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Wu D, Tang H, Qiu X, Song S, Chen S, Robinson CV. Native MS-guided lipidomics to define endogenous lipid microenvironments of eukaryotic receptors and transporters. Nat Protoc 2024:10.1038/s41596-024-01037-4. [PMID: 39174660 DOI: 10.1038/s41596-024-01037-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/06/2024] [Indexed: 08/24/2024]
Abstract
The mammalian membrane is composed of various eukaryotic lipids interacting with extensively post-translationally modified proteins. Probing interactions between these mammalian membrane proteins and their diverse and heterogeneous lipid cohort remains challenging. Recently, native mass spectrometry (MS) combined with bottom-up 'omics' approaches has provided valuable information to relate structural and functional lipids to membrane protein assemblies in eukaryotic membranes. Here we provide a step-by-step protocol to identify and provide relative quantification for endogenous lipids bound to mammalian membrane proteins and their complexes. Using native MS to guide our lipidomics strategies, we describe the necessary sample preparation steps, followed by native MS data acquisition, tailored lipidomics and data interpretation. We also highlight considerations for the integration of different levels of information from native MS and lipidomics and how to deal with the various challenges that arise during the experiments. This protocol begins with the preparation of membrane proteins from mammalian cells and tissues for native MS. The results enable not only direct assessment of copurified endogenous lipids but also determination of the apparent affinities of specific lipids. Detailed sample preparation for lipidomics analysis is also covered, along with comprehensive settings for liquid chromatography-MS analysis. This protocol is suitable for the identification and quantification of endogenous lipids, including fatty acids, sterols, glycerolipids, phospholipids and glycolipids and can be used to interrogate proteins from recombinant sources to native membranes.
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Affiliation(s)
- Di Wu
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Haiping Tang
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Xingyu Qiu
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Siyuan Song
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Siyun Chen
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
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2
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Timimi L, Wrobel AG, Chiduza GN, Maslen SL, Torres-Méndez A, Montaner B, Davis C, Minckley T, Hole KL, Serio A, Devine MJ, Skehel JM, Rubinstein JL, Schreiber A, Beale R. The V-ATPase/ATG16L1 axis is controlled by the V 1H subunit. Mol Cell 2024; 84:2966-2983.e9. [PMID: 39089251 DOI: 10.1016/j.molcel.2024.07.003] [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: 12/18/2023] [Revised: 05/15/2024] [Accepted: 07/05/2024] [Indexed: 08/03/2024]
Abstract
Defects in organellar acidification indicate compromised or infected compartments. Recruitment of the autophagy-related ATG16L1 complex to pathologically neutralized organelles targets ubiquitin-like ATG8 molecules to perturbed membranes. How this process is coupled to proton gradient disruption is unclear. Here, we reveal that the V1H subunit of the vacuolar ATPase (V-ATPase) proton pump binds directly to ATG16L1. The V1H/ATG16L1 interaction only occurs within fully assembled V-ATPases, allowing ATG16L1 recruitment to be coupled to increased V-ATPase assembly following organelle neutralization. Cells lacking V1H fail to target ATG8s during influenza infection or after activation of the immune receptor stimulator of interferon genes (STING). We identify a loop within V1H that mediates ATG16L1 binding. A neuronal V1H isoform lacks this loop and is associated with attenuated ATG8 targeting in response to ionophores in primary murine and human iPSC-derived neurons. Thus, V1H controls ATG16L1 recruitment following proton gradient dissipation, suggesting that the V-ATPase acts as a cell-intrinsic damage sensor.
