1
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Hevler JF, Heck AJR. Higher-Order Structural Organization of the Mitochondrial Proteome Charted by In Situ Cross-Linking Mass Spectrometry. Mol Cell Proteomics 2023; 22:100657. [PMID: 37805037 PMCID: PMC10651688 DOI: 10.1016/j.mcpro.2023.100657] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 09/14/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023] Open
Abstract
Mitochondria are densely packed with proteins, of which most are involved physically or more transiently in protein-protein interactions (PPIs). Mitochondria host among others all enzymes of the Krebs cycle and the oxidative phosphorylation pathway and are foremost associated with cellular bioenergetics. However, mitochondria are also important contributors to apoptotic cell death and contain their own genome indicating that they play additionally an eminent role in processes beyond bioenergetics. Despite intense efforts in identifying and characterizing mitochondrial protein complexes by structural biology and proteomics techniques, many PPIs have remained elusive. Several of these (membrane embedded) PPIs are less stable in vitro hampering their characterization by most contemporary methods in structural biology. Particularly in these cases, cross-linking mass spectrometry (XL-MS) has proven valuable for the in-depth characterization of mitochondrial protein complexes in situ. Here, we highlight experimental strategies for the analysis of proteome-wide PPIs in mitochondria using XL-MS. We showcase the ability of in situ XL-MS as a tool to map suborganelle interactions and topologies and aid in refining structural models of protein complexes. We describe some of the most recent technological advances in XL-MS that may benefit the in situ characterization of PPIs even further, especially when combined with electron microscopy and structural modeling.
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Affiliation(s)
- Johannes F Hevler
- Division of Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Albert J R Heck
- Division of Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands.
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2
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Mitochondrial cristae in health and disease. Int J Biol Macromol 2023; 235:123755. [PMID: 36812974 DOI: 10.1016/j.ijbiomac.2023.123755] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/20/2023] [Accepted: 02/09/2023] [Indexed: 02/22/2023]
Abstract
Mitochondria are centers of energy metabolism. The mitochondrial network is shaped by mitochondrial dynamics, including the processes of mitochondrial fission and fusion and cristae remodeling. The cristae folded by the inner mitochondrial membrane are sites of the mitochondrial oxidative phosphorylation (OXPHOS) system. However, the factors and their coordinated interplay in cristae remodeling and linked human diseases have not been fully demonstrated. In this review, we focus on key regulators of cristae structure, including the mitochondrial contact site and cristae organizing system, optic atrophy-1, mitochondrial calcium uniporter, and ATP synthase, which function in the dynamic remodeling of cristae. We summarized their contribution to sustaining functional cristae structure and abnormal cristae morphology, including a decreased number of cristae, enlarged cristae junctions, and cristae as concentric ring structures. These abnormalities directly impact cellular respiration and are caused by dysfunction or deletion of these regulators in diseases such as Parkinson's disease, Leigh syndrome, and dominant optic atrophy. Identifying the important regulators of cristae morphology and understanding their role in sustaining mitochondrial morphology could be applied to explore the pathologies of diseases and to develop relevant therapeutic tools.
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3
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Bassot A, Morio B, Bortoli S, Coumoul X. Le B-A-BA de la mitochondrie, une cheffe d’orchestre intracellulaire très dynamique. CAHIERS DE NUTRITION ET DE DIÉTÉTIQUE 2022. [DOI: 10.1016/j.cnd.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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4
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Ley-Ngardigal S, Bertolin G. Approaches to monitor ATP levels in living cells: where do we stand? FEBS J 2022; 289:7940-7969. [PMID: 34437768 DOI: 10.1111/febs.16169] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/30/2021] [Accepted: 08/25/2021] [Indexed: 01/14/2023]
Abstract
ATP is the most universal and essential energy molecule in cells. This is due to its ability to store cellular energy in form of high-energy phosphate bonds, which are extremely stable and readily usable by the cell. This energy is key for a variety of biological functions such as cell growth and division, metabolism, and signaling, and for the turnover of biomolecules. Understanding how ATP is produced and hydrolyzed with a spatiotemporal resolution is necessary to understand its functions both in physiological and in pathological contexts. In this review, first we will describe the organization of the electron transport chain and ATP synthase, the main molecular motor for ATP production in mitochondria. Second, we will review the biochemical assays currently available to estimate ATP quantities in cells, and we will compare their readouts, strengths, and weaknesses. Finally, we will explore the palette of genetically encoded biosensors designed for microscopy-based approaches, and show how their spatiotemporal resolution opened up the possibility to follow ATP levels in living cells.
