1
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Coupland CE, Karimi R, Bueler SA, Liang Y, Courbon GM, Di Trani JM, Wong CJ, Saghian R, Youn JY, Wang LY, Rubinstein JL. High-resolution electron cryomicroscopy of V-ATPase in native synaptic vesicles. Science 2024:eadp5577. [PMID: 38900912 DOI: 10.1126/science.adp5577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/16/2024] [Indexed: 06/22/2024]
Abstract
Intercellular communication in the nervous system occurs through the release of neurotransmitters into the synaptic cleft between neurons. In the presynaptic neuron, the proton pumping vesicular- or vacuolar-type ATPase (V-ATPase) powers neurotransmitter loading into synaptic vesicles (SVs), with the V1 complex dissociating from the membrane region of the enzyme before exocytosis. We isolated SVs from rat brain using SidK, a V-ATPase-binding bacterial effector protein. Single particle electron cryomicroscopy allowed high-resolution structure determination of V-ATPase within the native SV membrane. In the structure, regularly spaced cholesterol molecules decorate the enzyme's rotor and the abundant SV protein synaptophysin binds the complex stoichiometrically. ATP hydrolysis during vesicle loading results in loss of V1 from the SV membrane, suggesting that loading is sufficient to induce dissociation of the enzyme.
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Affiliation(s)
- Claire E Coupland
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Canada M5G 1X8
| | - Ryan Karimi
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Canada M5G 1X8
- Department of Medical Biophysics, The University of Toronto, Toronto, Canada M5G 1L7
| | - Stephanie A Bueler
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Canada M5G 1X8
| | - Yingke Liang
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Canada M5G 1X8
- Department of Biochemistry, The University of Toronto, Toronto, Canada M5S 1A8
| | - Gautier M Courbon
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Canada M5G 1X8
- Department of Medical Biophysics, The University of Toronto, Toronto, Canada M5G 1L7
| | - Justin M Di Trani
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Canada M5G 1X8
| | | | - Rayan Saghian
- Neuroscience and Mental Health Program, The Hospital for Sick Children, Toronto, Canada M5G 1X8
- Department of Physiology, The University of Toronto, Toronto, Canada M5S 1A8
| | - Ji-Young Youn
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Canada M5G 1X8
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada M5G 1X8
- Department of Molecular Genetics, The University of Toronto, Toronto, Canada M5S 1A8
| | - Lu-Yang Wang
- Neuroscience and Mental Health Program, The Hospital for Sick Children, Toronto, Canada M5G 1X8
- Department of Physiology, The University of Toronto, Toronto, Canada M5S 1A8
| | - John L Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Canada M5G 1X8
- Department of Medical Biophysics, The University of Toronto, Toronto, Canada M5G 1L7
- Department of Biochemistry, The University of Toronto, Toronto, Canada M5S 1A8
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2
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Zuccaro KE, Abriata LA, Pinto Meireles FT, Moss FR, Frost A, Dal Peraro M, Aydin H. Cardiolipin clustering promotes mitochondrial membrane dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595226. [PMID: 38826344 PMCID: PMC11142133 DOI: 10.1101/2024.05.21.595226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Cardiolipin (CL) is a mitochondria-specific phospholipid that forms heterotypic interactions with membrane-shaping proteins and regulates the dynamic remodeling and function of mitochondria. However, the precise mechanisms through which CL influences mitochondrial morphology are not well understood. In this study, employing molecular dynamics (MD) simulations, we observed CL localize near the membrane-binding sites of the mitochondrial fusion protein Optic Atrophy 1 (OPA1). To validate these findings experimentally, we developed a bromine-labeled CL probe to enhance cryoEM contrast and characterize the structure of OPA1 assemblies bound to the CL-brominated lipid bilayers. Our images provide direct evidence of interactions between CL and two conserved motifs within the paddle domain (PD) of OPA1, which control membrane-shaping mechanisms. We further observed a decrease in membrane remodeling activity for OPA1 in lipid compositions with increasing concentrations of monolyso-cardiolipin (MLCL). Suggesting that the partial replacement of CL by MLCL accumulation, as observed in Barth syndrome-associated mutations of the tafazzin phospholipid transacylase, compromises the stability of protein-membrane interactions. Our analyses provide insights into how biological membranes regulate the mechanisms governing mitochondrial homeostasis.
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Affiliation(s)
- Kelly E. Zuccaro
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA
| | - Luciano A. Abriata
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Protein Production and Structure Core Facility, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Fernando Teixeira Pinto Meireles
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Frank R. Moss
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Altos Labs, Bay Area Institute of Science, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Halil Aydin
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA
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3
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You H, Havey L, Li Z, Asara J, Guo R. Epstein-Barr-Virus-Driven Cardiolipin Synthesis Sustains Metabolic Remodeling During B-cell Lymphomagenesis. RESEARCH SQUARE 2024:rs.3.rs-4013392. [PMID: 38659762 PMCID: PMC11042403 DOI: 10.21203/rs.3.rs-4013392/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Epstein-Barr Virus (EBV) is associated with a range of B-cell malignancies, including Burkitt, Hodgkin, post-transplant, and AIDS-related lymphomas. Studies highlight EBV's transformative capability to induce oncometabolism in B-cells to support energy, biosynthetic precursors, and redox equivalents necessary for transition from quiescent to proliferation. Mitochondrial dysfunction presents an intrinsic barrier to EBV B-cell immortalization. Yet, how EBV maintains B-cell mitochondrial function and metabolic fluxes remains unclear. Here we show that EBV boosts cardiolipin(CL) biosynthesis, essential for mitochondrial cristae biogenesis, via EBNA2-induced CL enzyme transactivation. Pharmaceutical and CRISPR genetic analyses underscore the essentiality of CL biosynthesis in EBV-transformed B-cells. Metabolomic and isotopic tracing highlight CL's role in sustaining respiration, one-carbon metabolism, and aspartate synthesis, all vital for EBV-transformed B-cells. Targeting CL biosynthesis destabilizes mitochondrial one-carbon enzymes, causing synthetic lethality when coupled with a SHMT1/2 inhibitor. We demonstrate EBV-induced CL metabolism as a therapeutic target, offering new strategies against EBV-associated B-cell malignancies.
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Affiliation(s)
- Haixi You
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, USA
| | - Larissa Havey
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, USA
| | - Zhixuan Li
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston MA, USA
| | - John Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Rui Guo
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, USA
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4
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Fuentes JM, Morcillo P. The Role of Cardiolipin in Mitochondrial Function and Neurodegenerative Diseases. Cells 2024; 13:609. [PMID: 38607048 PMCID: PMC11012098 DOI: 10.3390/cells13070609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/13/2024] Open
Abstract
Cardiolipin (CL) is a mitochondria-exclusive phospholipid synthesized in the inner mitochondrial membrane. CL plays a key role in mitochondrial membranes, impacting a plethora of functions this organelle performs. Consequently, it is conceivable that abnormalities in the CL content, composition, and level of oxidation may negatively impact mitochondrial function and dynamics, with important implications in a variety of diseases. This review concentrates on papers published in recent years, combined with basic and underexplored research in CL. We capture new findings on its biological functions in the mitochondria, as well as its association with neurodegenerative diseases such as Alzheimer's disease or Parkinson's disease. Lastly, we explore the potential applications of CL as a biomarker and pharmacological target to mitigate mitochondrial dysfunction.
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Affiliation(s)
- José M. Fuentes
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, 10003 Cáceres, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas, Instituto de Salud Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Instituto Universitario de Investigación Biosanitaria de Extremadura (INUBE), 10003 Cáceres, Spain
| | - Patricia Morcillo
- Departmentof Neurology, Columbia University, New York, NY 10032, USA
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5
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Blanc FEC, Hummer G. Mechanism of proton-powered c-ring rotation in a mitochondrial ATP synthase. Proc Natl Acad Sci U S A 2024; 121:e2314199121. [PMID: 38451940 PMCID: PMC10945847 DOI: 10.1073/pnas.2314199121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/10/2024] [Indexed: 03/09/2024] Open
Abstract
Proton-powered c-ring rotation in mitochondrial ATP synthase is crucial to convert the transmembrane protonmotive force into torque to drive the synthesis of adenosine triphosphate (ATP). Capitalizing on recent cryo-EM structures, we aim at a structural and energetic understanding of how functional directional rotation is achieved. We performed multi-microsecond atomistic simulations to determine the free energy profiles along the c-ring rotation angle before and after the arrival of a new proton. Our results reveal that rotation proceeds by dynamic sliding of the ring over the a-subunit surface, during which interactions with conserved polar residues stabilize distinct intermediates. Ordered water chains line up for a Grotthuss-type proton transfer in one of these intermediates. After proton transfer, a high barrier prevents backward rotation and an overall drop in free energy favors forward rotation, ensuring the directionality of c-ring rotation required for the thermodynamically disfavored ATP synthesis. The essential arginine of the a-subunit stabilizes the rotated configuration through a salt bridge with the c-ring. Overall, we describe a complete mechanism for the rotation step of the ATP synthase rotor, thereby illuminating a process critical to all life at atomic resolution.
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Affiliation(s)
- Florian E. C. Blanc
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main60438, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main60438, Germany
- Institute for Biophysics, Goethe University Frankfurt, Frankfurt am Main60438, Germany
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6
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Nesterov SV, Plokhikh KS, Chesnokov YM, Mustafin DA, Goleva TN, Rogov AG, Vasilov RG, Yaguzhinsky LS. Safari with an Electron Gun: Visualization of Protein and Membrane Interactions in Mitochondria in Natural Environment. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:257-268. [PMID: 38622094 DOI: 10.1134/s0006297924020068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 04/17/2024]
Abstract
This paper presents new structural data about mitochondria using correlative light and electron microscopy (CLEM) and cryo-electron tomography. These state-of-the-art structural biology methods allow studying biological objects at nanometer scales under natural conditions. Non-invasiveness of these methods makes them comparable to observing animals in their natural environment on a safari. The paper highlights two areas of research that can only be accomplished using these methods. The study visualized location of the Aβ42 amyloid aggregates in relation to mitochondria to test a hypothesis of development of mitochondrial dysfunction in Alzheimer's disease. The results showed that the Aβ42 aggregates do not interact with mitochondria, although some of them are closely located. Therefore, the study demonstrated that mitochondrial dysfunction is not directly associated with the effects of aggregates on mitochondrial structure. Other processes should be considered as sources of mitochondrial dysfunction. Second unique area presented in this work is high-resolution visualization of the mitochondrial membranes and proteins in them. Analysis of the cryo-ET data reveals toroidal holes in the lamellar structures of cardiac mitochondrial cristae, where ATP synthases are located. The study proposes a new mechanism for sorting and clustering protein complexes in the membrane based on topology. According to this suggestion, position of the OXPHOS system proteins in the membrane is determined by its curvature. High-resolution tomography expands and complements existing ideas about the structural and functional organization of mitochondria. This makes it possible to study the previously inaccessible structural interactions of proteins with each other and with membranes in vivo.