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Affiliation(s)
- Lewis Timimi
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Division of Medicine, University College London, London WC1E 6JF, UK
| | - Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - George N Chiduza
- Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Sarah L Maslen
- Proteomics STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Antonio Torres-Méndez
- Neural Circuits & Evolution Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Beatriz Montaner
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Colin Davis
- Cellular Degradation Systems Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Taylor Minckley
- Neural Circuit Bioengineering and Disease Modelling Laboratory, The Francis Crick Institute, London NW1 1AT, UK; UK Dementia Research Institute at King's College London, London SE5 9RX, UK; Department of Basic and Clinical Neuroscience, Institute of Psychiatry Psychology & Neuroscience, King's College London, London SE5 9RX, UK
| | - Katriona L Hole
- Mitochondrial Neurobiology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Andrea Serio
- Neural Circuit Bioengineering and Disease Modelling Laboratory, The Francis Crick Institute, London NW1 1AT, UK; UK Dementia Research Institute at King's College London, London SE5 9RX, UK; Department of Basic and Clinical Neuroscience, Institute of Psychiatry Psychology & Neuroscience, King's College London, London SE5 9RX, UK
| | - Michael J Devine
- Mitochondrial Neurobiology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - J Mark Skehel
- Proteomics STP, The Francis Crick Institute, London NW1 1AT, UK
| | - John L Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Medical Biophysics, The University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Anne Schreiber
- Cellular Degradation Systems Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Rupert Beale
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Division of Medicine, University College London, London WC1E 6JF, UK.
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3
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Wang H, Tarsio M, Kane PM, Rubinstein JL. Structure of yeast RAVE bound to a partial V 1 complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.18.604153. [PMID: 39071316 PMCID: PMC11275763 DOI: 10.1101/2024.07.18.604153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Vacuolar-type ATPases (V-ATPases) are membrane-embedded proton pumps that acidify intracellular compartments in almost all eukaryotic cells. Homologous with ATP synthases, these multi-subunit enzymes consist of a soluble catalytic V 1 subcomplex and a membrane-embedded proton-translocating V O subcomplex. The V 1 and V O subcomplexes can undergo reversible dissociation to regulate proton pumping, with reassociation of V 1 and V O requiring the protein complex known as RAVE (regulator of the A TPase of v acuoles and e ndosomes). In the yeast Saccharomyces cerevisiae , RAVE consists of subunits Rav1p, Rav2p, and Skp1p. We used electron cryomicroscopy (cryo-EM) to determine a structure of yeast RAVE bound to V 1 . In the structure, RAVE is a L-shaped complex with Rav2p pointing toward the membrane and Skp1p distant from both the membrane and V 1 . Only Rav1p interacts with V 1 , binding to a region of subunit A not found in the corresponding ATP synthase subunit. When bound to RAVE, V 1 is in a rotational state suitable for binding the free V O complex, but it is partially disrupted in the structure, missing five of its 16 subunits. Other than these missing subunits and the conformation of the inhibitory subunit H, the V 1 complex with RAVE appears poised for reassembly with V O .
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4
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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; 385:168-174. [PMID: 38900912 DOI: 10.1126/science.adp5577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [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 a loss of the V1 region of V-ATPase 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, ON M5G 1X1, Canada
| | - Ryan Karimi
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 1X1, Canada
- Department of Medical Biophysics, The University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Stephanie A Bueler
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 1X1, Canada
| | - Yingke Liang
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 1X1, Canada
- Department of Biochemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Gautier M Courbon
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 1X1, Canada
- Department of Medical Biophysics, The University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Justin M Di Trani
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 1X1, Canada
| | - Cassandra J Wong
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada
| | - Rayan Saghian
- Neuroscience and Mental Health Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Physiology, The University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ji-Young Youn
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 1X1, Canada
- Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Molecular Genetics, The University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Lu-Yang Wang
- Neuroscience and Mental Health Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Physiology, The University of Toronto, Toronto, ON M5S 1A8, Canada
| | - John L Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 1X1, Canada
- Department of Medical Biophysics, The University of Toronto, Toronto, ON M5G 1L7, Canada