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Affiliation(s)
- Seyta Ley-Ngardigal
- CNRS, Univ Rennes, IGDR (Genetics and Development Institute of Rennes), Rennes, France.,LVMH Research Perfumes and Cosmetics, Saint-Jean-de-Braye, France
| | - Giulia Bertolin
- CNRS, Univ Rennes, IGDR (Genetics and Development Institute of Rennes), Rennes, France
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5
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Aass KR, Mjelle R, Kastnes MH, Tryggestad SS, van den Brink LM, Aass Roseth I, Westhrin M, Zahoor M, Moen SH, Vikene Nedal TM, Buene G, Misund K, Sponaas AM, Ma Q, Sundan A, Groen RW, Slørdahl TS, Waage A, Standal T. Intracellular IL-32 regulates mitochondrial metabolism, proliferation, and differentiation of malignant plasma cells. iScience 2022; 25:103605. [PMID: 35005550 PMCID: PMC8717606 DOI: 10.1016/j.isci.2021.103605] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 10/13/2021] [Accepted: 12/08/2021] [Indexed: 02/06/2023] Open
Abstract
Interleukin-32 (IL-32) is a nonclassical cytokine expressed in cancers, inflammatory diseases, and infections. Its expression is regulated by two different oxygen sensing systems; HIF1α and cysteamine dioxygenase (ADO), indicating that IL-32 may be involved in the response to hypoxia. We here demonstrate that endogenously expressed, intracellular IL-32 interacts with components of the mitochondrial respiratory chain and promotes oxidative phosphorylation. Knocking out IL-32 in three myeloma cell lines reduced cell survival and proliferation in vitro and in vivo. High-throughput transcriptomic and MS-metabolomic profiling of IL-32 KO cells revealed that cells depleted of IL-32 had perturbations in metabolic pathways, with accumulation of lipids, pyruvate precursors, and citrate. IL-32 was expressed in a subgroup of myeloma patients with inferior survival, and primary myeloma cells expressing IL-32 had a gene signature associated with immaturity, proliferation, and oxidative phosphorylation. In conclusion, we demonstrate a previously unrecognized role of IL-32 in the regulation of plasma cell metabolism. Intracellular IL-32 is an endogenous growth factor for malignant plasma cells IL-32 interacts with components of the electron transport chain IL-32 promotes oxidative phosphorylation IL-32 is expressed by immature, CD45 + highly proliferating malignant plasma cells
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Affiliation(s)
- Kristin Roseth Aass
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim 7491, Norway.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Robin Mjelle
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Martin H Kastnes
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim 7491, Norway.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Synne S Tryggestad
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim 7491, Norway.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Luca M van den Brink
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Ingrid Aass Roseth
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim 7491, Norway.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Marita Westhrin
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Muhammad Zahoor
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo 0372, Norway
| | - Siv H Moen
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim 7491, Norway.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Tonje M Vikene Nedal
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim 7491, Norway.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Glenn Buene
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim 7491, Norway.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Kristine Misund
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Anne-Marit Sponaas
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Qianli Ma
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim 7491, Norway.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Anders Sundan
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim 7491, Norway.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Richard Wj Groen
- Department of Hematology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam 1081, the Netherlands
| | - Tobias S Slørdahl
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim 7491, Norway.,Department of Hematology, St.Olavs University Hospital, Trondheim 7491, Norway
| | - Anders Waage
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim 7491, Norway.,Department of Hematology, St.Olavs University Hospital, Trondheim 7491, Norway
| | - Therese Standal
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim 7491, Norway.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim 7491, Norway.,Department of Hematology, St.Olavs University Hospital, Trondheim 7491, Norway
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6
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Dong SXM, Vizeacoumar FS, Bhanumathy KK, Alli N, Gonzalez-Lopez C, Gajanayaka N, Caballero R, Ali H, Freywald A, Cassol E, Angel JB, Vizeacoumar FJ, Kumar A. Identification of novel genes involved in apoptosis of HIV-infected macrophages using unbiased genome-wide screening. BMC Infect Dis 2021; 21:655. [PMID: 34233649 PMCID: PMC8261936 DOI: 10.1186/s12879-021-06346-7] [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: 11/15/2020] [Accepted: 06/15/2021] [Indexed: 12/01/2022] Open
Abstract
Background Macrophages, besides resting latently infected CD4+ T cells, constitute the predominant stable, major non-T cell HIV reservoirs. Therefore, it is essential to eliminate both latently infected CD4+ T cells and tissue macrophages to completely eradicate HIV in patients. Until now, most of the research focus is directed towards eliminating latently infected CD4+ T cells. However, few approaches have been directed at killing of HIV-infected macrophages either in vitro or in vivo. HIV infection dysregulates the expression of many host genes essential for the survival of infected cells. We postulated that exploiting this alteration may yield novel targets for the selective killing of infected macrophages. Methods We applied a pooled shRNA-based genome-wide approach by employing a lentivirus-based library of shRNAs to screen novel gene targets whose inhibition should selectively induce apoptosis in HIV-infected macrophages. Primary human MDMs were infected with HIV-eGFP and HIV-HSA viruses. Infected MDMs were transfected with siRNAs specific for the promising genes followed by analysis of apoptosis by flow cytometry using labelled Annexin-V in HIV-infected, HIV-exposed but uninfected bystander MDMs and uninfected MDMs. The results were analyzed using student’s t-test from at least four independent experiments. Results We validated 28 top hits in two independent HIV infection models. This culminated in the identification of four target genes, Cox7a2, Znf484, Cstf2t, and Cdk2, whose loss-of-function induced apoptosis preferentially in HIV-infected macrophages. Silencing these single genes killed significantly higher number of HIV-HSA-infected MDMs compared to the HIV-HSA-exposed, uninfected bystander macrophages, indicating the specificity in the killing of HIV-infected macrophages. The mechanism governing Cox7a2-mediated apoptosis of HIV-infected macrophages revealed that targeting respiratory chain complex II and IV genes also selectively induced apoptosis of HIV-infected macrophages possibly through enhanced ROS production. Conclusions We have identified above-mentioned novel genes and specifically the respiratory chain complex II and IV genes whose silencing may cause selective elimination of HIV-infected macrophages and eventually the HIV-macrophage reservoirs. The results highlight the potential of the identified genes as targets for eliminating HIV-infected macrophages in physiological environment as part of an HIV cure strategy. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06346-7.
