicroscopy. A respiratory supercomplex factor 2 was found to be bound at CIV distally positioned in the supercomplex. In addition to the redox-active metal sites, we found a metal ion, presumably Zn2+, coordinated in the CIII subunit Cor1, which is encoded by the same gene (qcr1) as the mitochondrial-processing peptidase subunit β. Our data show that the isolated CIII2CIV supercomplex displays proteolytic activity suggesting a dual role of CIII2 in S. pombe. As in the supercomplex from S. cerevisiae, subunit Cox5 of CIV faces towards one CIII monomer, but in S. pombe, the two complexes are rotated relative to each other by ~45°. This orientation yields equal distances between the cyt. c binding sites at CIV and at each of the two CIII monomers. The structure shows cyt. c bound at four positions, but only along one of the two symmetrical branches. Overall, this combined structural and functional study reveals the integration of peptidase activity with the CIII2 respiratory system and indicates a two-dimensional cyt. c diffusion mechanism within the CIII2-CIV supercomplex.
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Affiliation(s)
- Agnes Moe
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, StockholmSE-106 91, Sweden
| | - Anna-Roza Dimogkioka
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen72076, Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen72076, Germany
| | - Linda Näsvik Öjemyr
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, StockholmSE-106 91, Sweden
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, StockholmSE-106 91, Sweden
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7
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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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8
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González-Arzola K, Díaz-Quintana A. Mitochondrial Factors in the Cell Nucleus. Int J Mol Sci 2023; 24:13656. [PMID: 37686461 PMCID: PMC10563088 DOI: 10.3390/ijms241713656] [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: 07/18/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
The origin of eukaryotic organisms involved the integration of mitochondria into the ancestor cell, with a massive gene transfer from the original proteobacterium to the host nucleus. Thus, mitochondrial performance relies on a mosaic of nuclear gene products from a variety of genomes. The concerted regulation of their synthesis is necessary for metabolic housekeeping and stress response. This governance involves crosstalk between mitochondrial, cytoplasmic, and nuclear factors. While anterograde and retrograde regulation preserve mitochondrial homeostasis, the mitochondria can modulate a wide set of nuclear genes in response to an extensive variety of conditions, whose response mechanisms often merge. In this review, we summarise how mitochondrial metabolites and proteins-encoded either in the nucleus or in the organelle-target the cell nucleus and exert different actions modulating gene expression and the chromatin state, or even causing DNA fragmentation in response to common stress conditions, such as hypoxia, oxidative stress, unfolded protein stress, and DNA damage.
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Affiliation(s)
- Katiuska González-Arzola
- Centro Andaluz de Biología Molecular y Medicina Regenerativa—CABIMER, Consejo Superior de Investigaciones Científicas—Universidad de Sevilla—Universidad Pablo de Olavide, 41092 Seville, Spain
- Departamento de Bioquímica Vegetal y Biología Molecular, Universidad de Sevilla, 41012 Seville, Spain
| | - Antonio Díaz-Quintana
- Departamento de Bioquímica Vegetal y Biología Molecular, Universidad de Sevilla, 41012 Seville, Spain
- Instituto de Investigaciones Químicas—cicCartuja, Universidad de Sevilla—C.S.I.C, 41092 Seville, Spain
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9
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Zhai X, Bai J, Xu W, Yang X, Jia Z, Xia W, Wu X, Liang Q, Li B, Jia N. The molecular chaperone mtHSC70-1 interacts with DjA30 to regulate female gametophyte development and fertility in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1677-1698. [PMID: 37294615 DOI: 10.1111/tpj.16347] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/26/2023] [Indexed: 06/10/2023]
Abstract
Arabidopsis mitochondria-targeted heat shock protein 70 (mtHSC70-1) plays important roles in the establishment of cytochrome c oxidase-dependent respiration and redox homeostasis during the vegetative growth of plants. Here, we report that knocking out the mtHSC70-1 gene led to a decrease in plant fertility; the fertility defect of the mutant was completely rescued by introducing the mtHSC70-1 gene. mtHSC70-1 mutants also showed defects in female gametophyte (FG) development, including delayed mitosis, abnormal nuclear position, and ectopic gene expression in the embryo sacs. In addition, we found that an Arabidopsis mitochondrial J-protein gene (DjA30) mutant, j30+/- , had defects in FG development and fertility similar to those of mtHSC70-1 mutant. mtHSC70-1 and DjA30 had similar expression patterns in FGs and interacted in vivo, suggesting that these two proteins might cooperate during female gametogenesis. Further, respiratory chain complex IV activity in mtHSC70-1 and DjA30 mutant embryo sacs was markedly downregulated; this led to the accumulation of mitochondrial reactive oxygen species (ROS). Scavenging excess ROS by introducing Mn-superoxide dismutase 1 or catalase 1 gene into the mtHSC70-1 mutant rescued FG development and fertility. Altogether, our results suggest that mtHSC70-1 and DjA30 are essential for the maintenance of ROS homeostasis in the embryo sacs and provide direct evidence for the roles of ROS homeostasis in embryo sac maturation and nuclear patterning, which might determine the fate of gametic and accessory cells.
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Affiliation(s)
- Xiaoting Zhai
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Normal University, Shijiazhuang, 050024, China
- College of Agriculture and Forestry, Hebei North University, Zhangjiakou, 075000, China
| | - Jiaoteng Bai
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Normal University, Shijiazhuang, 050024, China
| | - Wenyan Xu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Normal University, Shijiazhuang, 050024, China
| | - Xiujuan Yang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Normal University, Shijiazhuang, 050024, China
| | - Zichao Jia
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Normal University, Shijiazhuang, 050024, China
| | - Wenxuan Xia
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Normal University, Shijiazhuang, 050024, China
| | - Xiaoqing Wu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Normal University, Shijiazhuang, 050024, China
| | - Qi Liang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Normal University, Shijiazhuang, 050024, China
| | - Bing Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Normal University, Shijiazhuang, 050024, China
| | - Ning Jia
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
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10
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Kaha M, Noda M, Maeda Y, Kaneko Y, Yoshino T, Tanaka T. Characterization of oil body-associated proteins obtained from oil bodies with different sizes in oleaginous diatom Fistulifera solaris. J Biosci Bioeng 2023; 135:359-368. [PMID: 36935336 DOI: 10.1016/j.jbiosc.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/08/2023] [Accepted: 01/13/2023] [Indexed: 03/19/2023]
Abstract
Oil body-associated proteins from the oleaginous diatom Fistulifera solaris were identified by proteomic analysis of oil bodies of various sizes (small, middle, and large) by time-dependent culturing upon nutrient-starvation at 36, 96 and 168 h. This diatom strain has the capability to accumulate neutral lipids and triacylglycerol. Liquid chromatography-tandem mass spectrometry analysis revealed 662 proteins in all oil body sizes. Among these, 132 proteins were predicted to be localized to the endoplasmic reticulum. Seventeen proteins that exhibited a positive correlation with gene expression and the oil body size were selected as novel candidates for oil body-associated proteins. Among the 17 protein candidates, two proteins encoded by fso:g8246 and fso:g10200 were confirmed to be localized on the surface of the oil body and endoplasmic reticulum. A protein encoded by fso:g2514, which is involved in sterol biosynthesis, was also identified. This protein was likely to localize to mitochondria; however, inhibitor assays suggested that it might play a role in lipid degradation. Our work provides new insights into the proteomics of microalgae and provides a valuable strategy for boosting lipid productivity in microalgae.
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Affiliation(s)
- Marshila Kaha
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Masayoshi Noda
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Yoshiaki Maeda
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan; Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan
| | - Yumika Kaneko
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Tomoko Yoshino
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Tsuyoshi Tanaka
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
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11
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Jia YZ, Liu J, Wang GQ, Pan H, Huang TZ, Liu R, Zhang Y. HIG1 domain family member 1A is a crucial regulator of disorders associated with hypoxia. Mitochondrion 2023; 69:171-182. [PMID: 36804467 DOI: 10.1016/j.mito.2023.02.009] [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: 06/08/2022] [Revised: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023]
Abstract
Mitochondria play a central role in cellular energy conversion, metabolism, and cell proliferation. The regulation of mitochondrial function by HIGD1A, which is located on the inner membrane of the mitochondria, is essential to maintain cell survival under hypoxic conditions. In recent years, there have been shown other cellular pathways and mechanisms involving HIGD1A diametrically or through its interaction. As a novel regulator, HIGD1A maintains mitochondrial integrity and enhances cell viability under hypoxic conditions, increasing cell resistance to hypoxia. HIGD1A mainly targets cytochrome c oxidase by regulating downstream signaling pathways, which affects the ATP generation system and subsequently alters mitochondrial respiratory function. In addition, HIGD1A plays a dual role in cell survival in distinct degree hypoxia regions of the tumor. Under mild and moderate anoxic areas, HIGD1A acts as a positive regulator to promote cell growth. However, HIGD1A plays a role in inhibiting cell growth but retaining cellular activity under severe anoxic areas. We speculate that HIGD1A engages in tumor recurrence and drug resistance mechanisms. This review will focus on data concerning how HIGD1A regulates cell viability under hypoxic conditions. Therefore, HIGD1A could be a potential therapeutic target for hypoxia-related diseases.