- Department of Biochemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada
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5
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Zhang Y, Lai Y, Zhou S, Ran T, Zhang Y, Zhao Z, Feng Z, Yu L, Xu J, Shi K, Wang J, Pang Y, Li L, Chen H, Guddat LW, Gao Y, Liu F, Rao Z, Gong H. Inhibition of M. tuberculosis and human ATP synthase by BDQ and TBAJ-587. Nature 2024; 631:409-414. [PMID: 38961288 DOI: 10.1038/s41586-024-07605-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 05/24/2024] [Indexed: 07/05/2024]
Abstract
Bedaquiline (BDQ), a first-in-class diarylquinoline anti-tuberculosis drug, and its analogue, TBAJ-587, prevent the growth and proliferation of Mycobacterium tuberculosis by inhibiting ATP synthase1,2. However, BDQ also inhibits human ATP synthase3. At present, how these compounds interact with either M. tuberculosis ATP synthase or human ATP synthase is unclear. Here we present cryogenic electron microscopy structures of M. tuberculosis ATP synthase with and without BDQ and TBAJ-587 bound, and human ATP synthase bound to BDQ. The two inhibitors interact with subunit a and the c-ring at the leading site, c-only sites and lagging site in M. tuberculosis ATP synthase, showing that BDQ and TBAJ-587 have similar modes of action. The quinolinyl and dimethylamino units of the compounds make extensive contacts with the protein. The structure of human ATP synthase in complex with BDQ reveals that the BDQ-binding site is similar to that observed for the leading site in M. tuberculosis ATP synthase, and that the quinolinyl unit also interacts extensively with the human enzyme. This study will improve researchers' understanding of the similarities and differences between human ATP synthase and M. tuberculosis ATP synthase in terms of the mode of BDQ binding, and will allow the rational design of novel diarylquinolines as anti-tuberculosis drugs.
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Affiliation(s)
- Yuying Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China
| | - Yuezheng Lai
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China
| | - Shan Zhou
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China
| | - Ting Ran
- Innovative Center for Pathogen Research, Guangzhou National Laboratory, Guangzhou, China
| | - Yue Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China
| | - Ziqing Zhao
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China
| | - Ziyan Feng
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China
| | - Long Yu
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China
| | - Jinxu Xu
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China
| | - Kun Shi
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China
| | - Jianyun Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China
| | - Yu Pang
- Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Research Institute, Capital Medical University, Beijing, China
| | - Liang Li
- Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Research Institute, Capital Medical University, Beijing, China
| | - Hongming Chen
- Innovative Center for Pathogen Research, Guangzhou National Laboratory, Guangzhou, China
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Fengjiang Liu
- Innovative Center for Pathogen Research, Guangzhou National Laboratory, Guangzhou, China.
| | - Zihe Rao
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China.
- Innovative Center for Pathogen Research, Guangzhou National Laboratory, Guangzhou, China.
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Laboratory of Structural Biology, Tsinghua University, Beijing, China.
| | - Hongri Gong
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China.
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6
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Wang C, Jiang W, Leitz J, Yang K, Esquivies L, Wang X, Shen X, Held RG, Adams DJ, Basta T, Hampton L, Jian R, Jiang L, Stowell MHB, Baumeister W, Guo Q, Brunger AT. Structure and topography of the synaptic V-ATPase-synaptophysin complex. Nature 2024; 631:899-904. [PMID: 38838737 PMCID: PMC11269182 DOI: 10.1038/s41586-024-07610-x] [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: 04/09/2024] [Accepted: 05/24/2024] [Indexed: 06/07/2024]
Abstract
Synaptic vesicles are organelles with a precisely defined protein and lipid composition1,2, yet the molecular mechanisms for the biogenesis of synaptic vesicles are mainly unknown. Here we discovered a well-defined interface between the synaptic vesicle V-ATPase and synaptophysin by in situ cryo-electron tomography and single-particle cryo-electron microscopy of functional synaptic vesicles isolated from mouse brains3. The synaptic vesicle V-ATPase is an ATP-dependent proton pump that establishes the proton gradient across the synaptic vesicle, which in turn drives the uptake of neurotransmitters4,5. Synaptophysin6 and its paralogues synaptoporin7 and synaptogyrin8 belong to a family of abundant synaptic vesicle proteins whose function is still unclear. We performed structural and functional studies of synaptophysin-knockout mice, confirming the identity of synaptophysin as an interaction partner with the V-ATPase. Although there is little change in the conformation of the V-ATPase upon interaction with synaptophysin, the presence of synaptophysin in synaptic vesicles profoundly affects the copy number of V-ATPases. This effect on the topography of synaptic vesicles suggests that synaptophysin assists in their biogenesis. In support of this model, we observed that synaptophysin-knockout mice exhibit severe seizure susceptibility, suggesting an imbalance of neurotransmitter release as a physiological consequence of the absence of synaptophysin.