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Affiliation(s)
- Simon X M Dong
- Apoptosis Research Center, Children's Hospital of Eastern Ontario, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,Department of Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Frederick S Vizeacoumar
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kalpana K Bhanumathy
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Nezeka Alli
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Niranjala Gajanayaka
- Apoptosis Research Center, Children's Hospital of Eastern Ontario, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Ramon Caballero
- Apoptosis Research Center, Children's Hospital of Eastern Ontario, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,Department of Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Hamza Ali
- Apoptosis Research Center, Children's Hospital of Eastern Ontario, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,Department of Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Andrew Freywald
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Edana Cassol
- Department of Health Sciences, Carleton University, Ottawa, ON, Canada
| | - Jonathan B Angel
- Department of Medicine, the Ottawa Health Research Institute, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Franco J Vizeacoumar
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada. .,Cancer Research, Saskatchewan Cancer Agency, 107 Wiggins Road, Saskatoon, SK, Canada.
| | - Ashok Kumar
- Apoptosis Research Center, Children's Hospital of Eastern Ontario, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada. .,Department of Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada. .,Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
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7
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Knapp-Wilson A, Pereira GC, Buzzard E, Ford HC, Richardson A, Corey RA, Neal C, Verkade P, Halestrap AP, Gold VAM, Kuwabara PE, Collinson I. Maintenance of complex I and its supercomplexes by NDUF-11 is essential for mitochondrial structure, function and health. J Cell Sci 2021; 134:jcs258399. [PMID: 34106255 PMCID: PMC8277142 DOI: 10.1242/jcs.258399] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 05/28/2021] [Indexed: 12/22/2022] Open
Abstract
Mitochondrial supercomplexes form around a conserved core of monomeric complex I and dimeric complex III; wherein a subunit of the former, NDUFA11, is conspicuously situated at the interface. We identified nduf-11 (B0491.5) as encoding the Caenorhabditis elegans homologue of NDUFA11. Animals homozygous for a CRISPR-Cas9-generated knockout allele of nduf-11 arrested at the second larval (L2) development stage. Reducing (but not eliminating) expression using RNAi allowed development to adulthood, enabling characterisation of the consequences: destabilisation of complex I and its supercomplexes and perturbation of respiratory function. The loss of NADH dehydrogenase activity was compensated by enhanced complex II activity, with the potential for detrimental reactive oxygen species (ROS) production. Cryo-electron tomography highlighted aberrant morphology of cristae and widening of both cristae junctions and the intermembrane space. The requirement of NDUF-11 for balanced respiration, mitochondrial morphology and development presumably arises due to its involvement in complex I and supercomplex maintenance. This highlights the importance of respiratory complex integrity for health and the potential for its perturbation to cause mitochondrial disease. This article has an associated First Person interview with Amber Knapp-Wilson, joint first author of the paper.
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Affiliation(s)
| | | | - Emma Buzzard
- Living Systems Institute, Stocker Road, University of Exeter, Exeter EX4 4QD, UK
- College of Life and Environmental Sciences,Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Holly C. Ford
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | | | - Robin A. Corey
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Chris Neal
- Wolfson Bioimaging Facility, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Paul Verkade
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | | | - Vicki A. M. Gold
- Living Systems Institute, Stocker Road, University of Exeter, Exeter EX4 4QD, UK
- College of Life and Environmental Sciences,Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | | | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
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8
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Zhu G, Zeng H, Zhang S, Juli J, Tai L, Zhang D, Pang X, Zhang Y, Lam SM, Zhu Y, Peng G, Michel H, Sun F. The Unusual Homodimer of a Heme‐Copper Terminal Oxidase Allows Itself to Utilize Two Electron Donors. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Guoliang Zhu
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Hui Zeng
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Max-von Laue-Straβe 3 60438 Frankfurt am Main Germany
| | - Shuangbo Zhang
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Jana Juli
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Max-von Laue-Straβe 3 60438 Frankfurt am Main Germany
| | - Linhua Tai
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Danyang Zhang
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Xiaoyun Pang
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
| | - Yan Zhang
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
| | - Sin Man Lam
- LipidALL Technologies Company Limited Changzhou 213022 Jiangsu Province China
- State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology Chinese Academy of Sciences No.1 West Beichen Road, Chaoyang District Beijing 100101 China
| | - Yun Zhu
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Guohong Peng
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Max-von Laue-Straβe 3 60438 Frankfurt am Main Germany
| | - Hartmut Michel
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Max-von Laue-Straβe 3 60438 Frankfurt am Main Germany
| | - Fei Sun
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
- Center for Biological Imaging Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
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9
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Zhu G, Zeng H, Zhang S, Juli J, Tai L, Zhang D, Pang X, Zhang Y, Lam SM, Zhu Y, Peng G, Michel H, Sun F. The Unusual Homodimer of a Heme-Copper Terminal Oxidase Allows Itself to Utilize Two Electron Donors. Angew Chem Int Ed Engl 2021; 60:13323-13330. [PMID: 33665933 PMCID: PMC8251803 DOI: 10.1002/anie.202016785] [Citation(s) in RCA: 4] [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: 12/18/2020] [Indexed: 02/03/2023]
Abstract
The heme-copper oxidase superfamily comprises cytochrome c and ubiquinol oxidases. These enzymes catalyze the transfer of electrons from different electron donors onto molecular oxygen. A B-family cytochrome c oxidase from the hyperthermophilic bacterium Aquifex aeolicus was discovered previously to be able to use both cytochrome c and naphthoquinol as electron donors. Its molecular mechanism as well as the evolutionary significance are yet unknown. Here we solved its 3.4 Å resolution electron cryo-microscopic structure and discovered a novel dimeric structure mediated by subunit I (CoxA2) that would be essential for naphthoquinol binding and oxidation. The unique structural features in both proton and oxygen pathways suggest an evolutionary adaptation of this oxidase to its hyperthermophilic environment. Our results add a new conceptual understanding of structural variation of cytochrome c oxidases in different species.