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Affiliation(s)
- Yin-Zhao Jia
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Jing Liu
- Key Laboratory of Coal Science and Technology of Ministry of Education, Taiyuan University of Technology, Taiyuan 030024, Shanxi, China
| | - Geng-Qiao Wang
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Hao Pan
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Tie-Zeng Huang
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Ran Liu
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Yong Zhang
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
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12
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Cryo-EM structure and function of S. pombe complex IV with bound respiratory supercomplex factor. Commun Chem 2023; 6:32. [PMID: 36797353 PMCID: PMC9935853 DOI: 10.1038/s42004-023-00827-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/31/2023] [Indexed: 02/18/2023] Open
Abstract
Fission yeast Schizosaccharomyces pombe serves as model organism for studying higher eukaryotes. We combined the use of cryo-EM and spectroscopy to investigate the structure and function of affinity purified respiratory complex IV (CIV) from S. pombe. The reaction sequence of the reduced enzyme with O2 proceeds over a time scale of µs-ms, similar to that of the mammalian CIV. The cryo-EM structure of CIV revealed eleven subunits as well as a bound hypoxia-induced gene 1 (Hig1) domain of respiratory supercomplex factor 2 (Rcf2). These results suggest that binding of Rcf2 does not require the presence of a CIII-CIV supercomplex, i.e. Rcf2 is a component of CIV. An AlphaFold-Multimer model suggests that the Hig1 domains of both Rcf1 and Rcf2 bind at the same site of CIV suggesting that their binding is mutually exclusive. Furthermore, the differential functional effect of Rcf1 or Rcf2 is presumably caused by interactions of CIV with their different non-Hig1 domain parts.
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13
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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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14
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Mitochondrial Respiratory Chain Supercomplexes: From Structure to Function. Int J Mol Sci 2022; 23:ijms232213880. [PMID: 36430359 PMCID: PMC9696846 DOI: 10.3390/ijms232213880] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 11/12/2022] Open
Abstract
Mitochondrial oxidative phospho rylation, the center of cellular metabolism, is pivotal for the energy production in eukaryotes. Mitochondrial oxidative phosphorylation relies on the mitochondrial respiratory chain, which consists of four main enzyme complexes and two mobile electron carriers. Mitochondrial enzyme complexes also assemble into respiratory chain supercomplexes (SCs) through specific interactions. The SCs not only have respiratory functions but also improve the efficiency of electron transfer and reduce the production of reactive oxygen species (ROS). Impaired assembly of SCs is closely related to various diseases, especially neurodegenerative diseases. Therefore, SCs play important roles in improving the efficiency of the mitochondrial respiratory chain, as well as maintaining the homeostasis of cellular metabolism. Here, we review the structure, assembly, and functions of SCs, as well as the relationship between mitochondrial SCs and diseases.
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15
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Mitochondrial HSC70-1 Regulates Polar Auxin Transport through ROS Homeostasis in Arabidopsis Roots. Antioxidants (Basel) 2022; 11:antiox11102035. [PMID: 36290758 PMCID: PMC9598091 DOI: 10.3390/antiox11102035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/08/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
Arabidopsis mitochondrial-localized heat shock protein 70-1 (mtHSC70-1) modulates vegetative growth by assisting mitochondrial complex IV assembly and maintaining reactive oxygen species (ROS) homeostasis. In addition, mtHSC70-1 affects embryo development, and this effect is mediated by auxin. However, whether mtHSC70-1 regulates vegetative growth through auxin and knowledge of the link between ROS homeostasis and auxin distribution remain unclear. Here, we found that mtHSC70-1 knockout seedlings (mthsc70-1a) displayed shortened roots, decreased fresh root weight and lateral root number, increased root width and abnormal root morphology. The introduction of the mtHSC70-1 gene into mthsc70-1a restored the growth and development of roots to the level of the wild type. However, sugar and auxin supplementation could not help the mutant roots restore to normal. Moreover, mthsc70-1a seedlings showed a decrease in meristem length and activity, auxin transport carrier (PINs and AUX1) and auxin abundances in root tips. The application of exogenous reducing agents upregulated the levels of PINs in the mutant roots. The introduction of antioxidant enzyme genes (MSD1 or CAT1) into the mthsc70-1a mutant rescued the PIN and local auxin abundances and root growth and development. Taken together, our data suggest that mtHSC70-1 regulates polar auxin transport through ROS homeostasis in Arabidopsis roots.
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Abstract
Higd1a is a conserved gene in evolution which is widely expressed in many tissues in mammals. Accumulating evidence has revealed multiple functions of Higd1a, as a mitochondrial inner membrane protein, in the regulation of metabolic homeostasis. It plays an important role in anti-apoptosis and promotes cellular survival in several cell types under hypoxic condition. And the survival of porcine Sertoli cells facilitated by Higd1a helps to support reproduction. In some cases, Higd1a can serve as a sign of metabolic stress. Over the past several years, a considerable amount of studies about how tumor fate is determined and how cancerous proliferation is regulated by Higd1a have been performed. In this review, we summarize the physiological functions of Higd1a in metabolic homeostasis and its pathophysiological roles in distinct diseases including cancer, nonalcoholic fatty liver disease (NAFLD), type II diabetes and mitochondrial diseases. The prospect of Higd1a with potential to preserve mammal health is also discussed. This review might pave the way for Higd1a-based research and application in clinical practice.
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17
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Salazar C, Barros M, Elorza AA, Ruiz LM. Dynamic Distribution of HIG2A between the Mitochondria and the Nucleus in Response to Hypoxia and Oxidative Stress. Int J Mol Sci 2021; 23:ijms23010389. [PMID: 35008815 PMCID: PMC8745331 DOI: 10.3390/ijms23010389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/13/2021] [Accepted: 12/24/2021] [Indexed: 01/06/2023] Open
Abstract
Mitochondrial respiratory supercomplex formation requires HIG2A protein, which also has been associated with cell proliferation and cell survival under hypoxia. HIG2A protein localizes in mitochondria and nucleus. DNA methylation and mRNA expression of the HIGD2A gene show significant alterations in several cancers, suggesting a role for HIG2A in cancer biology. The present work aims to understand the dynamics of the HIG2A subcellular localization under cellular stress. We found that HIG2A protein levels increase under oxidative stress. H2O2 shifts HIG2A localization to the mitochondria, while rotenone shifts it to the nucleus. HIG2A protein colocalized at a higher level in the nucleus concerning the mitochondrial network under normoxia and hypoxia (2% O2). Hypoxia (2% O2) significantly increases HIG2A nuclear colocalization in C2C12 cells. In HEK293 cells, chemical hypoxia with CoCl2 (>1% O2) and FCCP mitochondrial uncoupling, the HIG2A protein decreased its nuclear localization and shifted to the mitochondria. This suggests that the HIG2A distribution pattern between the mitochondria and the nucleus depends on stress and cell type. HIG2A protein expression levels increase under cellular stresses such as hypoxia and oxidative stress. Its dynamic distribution between mitochondria and the nucleus in response to stress factors suggests a new communication system between the mitochondria and the nucleus.
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Affiliation(s)
- Celia Salazar
- Institute of Biomedical Sciences, Faculty of Health Sciences, Universidad Autónoma de Chile, Santiago 8910060, Chile;
| | - Miriam Barros
- Confocal Microscopy Laboratory, Universidad Andres Bello, Santiago 8370146, Chile;
| | - Alvaro A. Elorza
- Institute of Biomedical Sciences, Faculty of Medicine, Universidad Andres Bello, Santiago 8370146, Chile;
- Institute of Biomedical Sciences, Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370146, Chile
- Millennium Institute in Immunology and Immunotherapy, Santiago 8331150, Chile
| | - Lina María Ruiz
- Institute of Biomedical Sciences, Faculty of Health Sciences, Universidad Autónoma de Chile, Santiago 8910060, Chile;
- Correspondence:
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18
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Morgenstern M, Peikert CD, Lübbert P, Suppanz I, Klemm C, Alka O, Steiert C, Naumenko N, Schendzielorz A, Melchionda L, Mühlhäuser WWD, Knapp B, Busch JD, Stiller SB, Dannenmaier S, Lindau C, Licheva M, Eickhorst C, Galbusera R, Zerbes RM, Ryan MT, Kraft C, Kozjak-Pavlovic V, Drepper F, Dennerlein S, Oeljeklaus S, Pfanner N, Wiedemann N, Warscheid B. Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context. Cell Metab 2021; 33:2464-2483.e18. [PMID: 34800366 PMCID: PMC8664129 DOI: 10.1016/j.cmet.2021.11.001] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/01/2021] [Accepted: 11/01/2021] [Indexed: 12/18/2022]
Abstract
Mitochondria are key organelles for cellular energetics, metabolism, signaling, and quality control and have been linked to various diseases. Different views exist on the composition of the human mitochondrial proteome. We classified >8,000 proteins in mitochondrial preparations of human cells and defined a mitochondrial high-confidence proteome of >1,100 proteins (MitoCoP). We identified interactors of translocases, respiratory chain, and ATP synthase assembly factors. The abundance of MitoCoP proteins covers six orders of magnitude and amounts to 7% of the cellular proteome with the chaperones HSP60-HSP10 being the most abundant mitochondrial proteins. MitoCoP dynamics spans three orders of magnitudes, with half-lives from hours to months, and suggests a rapid regulation of biosynthesis and assembly processes. 460 MitoCoP genes are linked to human diseases with a strong prevalence for the central nervous system and metabolism. MitoCoP will provide a high-confidence resource for placing dynamics, functions, and dysfunctions of mitochondria into the cellular context.