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Affiliation(s)
- Semen V Nesterov
- National Research Center "Kurchatov Institute", Moscow, 123182, Russia.
| | | | - Yuriy M Chesnokov
- National Research Center "Kurchatov Institute", Moscow, 123182, Russia
| | - Denis A Mustafin
- National Research Center "Kurchatov Institute", Moscow, 123182, Russia
| | - Tatyana N Goleva
- National Research Center "Kurchatov Institute", Moscow, 123182, Russia
| | - Anton G Rogov
- National Research Center "Kurchatov Institute", Moscow, 123182, Russia
| | - Raif G Vasilov
- National Research Center "Kurchatov Institute", Moscow, 123182, Russia
| | - Lev S Yaguzhinsky
- Belozersky Research Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
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7
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Britt M, Sawasato K, Moller E, Kidd G, Bogdanov M, Sukharev S. On the lipid dependence of bacterial mechanosensitive channel gating in situ. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576706. [PMID: 38328048 PMCID: PMC10849563 DOI: 10.1101/2024.01.22.576706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
For bacterial mechanosensitive channels acting as turgor-adjusting osmolyte release valves, membrane tension is the primary stimulus driving opening transitions. Because tension is transmitted through the surrounding lipid bilayer, it is possible that the presence or absence of different lipid species may influence the function of these channels. In this work, we characterize the lipid dependence of chromosome-encoded MscS and MscL in E. coli strains with genetically altered lipid composition. We use two previously generated strains that lack one or two major lipid species (PE, PG, or CL) and engineer a third strain that is highly enriched in CL due to the presence of hyperactive cardiolipin synthase ClsA. We characterize the functional behavior of these channels using patch-clamp and quantify the relative tension midpoints, closing rates, inactivation depth, and the rate of recovery back to the closed state. We also measure the osmotic survival of lipid-deficient strains, which characterizes the functional consequences of lipid-mediated channel function at the cell level. We find that the opening and closing behavior of MscS and MscL tolerate the absence of specific lipid species remarkably well. The lack of cardiolipin (CL), however, reduces the active MscS population relative to MscL and decreases the closing rate, slightly increasing the propensity of MscS toward inactivation and slowing the recovery process. The data points to the robustness of the osmolyte release system and the importance of cardiolipin for the adaptive behavior of MscS.
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8
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Fiebig A, Schnizlein MK, Pena-Rivera S, Trigodet F, Dubey AA, Hennessy MK, Basu A, Pott S, Dalal S, Rubin D, Sogin ML, Eren AM, Chang EB, Crosson S. Bile acid fitness determinants of a Bacteroides fragilis isolate from a human pouchitis patient. mBio 2024; 15:e0283023. [PMID: 38063424 PMCID: PMC10790697 DOI: 10.1128/mbio.02830-23] [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: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 12/19/2023] Open
Abstract
IMPORTANCE The Gram-negative bacterium Bacteroides fragilis is a common member of the human gut microbiota that colonizes multiple host niches and can influence human physiology through a variety of mechanisms. Identification of genes that enable B. fragilis to grow across a range of host environments has been impeded in part by the relatively limited genetic tractability of this species. We have developed a high-throughput genetic resource for a B. fragilis strain isolated from a UC pouchitis patient. Bile acids limit microbial growth and are altered in abundance in UC pouches, where B. fragilis often blooms. Using this resource, we uncovered pathways and processes that impact B. fragilis fitness in bile and that may contribute to population expansions during bouts of gut inflammation.
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Affiliation(s)
- Aretha Fiebig
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Matthew K. Schnizlein
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Selymar Pena-Rivera
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Florian Trigodet
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
- Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, Oldenburg, Germany
| | - Abhishek Anil Dubey
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Miette K. Hennessy
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Anindita Basu
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Sebastian Pott
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Sushila Dalal
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - David Rubin
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | | | - A. Murat Eren
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
- Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, Oldenburg, Germany
| | - Eugene B. Chang
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Sean Crosson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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9
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Guilvout I, Samsudin F, Huber RG, Bond PJ, Bardiaux B, Francetic O. Membrane platform protein PulF of the Klebsiella type II secretion system forms a trimeric ion channel essential for endopilus assembly and protein secretion. mBio 2024; 15:e0142323. [PMID: 38063437 PMCID: PMC10790770 DOI: 10.1128/mbio.01423-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 10/24/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Type IV pili and type II secretion systems are members of the widespread type IV filament (T4F) superfamily of nanomachines that assemble dynamic and versatile surface fibers in archaea and bacteria. The assembly and retraction of T4 filaments with diverse surface properties and functions require the plasma membrane platform proteins of the GspF/PilC superfamily. Generally considered dimeric, platform proteins are thought to function as passive transmitters of the mechanical energy generated by the ATPase motor, to somehow promote insertion of pilin subunits into the nascent pilus fibers. Here, we generate and experimentally validate structural predictions that support the trimeric state of a platform protein PulF from a type II secretion system. The PulF trimers form selective proton or sodium channels which might energize pilus assembly using the membrane potential. The conservation of the channel sequence and structural features implies a common mechanism for all T4F assembly systems. We propose a model of the oligomeric PulF-PulE ATPase complex that provides an essential framework to investigate and understand the pilus assembly mechanism.
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Affiliation(s)
- Ingrid Guilvout
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Biochemistry of Macromolecular Interactions Unit, Paris, France
| | | | | | - Peter J. Bond
- Bioinformatics Institute (A-STAR), Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Benjamin Bardiaux
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Structural Bioinformatics Unit, Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Bacterial Transmembrane Systems Unit, Paris, France
| | - Olivera Francetic
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Biochemistry of Macromolecular Interactions Unit, Paris, France
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10
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Li M, Gasanoff ES. Cationic Proteins Rich in Lysine Residue Trigger Formation of Non-bilayer Lipid Phases in Model and Biological Membranes: Biophysical Methods of Study. J Membr Biol 2023; 256:373-391. [PMID: 37735238 DOI: 10.1007/s00232-023-00292-y] [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: 06/17/2023] [Accepted: 09/05/2023] [Indexed: 09/23/2023]
Abstract
Cationic membrane-active toxins are the most abundant group of proteins in the venom of snakes and insects. Cationic proteins such as cobra venom cytotoxin and bee venom melittin are known for their pharmacological reactions including anticancer and antimicrobial effects which arise from the toxin-induced alteration in the dynamics and structure of plasma membranes and membranes of organelles. It has been established that these cationic toxins trigger the formation of non-bilayer lipid phase transitions in artificial and native mitochondrial membranes. Remarkably, the toxin-induced formation of non-bilayer lipid phase increases at certain conditions mitochondrial ATP synthase activity. This observation opens an intriguing avenue for using cationic toxins in the development of novel drugs for the treatment of cellular energy deficiency caused by aging and diseases. This observation also warrants a thorough investigation of the molecular mechanism(s) of lipid phase polymorphisms triggered by cationic proteins. This article presents a review on the application of powerful biophysical methods such as resonance spectroscopy (31P-, 1H-, 2H-nuclear magnetic resonance, and electron paramagnetic resonance), luminescence, and differential scanning microcalorimetry in studies of non-bilayer lipid phase transitions triggered by cationic proteins in artificial and biological membranes. A phenomenon of the triggered by cationic proteins the non-bilayer lipid phase transitions occurring within 10-2-10-11 s is discussed in the context of potential pharmacological applications of cationic proteins. Next to the ATP dimer is an inverted micelle made of cardiolipin that serves as a vehicle for the transport of H+ ions from the intra-crista space to the matrix. It is proposed that such inverted micelles are triggered by the high density of H+ ions and the cationic proteins rich in lysine residue which compete with the conserved lysine residues of the ATP synthase rotor for binding to cardiolipin in the inner mitochondrial membrane and perturb the bilayer lipid packing of cristae. Phospholipids with a blue polar head represent cardiolipin and those with a red polar head represent other phospholipids found in the crista membrane.
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Affiliation(s)
- Meiyi Li
- STEM Research Centre, Science Department, Chaoyang Kaiwen Academy, Beijing, 100018, China
| | - Edward S Gasanoff
- STEM Research Centre, Science Department, Chaoyang Kaiwen Academy, Beijing, 100018, China.
- Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, 119991, Russia.
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Valdivieso González D, Makowski M, Lillo MP, Cao‐García FJ, Melo MN, Almendro‐Vedia VG, López‐Montero I. Rotation of the c-Ring Promotes the Curvature Sorting of Monomeric ATP Synthases. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301606. [PMID: 37705095 PMCID: PMC10625105 DOI: 10.1002/advs.202301606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/07/2023] [Indexed: 09/15/2023]
Abstract
ATP synthases are proteins that catalyse the formation of ATP through the rotatory movement of their membrane-spanning subunit. In mitochondria, ATP synthases are found to arrange as dimers at the high-curved edges of cristae. Here, a direct link is explored between the rotatory movement of ATP synthases and their preference for curved membranes. An active curvature sorting of ATP synthases in lipid nanotubes pulled from giant vesicles is found. Coarse-grained simulations confirm the curvature-seeking behaviour of rotating ATP synthases, promoting reversible and frequent protein-protein contacts. The formation of transient protein dimers relies on the membrane-mediated attractive interaction of the order of 1.5 kB T produced by a hydrophobic mismatch upon protein rotation. Transient dimers are sustained by a conic-like arrangement characterized by a wedge angle of θ ≈ 50°, producing a dynamic coupling between protein shape and membrane curvature. The results suggest a new role of the rotational movement of ATP synthases for their dynamic self-assembly in biological membranes.
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Affiliation(s)
- David Valdivieso González
- Departamento Química FísicaUniversidad Complutense de MadridAvda. Complutense s/nMadrid28040Spain
- Instituto de Investigación Biomédica Hospital Doce de Octubre (imas12)Avenida de Córdoba s/nMadrid28041Spain
| | - Marcin Makowski
- Instituto de Medicina MolecularFacultade de MedicinaUniversidade de LisboaLisbon1649‐028Portugal
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaAv. da RepúblicaOeiras2780‐157Portugal
| | - M. Pilar Lillo
- Departamento Química Física BiológicaInstituto de Química‐Física “Blas Cabrera” (CSIC)Serrano 119Madrid28006Spain
| | - Francisco J. Cao‐García
- Departamento de Estructura de la MateriaFísica Térmica y ElectrónicaUniversidad Complutense de MadridPlaza de Ciencias 1Madrid28040Spain
- Instituto Madrileño de Estudios Avanzados en NanocienciaIMDEA NanocienciaC/ Faraday 9Madrid28049Spain
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaAv. da RepúblicaOeiras2780‐157Portugal
| | - Víctor G. Almendro‐Vedia
- Departamento Química FísicaUniversidad Complutense de MadridAvda. Complutense s/nMadrid28040Spain
- Instituto de Investigación Biomédica Hospital Doce de Octubre (imas12)Avenida de Córdoba s/nMadrid28041Spain
| | - Iván López‐Montero
- Departamento Química FísicaUniversidad Complutense de MadridAvda. Complutense s/nMadrid28040Spain
- Instituto de Investigación Biomédica Hospital Doce de Octubre (imas12)Avenida de Córdoba s/nMadrid28041Spain
- Instituto PluridisciplinarPaseo Juan XXIII 1Madrid28040Spain
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Fiebig A, Schnizlein MK, Pena-Rivera S, Trigodet F, Dubey AA, Hennessy M, Basu A, Pott S, Dalal S, Rubin D, Sogin ML, Murat Eren A, Chang EB, Crosson S. Bile acid fitness determinants of a Bacteroides fragilis isolate from a human pouchitis patient. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540287. [PMID: 37214927 PMCID: PMC10197588 DOI: 10.1101/2023.05.11.540287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Bacteroides fragilis comprises 1-5% of the gut microbiota in healthy humans but can expand to >50% of the population in ulcerative colitis (UC) patients experiencing inflammation. The mechanisms underlying such microbial blooms are poorly understood, but the gut of UC patients has physicochemical features that differ from healthy patients and likely impact microbial physiology. For example, levels of the secondary bile acid deoxycholate (DC) are highly reduced in the ileoanal J-pouch of UC colectomy patients. We isolated a B. fragilis strain from a UC patient with pouch inflammation (i.e. pouchitis) and developed it as a genetic model system to identify genes and pathways that are regulated by DC and that impact B. fragilis fitness in DC and crude bile. Treatment of B. fragilis with a physiologically relevant concentration of DC reduced cell growth and remodeled transcription of one-quarter of the genome. DC strongly induced expression of chaperones and select transcriptional regulators and efflux systems and downregulated protein synthesis genes. Using a barcoded collection of ≈50,000 unique insertional mutants, we further defined B. fragilis genes that contribute to fitness in media containing DC or crude bile. Genes impacting cell envelope functions including cardiolipin synthesis, cell surface glycosylation, and systems implicated in sodium-dependent bioenergetics were major bile acid fitness factors. As expected, there was limited overlap between transcriptionally regulated genes and genes that impacted fitness in bile when disrupted. Our study provides a genome-scale view of a B. fragilis bile response and genetic determinants of its fitness in DC and crude bile.