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Affiliation(s)
- Guoliang Zhu
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Hui Zeng
- Department of Molecular Membrane BiologyMax Planck Institute of BiophysicsMax-von Laue-Straβe 360438Frankfurt am MainGermany
| | - Shuangbo Zhang
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Jana Juli
- Department of Molecular Membrane BiologyMax Planck Institute of BiophysicsMax-von Laue-Straβe 360438Frankfurt am MainGermany
| | - Linhua Tai
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Danyang Zhang
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Xiaoyun Pang
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
| | - Yan Zhang
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
| | - Sin Man Lam
- LipidALL Technologies Company LimitedChangzhou213022Jiangsu ProvinceChina
- State Key Laboratory of Molecular Developmental BiologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesNo.1 West Beichen Road, Chaoyang DistrictBeijing100101China
| | - Yun Zhu
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Guohong Peng
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- Department of Molecular Membrane BiologyMax Planck Institute of BiophysicsMax-von Laue-Straβe 360438Frankfurt am MainGermany
| | - Hartmut Michel
- Department of Molecular Membrane BiologyMax Planck Institute of BiophysicsMax-von Laue-Straβe 360438Frankfurt am MainGermany
| | - Fei Sun
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
- Center for Biological ImagingInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
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10
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Organization of the Respiratory Supercomplexes in Cells with Defective Complex III: Structural Features and Metabolic Consequences. Life (Basel) 2021; 11:life11040351. [PMID: 33920624 PMCID: PMC8074069 DOI: 10.3390/life11040351] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/13/2022] Open
Abstract
The mitochondrial respiratory chain encompasses four oligomeric enzymatic complexes (complex I, II, III and IV) which, together with the redox carrier ubiquinone and cytochrome c, catalyze electron transport coupled to proton extrusion from the inner membrane. The protonmotive force is utilized by complex V for ATP synthesis in the process of oxidative phosphorylation. Respiratory complexes are known to coexist in the membrane as single functional entities and as supramolecular aggregates or supercomplexes (SCs). Understanding the assembly features of SCs has relevant biomedical implications because defects in a single protein can derange the overall SC organization and compromise the energetic function, causing severe mitochondrial disorders. Here we describe in detail the main types of SCs, all characterized by the presence of complex III. We show that the genetic alterations that hinder the assembly of Complex III, not just the activity, cause a rearrangement of the architecture of the SC that can help to preserve a minimal energetic function. Finally, the major metabolic disturbances associated with severe SCs perturbation due to defective complex III are discussed along with interventions that may circumvent these deficiencies.
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11
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Guo L. Mitochondria and the permeability transition pore in cancer metabolic reprogramming. Biochem Pharmacol 2021; 188:114537. [PMID: 33811907 DOI: 10.1016/j.bcp.2021.114537] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 02/07/2023]
Abstract
Mitochondria are a major source of ATP provision as well as cellular suicidal weapon store. Accumulating evidences demonstrate that mitochondrial bioenergetics, biosynthesis and signaling are important mediators of tumorigenesis. Metabolic plasticity enables cancer cell reprogramming to cope with cellular and environmental alterations, a process requires mitochondria biology. Mitochondrial metabolism emerges to be a promising arena for cancer therapeutic targets. The permeability transition pore (PTP) participates in physiological Ca2+ and ROS homeostasis as well as cell death depending on the open state. The hypothesis that PTP forms from F-ATP synthase provides clues to the potential collaborative role of mitochondrial respiration and PTP in regulating cancer cell fate and metabolic reprogramming.
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Affiliation(s)
- Lishu Guo
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, China.
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12
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Glancy B, Kane DA, Kavazis AN, Goodwin ML, Willis WT, Gladden LB. Mitochondrial lactate metabolism: history and implications for exercise and disease. J Physiol 2021; 599:863-888. [PMID: 32358865 PMCID: PMC8439166 DOI: 10.1113/jp278930] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 03/25/2020] [Indexed: 12/31/2022] Open
Abstract
Mitochondrial structures were probably observed microscopically in the 1840s, but the idea of oxidative phosphorylation (OXPHOS) within mitochondria did not appear until the 1930s. The foundation for research into energetics arose from Meyerhof's experiments on oxidation of lactate in isolated muscles recovering from electrical contractions in an O2 atmosphere. Today, we know that mitochondria are actually reticula and that the energy released from electron pairs being passed along the electron transport chain from NADH to O2 generates a membrane potential and pH gradient of protons that can enter the molecular machine of ATP synthase to resynthesize ATP. Lactate stands at the crossroads of glycolytic and oxidative energy metabolism. Based on reported research and our own modelling in silico, we contend that lactate is not directly oxidized in the mitochondrial matrix. Instead, the interim glycolytic products (pyruvate and NADH) are held in cytosolic equilibrium with the products of the lactate dehydrogenase (LDH) reaction and the intermediates of the malate-aspartate and glycerol 3-phosphate shuttles. This equilibrium supplies the glycolytic products to the mitochondrial matrix for OXPHOS. LDH in the mitochondrial matrix is not compatible with the cytoplasmic/matrix redox gradient; its presence would drain matrix reducing power and substantially dissipate the proton motive force. OXPHOS requires O2 as the final electron acceptor, but O2 supply is sufficient in most situations, including exercise and often acute illness. Recent studies suggest that atmospheric normoxia may constitute a cellular hyperoxia in mitochondrial disease. As research proceeds appropriate oxygenation levels should be carefully considered.