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Affiliation(s)
- Marcel Morgenstern
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Christian D Peikert
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Philipp Lübbert
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Ida Suppanz
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Cinzia Klemm
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Oliver Alka
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Conny Steiert
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Nataliia Naumenko
- Department of Cellular Biochemistry, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Alexander Schendzielorz
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Laura Melchionda
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Wignand W D Mühlhäuser
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Bettina Knapp
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Jakob D Busch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Sebastian B Stiller
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Stefan Dannenmaier
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Caroline Lindau
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Mariya Licheva
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Christopher Eickhorst
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Riccardo Galbusera
- Neurologic Clinic and Policlinic, Departments of Medicine, Clinical Research and Biomedical Engineering, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Ralf M Zerbes
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800 Melbourne, VIC, Australia
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Vera Kozjak-Pavlovic
- Department of Microbiology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Friedel Drepper
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Sven Dennerlein
- Department of Cellular Biochemistry, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Silke Oeljeklaus
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Nils Wiedemann
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
| | - Bettina Warscheid
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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Das S, Mukherjee S, Bedi M, Ghosh A. Mutations in the Yeast Cox12 Subunit Severely Compromise the Activity of the Mitochondrial Complex IV. BIOCHEMISTRY. BIOKHIMIIA 2021; 86:1607-1623. [PMID: 34937540 DOI: 10.1134/s0006297921120105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 10/25/2021] [Accepted: 11/21/2021] [Indexed: 06/14/2023]
Abstract
Cytochrome c oxidase 6B1 (COX6B1) is one of the less characterized subunits of the mitochondrial electron transport chain complex IV (CIV). Here, we studied the pathobiochemical and respiratory functions of Cox12 (yeast ortholog of COX6B1) using Saccharomyces cerevisiae BY4741 (cox12Δ) cells deficient by the Cox12 protein. The cells exhibited severe growth deficiency in the respiratory glycerol-ethanol medium, which could be reverted by complementation with the yeast COX12 or human COX6B1 genes. Cox12 with arginine 17 residue substituted by histidine (R17H) or cysteine (R17C) (mutations analogous to those observed in human patients) failed to complement the loss of Cox12 function. When cox12Δ cells were grown in rich respiratory/fermentative galactose medium, no changes in the expression of individual respiratory chain subunits were observed. Blue native PAGE/Western blotting analysis using antibodies against Rip1 and Cox1, which are specific components of complexes III (CIII) and IV (CIV), respectively, revealed no noticeable decrease in the native CIII2CIV2 and CIII2CIV1 supercomplexes (SCs). However, the association of the respiratory SC factor 2 (Rcf2) and Cox2 subunit within the SCs of cox12Δ cells was reduced, while the specific activity of CIV was downregulated by 90%. Both basal respiration and succinate-ADP stimulated state 3 respiration, as well as the mitochondrial membrane potential, were decreased in cox12Δ cells. Furthermore, cox12Δ cells and cells synthesizing Cox12 mutants R17H and R17C showed higher sensitivity to the H2O2-induced oxidative stress compared to the wild-type (WT) cells. In silico structural modeling of the WT yeast SCs revealed that Cox12 forms a network of interactions with Rcf2 and Cox2. Together, our results establish that Cox12 is essential for the CIV activity.
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Affiliation(s)
- Shubhojit Das
- Department of Biochemistry, University of Calcutta, Kolkata, 700019, India.
| | | | - Minakshi Bedi
- Department of Biochemistry, University of Calcutta, Kolkata, 700019, India.
| | - Alok Ghosh
- Department of Biochemistry, University of Calcutta, Kolkata, 700019, India.
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20
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Xu Z, Sun J, Chen Y, Zhang T, Qin Y, Hua D. HIG1 domain family member 1A disrupts proliferation, migration and invasion of colon adenocarcinoma cells. Bioengineered 2021; 12:10501-10511. [PMID: 34787061 PMCID: PMC8809935 DOI: 10.1080/21655979.2021.1999368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
HIG1 domain family member 1A (Higd-1a) interacts with dynamin-like 120 kDa protein to maintain the morphological and functional integrity of the mitochondria and thus plays an important role in the progression of malignant tumors. Higd-1a promotes the proliferation of pancreatic cancer cells and the growth of pancreatic cancer; however, no similar observations have been reported for colorectal cancer (CRC). This study, therefore, aimed to verify the role of Higd-1a in CRC. We downloaded data from the Genotype-Tissue Expression (GTEX) and The Cancer Genome Atlas (TCGA) databases and identified an association between Higd-1a levels in colon adenocarcinoma (COAD) tissues and poor survival using Kaplan-Meier curves. Subsequently, we overexpressed Higd-1a in the human COAD cell line HCT-8, knocked down Higd-1a expression in SW480 cells, and evaluated the effects via quantitative PCR (qPCR) and western blotting. MTT assays, colony formation assay, cell cycle analysis, annexin V-FITC/PI, wound-healing analysis, and transwell assay were used to test cell proliferation, formation of cell colonies, cell cycle progression, migration, invasiveness, and apoptosis. Higd-1a has low transcription levels in COAD tissue and suggests a poor prognosis. Higd-1a overexpression in HCT-8 cells weakened cell proliferation, formation of cell colonies, cell cycle progression, migration ability, and invasiveness, and increased apoptosis. Moreover, the decrease of Higd-1a in SW480 cells induced cell proliferation, formation of cell colonies, cell cycle progression, migration, and invasion, and inhibited apoptosis. Higd-1a is underexpressed in COAD cells and its overexpression impaired the proliferation, migration, and invasiveness of COAD cells.
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Affiliation(s)
- Zhenyu Xu
- Department of Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China.,Department of Oncology, The Affiliated Hospital of Jiangnan University, Wuxi, 214000, Jiangsu, China
| | - Junjie Sun
- Department of Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China.,Department of Oncology, The Affiliated Hospital of Jiangnan University, Wuxi, 214000, Jiangsu, China
| | - Yang Chen
- Department of pharmacy, The Affiliated Hospital of Jiangnan University, Wuxi, 214000, Jiangsu, China
| | - Ting Zhang
- Department of Oncology, The Affiliated Hospital of Jiangnan University, Wuxi, 214000, Jiangsu, China
| | - Yan Qin
- Department of pathology, The Affiliated Hospital of Jiangnan University, Wuxi, 214000, Jiangsu, China
| | - Dong Hua
- Department of Oncology, The Affiliated Hospital of Jiangnan University, Wuxi, 214000, Jiangsu, China
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21
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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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22
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Rcf proteins and their differential specificity for respiratory chain complexes: A unique role for Rcf2 on oxygen sensitive supercomplexes? BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119133. [PMID: 34450214 DOI: 10.1016/j.bbamcr.2021.119133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 08/18/2021] [Accepted: 08/21/2021] [Indexed: 11/22/2022]
Abstract
The respiratory chain, embedded in the inner mitochondrial membrane, is organized as a network of individual complexes, as well as large supercomplex structures. In the yeast S. cerevisiae, these supercomplexes consist of a dimeric cytochrome bc1-complex adjoined by one or two copies of cytochrome c oxidase. The formation of these complexes is a dynamic process and is regulated by various factors in order to adapt to environmental and metabolic changes. These adaptions occur at the level of enzyme regulation, complex assembly, as well as altered nuclear and mitochondrial transcription and translation. Members of the Rcf protein family (Rcf1, Rcf2 and Rcf3) are required for respiratory complex biogenesis and act mainly by regulating the assembly and enzyme activity of complex IV within supercomplexes. Rcf1 functions in the assembly process via the COX3 module, whereas Rcf2 and Rcf3 are responsible for enzymatic regulation. In this study, we have extended this knowledge to show that Rcf2 and Rcf3 can also associate with newly synthesized mitochondrial encoded proteins, such as Cox3, and therefore contribute to complex IV assembly. Since the Rcf proteins have overlapping regions of sequence similarities, we engineered novel fusion proteins of Rcf1 and Rcf3, with parts of Rcf2, to probe which of the Rcf protein domains can be attributed to their functions. The fusion proteins could compensate for the individual phenotypes of the complexIV assembly defect and the lack of complex IV regulation. Finally, the role of Rcf proteins for defined species of respiratory chain complexes in a hypoxic model was investigated, uncovering a unique association of Rcf2 with the hypoxic III2IV supercomplex. We therefore suggest an involvement of Rcf2 for adaption of the respiratory chain to altering oxygen levels.
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Adaptive optimization of the OXPHOS assembly line partially compensates lrpprc-dependent mitochondrial translation defects in mice. Commun Biol 2021; 4:989. [PMID: 34413467 PMCID: PMC8376967 DOI: 10.1038/s42003-021-02492-5] [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: 10/30/2020] [Accepted: 07/20/2021] [Indexed: 11/20/2022] Open
Abstract
Mouse models of genetic mitochondrial disorders are generally used to understand specific molecular defects and their biochemical consequences, but rarely to map compensatory changes allowing survival. Here we took advantage of the extraordinary mitochondrial resilience of hepatic Lrpprc knockout mice to explore this question using native proteomics profiling and lipidomics. In these mice, low levels of the mtRNA binding protein LRPPRC induce a global mitochondrial translation defect and a severe reduction (>80%) in the assembly and activity of the electron transport chain (ETC) complex IV (CIV). Yet, animals show no signs of overt liver failure and capacity of the ETC is preserved. Beyond stimulation of mitochondrial biogenesis, results show that the abundance of mitoribosomes per unit of mitochondria is increased and proteostatic mechanisms are induced in presence of low LRPPRC levels to preserve a balance in the availability of mitochondrial- vs nuclear-encoded ETC subunits. At the level of individual organelles, a stabilization of residual CIV in supercomplexes (SCs) is observed, pointing to a role of these supramolecular arrangements in preserving ETC function. While the SC assembly factor COX7A2L could not contribute to the stabilization of CIV, important changes in membrane glycerophospholipid (GPL), most notably an increase in SC-stabilizing cardiolipins species (CLs), were observed along with an increased abundance of other supramolecular assemblies known to be stabilized by, and/or participate in CL metabolism. Together these data reveal a complex in vivo network of molecular adjustments involved in preserving mitochondrial integrity in energy consuming organs facing OXPHOS defects, which could be therapeutically exploited. Cuillerier et al. investigate compensatory mechanisms underlying survival of mice with a liver-specific knockout of the mitochondrial mRNA-binding protein Lrpprc. They propose various mechanisms operating along the OXPHOS assembly line, including mitochondrial biogenesis, mitochondrial ribosome upregulation and preferential supercomplex assembly, that could compensate lack of LRPPRC and allow survival of these mice.