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Affiliation(s)
- Aretha Fiebig
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Matthew K. Schnizlein
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Selymar Pena-Rivera
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Florian Trigodet
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, Oldenburg, Germany
| | - Abhishek Anil Dubey
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Miette Hennessy
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Anindita Basu
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sebastian Pott
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sushila Dalal
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - David Rubin
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | | | - A. Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, Oldenburg, Germany
| | - Eugene B. Chang
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sean Crosson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
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13
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Lee MS, Webb TJ. Novel lipid antigens for NKT cells in cancer. Front Immunol 2023; 14:1173375. [PMID: 37908366 PMCID: PMC10613688 DOI: 10.3389/fimmu.2023.1173375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 10/02/2023] [Indexed: 11/02/2023] Open
Abstract
Cancer immunotherapy aims to unleash the power of the immune system against tumors without the side effects of traditional chemotherapy. Immunotherapeutic methods vary widely, but all follow the same basic principle: overcome the barriers utilized by cancers to avoid immune destruction. These approaches often revolve around classical T cells, such as with CAR T cells and neoantigen vaccines; however, the utility of the innate-like iNKT cell in cancer immunotherapy has gained significant recognition. iNKT cells parallel classic T cell recognition of peptide antigens presented on MHC through their recognition of lipid antigens presented on the MHC I-like molecule CD1d. Altered metabolism and a lipogenic phenotype are essential properties of tumor cells, representing a unique feature that may be exploited by iNKT cells. In this review, we will cover properties of iNKT cells, CD1d, and lipid antigen presentation. Next, we will discuss the cancer lipidome and how it may be exploited by iNKT cells through a window of opportunity. Finally, we will review, in detail, novel lipid antigens for iNKT cells in cancer.
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Affiliation(s)
- Michael S. Lee
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Tonya J. Webb
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, United States
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14
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Nesterov SV, Yaguzhinsky LS. Directed proton transfer from F o to F 1 extends the multifaceted proton functions in ATP synthase. Biophys Rev 2023; 15:859-873. [PMID: 37975013 PMCID: PMC10643803 DOI: 10.1007/s12551-023-01132-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/30/2023] [Indexed: 11/19/2023] Open
Abstract
The role of protons in ATP synthase is typically considered to be energy storage in the form of an electrochemical potential, as well as an operating element proving rotation. However, this review emphasizes that protons also act as activators of conformational changes in F1 and as direct participants in phosphorylation reaction. The protons transferred through Fo do not immediately leave to the bulk aqueous phase, but instead provide for the formation of a pH gradient between acidifying Fo and alkalizing F1. It facilitates a directed inter-subunit proton transfer to F1, where they are used in the ATP synthesis reaction. This ensures that the enzyme activity is not limited by a lack of protons in the alkaline mitochondrial matrix or chloroplast stroma. Up to one hundred protons bind to the carboxyl groups of the F1 subunit, altering the electrical interactions between the amino acids of the enzyme. This removes the inhibition of ATP synthase caused by the electrostatic attraction of charged amino acids of the stator and rotor and also makes the enzyme more prone to conformational changes. Protonation occurs during ATP synthesis initiation and during phosphorylation, while deprotonation blocks the rotation inhibiting both synthesis and hydrolysis. Thus, protons participate in the functioning of all main components of ATP synthase molecular machine making it effectively a proton-driven electric machine. The review highlights the key role of protons as a coupling factor in ATP synthase with multifaceted functions, including charge and energy transport, torque generation, facilitation of conformational changes, and participation in the ATP synthesis reaction.
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Affiliation(s)
- Semen V. Nesterov
- Kurchatov Complex of NBICS-Technologies, National Research Center Kurchatov Institute, 123182 Moscow, Russia
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Lev S. Yaguzhinsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
- Belozersky Research Institute for Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
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15
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Weindel CG, Ellzey LM, Martinez EL, Watson RO, Patrick KL. Gasdermins gone wild: new roles for GSDMs in regulating cellular homeostasis. Trends Cell Biol 2023; 33:773-787. [PMID: 37062616 PMCID: PMC10611448 DOI: 10.1016/j.tcb.2023.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/13/2023] [Accepted: 02/24/2023] [Indexed: 04/18/2023]
Abstract
Since their discovery, members of the gasdermin (GSDM) family of proteins have been firmly established as executors of pyroptosis, with the N-terminal fragment of most GSDMs capable of forming pores in the plasma membrane. More recent findings suggest that some GSDMs can drive additional cell death pathways, such as apoptosis and necroptosis, through mechanisms independent of plasma membrane perforation. There is also emerging evidence that by associating with cellular compartments such as mitochondria, peroxisomes, endosomes, and the nucleus, GSDMs regulate cell death-independent aspects of cellular homeostasis. Here, we review the diversity of GSDM function across several cell types and explore how various cellular stresses can promote relocalization - and thus refunctionalization - of GSDMs.
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Affiliation(s)
- Chi G Weindel
- Texas A&M University School of Medicine, Bryan, TX, USA
| | - Lily M Ellzey
- Texas A&M University School of Medicine, Bryan, TX, USA
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16
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Ivontsin LA, Mashkovtseva EV, Nartsissov YR. Membrane Lipid Composition Influences the Hydration of Proton Half-Channels in F oF 1-ATP Synthase. Life (Basel) 2023; 13:1816. [PMID: 37763220 PMCID: PMC10532555 DOI: 10.3390/life13091816] [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: 07/23/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
The membrane lipid composition plays an important role in the regulation of membrane protein activity. To probe its influence on proton half-channels' structure in FoF1-ATP synthase, we performed molecular dynamics simulations with the bacterial protein complex (PDB ID: 6VWK) embedded in three types of membranes: a model POPC, a lipid bilayer containing 25% (in vivo), and 75% (bacterial stress) of cardiolipin (CL). The structure proved to be stable regardless of the lipid composition. The presence of CL increased the hydration of half-channels. The merging of two water cavities at the inlet half-channel entrance and a long continuous chain of water molecules directly to cAsp61 from the periplasm were observed. Minor conformational changes in half-channels with the addition of CL caused extremely rare direct transitions between aGlu219-aAsp119, aGlu219-aHis245, and aGln252-cAsp61. Deeper penetration of water molecules (W1-W3) also increased the proton transport continuity. Stable spatial positions of significant amino acid (AA) residue aAsn214 were found under all simulation conditions indicate a prevailing influence of AA-AA or AA-W interactions on the side-chain dynamics. These results allowed us to put forward a model of the proton movement in ATP synthases under conditions close to in vivo and to evaluate the importance of membrane composition in simulations.
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Affiliation(s)
- Leonid A. Ivontsin
- Institute of Cytochemistry and Molecular Pharmacology, 24/14 6th Radialnaya Str., Moscow 115404, Russia; (E.V.M.); (Y.R.N.)
| | - Elena V. Mashkovtseva
- Institute of Cytochemistry and Molecular Pharmacology, 24/14 6th Radialnaya Str., Moscow 115404, Russia; (E.V.M.); (Y.R.N.)
| | - Yaroslav R. Nartsissov
- Institute of Cytochemistry and Molecular Pharmacology, 24/14 6th Radialnaya Str., Moscow 115404, Russia; (E.V.M.); (Y.R.N.)
- Biomedical Research Group, BiDiPharma GmbH, 5 Bültbek, 22962 Siek, Germany
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17
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Zhang Y, Pang C, Zhang C, Wang Y, Wang P, Chen Y, Wang J, Hu Y, Liu C, Liang H, Xie G, Ou J. HILPDA-mediated lipidomic remodelling promotes radiotherapy resistance in nasopharyngeal carcinoma by accelerating mitophagy. Cell Mol Life Sci 2023; 80:242. [PMID: 37552373 PMCID: PMC11072511 DOI: 10.1007/s00018-023-04891-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/22/2023] [Accepted: 07/20/2023] [Indexed: 08/09/2023]
Abstract
Radiotherapy resistance is a major obstacle to nasopharyngeal carcinoma (NPC) therapy and contributes to tumour recurrence and metastasis. Lipid metabolism is a key regulatory mechanism in cancer biology; however, its role in NPC radiotherapy resistance remains unclear. In this study, we identified hypoxia-inducible lipid droplet-associated protein (HILPDA) as a newly discovered regulator of radioresistance that induces not only lipid droplet (LD) formation but also intracellular lipid remodelling, notably changing mitochondrial cardiolipin (CL) levels. Additionally, we found that the upregulation of CL promotes mitophagy in response to irradiation exposure. Mechanistically, HILPDA inhibits PINK1-mediated CLS1 ubiquitination and degradation. The combination of a mitophagy inhibitor and irradiation significantly increases the radiosensitivity of NPC cells. Human cancer-derived data confirmed that the HILPDA-CLS1 pathway promotes NPC radioresistance. Collectively, these findings suggest that HILPDA plays a critical role in promoting NPC radioresistance and might be targeted to overcome radiotherapeutic resistance in NPC patients in the clinic.
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Affiliation(s)
- Yue Zhang
- Department of Oncology and Southwest Cancer Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Radiation Treatment Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Chen Pang
- Department of Oncology and Southwest Cancer Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Radiation Treatment Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Chi Zhang
- Department of Oncology and Southwest Cancer Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Yijie Wang
- Department of Oncology and Southwest Cancer Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Peng Wang
- Radiation Treatment Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Yanrong Chen
- Department of Oncology and Southwest Cancer Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Junyi Wang
- Department of Oncology and Southwest Cancer Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Ying Hu
- Department of Oncology and Southwest Cancer Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Chengxiang Liu
- Department of Oncology and Southwest Cancer Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Houjie Liang
- Department of Oncology and Southwest Cancer Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China.
- Radiation Treatment Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China.
| | - Ganfeng Xie
- Department of Oncology and Southwest Cancer Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China.
- Radiation Treatment Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China.
| | - Juanjuan Ou
- Department of Oncology and Southwest Cancer Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China.
- Radiation Treatment Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China.
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18
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Makowski M, Almendro-Vedia VG, Domingues MM, Franco OL, López-Montero I, Melo MN, Santos NC. Activity modulation of the Escherichia coli F 1F O ATP synthase by a designed antimicrobial peptide via cardiolipin sequestering. iScience 2023; 26:107004. [PMID: 37416464 PMCID: PMC10320169 DOI: 10.1016/j.isci.2023.107004] [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: 09/06/2022] [Revised: 02/13/2023] [Accepted: 05/26/2023] [Indexed: 07/08/2023] Open
Abstract
Most antimicrobial peptides (AMPs) exert their microbicidal activity through membrane permeabilization. The designed AMP EcDBS1R4 has a cryptic mechanism of action involving the membrane hyperpolarization of Escherichia coli, suggesting that EcDBS1R4 may hinder processes involved in membrane potential dissipation. We show that EcDBS1R4 can sequester cardiolipin, a phospholipid that interacts with several respiratory complexes of E. coli. Among these, F1FO ATP synthase uses membrane potential to fuel ATP synthesis. We found that EcDBS1R4 can modulate the activity of ATP synthase upon partition to membranes containing cardiolipin. Molecular dynamics simulations suggest that EcDBS1R4 alters the membrane environment of the transmembrane FO motor, impairing cardiolipin interactions with the cytoplasmic face of the peripheral stalk that binds the catalytic F1 domain to the FO domain. The proposed mechanism of action, targeting membrane protein function through lipid reorganization may open new venues of research on the mode of action and design of other AMPs.