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Affiliation(s)
- Brian Glancy
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Daniel A. Kane
- Department of Human Kinetics, St. Francis Xavier University, NS B2G 2W5, Antigonish, Canada
| | | | - Matthew L. Goodwin
- Department of Orthopaedic Surgery, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Wayne T. Willis
- College of Medicine, Department of Medicine, University of Arizona, Tucson, AZ 85724-5099, USA
| | - L. Bruce Gladden
- School of Kinesiology, Auburn University, Auburn, AL 36849-5323, USA
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13
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Ramírez-Camacho I, García-Niño W, Flores-García M, Pedraza-Chaverri J, Zazueta C. Alteration of mitochondrial supercomplexes assembly in metabolic diseases. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165935. [DOI: 10.1016/j.bbadis.2020.165935] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 01/05/2023]
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14
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Gazizova N, Rakhmatullina D, Minibayeva F. Effect of respiratory inhibitors on mitochondrial complexes and ADP/ATP translocators in the Triticum aestivum roots. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 151:601-607. [PMID: 32335383 DOI: 10.1016/j.plaphy.2020.04.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/06/2020] [Accepted: 04/10/2020] [Indexed: 06/11/2023]
Abstract
Effective functioning of the mitochondrial complexes of the oxidative phosphorylation (OXPHOS) system is necessary for ATP synthesis. The OXPHOS complexes exist both as individual forms and supercomplexes, whose formation and stability are supported by specific protein and lipid factors. In this paper, we report on the types and activities of OXPHOS complexes and supercomplexes from wheat (Triticum aestivum L.) root mitochondria analyzed by blue native polyacrylamide gel electrophoresis (BN-PAGE). The activity of OXPHOS complexes decreased when a mixture of rotenone, an inhibitor of complex I, and antimycin A, an inhibitor of complex III (R + AA) was applied to the BN-PAGE gels. By contrast, the types and activities of the OXPHOS complexes and supercomplexes did not change when they were isolated from the R + AA treated roots. However, the amount of the mitochondrial membrane-bound low molecular mass proteins in these roots markedly increased. The proteins were identified as ANT1 and ANT2 (ADP/ATP translocators) and ABA 8'-hydroxylase. We suggest that these low molecular mass proteins contribute to fine control mechanisms that stabilize mitochondrial supercomplexes and help to overcome an inhibitor-induced energy deficit by enhancing ADP/ATP transfer and ultimately improving the supply of ATP.
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Affiliation(s)
- Natalia Gazizova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, PO Box 30, Kazan, 420111, Russia.
| | - Daniya Rakhmatullina
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, PO Box 30, Kazan, 420111, Russia.
| | - Farida Minibayeva
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, PO Box 30, Kazan, 420111, Russia.
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15
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Prusinkiewicz MA, Gameiro SF, Ghasemi F, Dodge MJ, Zeng PYF, Maekebay H, Barrett JW, Nichols AC, Mymryk JS. Survival-Associated Metabolic Genes in Human Papillomavirus-Positive Head and Neck Cancers. Cancers (Basel) 2020; 12:E253. [PMID: 31968678 PMCID: PMC7017314 DOI: 10.3390/cancers12010253] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/12/2020] [Accepted: 01/16/2020] [Indexed: 12/12/2022] Open
Abstract
Human papillomavirus (HPV) causes an increasing number of head and neck squamous cell carcinomas (HNSCCs). Altered metabolism contributes to patient prognosis, but the impact of HPV status on HNSCC metabolism remains relatively uncharacterized. We hypothesize that metabolism-related gene expression differences unique to HPV-positive HNSCC influences patient survival. The Cancer Genome Atlas RNA-seq data from primary HNSCC patient samples were categorized as 73 HPV-positive, 442 HPV-negative, and 43 normal-adjacent control tissues. We analyzed 229 metabolic genes and identified numerous differentially expressed genes between HPV-positive and negative HNSCC patients. HPV-positive carcinomas exhibited lower expression levels of genes involved in glycolysis and higher levels of genes involved in the tricarboxylic acid cycle, oxidative phosphorylation, and β-oxidation than the HPV-negative carcinomas. Importantly, reduced expression of the metabolism-related genes SDHC, COX7A1, COX16, COX17, ELOVL6, GOT2, and SLC16A2 were correlated with improved patient survival only in the HPV-positive group. This work suggests that specific transcriptional alterations in metabolic genes may serve as predictive biomarkers of patient outcome and identifies potential targets for novel therapeutic intervention in HPV-positive head and neck cancers.
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Affiliation(s)
- Martin A. Prusinkiewicz
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Steven F. Gameiro
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Farhad Ghasemi
- Department of Surgery, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Mackenzie J. Dodge
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Peter Y. F. Zeng
- Department of Otolaryngology, Head & Neck Surgery, The University of Western Ontario, London, ON N6A 3K7, Canada; (P.Y.F.Z.)
| | - Hanna Maekebay
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - John W. Barrett
- Department of Otolaryngology, Head & Neck Surgery, The University of Western Ontario, London, ON N6A 3K7, Canada; (P.Y.F.Z.)
| | - Anthony C. Nichols
- Department of Otolaryngology, Head & Neck Surgery, The University of Western Ontario, London, ON N6A 3K7, Canada; (P.Y.F.Z.)
- Department of Oncology, The University of Western Ontario, London, ON N6A 3K7, Canada
- London Regional Cancer Program, Lawson Health Research Institute, London, ON N6C 2R5, Canada
| | - Joe S. Mymryk
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada
- Department of Otolaryngology, Head & Neck Surgery, The University of Western Ontario, London, ON N6A 3K7, Canada; (P.Y.F.Z.)