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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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Distinct Roles of Mitochondrial HIGD1A and HIGD2A in Respiratory Complex and Supercomplex Biogenesis. Cell Rep 2021; 31:107607. [PMID: 32375044 DOI: 10.1016/j.celrep.2020.107607] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 03/06/2020] [Accepted: 04/10/2020] [Indexed: 01/08/2023] Open
Abstract
The mitochondrial respiratory chain enzymes are organized as individual complexes and supercomplexes, whose biogenesis remains to be fully understood. To disclose the role of the human Hypoxia Inducible Gene Domain family proteins HIGD1A and HIGD2A in these processes, we generate and characterize HIGD-knockout (KO) cell lines. We show that HIGD2A controls and coordinates the modular assembly of isolated and supercomplexed complex IV (CIV) by acting on the COX3 assembly module. In contrast, HIGD1A regulates CIII and CIII-containing supercomplex biogenesis by supporting the incorporation of UQCRFS1. HIGD1A also clusters with COX4-1 and COX5A CIV subunits and, when overexpressed, suppresses the CIV biogenesis defect of HIGD2A-KO cells. We conclude that HIGD1A and HIGD2A have both independent and overlapping functions in the biogenesis of respiratory complexes and supercomplexes. Our data illuminate the existence of multiple pathways to assemble these structures by dynamic HIGD-mediated CIV biogenesis, potentially to adapt to changing environmental and nutritional conditions.
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26
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Zhou S, Pettersson P, Björck ML, Dawitz H, Brzezinski P, Mäler L, Ädelroth P. NMR structural analysis of the yeast cytochrome c oxidase subunit Cox13 and its interaction with ATP. BMC Biol 2021; 19:98. [PMID: 33971868 PMCID: PMC8111780 DOI: 10.1186/s12915-021-01036-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 04/22/2021] [Indexed: 11/29/2022] Open
Abstract
Background Mitochondrial respiration is organized in a series of enzyme complexes in turn forming dynamic supercomplexes. In Saccharomyces cerevisiae (baker’s yeast), Cox13 (CoxVIa in mammals) is a conserved peripheral subunit of Complex IV (cytochrome c oxidase, CytcO), localized at the interface of dimeric bovine CytcO, which has been implicated in the regulation of the complex. Results Here, we report the solution NMR structure of Cox13, which forms a dimer in detergent micelles. Each Cox13 monomer has three short helices (SH), corresponding to disordered regions in X-ray or cryo-EM structures of homologous proteins. Dimer formation is mainly induced by hydrophobic interactions between the transmembrane (TM) helix of each monomer. Furthermore, an analysis of chemical shift changes upon addition of ATP revealed that ATP binds at a conserved region of the C terminus with considerable conformational flexibility. Conclusions Together with functional analysis of purified CytcO, we suggest that this ATP interaction is inhibitory of catalytic activity. Our results shed light on the structural flexibility of an important subunit of yeast CytcO and provide structure-based insight into how ATP could regulate mitochondrial respiration. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01036-x.
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Affiliation(s)
- Shu Zhou
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Current address: High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Pontus Pettersson
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Markus L Björck
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Hannah Dawitz
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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27
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Kell DB. A protet-based, protonic charge transfer model of energy coupling in oxidative and photosynthetic phosphorylation. Adv Microb Physiol 2021; 78:1-177. [PMID: 34147184 DOI: 10.1016/bs.ampbs.2021.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Textbooks of biochemistry will explain that the otherwise endergonic reactions of ATP synthesis can be driven by the exergonic reactions of respiratory electron transport, and that these two half-reactions are catalyzed by protein complexes embedded in the same, closed membrane. These views are correct. The textbooks also state that, according to the chemiosmotic coupling hypothesis, a (or the) kinetically and thermodynamically competent intermediate linking the two half-reactions is the electrochemical difference of protons that is in equilibrium with that between the two bulk phases that the coupling membrane serves to separate. This gradient consists of a membrane potential term Δψ and a pH gradient term ΔpH, and is known colloquially as the protonmotive force or pmf. Artificial imposition of a pmf can drive phosphorylation, but only if the pmf exceeds some 150-170mV; to achieve in vivo rates the imposed pmf must reach 200mV. The key question then is 'does the pmf generated by electron transport exceed 200mV, or even 170mV?' The possibly surprising answer, from a great many kinds of experiment and sources of evidence, including direct measurements with microelectrodes, indicates it that it does not. Observable pH changes driven by electron transport are real, and they control various processes; however, compensating ion movements restrict the Δψ component to low values. A protet-based model, that I outline here, can account for all the necessary observations, including all of those inconsistent with chemiosmotic coupling, and provides for a variety of testable hypotheses by which it might be refined.
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Affiliation(s)
- Douglas B Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative, Biology, University of Liverpool, Liverpool, United Kingdom; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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Nesci S, Trombetti F, Pagliarani A, Ventrella V, Algieri C, Tioli G, Lenaz G. Molecular and Supramolecular Structure of the Mitochondrial Oxidative Phosphorylation System: Implications for Pathology. Life (Basel) 2021; 11:242. [PMID: 33804034 PMCID: PMC7999509 DOI: 10.3390/life11030242] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 02/07/2023] Open
Abstract
Under aerobic conditions, mitochondrial oxidative phosphorylation (OXPHOS) converts the energy released by nutrient oxidation into ATP, the currency of living organisms. The whole biochemical machinery is hosted by the inner mitochondrial membrane (mtIM) where the protonmotive force built by respiratory complexes, dynamically assembled as super-complexes, allows the F1FO-ATP synthase to make ATP from ADP + Pi. Recently mitochondria emerged not only as cell powerhouses, but also as signaling hubs by way of reactive oxygen species (ROS) production. However, when ROS removal systems and/or OXPHOS constituents are defective, the physiological ROS generation can cause ROS imbalance and oxidative stress, which in turn damages cell components. Moreover, the morphology of mitochondria rules cell fate and the formation of the mitochondrial permeability transition pore in the mtIM, which, most likely with the F1FO-ATP synthase contribution, permeabilizes mitochondria and leads to cell death. As the multiple mitochondrial functions are mutually interconnected, changes in protein composition by mutations or in supercomplex assembly and/or in membrane structures often generate a dysfunctional cascade and lead to life-incompatible diseases or severe syndromes. The known structural/functional changes in mitochondrial proteins and structures, which impact mitochondrial bioenergetics because of an impaired or defective energy transduction system, here reviewed, constitute the main biochemical damage in a variety of genetic and age-related diseases.
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Affiliation(s)
- Salvatore Nesci
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, 40064 Ozzano Emilia, Italy; (F.T.); (V.V.); (C.A.)
| | - Fabiana Trombetti
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, 40064 Ozzano Emilia, Italy; (F.T.); (V.V.); (C.A.)
| | - Alessandra Pagliarani
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, 40064 Ozzano Emilia, Italy; (F.T.); (V.V.); (C.A.)
| | - Vittoria Ventrella
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, 40064 Ozzano Emilia, Italy; (F.T.); (V.V.); (C.A.)
| | - Cristina Algieri
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, 40064 Ozzano Emilia, Italy; (F.T.); (V.V.); (C.A.)
| | - Gaia Tioli
- Department of Biomedical and Neuromotor Sciences, Alma Mater Studiorum University of Bologna, 40138 Bologna, Italy;
| | - Giorgio Lenaz
- Department of Biomedical and Neuromotor Sciences, Alma Mater Studiorum University of Bologna, 40138 Bologna, Italy;
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29
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Mitochondrial Structure and Bioenergetics in Normal and Disease Conditions. Int J Mol Sci 2021; 22:ijms22020586. [PMID: 33435522 PMCID: PMC7827222 DOI: 10.3390/ijms22020586] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/03/2021] [Accepted: 01/04/2021] [Indexed: 02/06/2023] Open
Abstract
Mitochondria are ubiquitous intracellular organelles found in almost all eukaryotes and involved in various aspects of cellular life, with a primary role in energy production. The interest in this organelle has grown stronger with the discovery of their link to various pathologies, including cancer, aging and neurodegenerative diseases. Indeed, dysfunctional mitochondria cannot provide the required energy to tissues with a high-energy demand, such as heart, brain and muscles, leading to a large spectrum of clinical phenotypes. Mitochondrial defects are at the origin of a group of clinically heterogeneous pathologies, called mitochondrial diseases, with an incidence of 1 in 5000 live births. Primary mitochondrial diseases are associated with genetic mutations both in nuclear and mitochondrial DNA (mtDNA), affecting genes involved in every aspect of the organelle function. As a consequence, it is difficult to find a common cause for mitochondrial diseases and, subsequently, to offer a precise clinical definition of the pathology. Moreover, the complexity of this condition makes it challenging to identify possible therapies or drug targets.