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Affiliation(s)
- Marcin Makowski
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Víctor G. Almendro-Vedia
- Instituto Pluridisciplinar, Universidad Complutense de Madrid, Ps Juan XXIII 1, 28040 Madrid, Spain
- Universidad Complutense de Madrid, Departamento de Química Física, 28040 Madrid, Spain
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
| | - Marco M. Domingues
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - Octavio L. Franco
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, 71966-700 Federal District, Brazil
- S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, 79117-900 Mato Grosso do Sul, Brazil
| | - Iván López-Montero
- Instituto Pluridisciplinar, Universidad Complutense de Madrid, Ps Juan XXIII 1, 28040 Madrid, Spain
- Universidad Complutense de Madrid, Departamento de Química Física, 28040 Madrid, Spain
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Nuno C. Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
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19
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Shrestha RK, Founds MW, Shepard SJ, Rothrock MM, Defnet AE, Steed PR. Mutational analysis of a conserved positive charge in the c-ring of E. coli ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148962. [PMID: 36822493 PMCID: PMC9998364 DOI: 10.1016/j.bbabio.2023.148962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 01/25/2023] [Accepted: 02/13/2023] [Indexed: 02/25/2023]
Abstract
F1Fo ATP synthase is a ubiquitous molecular motor that utilizes a rotary mechanism to synthesize adenosine triphosphate (ATP), the fundamental energy currency of life. The membrane-embedded Fo motor converts the electrochemical gradient of protons into rotation, which is then used to drive the conformational changes in the soluble F1 motor that catalyze ATP synthesis. In E. coli, the Fo motor is composed of a c10 ring (rotor) alongside subunit a (stator), which together provide two aqueous half channels that facilitate proton translocation. Previous work has suggested that Arg50 and Thr51 on the cytoplasmic side of each subunit c are involved in the proton translocation process, and positive charge is conserved in this region of subunit c. To further investigate the role of these residues and the chemical requirements for activity at these positions, we generated 13 substitution mutants and assayed their in vitro ATP synthesis, H+ pumping, and passive H+ permeability activities, as well as the ability of mutants to carry out oxidative phosphorylation in vivo. While polar and hydrophobic mutations were generally tolerated in either position, introduction of negative charge or removal of polarity caused a substantial defect. We discuss the possible effects of altered electrostatics on the interaction between the rotor and stator, water structure in the aqueous channel, and interaction of the rotor with cardiolipin.
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Affiliation(s)
- Rashmi K Shrestha
- Department of Chemistry & Biochemistry, University of North Carolina Asheville, One University Heights, Asheville, NC 28804, United States of America
| | - Michael W Founds
- Department of Chemistry & Biochemistry, University of North Carolina Asheville, One University Heights, Asheville, NC 28804, United States of America
| | - Sam J Shepard
- Department of Chemistry & Biochemistry, University of North Carolina Asheville, One University Heights, Asheville, NC 28804, United States of America
| | - Mallory M Rothrock
- Department of Chemistry & Biochemistry, University of North Carolina Asheville, One University Heights, Asheville, NC 28804, United States of America
| | - Amy E Defnet
- Department of Chemistry & Biochemistry, University of North Carolina Asheville, One University Heights, Asheville, NC 28804, United States of America
| | - P Ryan Steed
- Department of Chemistry & Biochemistry, University of North Carolina Asheville, One University Heights, Asheville, NC 28804, United States of America.
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20
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Ren M, Xu Y, Phoon CKL, Erdjument-Bromage H, Neubert TA, Schlame M. Knockout of cardiolipin synthase disrupts postnatal cardiac development by inhibiting the maturation of mitochondrial cristae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.09.531996. [PMID: 36945411 PMCID: PMC10029008 DOI: 10.1101/2023.03.09.531996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Background Cardiomyocyte maturation requires a massive increase in respiratory enzymes and their assembly into long-lived complexes of oxidative phosphorylation (OXPHOS). The molecular mechanisms underlying the maturation of cardiac mitochondria have not been established. Methods To determine whether the mitochondria-specific lipid cardiolipin is involved in cardiac maturation, we created a cardiomyocyte-restricted knockout (KO) of cardiolipin synthase ( Crls1 ) in mice and studied the postnatal development of the heart. We also measured the turnover rates of proteins and lipids in cardiolipin-deficient flight muscle from Drosophila, a tissue that has mitochondria with high OXPHOS activity like the heart. Results Crls1KO mice survived the prenatal period but failed to accumulate OXPHOS proteins during postnatal maturation and succumbed to heart failure at the age of 2 weeks. Turnover measurements showed that the exceptionally long half-life of OXPHOS proteins is critically dependent on cardiolipin. Conclusions Cardiolipin is essential for the postnatal maturation of cardiomyocytes because it allows mitochondrial cristae to accumulate OXPHOS proteins to a high concentration and to shield them from degradation.
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21
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Supramolecular organization and dynamics of mannosylated phosphatidylinositol lipids in the mycobacterial plasma membrane. Proc Natl Acad Sci U S A 2023; 120:e2212755120. [PMID: 36693100 PMCID: PMC9945971 DOI: 10.1073/pnas.2212755120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis (TB), a disease that claims ~1.6 million lives annually. The current treatment regime is long and expensive, and missed doses contribute to drug resistance. Therefore, development of new anti-TB drugs remains one of the highest public health priorities. Mtb has evolved a complex cell envelope that represents a formidable barrier to antibiotics. The Mtb cell envelop consists of four distinct layers enriched for Mtb specific lipids and glycans. Although the outer membrane, comprised of mycolic acid esters, has been extensively studied, less is known about the plasma membrane, which also plays a critical role in impacting antibiotic efficacy. The Mtb plasma membrane has a unique lipid composition, with mannosylated phosphatidylinositol lipids (phosphatidyl-myoinositol mannosides, PIMs) comprising more than 50% of the lipids. However, the role of PIMs in the structure and function of the membrane remains elusive. Here, we used multiscale molecular dynamics (MD) simulations to understand the structure-function relationship of the PIM lipid family and decipher how they self-organize to shape the biophysical properties of mycobacterial plasma membranes. We assess both symmetric and asymmetric assemblies of the Mtb plasma membrane and compare this with residue distributions of Mtb integral membrane protein structures. To further validate the model, we tested known anti-TB drugs and demonstrated that our models agree with experimental results. Thus, our work sheds new light on the organization of the mycobacterial plasma membrane. This paves the way for future studies on antibiotic development and understanding Mtb membrane protein function.
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22
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Nesterov SV, Yaguzhinsky LS, Vasilov RG, Kadantsev VN, Goltsov AN. Contribution of the Collective Excitations to the Coupled Proton and Energy Transport along Mitochondrial Cristae Membrane in Oxidative Phosphorylation System. ENTROPY (BASEL, SWITZERLAND) 2022; 24:1813. [PMID: 36554218 PMCID: PMC9778164 DOI: 10.3390/e24121813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
The results of many experimental and theoretical works indicate that after transport of protons across the mitochondrial inner membrane (MIM) in the oxidative phosphorylation (OXPHOS) system, they are retained on the membrane-water interface in nonequilibrium state with free energy excess due to low proton surface-to-bulk release. This well-established phenomenon suggests that proton trapping on the membrane interface ensures vectorial lateral transport of protons from proton pumps to ATP synthases (proton acceptors). Despite the key role of the proton transport in bioenergetics, the molecular mechanism of proton transfer in the OXPHOS system is not yet completely established. Here, we developed a dynamics model of long-range transport of energized protons along the MIM accompanied by collective excitation of localized waves propagating on the membrane surface. Our model is based on the new data on the macromolecular organization of the OXPHOS system showing the well-ordered structure of respirasomes and ATP synthases on the cristae membrane folds. We developed a two-component dynamics model of the proton transport considering two coupled subsystems: the ordered hydrogen bond (HB) chain of water molecules and lipid headgroups of MIM. We analytically obtained a two-component soliton solution in this model, which describes the motion of the proton kink, corresponding to successive proton hops in the HB chain, and coherent motion of a compression soliton in the chain of lipid headgroups. The local deformation in a soliton range facilitates proton jumps due to water molecules approaching each other in the HB chain. We suggested that the proton-conducting structures formed along the cristae membrane surface promote direct lateral proton transfer in the OXPHOS system. Collective excitations at the water-membrane interface in a form of two-component soliton ensure the coupled non-dissipative transport of charge carriers and elastic energy of MIM deformation to ATP synthases that may be utilized in ATP synthesis providing maximal efficiency in mitochondrial bioenergetics.
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Affiliation(s)
- Semen V. Nesterov
- Kurchatov Complex of NBICS-Technologies, National Research Center Kurchatov Institute, 123182 Moscow, Russia
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Lev S. Yaguzhinsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
- Department of Bioenergetics, Institute of Cytochemistry and Molecular Pharmacology, 115404 Moscow, Russia
- Belozersky Research Institute for Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Raif G. Vasilov
- Kurchatov Complex of NBICS-Technologies, National Research Center Kurchatov Institute, 123182 Moscow, Russia
| | - Vasiliy N. Kadantsev
- Institute for Artificial Intelligence, Russian Technological University (MIREA), 119454 Moscow, Russia
| | - Alexey N. Goltsov
- Institute for Artificial Intelligence, Russian Technological University (MIREA), 119454 Moscow, Russia
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23
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Prola A, Pilot-Storck F. Cardiolipin Alterations during Obesity: Exploring Therapeutic Opportunities. BIOLOGY 2022; 11:1638. [PMID: 36358339 PMCID: PMC9687765 DOI: 10.3390/biology11111638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/31/2022] [Accepted: 11/03/2022] [Indexed: 08/13/2023]
Abstract
Cardiolipin is a specific phospholipid of the mitochondrial inner membrane that participates in many aspects of its organization and function, hence promoting proper mitochondrial ATP production. Here, we review recent data that have investigated alterations of cardiolipin in different tissues in the context of obesity and the related metabolic syndrome. Data relating perturbations of cardiolipin content or composition are accumulating and suggest their involvement in mitochondrial dysfunction in tissues from obese patients. Conversely, cardiolipin modulation is a promising field of investigation in a search for strategies for obesity management. Several ways to restore cardiolipin content, composition or integrity are emerging and may contribute to the improvement of mitochondrial function in tissues facing excessive fat storage. Inversely, reduction of mitochondrial efficiency in a controlled way may increase energy expenditure and help fight against obesity and in this perspective, several options aim at targeting cardiolipin to achieve a mild reduction of mitochondrial coupling. Far from being just a victim of the deleterious consequences of obesity, cardiolipin may ultimately prove to be a possible weapon to fight against obesity in the future.
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Affiliation(s)
- Alexandre Prola
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Fanny Pilot-Storck
- Team Relaix, INSERM, IMRB, Université Paris-Est Créteil, F-94010 Créteil, France
- EnvA, IMRB, F-94700 Maisons-Alfort, France
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24
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Luévano-Martínez LA, Pinto IFD, Yoshinaga MY, Miyamoto S. In yeast, cardiolipin unsaturation level plays a key role in mitochondrial function and inner membrane integrity. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148587. [PMID: 35780857 DOI: 10.1016/j.bbabio.2022.148587] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/07/2022] [Accepted: 06/24/2022] [Indexed: 12/27/2022]
Abstract
Cardiolipin is the signature phospholipid of the mitochondrial inner membrane. It participates in shaping the inner membrane as well as in modulating the activity of many membrane-bound proteins. The acyl chain composition of cardiolipin is finely tuned post-biosynthesis depending on the surrounding phospholipids to produce mature or unsaturated cardiolipin. However, experimental evidence showing that immature and mature cardiolipin are functionally equivalents for mitochondria poses doubts on the relevance of cardiolipin remodeling. In this work, we studied the role of cardiolipin acyl chain composition in mitochondrial bioenergetics, including a detailed bioenergetic profile of yeast mitochondria. Cardiolipin acyl chains were modified by genetic and nutritional manipulation. We found that both the bioenergetic efficiency and osmotic stability of mitochondria are dependent on the unsaturation level of cardiolipin acyl chains. It is proposed that cardiolipin remodeling and, consequently, mature cardiolipins play an important role in mitochondrial inner membrane integrity and functionality.