- Department of Oncology, The University of Western Ontario, London, ON N6A 3K7, Canada
- London Regional Cancer Program, Lawson Health Research Institute, London, ON N6C 2R5, Canada
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16
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Xie T, Wu Z, Gu J, Guo R, Yan X, Duan H, Liu X, Liu W, Liang L, Wan H, Luo Y, Tang D, Shi H, Hu J. The global motion affecting electron transfer in Plasmodium falciparum type II NADH dehydrogenases: a novel non-competitive mechanism for quinoline ketone derivative inhibitors. Phys Chem Chem Phys 2019; 21:18105-18118. [PMID: 31396604 DOI: 10.1039/c9cp02645b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
With the emergence of drug-resistant Plasmodium falciparum, the treatment of malaria has become a significant challenge; therefore, the development of antimalarial drugs acting on new targets is extremely urgent. In Plasmodium falciparum, type II nicotinamide adenine dinucleotide (NADH) dehydrogenase (NDH-2) is responsible for catalyzing the transfer of two electrons from NADH to flavin adenine dinucleotide (FAD), which in turn transfers the electrons to coenzyme Q (CoQ). As an entry enzyme for oxidative phosphorylation, NDH-2 has become one of the popular targets for the development of new antimalarial drugs. In this study, reliable motion trajectories of the NDH-2 complex with its co-factors (NADH and FAD) and inhibitor, RYL-552, were obtained by comparative molecular dynamics simulations. The influence of cofactor binding on the global motion of NDH-2 was explored through conformational clustering, principal component analysis and free energy landscape. The molecular interactions of NDH-2 before and after its binding with the inhibitor RYL-552 were analyzed, and the key residues and important hydrogen bonds were also determined. The results show that the association of RYL-552 results in the weakening of intramolecular hydrogen bonds and large allosterism of NDH-2. There was a significant positive correlation between the angular change of the key pocket residues in the NADH-FAD-pockets that represents the global functional motion and the change in distance between NADH-C4 and FAD-N5 that represents the electron transfer efficiency. Finally, the possible non-competitive inhibitory mechanism of RYL-552 was proposed. Specifically, the association of inhibitors with NDH-2 significantly affects the global motion mode of NDH-2, leading to widening of the distance between NADH and FAD through cooperative motion induction; this reduces the electron transfer efficiency of the mitochondrial respiratory chain. The simulation results provide useful theoretical guidance for subsequent antimalarial drug design based on the NDH-2 structure and the respiratory chain electron transfer mechanism.
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Affiliation(s)
- Tao Xie
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, Chengdu, 610106, China.
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17
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Zong S, Gu J, Liu T, Guo R, Wu M, Yang M. UQCRFS1N assembles mitochondrial respiratory complex-III into an asymmetric 21-subunit dimer. Protein Cell 2019; 9:586-591. [PMID: 29511933 PMCID: PMC5966358 DOI: 10.1007/s13238-018-0515-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
- Shuai Zong
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jinke Gu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Tianya Liu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Runyu Guo
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Meng Wu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Maojun Yang
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China. .,School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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18
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Šribar J, Kovačič L, Oberčkal J, Ivanušec A, Petan T, Fox JW, Križaj I. The neurotoxic secreted phospholipase A 2 from the Vipera a. ammodytes venom targets cytochrome c oxidase in neuronal mitochondria. Sci Rep 2019; 9:283. [PMID: 30670719 PMCID: PMC6342964 DOI: 10.1038/s41598-018-36461-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 11/16/2018] [Indexed: 12/30/2022] Open
Abstract
The β-neurotoxic secreted phospholipases A2 (sPLA2s) block neuro-muscular transmission by poisoning nerve terminals. Damage inflicted by such sPLA2s (β-ntx) on neuronal mitochondria is characteristic, very similar to that induced by structurally homologous endogenous group IIA sPLA2 when its activity is elevated, as, for example, in the early phase of Alzheimer's disease. Using ammodytoxin (Atx), the β-ntx from the venom of the nose-horned viper (Vipera a. ammodytes), the sPLA2 receptor R25 has been detected in neuronal mitochondria. This receptor has been purified from porcine cerebral cortex mitochondria by a new Atx-affinity-based chromatographic procedure. Mass spectrometry analysis revealed R25 to be the subunit II of cytochrome c oxidase (CCOX), an essential constituent of the respiratory chain complex. CCOX was confirmed as being the first intracellular membrane receptor for sPLA2 by alternative Atx-affinity-labellings of purified CCOX, supported also by the encounter of Atx and CCOX in PC12 cells. This discovery suggests the explanation of the mechanism by which β-ntx hinders production of ATP in poisoned nerve endings. It also provides a new insight into the potential function and dysfunction of endogenous GIIA sPLA2 in mitochondria.
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Affiliation(s)
- Jernej Šribar
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
| | - Lidija Kovačič
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
| | - Jernej Oberčkal
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
| | - Adrijan Ivanušec
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000, Ljubljana, Slovenia
| | - Toni Petan
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
| | - Jay W Fox
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, 22908, USA
| | - Igor Križaj
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia.
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Ounpuu L, Truu L, Shevchuk I, Chekulayev V, Klepinin A, Koit A, Tepp K, Puurand M, Rebane-Klemm E, Käämbre T. Comparative analysis of the bioenergetics of human adenocarcinoma Caco-2 cell line and postoperative tissue samples from colorectal cancer patients. Biochem Cell Biol 2018; 96:1-10. [PMID: 30058357 DOI: 10.1139/bcb-2018-0076] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The aim of this work was to explore the key bioenergetic properties for mitochondrial respiration in the widely-used Caco-2 cell line and in human colorectal cancer (HCC) postoperational tissue samples. Oxygraphy and metabolic control analysis (MCA) were applied to estimate the function of oxidative phosphorylation in cultured Caco-2 cells and HCC tissue samples. The mitochondria of Caco-2 cells and HCC tissues displayed larger functional activity of respiratory complex (C)II compared with CI, whereas in normal colon tissue an inverse pattern in the ratio of CI to CII activity was observed. MCA showed that the respiration in Caco-2 and HCC tissue cells is regulated by different parts of electron transport chain. In HCC tissues, this control is performed essentially at the level of respiratory chain complexes I-IV, whereas in Caco-2 cells at the level of CIV (cytochrome c oxidase) and the ATP synthasome. The differences we found in the regulation of respiratory chain activity and glycose index could represent an adaptive response to distinct growth conditions; this highlights the importance of proper validation of results obtained from in-vitro models before their extrapolation to the more complex in-vivo systems.