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Affiliation(s)
- Chuchu Wang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
- Department of Photon Science, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Wenhong Jiang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Jeremy Leitz
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
- Department of Photon Science, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Kailu Yang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
- Department of Photon Science, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Luis Esquivies
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
- Department of Photon Science, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Xing Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xiaotao Shen
- Department of Genetics, Stanford University, Stanford, CA, USA
- Stanford Center for Genomics and Personalized Medicine, Stanford University, Stanford, CA, USA
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Richard G Held
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
- Department of Photon Science, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Daniel J Adams
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Tamara Basta
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Lucas Hampton
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Ruiqi Jian
- Department of Genetics, Stanford University, Stanford, CA, USA
- Stanford Center for Genomics and Personalized Medicine, Stanford University, Stanford, CA, USA
| | - Lihua Jiang
- Department of Genetics, Stanford University, Stanford, CA, USA
- Stanford Center for Genomics and Personalized Medicine, Stanford University, Stanford, CA, USA
| | - Michael H B Stowell
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Wolfgang Baumeister
- Department of Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Qiang Guo
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.
- Department of Structural Biology, Stanford University, Stanford, CA, USA.
- Department of Photon Science, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
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7
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Yanagisawa S, Bukhari ZA, Parra KJ, Frasch WD. Eukaryotic yeast V 1-ATPase rotary mechanism insights revealed by high-resolution single-molecule studies. Front Mol Biosci 2024; 11:1269040. [PMID: 38567099 PMCID: PMC10985318 DOI: 10.3389/fmolb.2024.1269040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 02/07/2024] [Indexed: 04/04/2024] Open
Abstract
Vacuolar ATP-dependent proton pumps (V-ATPases) belong to a super-family of rotary ATPases and ATP synthases. The V1 complex consumes ATP to drive rotation of a central rotor that pumps protons across membranes via the Vo complex. Eukaryotic V-ATPases are regulated by reversible disassembly of subunit C, V1 without C, and VO. ATP hydrolysis is thought to generate an unknown rotary state that initiates regulated disassembly. Dissociated V1 is inhibited by subunit H that traps it in a specific rotational position. Here, we report the first single-molecule studies with high resolution of time and rotational position of Saccharomyces cerevisiae V1-ATPase lacking subunits H and C (V1ΔHC), which resolves previously elusive dwells and angular velocity changes. Rotation occurred in 120° power strokes separated by dwells comparable to catalytic dwells observed in other rotary ATPases. However, unique V1ΔHC rotational features included: 1) faltering power stroke rotation during the first 60°; 2) a dwell often occurring ∼45° after the catalytic dwell, which did not increase in duration at limiting MgATP; 3) a second dwell, ∼2-fold longer occurring 112° that increased in duration and occurrence at limiting MgATP; 4) limiting MgATP-dependent decreases in power stroke angular velocity where dwells were not observed. The results presented here are consistent with MgATP binding to the empty catalytic site at 112° and MgADP released at ∼45°, and provide important new insight concerning the molecular basis for the differences in rotary positions of substrate binding and product release between V-type and F-type ATPases.