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Affiliation(s)
- Luis Alberto Luévano-Martínez
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, N.L, Mexico.
| | | | - Marcos Yukio Yoshinaga
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Sayuri Miyamoto
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
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25
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The effects of cardiolipin on the structural dynamics of the mitochondrial ADP/ATP carrier in its cytosol-open state. J Lipid Res 2022; 63:100227. [PMID: 35569528 PMCID: PMC9189224 DOI: 10.1016/j.jlr.2022.100227] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 11/21/2022] Open
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26
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Mohr B, Shmilovich K, Kleinwächter IS, Schneider D, Ferguson AL, Bereau T. Data-driven discovery of cardiolipin-selective small molecules by computational active learning. Chem Sci 2022; 13:4498-4511. [PMID: 35656132 PMCID: PMC9019913 DOI: 10.1039/d2sc00116k] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/24/2022] [Indexed: 12/23/2022] Open
Abstract
Subtle variations in the lipid composition of mitochondrial membranes can have a profound impact on mitochondrial function. The inner mitochondrial membrane contains the phospholipid cardiolipin, which has been demonstrated to act as a biomarker for a number of diverse pathologies. Small molecule dyes capable of selectively partitioning into cardiolipin membranes enable visualization and quantification of the cardiolipin content. Here we present a data-driven approach that combines a deep learning-enabled active learning workflow with coarse-grained molecular dynamics simulations and alchemical free energy calculations to discover small organic compounds able to selectively permeate cardiolipin-containing membranes. By employing transferable coarse-grained models we efficiently navigate the all-atom design space corresponding to small organic molecules with molecular weight less than ≈500 Da. After direct simulation of only 0.42% of our coarse-grained search space we identify molecules with considerably increased levels of cardiolipin selectivity compared to a widely used cardiolipin probe 10-N-nonyl acridine orange. Our accumulated simulation data enables us to derive interpretable design rules linking coarse-grained structure to cardiolipin selectivity. The findings are corroborated by fluorescence anisotropy measurements of two compounds conforming to our defined design rules. Our findings highlight the potential of coarse-grained representations and multiscale modelling for materials discovery and design.
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Affiliation(s)
- Bernadette Mohr
- Van't Hoff Institute for Molecular Sciences and Informatics Institute, University of Amsterdam Amsterdam 1098 XH The Netherlands
| | - Kirill Shmilovich
- Pritzker School of Molecular Engineering, University of Chicago Chicago Illinois 60637 USA
| | - Isabel S Kleinwächter
- Department of Chemistry - Biochemistry, Johannes Gutenberg University Mainz 55128 Mainz Germany
| | - Dirk Schneider
- Department of Chemistry - Biochemistry, Johannes Gutenberg University Mainz 55128 Mainz Germany
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago Chicago Illinois 60637 USA
| | - Tristan Bereau
- Van't Hoff Institute for Molecular Sciences and Informatics Institute, University of Amsterdam Amsterdam 1098 XH The Netherlands .,Max Planck Institute for Polymer Research 55128 Mainz Germany
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27
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Structural and functional roles of non-bilayer lipid phases of chloroplast thylakoid membranes and mitochondrial inner membranes. Prog Lipid Res 2022; 86:101163. [DOI: 10.1016/j.plipres.2022.101163] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 12/11/2022]
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28
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Dewar CE, Oeljeklaus S, Wenger C, Warscheid B, Schneider A. Characterization of a highly diverged mitochondrial ATP synthase F o subunit in Trypanosoma brucei. J Biol Chem 2022; 298:101829. [PMID: 35293314 PMCID: PMC9034290 DOI: 10.1016/j.jbc.2022.101829] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 03/02/2022] [Accepted: 03/04/2022] [Indexed: 11/24/2022] Open
Abstract
The mitochondrial F1Fo ATP synthase of the parasite Trypanosoma brucei has been previously studied in detail. This unusual enzyme switches direction in functionality during the life cycle of the parasite, acting as an ATP synthase in the insect stages, and as an ATPase to generate mitochondrial membrane potential in the mammalian bloodstream stages. Whereas the trypanosome F1 moiety is relatively highly conserved in structure and composition, the Fo subcomplex and the peripheral stalk have been shown to be more variable. Interestingly, a core subunit of the latter, the normally conserved subunit b, has been resistant to identification by sequence alignment or biochemical methods. Here, we identified a 17 kDa mitochondrial protein of the inner membrane, Tb927.8.3070, that is essential for normal growth, efficient oxidative phosphorylation, and membrane potential maintenance. Pull-down experiments and native PAGE analysis indicated that the protein is both associated with the F1Fo ATP synthase and integral to its assembly. In addition, its knockdown reduced the levels of Fo subunits, but not those of F1, and disturbed the cell cycle. Finally, analysis of structural homology using the HHpred algorithm showed that this protein has structural similarities to Fo subunit b of other species, indicating that this subunit may be a highly diverged form of the elusive subunit b.
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Affiliation(s)
- Caroline E Dewar
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Silke Oeljeklaus
- Department of Biochemistry, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - Christoph Wenger
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Bettina Warscheid
- Department of Biochemistry, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
| | - André Schneider
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
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29
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Murakami A, Nagao K, Sakaguchi R, Kida K, Hara Y, Mori Y, Okabe K, Harada Y, Umeda M. Cell-autonomous control of intracellular temperature by unsaturation of phospholipid acyl chains. Cell Rep 2022; 38:110487. [PMID: 35294880 DOI: 10.1016/j.celrep.2022.110487] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 12/03/2021] [Accepted: 02/14/2022] [Indexed: 11/25/2022] Open
Abstract
Intracellular temperature affects a wide range of cellular functions in living organisms. However, it remains unclear whether temperature in individual animal cells is controlled autonomously as a response to fluctuations in environmental temperature. Using two distinct intracellular thermometers, we find that the intracellular temperature of steady-state Drosophila S2 cells is maintained in a manner dependent on Δ9-fatty acid desaturase DESAT1, which introduces a double bond at the Δ9 position of the acyl moiety of acyl-CoA. The DESAT1-mediated increase of intracellular temperature is caused by the enhancement of F1Fo-ATPase-dependent mitochondrial respiration, which is coupled with thermogenesis. We also reveal that F1Fo-ATPase-dependent mitochondrial respiration is potentiated by cold exposure through the remodeling of mitochondrial cristae structures via DESAT1-dependent unsaturation of mitochondrial phospholipid acyl chains. Based on these findings, we propose a cell-autonomous mechanism for intracellular temperature control during environmental temperature changes.
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Affiliation(s)
- Akira Murakami
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan; Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Kohjiro Nagao
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan.
| | - Reiko Sakaguchi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Keisuke Kida
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Yuji Hara
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Yasuo Mori
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Kohki Okabe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yoshie Harada
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Masato Umeda
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan.
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30
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Małecki JM, Davydova E, Falnes PØ. Protein methylation in mitochondria. J Biol Chem 2022; 298:101791. [PMID: 35247388 PMCID: PMC9006661 DOI: 10.1016/j.jbc.2022.101791] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/18/2022] [Accepted: 02/22/2022] [Indexed: 12/15/2022] Open
Abstract
Many proteins are modified by posttranslational methylation, introduced by a number of methyltransferases (MTases). Protein methylation plays important roles in modulating protein function and thus in optimizing and regulating cellular and physiological processes. Research has mainly focused on nuclear and cytosolic protein methylation, but it has been known for many years that also mitochondrial proteins are methylated. During the last decade, significant progress has been made on identifying the MTases responsible for mitochondrial protein methylation and addressing its functional significance. In particular, several novel human MTases have been uncovered that methylate lysine, arginine, histidine, and glutamine residues in various mitochondrial substrates. Several of these substrates are key components of the bioenergetics machinery, e.g., respiratory Complex I, citrate synthase, and the ATP synthase. In the present review, we report the status of the field of mitochondrial protein methylation, with a particular emphasis on recently discovered human MTases. We also discuss evolutionary aspects and functional significance of mitochondrial protein methylation and present an outlook for this emergent research field.
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Affiliation(s)
- Jędrzej M Małecki
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway.
| | - Erna Davydova
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Pål Ø Falnes
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway.
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31
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High-throughput functional characterization of protein phosphorylation sites in yeast. Nat Biotechnol 2022; 40:382-390. [PMID: 34663920 PMCID: PMC7612524 DOI: 10.1038/s41587-021-01051-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/09/2021] [Indexed: 12/11/2022]
Abstract
Phosphorylation is a critical post-translational modification involved in the regulation of almost all cellular processes. However, fewer than 5% of thousands of recently discovered phosphosites have been functionally annotated. In this study, we devised a chemical genetic approach to study the functional relevance of phosphosites in Saccharomyces cerevisiae. We generated 474 yeast strains with mutations in specific phosphosites that were screened for fitness in 102 conditions, along with a gene deletion library. Of these phosphosites, 42% exhibited growth phenotypes, suggesting that these are more likely functional. We inferred their function based on the similarity of their growth profiles with that of gene deletions and validated a subset by thermal proteome profiling and lipidomics. A high fraction exhibited phenotypes not seen in the corresponding gene deletion, suggestive of a gain-of-function effect. For phosphosites conserved in humans, the severity of the yeast phenotypes is indicative of their human functional relevance. This high-throughput approach allows for functionally characterizing individual phosphosites at scale.
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32
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Yang Z, Wang L, Yang C, Pu S, Guo Z, Wu Q, Zhou Z, Zhao H. Mitochondrial Membrane Remodeling. Front Bioeng Biotechnol 2022; 9:786806. [PMID: 35059386 PMCID: PMC8763711 DOI: 10.3389/fbioe.2021.786806] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/22/2021] [Indexed: 02/05/2023] Open
Abstract
Mitochondria are key regulators of many important cellular processes and their dysfunction has been implicated in a large number of human disorders. Importantly, mitochondrial function is tightly linked to their ultrastructure, which possesses an intricate membrane architecture defining specific submitochondrial compartments. In particular, the mitochondrial inner membrane is highly folded into membrane invaginations that are essential for oxidative phosphorylation. Furthermore, mitochondrial membranes are highly dynamic and undergo constant membrane remodeling during mitochondrial fusion and fission. It has remained enigmatic how these membrane curvatures are generated and maintained, and specific factors involved in these processes are largely unknown. This review focuses on the current understanding of the molecular mechanism of mitochondrial membrane architectural organization and factors critical for mitochondrial morphogenesis, as well as their functional link to human diseases.
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Affiliation(s)
- Ziyun Yang
- School of Life Sciences, Guangxi Normal University, Guilin, China.,Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China.,Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Liang Wang
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, West China Medical School, Sichuan University, High-Tech Development Zone, Chengdu, China
| | - Cheng Yang
- School of Life Sciences, Guangxi Normal University, Guilin, China.,Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China.,Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Shiming Pu
- School of Life Sciences, Guangxi Normal University, Guilin, China.,Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China.,Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Ziqi Guo
- School of Life Sciences, Guangxi Normal University, Guilin, China.,Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China.,Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Qiong Wu
- School of Life Sciences, Guangxi Normal University, Guilin, China.,Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China.,Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Zuping Zhou
- School of Life Sciences, Guangxi Normal University, Guilin, China.,Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China.,Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Hongxia Zhao
- School of Life Sciences, Guangxi Normal University, Guilin, China.,Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China.,Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China.,Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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33
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Dudek J, Maack C. Mechano-energetic aspects of Barth syndrome. J Inherit Metab Dis 2022; 45:82-98. [PMID: 34423473 DOI: 10.1002/jimd.12427] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/28/2021] [Accepted: 08/19/2021] [Indexed: 12/22/2022]
Abstract
Energy-demanding organs like the heart are strongly dependent on oxidative phosphorylation in mitochondria. Oxidative phosphorylation is governed by the respiratory chain located in the inner mitochondrial membrane. The inner mitochondrial membrane is the only cellular membrane with significant amounts of the phospholipid cardiolipin, and cardiolipin was found to directly interact with a number of essential protein complexes, including respiratory chain complexes I to V. An inherited defect in the biogenesis of cardiolipin causes Barth syndrome, which is associated with cardiomyopathy, skeletal myopathy, neutropenia and growth retardation. Energy conversion is dependent on reducing equivalents, which are replenished by oxidative metabolism in the Krebs cycle. Cardiolipin deficiency in Barth syndrome also affects Krebs cycle activity, metabolite transport and mitochondrial morphology. During excitation-contraction coupling, calcium (Ca2+ ) released from the sarcoplasmic reticulum drives sarcomeric contraction. At the same time, Ca2+ influx into mitochondria drives the activation of Krebs cycle dehydrogenases and the regeneration of reducing equivalents. Reducing equivalents are essential not only for energy conversion, but also for maintaining a redox buffer, which is required to detoxify reactive oxygen species (ROS). Defects in CL may also affect Ca2+ uptake into mitochondria and thereby hamper energy supply and demand matching, but also detoxification of ROS. Here, we review the impact of cardiolipin deficiency on mitochondrial function in Barth syndrome and discuss potential therapeutic strategies.