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30
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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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31
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Domesticated and optimized mitochondria: Mitochondrial modifications based on energetic status and cellular stress. Life Sci 2020; 265:118766. [PMID: 33245965 DOI: 10.1016/j.lfs.2020.118766] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/28/2020] [Accepted: 11/11/2020] [Indexed: 12/15/2022]
Abstract
Mitochondria are the main source of energy and play an important role in coupling intracellular and intercellular metabolic cooperation. Cellular stress and energetic status can affect various mitochondrial behaviors, including mitochondrial biogenesis, mitophagy, assembly of respiratory chain supercomplexes and mitochondrial distribution. These modifications usually result in adaptive adjustment of mitochondrial output and resistance to cellular stress. However, when the pro-death signals triggered by excessive damage converge to mitochondria, mitochondrial reserve and functional status can profoundly determine the direction of cell death, and even affect the survival and death of surrounding or distant tissues. In this review, we discuss multiple mitochondrial modifications in eukaryotes based on metabolic status and cellular stress, and review the emerging knowledge about the effects of mitochondrial dysfunction on the fate of cells and surrounding tissues.
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32
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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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Zhao Y, Yang N, Deng Y, Tao K, Jin H, Hou T. Mechanism of Action of Novel Pyrazole Carboxamide Containing a Diarylamine Scaffold against Rhizoctonia solani. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:11068-11076. [PMID: 32924467 DOI: 10.1021/acs.jafc.9b06937] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In the last few decades, Rhizoctonia solani causing rice sheath blight has resulted in a lot of economic losses in the world. Therefore, many novel pyrazole carboxamide fungicides have been intensively researched and employed to fight against it. In this regard, in recent years, our group reported a novel pyrazole carboxamide containing a diarylamine scaffold with good antifungal activity against rice sheath blight in the pot test and field trial. Following this project, the antifungal mechanism of action of the pyrazole carboxamide has been elucidated in this work. The antifungal result showed that compound SCU2028, N-[2-[(3-chlorophenyl)amino]-phenyl]-3-(difluoromethyl)-1-methyl-1H-pyrazole-4-carboxamide, was equivalent to the commercial fungicide thifluzamide and its EC50 value was 0.022 mg/L against R. solani. Also, the observation results by scanning electron microscopy and transmission electron microscopy showed that it could destroy the fungus' cell walls or membranes and result in the leakage of contents and increase of the number of mitochondria and abnormal morphology. Meanwhile, the result on the mitochondrial membrane potential (MMP) showed that it could decrease R. solani's MMP. Furthermore, the results by label-free quantitative proteomic analysis showed that 1153 proteins were found after R. solani was treated with compound SCU2028, including 212 proteins in the control group and 257 proteins in the treatment group. A total of 142 differential proteins were obtained, of which 92 proteins were upregulated and 50 proteins were downregulated. The differentially expressed proteins affected a series of physiological and biochemical pathways in the mitochondria, endoplasmic reticulum, ribosome, and other related GO and KEGG pathways. In particular, the inhibition of the respiratory chain caused by the TCA cycle and oxidative phosphorylation KEGG pathway indicated that complex II (succinate dehydrogenase) and complex IV (cytochrome oxidase) might be compound SCU2028's main action targets. In addition, multiple experiments of qRT-PCR, enzyme activity detection, and molecular docking confirmed complex II and complex IV as targets. It could be seen that these findings provided a theoretical support for further research and development of the pyrazole carboxamide fungicides.
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Affiliation(s)
- Yongtian Zhao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
- College of Agroforestry and Health, Sichuan Radio and TV University, Chengdu, Sichuan 610073, China
| | - Na Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Yiming Deng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Ke Tao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Hong Jin
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Taiping Hou
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
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Saldana-Caboverde A, Nissanka N, Garcia S, Lombès A, Diaz F. Hypoxia Promotes Mitochondrial Complex I Abundance via HIF-1α in Complex III and Complex IV Eficient Cells. Cells 2020; 9:cells9102197. [PMID: 33003371 PMCID: PMC7599499 DOI: 10.3390/cells9102197] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 11/16/2022] Open
Abstract
Murine fibroblasts deficient in mitochondria respiratory complexes III (CIII) and IV (CIV) produced by either the ablation of Uqcrfs1 (encoding for Rieske iron sulfur protein, RISP) or Cox10 (encoding for protoheme IX farnesyltransferase, COX10) genes, respectively, showed a pleiotropic effect in complex I (CI). Exposure to 1-5% oxygen increased the levels of CI in both RISP and COX10 KO fibroblasts. De novo assembly of the respiratory complexes occurred at a faster rate and to higher levels in 1% oxygen compared to normoxia in both RISP and COX10 KO fibroblasts. Hypoxia did not affect the levels of assembly of CIII in the COX10 KO fibroblasts nor abrogated the genetic defect impairing CIV assembly. Mitochondrial signaling involving reactive oxygen species (ROS) has been implicated as necessary for HIF-1α stabilization in hypoxia. We did not observe increased ROS production in hypoxia. Exposure to low oxygen levels stabilized HIF-1α and increased CI levels in RISP and COX10 KO fibroblasts. Knockdown of HIF-1α during hypoxic conditions abrogated the beneficial effect of hypoxia on the stability/assembly of CI. These findings demonstrate that oxygen and HIF-1α regulate the assembly of respiratory complexes.
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Affiliation(s)
- Amy Saldana-Caboverde
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; (A.S.-C.); (N.N.); (S.G.)
| | - Nadee Nissanka
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; (A.S.-C.); (N.N.); (S.G.)
| | - Sofia Garcia
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; (A.S.-C.); (N.N.); (S.G.)
| | - Anne Lombès
- Institut Cochin, Unité U1016, INSERM, UMR 8104, CNRS, Université Paris 5, F-75014 Paris, France;
| | - Francisca Diaz
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; (A.S.-C.); (N.N.); (S.G.)
- Correspondence: ; Tel.: +1-305-243-7489
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35
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Zhou S, Pettersson P, Huang J, Brzezinski P, Pomès R, Mäler L, Ädelroth P. NMR Structure and Dynamics Studies of Yeast Respiratory Supercomplex Factor 2. Structure 2020; 29:275-283.e4. [PMID: 32905793 DOI: 10.1016/j.str.2020.08.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/12/2020] [Accepted: 08/19/2020] [Indexed: 12/22/2022]
Abstract
The Saccharomyces cerevisiae respiratory supercomplex factor 2 (Rcf2) is a 224-residue protein located in the mitochondrial inner membrane where it is involved in the formation of supercomplexes composed of cytochrome bc1 and cytochrome c oxidase. We previously demonstrated that Rcf2 forms a dimer in dodecylphosphocholine micelles, and here we report the solution NMR structure of this Rcf2 dimer. Each Rcf2 monomer has two soluble α helices and five putative transmembrane (TM) α helices, including an unexpectedly charged TM helix at the C terminus, which mediates dimer formation. The NOE contacts indicate the presence of inter-monomer salt bridges and hydrogen bonds at the dimer interface, which stabilize the Rcf2 dimer structure. Moreover, NMR chemical shift change mapping upon lipid titrations as well as molecular dynamics analysis reveal possible structural changes upon embedding Rcf2 into a native lipid environment. Our results contribute to the understanding of respiratory supercomplex formation and regulation.
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Affiliation(s)
- Shu Zhou
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden; High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Pontus Pettersson
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Jingjing Huang
- Molecular Medicine, The Hospital for Sick Children, Toronto, Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 0A4, Canada
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Régis Pomès
- Molecular Medicine, The Hospital for Sick Children, Toronto, Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 0A4, Canada
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden.
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden.
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36
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Liu Y, Liu Y, Tong C, Cong P, Shi X, Shi L, Hou M, Jin H, Bao Y. Quantitative analysis of the global proteome in lung from mice with blast injury. Exp Lung Res 2020; 46:308-319. [PMID: 32748703 DOI: 10.1080/01902148.2020.1801896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
AIM OF THE STUDY The mechanism by which primary shock wave causes lung injury is unclear. The aim of this study is to find the changes of protein that can be helpful in understanding blast-induced lung injury. MATERIAL AND METHODS A quantitative analysis of their global proteome was conducted in lung from mice with blast injury using LC-MS/MS. Protein annotation, unsupervised hierarchical clustering, functional classification, functional enrichment and cluster, and protein-protein interaction analyses were performed. Furthermore, western blotting was used to validate the changed protein levels. RESULTS A total of 6498 proteins were identified, of which 5520 proteins were quantified. The fold-change cutoff was set at 1.2; 132 proteins were upregulated, and 104 proteins were downregulated. The bioinformatics analysis indicated that the differentially expressed proteins were involved in the cholesterol metabolism, asthma, nonalcoholic fatty liver disease. Remarkably, the processes related to the change of oxidative phosphorylation including the NADH dehydrogenase, Cytochrome C reductase, Cytochrome C oxidase and F-type ATPase were significantly upregulated, which were further verified by western blotting. CONCLUSION These results confirmed that the oxidative phosphorylation is critical to blast-induced lung injury. LC/MS-based profiling presented candidate target/pathways that could be explored for future therapeutic development.