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Affiliation(s)
- Lyudmila Ounpuu
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
| | - Laura Truu
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
| | - Igor Shevchuk
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
| | - Vladimir Chekulayev
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
| | - Aleksandr Klepinin
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
| | - Andre Koit
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
| | - Kersti Tepp
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
| | - Marju Puurand
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
| | - Egle Rebane-Klemm
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
| | - Tuuli Käämbre
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
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20
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Zong S, Wu M, Gu J, Liu T, Guo R, Yang M. Structure of the intact 14-subunit human cytochrome c oxidase. Cell Res 2018; 28:1026-1034. [PMID: 30030519 DOI: 10.1038/s41422-018-0071-1] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 06/23/2018] [Accepted: 07/03/2018] [Indexed: 01/14/2023] Open
Abstract
Respiration is one of the most basic features of living organisms, and the electron transport chain complexes are probably the most complicated protein system in mitochondria. Complex-IV is the terminal enzyme of the electron transport chain, existing either as randomly scattered complexes or as a component of supercomplexes. NDUFA4 was previously assumed as a subunit of complex-I, but recent biochemical data suggested it may be a subunit of complex-IV. However, no structural evidence supporting this notion was available till now. Here we obtained the 3.3 Å resolution structure of complex-IV derived from the human supercomplex I1III2IV1 and assigned the NDUFA4 subunit into complex-IV. Intriguingly, NDUFA4 lies exactly at the dimeric interface observed in previously reported crystal structures of complex-IV homodimer which would preclude complex-IV dimerization. Combining previous structural and biochemical data shown by us and other groups, we propose that the intact complex-IV is a monomer containing 14 subunits.
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Affiliation(s)
- Shuai Zong
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Meng Wu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jinke Gu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Tianya Liu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Runyu Guo
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Maojun Yang
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China. .,School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.
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21
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Guo R, Gu J, Zong S, Wu M, Yang M. Structure and mechanism of mitochondrial electron transport chain. Biomed J 2018; 41:9-20. [PMID: 29673555 PMCID: PMC6138618 DOI: 10.1016/j.bj.2017.12.001] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 11/16/2017] [Accepted: 12/01/2017] [Indexed: 12/22/2022] Open
Abstract
Respiration is one of the most vital and basic features of living organisms. In mammals, respiration is accomplished by respiratory chain complexes located on the mitochondrial inner membrane. In the past century, scientists put tremendous efforts in understanding these complexes, but failed to solve the high resolution structure until recently. In 2016, three research groups reported the structure of respiratory chain supercomplex from different species, and fortunately the structure solved by our group has the highest resolution. In this review, we will compare the recently solved structures of respirasome, probe into the relationship between cristae shape and respiratory chain organization, and discuss the highly disputed issues afterwards. Besides, our group reported the first high resolution structure of respirasome and medium resolution structure of megacomplex from cultured human cells this year. Definitely, these supercomplex structures will provide precious information for conquering the mitochondrial malfunction diseases.
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Affiliation(s)
- Runyu Guo
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing, China; Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jinke Gu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing, China; Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Shuai Zong
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing, China; Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Meng Wu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing, China; Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Maojun Yang
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing, China; Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.
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22
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Solution NMR structure of yeast Rcf1, a protein involved in respiratory supercomplex formation. Proc Natl Acad Sci U S A 2018; 115:3048-3053. [PMID: 29507228 DOI: 10.1073/pnas.1712061115] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The Saccharomyces cerevisiae respiratory supercomplex factor 1 (Rcf1) protein is located in the mitochondrial inner membrane where it is involved in formation of supercomplexes composed of respiratory complexes III and IV. We report the solution structure of Rcf1, which forms a dimer in dodecylphosphocholine (DPC) micelles, where each monomer consists of a bundle of five transmembrane (TM) helices and a short flexible soluble helix (SH). Three TM helices are unusually charged and provide the dimerization interface consisting of 10 putative salt bridges, defining a "charge zipper" motif. The dimer structure is supported by molecular dynamics (MD) simulations in DPC, although the simulations show a more dynamic dimer interface than the NMR data. Furthermore, CD and NMR data indicate that Rcf1 undergoes a structural change when reconstituted in liposomes, which is supported by MD data, suggesting that the dimer structure is unstable in a planar membrane environment. Collectively, these data indicate a dynamic monomer-dimer equilibrium. Furthermore, the Rcf1 dimer interacts with cytochrome c, suggesting a role as an electron-transfer bridge between complexes III and IV. The Rcf1 structure will help in understanding its functional roles at a molecular level.