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Affiliation(s)
- Jan Dudek
- Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, Würzburg, Germany
| | - Christoph Maack
- Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, Würzburg, Germany
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34
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Characterization of a Novel Splicing Variant in Acylglycerol Kinase (AGK) Associated with Fatal Sengers Syndrome. Int J Mol Sci 2021; 22:ijms222413484. [PMID: 34948281 PMCID: PMC8708263 DOI: 10.3390/ijms222413484] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 12/26/2022] Open
Abstract
Mitochondrial functional integrity depends on protein and lipid homeostasis in the mitochondrial membranes and disturbances in their accumulation can cause disease. AGK, a mitochondrial acylglycerol kinase, is not only involved in lipid signaling but is also a component of the TIM22 complex in the inner mitochondrial membrane, which mediates the import of a subset of membrane proteins. AGK mutations can alter both phospholipid metabolism and mitochondrial protein biogenesis, contributing to the pathogenesis of Sengers syndrome. We describe the case of an infant carrying a novel homozygous AGK variant, c.518+1G>A, who was born with congenital cataracts, pielic ectasia, critical congenital dilated myocardiopathy, and hyperlactacidemia and died 20 h after birth. Using the patient’s DNA, we performed targeted sequencing of 314 nuclear genes encoding respiratory chain complex subunits and proteins implicated in mitochondrial oxidative phosphorylation (OXPHOS). A decrease of 96-bp in the length of the AGK cDNA sequence was detected. Decreases in the oxygen consumption rate (OCR) and the OCR:ECAR (extracellular acidification rate) ratio in the patient’s fibroblasts indicated reduced electron flow through the respiratory chain, and spectrophotometry revealed decreased activity of OXPHOS complexes I and V. We demonstrate a clear defect in mitochondrial function in the patient’s fibroblasts and describe the possible molecular mechanism underlying the pathogenicity of this novel AGK variant. Experimental validation using in vitro analysis allowed an accurate characterization of the disease-causing variant.
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35
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Iovine JC, Claypool SM, Alder NN. Mitochondrial compartmentalization: emerging themes in structure and function. Trends Biochem Sci 2021; 46:902-917. [PMID: 34244035 PMCID: PMC11008732 DOI: 10.1016/j.tibs.2021.06.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/26/2021] [Accepted: 06/04/2021] [Indexed: 11/27/2022]
Abstract
Within cellular structures, compartmentalization is the concept of spatial segregation of macromolecules, metabolites, and biochemical pathways. Therefore, this concept bridges organellar structure and function. Mitochondria are morphologically complex, partitioned into several subcompartments by a topologically elaborate two-membrane system. They are also dynamically polymorphic, undergoing morphogenesis events with an extent and frequency that is only now being appreciated. Thus, mitochondrial compartmentalization is something that must be considered both spatially and temporally. Here, we review new developments in how mitochondrial structure is established and regulated, the factors that underpin the distribution of lipids and proteins, and how they spatially demarcate locations of myriad mitochondrial processes. Consistent with its pre-eminence, disturbed mitochondrial compartmentalization contributes to the dysfunction associated with heritable and aging-related diseases.
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Affiliation(s)
- Joseph C Iovine
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Steven M Claypool
- Department of Physiology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nathan N Alder
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
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36
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Xu Y, Erdjument-Bromage H, Phoon CKL, Neubert TA, Ren M, Schlame M. Cardiolipin remodeling enables protein crowding in the inner mitochondrial membrane. EMBO J 2021; 40:e108428. [PMID: 34661298 DOI: 10.15252/embj.2021108428] [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] [Received: 04/07/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 11/09/2022] Open
Abstract
Mitochondrial cristae are extraordinarily crowded with proteins, which puts stress on the bilayer organization of lipids. We tested the hypothesis that the high concentration of proteins drives the tafazzin-catalyzed remodeling of fatty acids in cardiolipin, thereby reducing bilayer stress in the membrane. Specifically, we tested whether protein crowding induces cardiolipin remodeling and whether the lack of cardiolipin remodeling prevents the membrane from accumulating proteins. In vitro, the incorporation of large amounts of proteins into liposomes altered the outcome of the remodeling reaction. In yeast, the concentration of proteins involved in oxidative phosphorylation (OXPHOS) correlated with the cardiolipin composition. Genetic ablation of either remodeling or biosynthesis of cardiolipin caused a substantial drop in the surface density of OXPHOS proteins in the inner membrane of the mouse heart and Drosophila flight muscle mitochondria. Our data suggest that OXPHOS protein crowding induces cardiolipin remodelling and that remodeled cardiolipin supports the high concentration of these proteins in the inner mitochondrial membrane.
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Affiliation(s)
- Yang Xu
- Department of Anesthesiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Hediye Erdjument-Bromage
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY, USA.,Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, USA
| | - Colin K L Phoon
- Department of Pediatrics, New York University Grossman School of Medicine, New York, NY, USA
| | - Thomas A Neubert
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY, USA.,Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, USA
| | - Mindong Ren
- Department of Anesthesiology, New York University Grossman School of Medicine, New York, NY, USA.,Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, USA
| | - Michael Schlame
- Department of Anesthesiology, New York University Grossman School of Medicine, New York, NY, USA.,Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, USA
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37
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Nirody JA, Budin I, Rangamani P. ATP synthase: Evolution, energetics, and membrane interactions. J Gen Physiol 2021; 152:152111. [PMID: 32966553 PMCID: PMC7594442 DOI: 10.1085/jgp.201912475] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/24/2020] [Indexed: 12/24/2022] Open
Abstract
The synthesis of ATP, life’s “universal energy currency,” is the most prevalent chemical reaction in biological systems and is responsible for fueling nearly all cellular processes, from nerve impulse propagation to DNA synthesis. ATP synthases, the family of enzymes that carry out this endless task, are nearly as ubiquitous as the energy-laden molecule they are responsible for making. The F-type ATP synthase (F-ATPase) is found in every domain of life and has facilitated the survival of organisms in a wide range of habitats, ranging from the deep-sea thermal vents to the human intestine. Accordingly, there has been a large amount of work dedicated toward understanding the structural and functional details of ATP synthases in a wide range of species. Less attention, however, has been paid toward integrating these advances in ATP synthase molecular biology within the context of its evolutionary history. In this review, we present an overview of several structural and functional features of the F-type ATPases that vary across taxa and are purported to be adaptive or otherwise evolutionarily significant: ion channel selectivity, rotor ring size and stoichiometry, ATPase dimeric structure and localization in the mitochondrial inner membrane, and interactions with membrane lipids. We emphasize the importance of studying these features within the context of the enzyme’s particular lipid environment. Just as the interactions between an organism and its physical environment shape its evolutionary trajectory, ATPases are impacted by the membranes within which they reside. We argue that a comprehensive understanding of the structure, function, and evolution of membrane proteins—including ATP synthase—requires such an integrative approach.
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Affiliation(s)
- Jasmine A Nirody
- Center for Studies in Physics and Biology, The Rockefeller University, New York, NY.,All Souls College, University of Oxford, Oxford, UK
| | - Itay Budin
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA
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Corey RA, Song W, Duncan AL, Ansell TB, Sansom MSP, Stansfeld PJ. Identification and assessment of cardiolipin interactions with E. coli inner membrane proteins. SCIENCE ADVANCES 2021; 7:eabh2217. [PMID: 34417182 PMCID: PMC8378812 DOI: 10.1126/sciadv.abh2217] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/30/2021] [Indexed: 05/03/2023]
Abstract
Integral membrane proteins are localized and/or regulated by lipids present in the surrounding bilayer. While bacteria have relatively simple membranes, there is ample evidence that many bacterial proteins bind to specific lipids, especially the anionic lipid cardiolipin. Here, we apply molecular dynamics simulations to assess lipid binding to 42 different Escherichia coli inner membrane proteins. Our data reveal an asymmetry between the membrane leaflets, with increased anionic lipid binding to the inner leaflet regions of the proteins, particularly for cardiolipin. From our simulations, we identify >700 independent cardiolipin binding sites, allowing us to identify the molecular basis of a prototypical cardiolipin binding site, which we validate against structures of bacterial proteins bound to cardiolipin. This allows us to construct a set of metrics for defining a high-affinity cardiolipin binding site on bacterial membrane proteins, paving the way for a heuristic approach to defining other protein-lipid interactions.
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Affiliation(s)
- Robin A Corey
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Wanling Song
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - T Bertie Ansell
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
- School of Life Sciences and Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
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Cardiolipin, Non-Bilayer Structures and Mitochondrial Bioenergetics: Relevance to Cardiovascular Disease. Cells 2021; 10:cells10071721. [PMID: 34359891 PMCID: PMC8304834 DOI: 10.3390/cells10071721] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/19/2021] [Accepted: 06/29/2021] [Indexed: 12/23/2022] Open
Abstract
The present review is an attempt to conceptualize a contemporary understanding about the roles that cardiolipin, a mitochondrial specific conical phospholipid, and non-bilayer structures, predominantly found in the inner mitochondrial membrane (IMM), play in mitochondrial bioenergetics. This review outlines the link between changes in mitochondrial cardiolipin concentration and changes in mitochondrial bioenergetics, including changes in the IMM curvature and surface area, cristae density and architecture, efficiency of electron transport chain (ETC), interaction of ETC proteins, oligomerization of respiratory complexes, and mitochondrial ATP production. A relationship between cardiolipin decline in IMM and mitochondrial dysfunction leading to various diseases, including cardiovascular diseases, is thoroughly presented. Particular attention is paid to the targeting of cardiolipin by Szeto–Schiller tetrapeptides, which leads to rejuvenation of important mitochondrial activities in dysfunctional and aging mitochondria. The role of cardiolipin in triggering non-bilayer structures and the functional roles of non-bilayer structures in energy-converting membranes are reviewed. The latest studies on non-bilayer structures induced by cobra venom peptides are examined in model and mitochondrial membranes, including studies on how non-bilayer structures modulate mitochondrial activities. A mechanism by which non-bilayer compartments are formed in the apex of cristae and by which non-bilayer compartments facilitate ATP synthase dimerization and ATP production is also presented.
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Almendro-Vedia V, Natale P, Valdivieso González D, Lillo MP, Aragones JL, López-Montero I. How rotating ATP synthases can modulate membrane structure. Arch Biochem Biophys 2021; 708:108939. [PMID: 34052190 DOI: 10.1016/j.abb.2021.108939] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 01/03/2023]
Abstract
F1Fo-ATP synthase (ATP synthase) is a central membrane protein that synthetizes most of the ATP in the cell through a rotational movement driven by a proton gradient across the hosting membrane. In mitochondria, ATP synthases can form dimers through specific interactions between some subunits of the protein. The dimeric form of ATP synthase provides the protein with a spontaneous curvature that sustain their arrangement at the rim of the high-curvature edges of mitochondrial membrane (cristae). Also, a direct interaction with cardiolipin, a lipid present in the inner mitochondrial membrane, induces the dimerization of ATP synthase molecules along cristae. The deletion of those biochemical interactions abolishes the protein dimerization producing an altered mitochondrial function and morphology. Mechanically, membrane bending is one of the key deformation modes by which mitochondrial membranes can be shaped. In particular, bending rigidity and spontaneous curvature are important physical factors for membrane remodelling. Here, we discuss a complementary mechanism whereby the rotatory movement of the ATP synthase might modify the mechanical properties of lipid bilayers and contribute to the formation and regulation of the membrane invaginations.