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Affiliation(s)
- Ying Liu
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun, China.,Emergency Medicine Department of General Hospital of Northern Theater Command, Laboratory of Rescue Center of Severe Wound and Trauma PLA, Shenyang, China
| | - Yunen Liu
- Emergency Medicine Department of General Hospital of Northern Theater Command, Laboratory of Rescue Center of Severe Wound and Trauma PLA, Shenyang, China
| | - Changci Tong
- Emergency Medicine Department of General Hospital of Northern Theater Command, Laboratory of Rescue Center of Severe Wound and Trauma PLA, Shenyang, China
| | - Peifang Cong
- Emergency Medicine Department of General Hospital of Northern Theater Command, Laboratory of Rescue Center of Severe Wound and Trauma PLA, Shenyang, China
| | - Xiuyun Shi
- Emergency Medicine Department of General Hospital of Northern Theater Command, Laboratory of Rescue Center of Severe Wound and Trauma PLA, Shenyang, China
| | - Lin Shi
- Emergency Medicine Department of General Hospital of Northern Theater Command, Laboratory of Rescue Center of Severe Wound and Trauma PLA, Shenyang, China
| | - Mingxiao Hou
- Emergency Medicine Department of General Hospital of Northern Theater Command, Laboratory of Rescue Center of Severe Wound and Trauma PLA, Shenyang, China
| | - Hongxu Jin
- Emergency Medicine Department of General Hospital of Northern Theater Command, Laboratory of Rescue Center of Severe Wound and Trauma PLA, Shenyang, China
| | - Yongli Bao
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun, China
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37
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Linden A, Deckers M, Parfentev I, Pflanz R, Homberg B, Neumann P, Ficner R, Rehling P, Urlaub H. A Cross-linking Mass Spectrometry Approach Defines Protein Interactions in Yeast Mitochondria. Mol Cell Proteomics 2020; 19:1161-1178. [PMID: 32332106 PMCID: PMC7338081 DOI: 10.1074/mcp.ra120.002028] [Citation(s) in RCA: 24] [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: 03/09/2020] [Revised: 04/24/2020] [Indexed: 12/13/2022] Open
Abstract
Protein cross-linking and the analysis of cross-linked peptides by mass spectrometry is currently receiving much attention. Not only is this approach applied to isolated complexes to provide information about spatial arrangements of proteins, but it is also increasingly applied to entire cells and their organelles. As in quantitative proteomics, the application of isotopic labeling further makes it possible to monitor quantitative changes in the protein-protein interactions between different states of a system. Here, we cross-linked mitochondria from Saccharomyces cerevisiae grown on either glycerol- or glucose-containing medium to monitor protein-protein interactions under non-fermentative and fermentative conditions. We investigated qualitatively the protein-protein interactions of the 400 most abundant proteins applying stringent data-filtering criteria, i.e. a minimum of two cross-linked peptide spectrum matches and a cut-off in the spectrum scoring of the used search engine. The cross-linker BS3 proved to be equally suited for connecting proteins in all compartments of mitochondria when compared with its water-insoluble but membrane-permeable derivative DSS. We also applied quantitative cross-linking to mitochondria of both the growth conditions using stable-isotope labeled BS3. Significant differences of cross-linked proteins under glycerol and glucose conditions were detected, however, mainly because of the different copy numbers of these proteins in mitochondria under both the conditions. Results obtained from the glycerol condition indicate that the internal NADH:ubiquinone oxidoreductase Ndi1 is part of an electron transport chain supercomplex. We have also detected several hitherto uncharacterized proteins and identified their interaction partners. Among those, Min8 was found to be associated with cytochrome c oxidase. BN-PAGE analyses of min8Δ mitochondria suggest that Min8 promotes the incorporation of Cox12 into cytochrome c oxidase.
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Affiliation(s)
- Andreas Linden
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Markus Deckers
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Iwan Parfentev
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ralf Pflanz
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Bettina Homberg
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-University Göttingen, Göttingen, Germany
| | - Ralf Ficner
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany; Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-University Göttingen, Göttingen, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany; Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany.
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38
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Hock DH, Reljic B, Ang CS, Muellner-Wong L, Mountford HS, Compton AG, Ryan MT, Thorburn DR, Stroud DA. HIGD2A is Required for Assembly of the COX3 Module of Human Mitochondrial Complex IV. Mol Cell Proteomics 2020; 19:1145-1160. [PMID: 32317297 PMCID: PMC7338084 DOI: 10.1074/mcp.ra120.002076] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Indexed: 12/14/2022] Open
Abstract
Assembly factors play a critical role in the biogenesis of mitochondrial respiratory chain complexes I-IV where they assist in the membrane insertion of subunits, attachment of co-factors, and stabilization of assembly intermediates. The major fraction of complexes I, III and IV are present together in large molecular structures known as respiratory chain supercomplexes. Several assembly factors have been proposed as required for supercomplex assembly, including the hypoxia inducible gene 1 domain family member HIGD2A. Using gene-edited human cell lines and extensive steady state, translation and affinity enrichment proteomics techniques we show that loss of HIGD2A leads to defects in the de novo biogenesis of mtDNA-encoded COX3, subsequent accumulation of complex IV intermediates and turnover of COX3 partner proteins. Deletion of HIGD2A also leads to defective complex IV activity. The impact of HIGD2A loss on complex IV was not altered by growth under hypoxic conditions, consistent with its role being in basal complex IV assembly. Although in the absence of HIGD2A we show that mitochondria do contain an altered supercomplex assembly, we demonstrate it to harbor a crippled complex IV lacking COX3. Our results redefine HIGD2A as a classical assembly factor required for building the COX3 module of complex IV.
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Affiliation(s)
- Daniella H Hock
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Boris Reljic
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Ching-Seng Ang
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria, Australia
| | - Linden Muellner-Wong
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Hayley S Mountford
- Brain and Mitochondrial Research, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Alison G Compton
- Brain and Mitochondrial Research, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - David R Thorburn
- Brain and Mitochondrial Research, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia; Mitochondrial Laboratory, Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - David A Stroud
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia.
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39
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Hartley AM, Meunier B, Pinotsis N, Maréchal A. Rcf2 revealed in cryo-EM structures of hypoxic isoforms of mature mitochondrial III-IV supercomplexes. Proc Natl Acad Sci U S A 2020; 117:9329-9337. [PMID: 32291341 PMCID: PMC7196821 DOI: 10.1073/pnas.1920612117] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The organization of the mitochondrial electron transport chain proteins into supercomplexes (SCs) is now undisputed; however, their assembly process, or the role of differential expression isoforms, remain to be determined. In Saccharomyces cerevisiae, cytochrome c oxidase (CIV) forms SCs of varying stoichiometry with cytochrome bc1 (CIII). Recent studies have revealed, in normoxic growth conditions, an interface made exclusively by Cox5A, the only yeast respiratory protein that exists as one of two isoforms depending on oxygen levels. Here we present the cryo-EM structures of the III2-IV1 and III2-IV2 SCs containing the hypoxic isoform Cox5B solved at 3.4 and 2.8 Å, respectively. We show that the change of isoform does not affect SC formation or activity, and that SC stoichiometry is dictated by the level of CIII/CIV biosynthesis. Comparison of the CIV5B- and CIV5A-containing SC structures highlighted few differences, found mainly in the region of Cox5. Additional density was revealed in all SCs, independent of the CIV isoform, in a pocket formed by Cox1, Cox3, Cox12, and Cox13, away from the CIII-CIV interface. In the CIV5B-containing hypoxic SCs, this could be confidently assigned to the hypoxia-induced gene 1 (Hig1) type 2 protein Rcf2. With conserved residues in mammalian Hig1 proteins and Cox3/Cox12/Cox13 orthologs, we propose that Hig1 type 2 proteins are stoichiometric subunits of CIV, at least when within a III-IV SC.
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Affiliation(s)
- Andrew M Hartley
- Institute of Structural and Molecular Biology, Birkbeck College, WC1E 7HX London, United Kingdom
| | - Brigitte Meunier
- Institute for Integrative Biology of the Cell (I2BC), CNRS, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Nikos Pinotsis
- Institute of Structural and Molecular Biology, Birkbeck College, WC1E 7HX London, United Kingdom
| | - Amandine Maréchal
- Institute of Structural and Molecular Biology, Birkbeck College, WC1E 7HX London, United Kingdom;
- Institute of Structural and Molecular Biology, University College London, WC1E 6BT London, United Kingdom
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40
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Mukherjee S, Ghosh A. Molecular mechanism of mitochondrial respiratory chain assembly and its relation to mitochondrial diseases. Mitochondrion 2020; 53:1-20. [PMID: 32304865 DOI: 10.1016/j.mito.2020.04.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 03/28/2020] [Accepted: 04/07/2020] [Indexed: 12/17/2022]
Abstract
The mitochondrial respiratory chain (MRC) is comprised of ~92 nuclear and mitochondrial DNA-encoded protein subunits that are organized into five different multi-subunit respiratory complexes. These complexes produce 90% of the ATP required for cell sustenance. Specific sets of subunits are assembled in a modular or non-modular fashion to construct the MRC complexes. The complete assembly process is gradually chaperoned by a myriad of assembly factors that must coordinate with several other prosthetic groups to reach maturity, makingthe entire processextensively complicated. Further, the individual respiratory complexes can be integrated intovarious giant super-complexes whose functional roles have yet to be explored. Mutations in the MRC subunits and in the related assembly factors often give rise to defects in the proper assembly of the respiratory chain, which then manifests as a group of disorders called mitochondrial diseases, the most common inborn errors of metabolism. This review summarizes the current understanding of the biogenesis of individual MRC complexes and super-complexes, and explores how mutations in the different subunits and assembly factors contribute to mitochondrial disease pathology.