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Derbikova KS, Levitsky SA, Chicherin IV, Vinogradova EN, Kamenski PA. Activation of Yeast Mitochondrial Translation: Who Is in Charge? BIOCHEMISTRY (MOSCOW) 2018; 83:87-97. [DOI: 10.1134/s0006297918020013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part I. [4Fe-4S] + [2Fe-2S] iron-sulfur proteins. J Struct Biol 2017; 200:1-19. [DOI: 10.1016/j.jsb.2017.05.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/25/2017] [Indexed: 01/08/2023]
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Borrero-de Acuña JM, Timmis KN, Jahn M, Jahn D. Protein complex formation during denitrification by Pseudomonas aeruginosa. Microb Biotechnol 2017; 10:1523-1534. [PMID: 28857512 PMCID: PMC5658584 DOI: 10.1111/1751-7915.12851] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 12/18/2022] Open
Abstract
The most efficient means of generating cellular energy is through aerobic respiration. Under anaerobic conditions, several prokaryotes can replace oxygen by nitrate as final electron acceptor. During denitrification, nitrate is reduced via nitrite, NO and N2O to molecular nitrogen (N2) by four membrane‐localized reductases with the simultaneous formation of an ion gradient for ATP synthesis. These four multisubunit enzyme complexes are coupled in four electron transport chains to electron donating primary dehydrogenases and intermediate electron transfer proteins. Many components require membrane transport and insertion, complex assembly and cofactor incorporation. All these processes are mediated by fine‐tuned stable and transient protein–protein interactions. Recently, an interactomic approach was used to determine the exact protein–protein interactions involved in the assembly of the denitrification apparatus of Pseudomonas aeruginosa. Both subunits of the NO reductase NorBC, combined with the flavoprotein NosR, serve as a membrane‐localized assembly platform for the attachment of the nitrate reductase NarGHI, the periplasmic nitrite reductase NirS via its maturation factor NirF and the N2O reductase NosZ through NosR. A nitrate transporter (NarK2), the corresponding regulatory system NarXL, various nitrite (NirEJMNQ) and N2O reductase (NosFL) maturation proteins are also part of the complex. Primary dehydrogenases, ATP synthase, most enzymes of the TCA cycle, and the SEC protein export system, as well as a number of other proteins, were found to interact with the denitrification complex. Finally, a protein complex composed of the flagella protein FliC, nitrite reductase NirS and the chaperone DnaK required for flagella formation was found in the periplasm of P. aeruginosa. This work demonstrated that the interactomic approach allows for the identification and characterization of stable and transient protein–protein complexes and interactions involved in the assembly and function of multi‐enzyme complexes.
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Affiliation(s)
| | - Kenneth N Timmis
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, Braunschweig, Germany
| | - Martina Jahn
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, Braunschweig, Germany
| | - Dieter Jahn
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology BRICS, Technische Universität Braunschweig, Rebenring 56, Braunschweig, Germany
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26
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Guo R, Zong S, Wu M, Gu J, Yang M. Architecture of Human Mitochondrial Respiratory Megacomplex I 2III 2IV 2. Cell 2017; 170:1247-1257.e12. [PMID: 28844695 DOI: 10.1016/j.cell.2017.07.050] [Citation(s) in RCA: 322] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 06/20/2017] [Accepted: 07/28/2017] [Indexed: 01/01/2023]
Abstract
The respiratory megacomplex represents the highest-order assembly of respiratory chain complexes, and it allows mitochondria to respond to energy-requiring conditions. To understand its architecture, we examined the human respiratory chain megacomplex-I2III2IV2 (MCI2III2IV2) with 140 subunits and a subset of associated cofactors using cryo-electron microscopy. The MCI2III2IV2 forms a circular structure with the dimeric CIII located in the center, where it is surrounded by two copies each of CI and CIV. Two cytochrome c (Cyt.c) molecules are positioned to accept electrons on the surface of the c1 state CIII dimer. Analyses indicate that CII could insert into the gaps between CI and CIV to form a closed ring, which we termed the electron transport chain supercomplex. The structure not only reveals the precise assignment of individual subunits of human CI and CIII, but also enables future in-depth analysis of the electron transport chain as a whole.
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Affiliation(s)
- Runyu Guo
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Shuai Zong
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Meng Wu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Jinke Gu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Maojun Yang
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China.
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27
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Jang S, Javadov S. Association between ROS production, swelling and the respirasome integrity in cardiac mitochondria. Arch Biochem Biophys 2017; 630:1-8. [PMID: 28736227 DOI: 10.1016/j.abb.2017.07.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 06/05/2017] [Accepted: 07/17/2017] [Indexed: 02/04/2023]
Abstract
Although mitochondrial Ca2+ overload and ROS production play a critical role in mitochondria-mediated cell death, a cause-effect relationship between them remains elusive. This study elucidated the crosstalk between mitochondrial swelling, ROS production, and electron transfer chain (ETC) supercomplexes in rat heart mitochondria in response to Ca2+ and tert-butyl hydroperoxide (TBH), a lipid-soluble organic peroxide. Results showed that ROS production induced by TBH was significantly increased in the presence of Ca2+ in a dose-dependent manner. TBH markedly inhibited the state 3 respiration rate with no effect on the mitochondrial swelling. Ca2+ exerted a slight effect on mitochondrial respiration that was greatly aggravated by TBH. Analysis of supercomplexes revealed a minor difference in the presence of TBH and/or Ca2+. However, incubation of mitochondria in the presence of high Ca2+ (1 mM) or inhibitors of ETC complexes (rotenone and antimycin A) induced disintegration of the main supercomplex, respirasome. Thus, PTP-dependent swelling of mitochondria solely depends on Ca2+ but not ROS. TBH has no effect on the respirasome while Ca2+ induces disintegration of the supercomplex only at a high concentration. Intactness of individual ETC complexes I and III is important for maintenance of the structural integrity of the respirasome.
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Affiliation(s)
- Sehwan Jang
- Department of Physiology, University of Puerto Rico School of Medicine, San Juan, Puerto Rico
| | - Sabzali Javadov
- Department of Physiology, University of Puerto Rico School of Medicine, San Juan, Puerto Rico.
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28
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Affiliation(s)
- Hao Cheng
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
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29
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Structure of Mammalian Respiratory Supercomplex I 1 III 2 IV 1. Cell 2016; 167:1598-1609.e10. [DOI: 10.1016/j.cell.2016.11.012] [Citation(s) in RCA: 251] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 10/27/2016] [Accepted: 11/03/2016] [Indexed: 01/14/2023]
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