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Affiliation(s)
- Seiga Yanagisawa
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Zain A. Bukhari
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Karlett J. Parra
- Department of Biochemistry and Molecular Biology, University of New Mexico School of Medicine, Albuquerque, NM, United States
| | - Wayne D. Frasch
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
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8
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Jiang YT, Yang LH, Zheng JX, Geng XC, Bai YX, Wang YC, Xue HW, Lin WH. Vacuolar H +-ATPase and BZR1 form a feedback loop to regulate the homeostasis of BR signaling in Arabidopsis. MOLECULAR PLANT 2023; 16:1976-1989. [PMID: 37837193 DOI: 10.1016/j.molp.2023.10.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 09/29/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
Abstract
Brassinosteroid (BR) is a vital plant hormone that regulates plant growth and development. BRASSINAZOLE RESISTANT 1 (BZR1) is a key transcription factor in BR signaling, and its nucleocytoplasmic localization is crucial for BR signaling. However, the mechanisms that regulate BZR1 nucleocytoplasmic distribution and thus the homeostasis of BR signaling remain largely unclear. The vacuole is the largest organelle in mature plant cells and plays a key role in maintenance of cellular pH, storage of intracellular substances, and transport of ions. In this study, we uncovered a novel mechanism of BR signaling homeostasis regulated by the vacuolar H+-ATPase (V-ATPase) and BZR1 feedback loop. Our results revealed that the vha-a2 vha-a3 mutant (vha2, lacking V-ATPase activity) exhibits enhanced BR signaling with increased total amount of BZR1, nuclear-localized BZR1, and the ratio of BZR1/phosphorylated BZR1 in the nucleus. Further biochemical assays revealed that VHA-a2 and VHA-a3 of V-ATPase interact with the BZR1 protein through a domain that is conserved across multiple species. VHA-a2 and VHA-a3 negatively regulate BR signaling by interacting with BZR1 and promoting its retention in the tonoplast. Interestingly, a series of molecular analyses demonstrated that nuclear-localized BZR1 could bind directly to specific motifs in the promoters of VHA-a2 and VHA-a3 to promote their expression. Taken together, these results suggest that V-ATPase and BZR1 may form a feedback regulatory loop to maintain the homeostasis of BR signaling in Arabidopsis, providing new insights into vacuole-mediated regulation of hormone signaling.
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Affiliation(s)
- Yu-Tong Jiang
- School of Life Sciences and Biotechnology, The Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, Shanghai 200240, China; School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lu-Han Yang
- School of Life Sciences and Biotechnology, The Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ji-Xuan Zheng
- Zhiyuan College, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xian-Chen Geng
- School of Life Sciences and Biotechnology, The Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yu-Xuan Bai
- Zhiyuan College, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yu-Chen Wang
- Zhiyuan College, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hong-Wei Xue
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, Shanghai 200240, China; School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wen-Hui Lin
- School of Life Sciences and Biotechnology, The Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, Shanghai 200240, China.
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9
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Mitra C, Winkley S, Kane PM. Human V-ATPase a-subunit isoforms bind specifically to distinct phosphoinositide phospholipids. J Biol Chem 2023; 299:105473. [PMID: 37979916 PMCID: PMC10755780 DOI: 10.1016/j.jbc.2023.105473] [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: 05/12/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 11/20/2023] Open
Abstract
Vacuolar H+-ATPases (V-ATPases) are highly conserved multisubunit enzymes that maintain the distinct pH of eukaryotic organelles. The integral membrane a-subunit is encoded by tissue- and organelle-specific isoforms, and its cytosolic N-terminal domain (aNT) modulates organelle-specific regulation and targeting of V-ATPases. Organelle membranes have specific phosphatidylinositol phosphate (PIP) lipid enrichment linked to maintenance of organelle pH. In yeast, the aNT domains of the two a-subunit isoforms bind PIP lipids enriched in the organelle membranes where they reside; these interactions affect activity and regulatory properties of the V-ATPases containing each isoform. Humans have four a-subunit isoforms, and we hypothesize that the aNT domains of these isoforms will also bind to specific PIP lipids. The a1 and a2 isoforms of human V-ATPase a-subunits are localized to endolysosomes and Golgi, respectively. We determined that bacterially expressed Hua1NT and Hua2NT bind specifically to endolysosomal PIP lipids PI(3)P and PI(3,5)P2 and Golgi enriched PI(4)P, respectively. Despite the lack of canonical PIP-binding sites, we identified potential binding sites in the HuaNT domains by sequence comparisons and existing subunit structures and models. We found that mutations at a similar location in the distal loops of both HuaNT isoforms compromise binding to their cognate PIP lipids, suggesting that these loops encode PIP specificity of the a-subunit isoforms. These data suggest a mechanism through which PIP lipid binding could stabilize and activate V-ATPases in distinct organelles.