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Affiliation(s)
- Soumyajit Mukherjee
- Department of Biochemistry, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, India
| | - Alok Ghosh
- Department of Biochemistry, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, India.
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41
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Pfanner N, Warscheid B, Wiedemann N. Mitochondrial proteins: from biogenesis to functional networks. Nat Rev Mol Cell Biol 2020; 20:267-284. [PMID: 30626975 DOI: 10.1038/s41580-018-0092-0] [Citation(s) in RCA: 516] [Impact Index Per Article: 129.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Mitochondria are essential for the viability of eukaryotic cells as they perform crucial functions in bioenergetics, metabolism and signalling and have been associated with numerous diseases. Recent functional and proteomic studies have revealed the remarkable complexity of mitochondrial protein organization. Protein machineries with diverse functions such as protein translocation, respiration, metabolite transport, protein quality control and the control of membrane architecture interact with each other in dynamic networks. In this Review, we discuss the emerging role of the mitochondrial protein import machinery as a key organizer of these mitochondrial protein networks. The preprotein translocases that reside on the mitochondrial membranes not only function during organelle biogenesis to deliver newly synthesized proteins to their final mitochondrial destination but also cooperate with numerous other mitochondrial protein complexes that perform a wide range of functions. Moreover, these protein networks form membrane contact sites, for example, with the endoplasmic reticulum, that are key for integration of mitochondria with cellular function, and defects in protein import can lead to diseases.
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Affiliation(s)
- Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
| | - Bettina Warscheid
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.,Institute of Biology II, Biochemistry - Functional Proteomics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Nils Wiedemann
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
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42
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Timón-Gómez A, Barrientos A. Mitochondrial respiratory chain composition and organization in response to changing oxygen levels. ACTA ACUST UNITED AC 2020; 2. [PMID: 32551463 DOI: 10.36069/jols/20200601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mitochondria are the major consumer of oxygen in eukaryotic cells, owing to the requirement of oxygen to generate ATP through the mitochondrial respiratory chain (MRC) and the oxidative phosphorylation system (OXPHOS). This aerobic energy transduction is more efficient than anaerobic processes such as glycolysis. Hypoxia, a condition in which environmental or intracellular oxygen levels are below the standard range, triggers an adaptive signaling pathway within the cell. When oxygen concentrations are low, hypoxia-inducible factors (HIFs) become stabilized and activated to mount a transcriptional response that triggers modulation of cellular metabolism to adjust to hypoxic conditions. Mitochondrial aerobic metabolism is one of the main targets of the hypoxic response to regulate its functioning and efficiency in the presence of decreased oxygen levels. During evolution, eukaryotic cells and tissues have increased the plasticity of their mitochondrial OXPHOS system to cope with metabolic needs in different oxygen contexts. In mammalian mitochondria, two factors contribute to this plasticity. First, several subunits of the multimeric MRC complexes I and IV exist in multiple tissue-specific and condition-specific isoforms. Second, the MRC enzymes can coexist organized as individual entities or forming supramolecular structures known as supercomplexes, perhaps in a dynamic manner to respond to environmental conditions and cellular metabolic demands. In this review, we will summarize the information currently available on oxygen-related changes in MRC composition and organization and will discuss gaps of knowledge and research opportunities in the field.
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Affiliation(s)
- Alba Timón-Gómez
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Antoni Barrientos
- department of Neurology and Department of Biochemistry and Molecular Biology. University of Miami Miller School of Medicine, Miami, FL 33136
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43
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Pacheu-Grau D, Wasilewski M, Oeljeklaus S, Gibhardt CS, Aich A, Chudenkova M, Dennerlein S, Deckers M, Bogeski I, Warscheid B, Chacinska A, Rehling P. COA6 Facilitates Cytochrome c Oxidase Biogenesis as Thiol-reductase for Copper Metallochaperones in Mitochondria. J Mol Biol 2020; 432:2067-2079. [PMID: 32061935 PMCID: PMC7254062 DOI: 10.1016/j.jmb.2020.01.036] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/23/2020] [Accepted: 01/27/2020] [Indexed: 12/15/2022]
Abstract
The mitochondrial cytochrome c oxidase, the terminal enzyme of the respiratory chain, contains heme and copper centers for electron transfer. The conserved COX2 subunit contains the CuA site, a binuclear copper center. The copper chaperones SCO1, SCO2, and COA6, are required for CuA center formation. Loss of function of these chaperones and the concomitant cytochrome c oxidase deficiency cause severe human disorders. Here we analyzed the molecular function of COA6 and the consequences of COA6 deficiency for mitochondria. Our analyses show that loss of COA6 causes combined complex I and complex IV deficiency and impacts membrane potential-driven protein transport across the inner membrane. We demonstrate that COA6 acts as a thiol-reductase to reduce disulfide bridges of critical cysteine residues in SCO1 and SCO2. Cysteines within the CX3CXNH domain of SCO2 mediate its interaction with COA6 but are dispensable for SCO2–SCO1 interaction. Our analyses define COA6 as thiol-reductase, which is essential for CuA biogenesis. Loss of COA6 affects respiratory chain complexes IV and I. Decreased membrane potential-driven protein import due to loss of COA6. Cysteine residues in the CX3CXNH motif of SCO2 mediate COA6 interaction. COA6 acts as thiol reductase for copper metallochaperones during CuA biogenesis.
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Affiliation(s)
- David Pacheu-Grau
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany.
| | - Michał Wasilewski
- Laboratory of Mitochondrial Biogenesis, Centre of New Technologies, University of Warsaw, Warsaw, Poland; ReMedy International Research Agenda Unit, Centre of New Technologies, University of Warsaw, Poland
| | - Silke Oeljeklaus
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, D-79104 Freiburg, Germany
| | - Christine Silvia Gibhardt
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Abhishek Aich
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Margarita Chudenkova
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Sven Dennerlein
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Markus Deckers
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Ivan Bogeski
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Bettina Warscheid
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, D-79104 Freiburg, Germany
| | - Agnieszka Chacinska
- Laboratory of Mitochondrial Biogenesis, Centre of New Technologies, University of Warsaw, Warsaw, Poland; ReMedy International Research Agenda Unit, Centre of New Technologies, University of Warsaw, Poland
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany; Max-Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany.
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44
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Protasoni M, Pérez‐Pérez R, Lobo‐Jarne T, Harbour ME, Ding S, Peñas A, Diaz F, Moraes CT, Fearnley IM, Zeviani M, Ugalde C, Fernández‐Vizarra E. Respiratory supercomplexes act as a platform for complex III-mediated maturation of human mitochondrial complexes I and IV. EMBO J 2020; 39:e102817. [PMID: 31912925 PMCID: PMC6996572 DOI: 10.15252/embj.2019102817] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 11/02/2019] [Accepted: 11/26/2019] [Indexed: 02/02/2023] Open
Abstract
Mitochondrial respiratory chain (MRC) enzymes associate in supercomplexes (SCs) that are structurally interdependent. This may explain why defects in a single component often produce combined enzyme deficiencies in patients. A case in point is the alleged destabilization of complex I in the absence of complex III. To clarify the structural and functional relationships between complexes, we have used comprehensive proteomic, functional, and biogenetical approaches to analyze a MT-CYB-deficient human cell line. We show that the absence of complex III blocks complex I biogenesis by preventing the incorporation of the NADH module rather than decreasing its stability. In addition, complex IV subunits appeared sequestered within complex III subassemblies, leading to defective complex IV assembly as well. Therefore, we propose that complex III is central for MRC maturation and SC formation. Our results challenge the notion that SC biogenesis requires the pre-formation of fully assembled individual complexes. In contrast, they support a cooperative-assembly model in which the main role of complex III in SCs is to provide a structural and functional platform for the completion of overall MRC biogenesis.
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Affiliation(s)
- Margherita Protasoni
- Medical Research Council‐Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | | | | | - Michael E Harbour
- Medical Research Council‐Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | - Shujing Ding
- Medical Research Council‐Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | - Ana Peñas
- Instituto de Investigación Hospital 12 de Octubre (i+12)MadridSpain
| | - Francisca Diaz
- Department of NeurologyMiller School of MedicineUniversity of MiamiMiamiFLUSA
| | - Carlos T Moraes
- Department of NeurologyMiller School of MedicineUniversity of MiamiMiamiFLUSA
| | - Ian M Fearnley
- Medical Research Council‐Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | - Massimo Zeviani
- Medical Research Council‐Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
- Department of NeurosciencesUniversity of PadovaPadovaItaly
| | - Cristina Ugalde
- Instituto de Investigación Hospital 12 de Octubre (i+12)MadridSpain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723MadridSpain
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45
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Dawitz H, Schäfer J, Schaart JM, Magits W, Brzezinski P, Ott M. Rcf1 Modulates Cytochrome c Oxidase Activity Especially Under Energy-Demanding Conditions. Front Physiol 2020; 10:1555. [PMID: 32009973 PMCID: PMC6971206 DOI: 10.3389/fphys.2019.01555] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 12/10/2019] [Indexed: 12/17/2022] Open
Abstract
The mitochondrial respiratory chain is assembled into supercomplexes. Previously, two respiratory supercomplex-associated proteins, Rcf1 and Rcf2, were identified in Saccharomyces cerevisiae, which were initially suggested to mediate supercomplex formation. Recent evidence suggests that these factors instead are involved in cytochrome c oxidase biogenesis. We demonstrate here that Rcf1 mediates proper function of cytochrome c oxidase, while binding of Rcf2 results in a decrease of cytochrome c oxidase activity. Chemical crosslink experiments demonstrate that the conserved Hig-domain as well as the fungi specific C-terminus of Rcf1 are involved in molecular interactions with the cytochrome c oxidase subunit Cox3. We propose that Rcf1 modulates cytochrome c oxidase activity by direct binding to the oxidase to trigger changes in subunit Cox1, which harbors the catalytic site. Additionally, Rcf1 interaction with cytochrome c oxidase in the supercomplexes increases under respiratory conditions. These observations indicate that Rcf1 could enable the tuning of the respiratory chain depending on metabolic needs or repair damages at the catalytic site.