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Affiliation(s)
- Víctor Almendro-Vedia
- Departamento Química Física, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain; Instituto de Investigación Hospital Doce de Octubre (imas12), Avenida de Córdoba s/n, 28041, Madrid, Spain
| | - Paolo Natale
- Departamento Química Física, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain; Instituto de Investigación Hospital Doce de Octubre (imas12), Avenida de Córdoba s/n, 28041, Madrid, Spain
| | - David Valdivieso González
- Departamento Química Física, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain; Instituto de Investigación Hospital Doce de Octubre (imas12), Avenida de Córdoba s/n, 28041, Madrid, Spain
| | - M Pilar Lillo
- Departamento Química Física Biológica, Instituto de Química-Física "Rocasolano" (CSIC), Serrano 119, 28006, Madrid, Spain
| | - Juan L Aragones
- Departamento de Física Teórica de la Materia Condensada, Instituto Nicolás Cabrera and Condensed Matter Physics Centre (IFIMAC), Universidad Autónoma de Madrid, E-28049, Madrid, Spain
| | - Iván López-Montero
- Departamento Química Física, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain; Instituto de Investigación Hospital Doce de Octubre (imas12), Avenida de Córdoba s/n, 28041, Madrid, Spain.
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41
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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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42
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Cardiolipin enhances the enzymatic activity of cytochrome bd and cytochrome bo 3 solubilized in dodecyl-maltoside. Sci Rep 2021; 11:8006. [PMID: 33850195 PMCID: PMC8044227 DOI: 10.1038/s41598-021-87354-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 03/25/2021] [Indexed: 02/01/2023] Open
Abstract
Cardiolipin (CL) is a lipid that is found in the membranes of bacteria and the inner membranes of mitochondria. CL can increase the activity of integral membrane proteins, in particular components of respiratory pathways. We here report that CL activated detergent-solubilized cytochrome bd, a terminal oxidase from Escherichia coli. CL enhanced the oxygen consumption activity ~ twofold and decreased the apparent KM value for ubiquinol-1 as substrate from 95 µM to 35 µM. Activation by CL was also observed for cytochrome bd from two Gram-positive species, Geobacillus thermodenitrificans and Corynebacterium glutamicum, and for cytochrome bo3 from E. coli. Taken together, CL can enhance the activity of detergent-solubilized cytochrome bd and cytochrome bo3.
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43
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Falabella M, Vernon HJ, Hanna MG, Claypool SM, Pitceathly RDS. Cardiolipin, Mitochondria, and Neurological Disease. Trends Endocrinol Metab 2021; 32:224-237. [PMID: 33640250 PMCID: PMC8277580 DOI: 10.1016/j.tem.2021.01.006] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 02/07/2023]
Abstract
Over the past decade, it has become clear that lipid homeostasis is central to cellular metabolism. Lipids are particularly abundant in the central nervous system (CNS) where they modulate membrane fluidity, electric signal transduction, and synaptic stabilization. Abnormal lipid profiles reported in Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS), and traumatic brain injury (TBI), are further support for the importance of lipid metablism in the nervous system. Cardiolipin (CL), a mitochondria-exclusive phospholipid, has recently emerged as a focus of neurodegenerative disease research. Aberrant CL content, structure, and localization are linked to impaired neurogenesis and neuronal dysfunction, contributing to aging and the pathogenesis of several neurodegenerative diseases, such as AD and PD. Furthermore, the highly tissue-specific acyl chain composition of CL confers it significant potential as a biomarker to diagnose and monitor the progression in several neurological diseases. CL also represents a potential target for pharmacological strategies aimed at treating neurodegeneration. Given the equipoise that currently exists between CL metabolism, mitochondrial function, and neurological disease, we review the role of CL in nervous system physiology and monogenic and neurodegenerative disease pathophysiology, in addition to its potential application as a biomarker and pharmacological target.
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Affiliation(s)
- Micol Falabella
- Department of Neuromuscular Diseases, University College London Queen Square Institute of Neurology, London, UK
| | - Hilary J Vernon
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael G Hanna
- Department of Neuromuscular Diseases, University College London Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Steven M Claypool
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert D S Pitceathly
- Department of Neuromuscular Diseases, University College London Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK.
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44
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Deng Z, Yuan B, Yang K. Cardiolipin Selectively Binds to the Interface of VsSemiSWEET and Regulates Its Dimerization. J Phys Chem Lett 2021; 12:1940-1946. [PMID: 33591759 DOI: 10.1021/acs.jpclett.1c00022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Lipid-regulated oligomerization of membrane proteins plays a critical role in many cell-transduction pathways. However, molecular details of such processes are often hard to define experimentally. Here we reveal the key role of interfacial cardiolipin in regulating the functional dimerization of VsSemiSWEET (one of the smallest transporters) using molecular dynamics simulations. Four binding sites for cardiolipins are identified by calculating the spatiotemporal density distribution of cardiolipins and the free energy surface. Two types of dimerization modes (i.e., arm-to-body and body-to-body) are observed in the assembly process of VsSemiSWEET protomers. Binding of enough cardiolipin molecules at the dimer interface on the cytoplasmic side is found to be crucial in adjusting the monomer-dimer equilibrium and regulating the formation of functional dimers with proper conformation. Our results provide useful information on the relationship between lipid binding and functional dimerization of VsSemiSWEET and are helpful to understand the molecular mechanism of biological function of sugar transporters.
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Affiliation(s)
- Zhixiong Deng
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, P.R. China
| | - Bing Yuan
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, P.R. China
| | - Kai Yang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, P.R. China
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45
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Prola A, Blondelle J, Vandestienne A, Piquereau J, Denis RGP, Guyot S, Chauvin H, Mourier A, Maurer M, Henry C, Khadhraoui N, Gallerne C, Molinié T, Courtin G, Guillaud L, Gressette M, Solgadi A, Dumont F, Castel J, Ternacle J, Demarquoy J, Malgoyre A, Koulmann N, Derumeaux G, Giraud MF, Joubert F, Veksler V, Luquet S, Relaix F, Tiret L, Pilot-Storck F. Cardiolipin content controls mitochondrial coupling and energetic efficiency in muscle. SCIENCE ADVANCES 2021; 7:7/1/eabd6322. [PMID: 33523852 PMCID: PMC7775760 DOI: 10.1126/sciadv.abd6322] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/04/2020] [Indexed: 05/11/2023]
Abstract
Unbalanced energy partitioning participates in the rise of obesity, a major public health concern in many countries. Increasing basal energy expenditure has been proposed as a strategy to fight obesity yet raises efficiency and safety concerns. Here, we show that mice deficient for a muscle-specific enzyme of very-long-chain fatty acid synthesis display increased basal energy expenditure and protection against high-fat diet-induced obesity. Mechanistically, muscle-specific modulation of the very-long-chain fatty acid pathway was associated with a reduced content of the inner mitochondrial membrane phospholipid cardiolipin and a blunted coupling efficiency between the respiratory chain and adenosine 5'-triphosphate (ATP) synthase, which was restored by cardiolipin enrichment. Our study reveals that selective increase of lipid oxidative capacities in skeletal muscle, through the cardiolipin-dependent lowering of mitochondrial ATP production, provides an effective option against obesity at the whole-body level.
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Affiliation(s)
- Alexandre Prola
- Université Paris-Est Créteil, INSERM, IMRB, Team Relaix, F-94010 Créteil, France
- EnvA, IMRB, F-94700 Maisons-Alfort, France
- EFS, IMRB, F-94010 Créteil, France
| | - Jordan Blondelle
- Université Paris-Est Créteil, INSERM, IMRB, Team Relaix, F-94010 Créteil, France
- EnvA, IMRB, F-94700 Maisons-Alfort, France
- EFS, IMRB, F-94010 Créteil, France
| | - Aymeline Vandestienne
- Université Paris-Est Créteil, INSERM, IMRB, Team Relaix, F-94010 Créteil, France
- EnvA, IMRB, F-94700 Maisons-Alfort, France
- EFS, IMRB, F-94010 Créteil, France
| | - Jérôme Piquereau
- UMR-S 1180, INSERM, Université Paris-Sud, Université Paris-Saclay, F-92296 Châtenay-Malabry, France
| | | | - Stéphane Guyot
- Université Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, F-21000 Dijon, France
| | - Hadrien Chauvin
- Université Paris-Est Créteil, INSERM, IMRB, Team Relaix, F-94010 Créteil, France
- EnvA, IMRB, F-94700 Maisons-Alfort, France
- EFS, IMRB, F-94010 Créteil, France
| | - Arnaud Mourier
- Université Bordeaux, CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Marie Maurer
- Université Paris-Est Créteil, INSERM, IMRB, Team Relaix, F-94010 Créteil, France
- EnvA, IMRB, F-94700 Maisons-Alfort, France
- EFS, IMRB, F-94010 Créteil, France
| | - Céline Henry
- PAPPSO, Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, F-78350 Jouy-en-Josas, France
| | - Nahed Khadhraoui
- Université Paris-Est Créteil, INSERM, IMRB, Team Relaix, F-94010 Créteil, France
- EnvA, IMRB, F-94700 Maisons-Alfort, France
- EFS, IMRB, F-94010 Créteil, France
| | - Cindy Gallerne
- Université Paris-Est Créteil, INSERM, IMRB, Team Relaix, F-94010 Créteil, France
- EnvA, IMRB, F-94700 Maisons-Alfort, France
- EFS, IMRB, F-94010 Créteil, France
| | - Thibaut Molinié
- Université Bordeaux, CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Guillaume Courtin
- Université Paris-Est Créteil, INSERM, IMRB, Team Relaix, F-94010 Créteil, France
- EnvA, IMRB, F-94700 Maisons-Alfort, France
- EFS, IMRB, F-94010 Créteil, France
| | - Laurent Guillaud
- Université Paris-Est Créteil, INSERM, IMRB, Team Relaix, F-94010 Créteil, France
- EnvA, IMRB, F-94700 Maisons-Alfort, France
- EFS, IMRB, F-94010 Créteil, France
| | - Mélanie Gressette
- UMR-S 1180, INSERM, Université Paris-Sud, Université Paris-Saclay, F-92296 Châtenay-Malabry, France
| | - Audrey Solgadi
- UMS IPSIT, Université Paris-Saclay, F-92296 Châtenay-Malabry, France
| | - Florent Dumont
- UMS IPSIT, Université Paris-Saclay, F-92296 Châtenay-Malabry, France
| | - Julien Castel
- Université de Paris, BFA, UMR 8251, CNRS, F-75014 Paris, France
| | - Julien Ternacle
- Université Paris-Est Créteil, INSERM, IMRB, Team Derumeaux, F-94010 Creteil, France
| | - Jean Demarquoy
- Université Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, F-21000 Dijon, France
| | - Alexandra Malgoyre
- Département Environnements Opérationnels, Unité de Physiologie des Exercices et Activités en Conditions Extrêmes, Institut de Recherche Biomédicale des Armées, F-91220 Brétigny-Sur-Orge, France
- LBEPS, Université Evry, IRBA, Université Paris-Saclay, F-91025 Evry, France
| | - Nathalie Koulmann
- Département Environnements Opérationnels, Unité de Physiologie des Exercices et Activités en Conditions Extrêmes, Institut de Recherche Biomédicale des Armées, F-91220 Brétigny-Sur-Orge, France
- LBEPS, Université Evry, IRBA, Université Paris-Saclay, F-91025 Evry, France
- École du Val de Grâce, Place Alphonse Laveran, F-75005 Paris, France
| | - Geneviève Derumeaux
- Université Paris-Est Créteil, INSERM, IMRB, Team Derumeaux, F-94010 Creteil, France
| | | | - Frédéric Joubert
- Laboratoire Jean Perrin, CNRS, Sorbonne Université, UMR 8237, Paris, F-75005, France
| | - Vladimir Veksler
- UMR-S 1180, INSERM, Université Paris-Sud, Université Paris-Saclay, F-92296 Châtenay-Malabry, France
| | - Serge Luquet
- Université de Paris, BFA, UMR 8251, CNRS, F-75014 Paris, France
| | - Frédéric Relaix
- Université Paris-Est Créteil, INSERM, IMRB, Team Relaix, F-94010 Créteil, France.
- EnvA, IMRB, F-94700 Maisons-Alfort, France
- EFS, IMRB, F-94010 Créteil, France
| | - Laurent Tiret
- Université Paris-Est Créteil, INSERM, IMRB, Team Relaix, F-94010 Créteil, France.