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Affiliation(s)
- Hannah Dawitz
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Jacob Schäfer
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Judith M Schaart
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Wout Magits
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Martin Ott
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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Novack GV, Galeano P, Castaño EM, Morelli L. Mitochondrial Supercomplexes: Physiological Organization and Dysregulation in Age-Related Neurodegenerative Disorders. Front Endocrinol (Lausanne) 2020; 11:600. [PMID: 33042002 PMCID: PMC7518391 DOI: 10.3389/fendo.2020.00600] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 07/22/2020] [Indexed: 12/16/2022] Open
Abstract
Several studies suggest that the assembly of mitochondrial respiratory complexes into structures known as supercomplexes (SCs) may increase the efficiency of the electron transport chain, reducing the rate of production of reactive oxygen species. Therefore, the study of the (dis)assembly of SCs may be relevant for the understanding of mitochondrial dysfunction reported in brain aging and major neurodegenerative disorders such as Alzheimer's disease (AD) and Parkinson's disease (PD). Here we briefly reviewed the biogenesis and structural properties of SCs, the impact of mtDNA mutations and mitochondrial dynamics on SCs assembly, the role of lipids on stabilization of SCs and the methodological limitations for the study of SCs. More specifically, we summarized what is known about mitochondrial dysfunction and SCs organization and activity in aging, AD and PD. We focused on the critical variables to take into account when postmortem tissues are used to study the (dis)assembly of SCs. Since few works have been performed to study SCs in AD and PD, the impact of SCs dysfunction on the alteration of brain energetics in these diseases remains poorly understood. The convergence of future progress in the study of SCs structure at high resolution and the refinement of animal models of AD and PD, as well as the use of iPSC-based and somatic cell-derived neurons, will be critical in understanding the biological relevance of the structural remodeling of SCs.
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Lian J, Schultz C, Cao M, HamediRad M, Zhao H. Multi-functional genome-wide CRISPR system for high throughput genotype-phenotype mapping. Nat Commun 2019; 10:5794. [PMID: 31857575 PMCID: PMC6923430 DOI: 10.1038/s41467-019-13621-4] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 11/12/2019] [Indexed: 01/20/2023] Open
Abstract
Genome-scale engineering is an indispensable tool to understand genome functions due to our limited knowledge of cellular networks. Unfortunately, most existing methods for genome-wide genotype–phenotype mapping are limited to a single mode of genomic alteration, i.e. overexpression, repression, or deletion. Here we report a multi-functional genome-wide CRISPR (MAGIC) system to precisely control the expression level of defined genes to desired levels throughout the whole genome. By combining the tri-functional CRISPR system and array-synthesized oligo pools, MAGIC is used to create, to the best of our knowledge, one of the most comprehensive and diversified genomic libraries in yeast ever reported. The power of MAGIC is demonstrated by the identification of previously uncharacterized genetic determinants of complex phenotypes, particularly those having synergistic interactions when perturbed to different expression levels. MAGIC represents a powerful synthetic biology tool to investigate fundamental biological questions as well as engineer complex phenotypes for biotechnological applications. Genome-scale engineering is generally limited to single methods of alteration such as overexpression, repression or deletion. Here the authors present a tri-functional CRISPR system that can engineer complex synergistic interactions in a genome-wide manner.
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Affiliation(s)
- Jiazhang Lian
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, 310027, Hangzhou, China
| | - Carl Schultz
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Mingfeng Cao
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Mohammad HamediRad
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Lifefoundry Inc., 60 Hazelwood Dr., Champaign, IL, 61820, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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Nagao T, Shintani Y, Hayashi T, Kioka H, Kato H, Nishida Y, Yamazaki S, Tsukamoto O, Yashirogi S, Yazawa I, Asano Y, Shinzawa-Itoh K, Imamura H, Suzuki T, Suzuki T, Goto YI, Takashima S. Higd1a improves respiratory function in the models of mitochondrial disorder. FASEB J 2019; 34:1859-1871. [PMID: 31914602 DOI: 10.1096/fj.201800389r] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/26/2018] [Accepted: 06/12/2018] [Indexed: 12/22/2022]
Abstract
The respiratory chain (RC) transports electrons to form a proton motive force that is required for ATP synthesis in the mitochondria. RC disorders cause mitochondrial diseases that have few effective treatments; therefore, novel therapeutic strategies are critically needed. We previously identified Higd1a as a positive regulator of cytochrome c oxidase (CcO) in the RC. Here, we test that Higd1a has a beneficial effect by increasing CcO activity in the models of mitochondrial dysfunction. We first demonstrated the tissue-protective effects of Higd1a via in situ measurement of mitochondrial ATP concentrations ([ATP]mito) in a zebrafish hypoxia model. Heart-specific Higd1a overexpression mitigated the decline in [ATP]mito under hypoxia and preserved cardiac function in zebrafish. Based on the in vivo results, we examined the effects of exogenous HIGD1A on three cellular models of mitochondrial disease; notably, HIGD1A improved respiratory function that was coupled with increased ATP synthesis and demonstrated cellular protection in all three models. Finally, enzyme kinetic analysis revealed that Higd1a significantly increased the maximal velocity of the reaction between CcO and cytochrome c without changing the affinity between them, indicating that Higd1a is a positive modulator of CcO. These results corroborate that Higd1a, or its mimic, provides therapeutic options for the treatment of mitochondrial diseases.
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Affiliation(s)
- Takemasa Nagao
- Department of Medical Biochemistry, Graduate School of Frontier Biological Science, Osaka University, Suita, Japan
| | - Yasunori Shintani
- Department of Medical Biochemistry, Graduate School of Frontier Biological Science, Osaka University, Suita, Japan
| | - Takaharu Hayashi
- Department of Cardiovascular Medicine, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Hidetaka Kioka
- Department of Cardiovascular Medicine, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Hisakazu Kato
- Department of Medical Biochemistry, Graduate School of Frontier Biological Science, Osaka University, Suita, Japan
| | - Yuya Nishida
- Department of Medical Biochemistry, Graduate School of Frontier Biological Science, Osaka University, Suita, Japan.,Japan Science and Technology Agency-Core Research for Evolutional Science and Technology (CREST), Kawaguchi, Japan
| | - Satoru Yamazaki
- Department of Cell Biology, National Cerebral and Cardiovascular Center, Suita, Japan
| | - Osamu Tsukamoto
- Department of Medical Biochemistry, Graduate School of Frontier Biological Science, Osaka University, Suita, Japan
| | - Shohei Yashirogi
- Department of Medical Biochemistry, Graduate School of Frontier Biological Science, Osaka University, Suita, Japan
| | - Issei Yazawa
- Department of Medical Biochemistry, Graduate School of Frontier Biological Science, Osaka University, Suita, Japan
| | - Yoshihiro Asano
- Department of Cardiovascular Medicine, Graduate School of Medicine, Osaka University, Suita, Japan
| | | | - Hiromi Imamura
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Yu-Ichi Goto
- Department of Child Neurology, National Center Hospital of Neurology and Psychiatry (NCNP), Kodaira, Japan
| | - Seiji Takashima
- Department of Medical Biochemistry, Graduate School of Frontier Biological Science, Osaka University, Suita, Japan.,Japan Science and Technology Agency-Core Research for Evolutional Science and Technology (CREST), Kawaguchi, Japan
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Barros MH, McStay GP. Modular biogenesis of mitochondrial respiratory complexes. Mitochondrion 2019; 50:94-114. [PMID: 31669617 DOI: 10.1016/j.mito.2019.10.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/04/2019] [Accepted: 10/10/2019] [Indexed: 11/29/2022]
Abstract
Mitochondrial function relies on the activity of oxidative phosphorylation to synthesise ATP and generate an electrochemical gradient across the inner mitochondrial membrane. These coupled processes are mediated by five multi-subunit complexes that reside in this inner membrane. These complexes are the product of both nuclear and mitochondrial gene products. Defects in the function or assembly of these complexes can lead to mitochondrial diseases due to deficits in energy production and mitochondrial functions. Appropriate biogenesis and function are mediated by a complex number of assembly factors that promote maturation of specific complex subunits to form the active oxidative phosphorylation complex. The understanding of the biogenesis of each complex has been informed by studies in both simple eukaryotes such as Saccharomyces cerevisiae and human patients with mitochondrial diseases. These studies reveal each complex assembles through a pathway using specific subunits and assembly factors to form kinetically distinct but related assembly modules. The current understanding of these complexes has embraced the revolutions in genomics and proteomics to further our knowledge on the impact of mitochondrial biology in genetics, medicine, and evolution.
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Affiliation(s)
- Mario H Barros
- Departamento de Microbiologia - Instituto de Ciências Biomédicas, Universidade de São Paulo, Brazil.
| | - Gavin P McStay
- Department of Biological Sciences, Staffordshire University, Stoke-on-Trent, United Kingdom.
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