- EnvA, IMRB, F-94700 Maisons-Alfort, France
- EFS, IMRB, F-94010 Créteil, France
| | - Fanny Pilot-Storck
- Université Paris-Est Créteil, INSERM, IMRB, Team Relaix, F-94010 Créteil, France.
- EnvA, IMRB, F-94700 Maisons-Alfort, France
- EFS, IMRB, F-94010 Créteil, France
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46
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Mao X, Yao S, Yi Q, Xu ZM, Cang X. Function-related asymmetry of the specific cardiolipin binding sites on the mitochondrial ADP/ATP carrier. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2021; 1863:183466. [PMID: 32871114 DOI: 10.1016/j.bbamem.2020.183466] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/16/2020] [Accepted: 08/24/2020] [Indexed: 01/04/2023]
Abstract
The ADP/ATP carrier (AAC) transports matrix ATP and cytosolic ADP across the inner mitochondrial membrane (IMM). It is well known that cardiolipin (CL) plays an important role in regulating the function of AAC, yet the underlying mechanism still remains elusive. AAC is composed of three homologous domains, and three specific CL binding sites are located at the domain-domain interfaces near the matrix side. Here we report an in-depth investigation on the dynamic properties of the bound CL within the three specific sites through all-atom molecular dynamics simulations of up to 13 μs in total. Our results highlight the importance of the basic and polar residues in CL binding. The basic residues from the linker helix and/or the [Y/W/F][K/R]G motif enable the bound CL to form an intra-domain binding mode, and the canonical inter-domain binding mode only forms when these basic residues are occupied by an additional phospholipid. Of special significance, differences in the basic and polar residues lead to remarkable asymmetry among the three specific CL binding sites. We found that the bound CL at the interface of domains 2 and 3 predominantly adopts inter-domain binding mode, while CLs at the other two sites have much more intra-domain populations. This is consistent with the asymmetric crystal structure of the matrix state (m-state) AAC which implies an asymmetric transport mechanism. The dynamic equilibrium between the inter-domain and intra-domain binding modes observed in our simulations could be highly important for the bound CLs to adapt to the movements during state transitions.
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Affiliation(s)
- Xiaoting Mao
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China; Institute of Genetics, Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Shihao Yao
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China; Institute of Genetics, Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Qiuzi Yi
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China; Institute of Genetics, Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Zhe-Ming Xu
- Department of Urology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health and National Children's Regional Medical Center, Hangzhou, Zhejiang 310052, China
| | - Xiaohui Cang
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China; Institute of Genetics, Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.
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47
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Corrado M, Edwards-Hicks J, Villa M, Flachsmann LJ, Sanin DE, Jacobs M, Baixauli F, Stanczak M, Anderson E, Azuma M, Quintana A, Curtis JD, Clapes T, Grzes KM, Kabat AM, Kyle R, Patterson AE, Geltink RK, Amulic B, Steward CG, Strathdee D, Trompouki E, O'Sullivan D, Pearce EJ, Pearce EL. Dynamic Cardiolipin Synthesis Is Required for CD8 + T Cell Immunity. Cell Metab 2020; 32:981-995.e7. [PMID: 33264603 PMCID: PMC7721104 DOI: 10.1016/j.cmet.2020.11.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 08/25/2020] [Accepted: 11/08/2020] [Indexed: 12/31/2022]
Abstract
Mitochondria constantly adapt to the metabolic needs of a cell. This mitochondrial plasticity is critical to T cells, which modulate metabolism depending on antigen-driven signals and environment. We show here that de novo synthesis of the mitochondrial membrane-specific lipid cardiolipin maintains CD8+ T cell function. T cells deficient for the cardiolipin-synthesizing enzyme PTPMT1 had reduced cardiolipin and responded poorly to antigen because basal cardiolipin levels were required for activation. However, neither de novo cardiolipin synthesis, nor its Tafazzin-dependent remodeling, was needed for T cell activation. In contrast, PTPMT1-dependent cardiolipin synthesis was vital when mitochondrial fitness was required, most notably during memory T cell differentiation or nutrient stress. We also found CD8+ T cell defects in a small cohort of patients with Barth syndrome, where TAFAZZIN is mutated, and in a Tafazzin-deficient mouse model. Thus, the dynamic regulation of a single mitochondrial lipid is crucial for CD8+ T cell immunity.
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Affiliation(s)
- Mauro Corrado
- Max-Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Joy Edwards-Hicks
- Max-Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Matteo Villa
- Max-Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Lea J Flachsmann
- Max-Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - David E Sanin
- Max-Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Maaike Jacobs
- Max-Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Francesc Baixauli
- Max-Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Michal Stanczak
- Max-Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Eve Anderson
- Cancer Research UK Beatson Institute, Glasgow G61 1 BD, UK
| | - Mai Azuma
- Max-Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Andrea Quintana
- Max-Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Jonathan D Curtis
- Max-Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Thomas Clapes
- Max-Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Katarzyna M Grzes
- Max-Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Agnieszka M Kabat
- Max-Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Ryan Kyle
- Max-Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Annette E Patterson
- Max-Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Ramon Klein Geltink
- Max-Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Borko Amulic
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TH, UK
| | - Colin G Steward
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TH, UK
| | | | - Eirini Trompouki
- Max-Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - David O'Sullivan
- Max-Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Edward J Pearce
- Max-Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79098 Freiburg im Breisgau, Germany
| | - Erika L Pearce
- Max-Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
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Makowski M, Felício MR, Fensterseifer ICM, Franco OL, Santos NC, Gonçalves S. EcDBS1R4, an Antimicrobial Peptide Effective against Escherichia coli with In Vitro Fusogenic Ability. Int J Mol Sci 2020; 21:ijms21239104. [PMID: 33265989 PMCID: PMC7730630 DOI: 10.3390/ijms21239104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 01/18/2023] Open
Abstract
Discovering antibiotic molecules able to hold the growing spread of antimicrobial resistance is one of the most urgent endeavors that public health must tackle. The case of Gram-negative bacterial pathogens is of special concern, as they are intrinsically resistant to many antibiotics, due to an outer membrane that constitutes an effective permeability barrier. Antimicrobial peptides (AMPs) have been pointed out as potential alternatives to conventional antibiotics, as their main mechanism of action is membrane disruption, arguably less prone to elicit resistance in pathogens. Here, we investigate the in vitro activity and selectivity of EcDBS1R4, a bioinspired AMP. To this purpose, we have used bacterial cells and model membrane systems mimicking both the inner and the outer membranes of Escherichia coli, and a variety of optical spectroscopic methodologies. EcDBS1R4 is effective against the Gram-negative E. coli, ineffective against the Gram-positive Staphylococcus aureus and noncytotoxic for human cells. EcDBS1R4 does not form stable pores in E. coli, as the peptide does not dissipate its membrane potential, suggesting an unusual mechanism of action. Interestingly, EcDBS1R4 promotes a hemi-fusion of vesicles mimicking the inner membrane of E. coli. This fusogenic ability of EcDBS1R4 requires the presence of phospholipids with a negative curvature and a negative charge. This finding suggests that EcDBS1R4 promotes a large lipid spatial reorganization able to reshape membrane curvature, with interesting biological implications herein discussed.
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Affiliation(s)
- Marcin Makowski
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (M.M.); (M.R.F.)
| | - Mário R. Felício
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (M.M.); (M.R.F.)
| | - Isabel C. M. Fensterseifer
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília 71966-700, Brazil; (I.C.M.F.); (O.L.F.)
- S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande 79117-010, Brazil
| | - Octávio L. Franco
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília 71966-700, Brazil; (I.C.M.F.); (O.L.F.)
- S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande 79117-010, Brazil
| | - Nuno C. Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (M.M.); (M.R.F.)
- Correspondence: (N.C.S.); (S.G.)
| | - Sónia Gonçalves
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (M.M.); (M.R.F.)
- Correspondence: (N.C.S.); (S.G.)
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49
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Serricchio M, Hierro-Yap C, Schädeli D, Ben Hamidane H, Hemphill A, Graumann J, Zíková A, Bütikofer P. Depletion of cardiolipin induces major changes in energy metabolism in Trypanosoma brucei bloodstream forms. FASEB J 2020; 35:e21176. [PMID: 33184899 DOI: 10.1096/fj.202001579rr] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/26/2020] [Indexed: 01/09/2023]
Abstract
The mitochondrial inner membrane glycerophospholipid cardiolipin (CL) associates with mitochondrial proteins to regulate their activities and facilitate protein complex and supercomplex formation. Loss of CL leads to destabilized respiratory complexes and mitochondrial dysfunction. The role of CL in an organism lacking a conventional electron transport chain (ETC) has not been elucidated. Trypanosoma brucei bloodstream forms use an unconventional ETC composed of glycerol-3-phosphate dehydrogenase and alternative oxidase (AOX), while the mitochondrial membrane potential (ΔΨm) is generated by the hydrolytic action of the Fo F1 -ATP synthase (aka Fo F1 -ATPase). We now report that the inducible depletion of cardiolipin synthase (TbCls) is essential for survival of T brucei bloodstream forms. Loss of CL caused a rapid drop in ATP levels and a decline in the ΔΨm. Unbiased proteomic analyses revealed a reduction in the levels of many mitochondrial proteins, most notably of Fo F1 -ATPase subunits and AOX, resulting in a strong decline of glycerol-3-phosphate-stimulated oxygen consumption. The changes in cellular respiration preceded the observed decrease in Fo F1 -ATPase stability, suggesting that the AOX-mediated ETC is the first pathway responding to the decline in CL. Select proteins and pathways involved in glucose and amino acid metabolism were upregulated to counteract the CL depletion-induced drop in cellular ATP.
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Affiliation(s)
- Mauro Serricchio
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Carolina Hierro-Yap
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - David Schädeli
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | | | - Andrew Hemphill
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Johannes Graumann
- Weill Cornell Medicine - Qatar, Doha, State of Qatar.,Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Alena Zíková
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Peter Bütikofer
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
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50
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Metabolic Alterations Caused by Defective Cardiolipin Remodeling in Inherited Cardiomyopathies. Life (Basel) 2020; 10:life10110277. [PMID: 33187128 PMCID: PMC7697959 DOI: 10.3390/life10110277] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/04/2020] [Accepted: 11/06/2020] [Indexed: 12/21/2022] Open
Abstract
The heart is the most energy-consuming organ in the human body. In heart failure, the homeostasis of energy supply and demand is endangered by an increase in cardiomyocyte workload, or by an insufficiency in energy-providing processes. Energy metabolism is directly associated with mitochondrial redox homeostasis. The production of toxic reactive oxygen species (ROS) may overwhelm mitochondrial and cellular ROS defense mechanisms in case of heart failure. Mitochondria are essential cell organelles and provide 95% of the required energy in the heart. Metabolic remodeling, changes in mitochondrial structure or function, and alterations in mitochondrial calcium signaling diminish mitochondrial energy provision in many forms of cardiomyopathy. The mitochondrial respiratory chain creates a proton gradient across the inner mitochondrial membrane, which couples respiration with oxidative phosphorylation and the preservation of energy in the chemical bonds of ATP. Akin to other mitochondrial enzymes, the respiratory chain is integrated into the inner mitochondrial membrane. The tight association with the mitochondrial phospholipid cardiolipin (CL) ensures its structural integrity and coordinates enzymatic activity. This review focuses on how changes in mitochondrial CL may be associated with heart failure. Dysfunctional CL has been found in diabetic cardiomyopathy, ischemia reperfusion injury and the aging heart. Barth syndrome (BTHS) is caused by an inherited defect in the biosynthesis of cardiolipin. Moreover, a dysfunctional CL pool causes other types of rare inherited cardiomyopathies, such as Sengers syndrome and Dilated Cardiomyopathy with Ataxia (DCMA). Here we review the impact of cardiolipin deficiency on mitochondrial functions in cellular and animal models. We describe the molecular mechanisms concerning mitochondrial dysfunction as an incitement of cardiomyopathy and discuss potential therapeutic strategies.
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