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Affiliation(s)
- Connie Mitra
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Samuel Winkley
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Patricia M Kane
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA.
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Burton-Smith RN, Song C, Ueno H, Murata T, Iino R, Murata K. Six states of Enterococcus hirae V-type ATPase reveals non-uniform rotor rotation during turnover. Commun Biol 2023; 6:755. [PMID: 37507515 PMCID: PMC10382590 DOI: 10.1038/s42003-023-05110-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
The vacuolar-type ATPase from Enterococcus hirae (EhV-ATPase) is a thus-far unique adaptation of V-ATPases, as it performs Na+ transport and demonstrates an off-axis rotor assembly. Recent single molecule studies of the isolated V1 domain have indicated that there are subpauses within the three major states of the pseudo three-fold symmetric rotary enzyme. However, there was no structural evidence for these. Herein we activate the EhV-ATPase complex with ATP and identified multiple structures consisting of a total of six states of this complex by using cryo-electron microscopy. The orientations of the rotor complex during turnover, especially in the intermediates, are not as perfectly uniform as expected. The densities in the nucleotide binding pockets in the V1 domain indicate the different catalytic conditions for the six conformations. The off-axis rotor and its' interactions with the stator a-subunit during rotation suggests that this non-uniform rotor rotation is performed through the entire complex.
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Affiliation(s)
- Raymond N Burton-Smith
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan
| | - Chihong Song
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan
- Department of Physiological Sciences, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan
| | - Hiroshi Ueno
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8656, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage-Ku, Chiba, 263-8522, Japan
| | - Ryota Iino
- Institute for Molecular Science, National Institute for Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
- Department of Functional Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8585, Japan
| | - Kazuyoshi Murata
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan.
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan.
- Department of Physiological Sciences, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan.
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Yang SZ, Peng LT. Significance of the plasma membrane H +-ATPase and V-ATPase for growth and pathogenicity in pathogenic fungi. ADVANCES IN APPLIED MICROBIOLOGY 2023; 124:31-53. [PMID: 37597947 DOI: 10.1016/bs.aambs.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/21/2023]
Abstract
Pathogenic fungi are widespread and cause a variety of diseases in human beings and other organisms. At present, limited classes of antifungal agents are available to treat invasive fungal diseases. With the wide use of the commercial antifungal agents, drug resistance of pathogenic fungi are continuously increasing. Therefore, exploring effective antifungal agents with novel drug targets is urgently needed to cope with the challenges that the antifungal area faces. pH homeostasis is vital for multiple cellular processes, revealing the potential for defining novel drug targets. Fungi have evolved a number of strategies to maintain a stable pH internal environment in response to rapid metabolism and a dramatically changing extracellular environment. Among them, plasma membrane H+-ATPase (PMA) and vacuolar H+-ATPase (V-ATPase) play a central role in the regulation of pH homeostasis system. In this chapter, we will summarize the current knowledge about pH homeostasis and its regulation mechanisms in pathogenic fungi, especially for the recent advances in PMA and V-ATPase, which would help in revealing the regulating mechanism of pH on cell growth and pathogenicity, and further designing effective drugs and identify new targets for combating fungal diseases.
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Affiliation(s)
- S Z Yang
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China.
| | - L T Peng
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
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Tuli F, Kane PM. The cytosolic N-terminal domain of V-ATPase a-subunits is a regulatory hub targeted by multiple signals. Front Mol Biosci 2023; 10:1168680. [PMID: 37398550 PMCID: PMC10313074 DOI: 10.3389/fmolb.2023.1168680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/05/2023] [Indexed: 07/04/2023] Open
Abstract
Vacuolar H+-ATPases (V-ATPases) acidify several organelles in all eukaryotic cells and export protons across the plasma membrane in a subset of cell types. V-ATPases are multisubunit enzymes consisting of a peripheral subcomplex, V1, that is exposed to the cytosol and an integral membrane subcomplex, Vo, that contains the proton pore. The Vo a-subunit is the largest membrane subunit and consists of two domains. The N-terminal domain of the a-subunit (aNT) interacts with several V1 and Vo subunits and serves to bridge the V1 and Vo subcomplexes, while the C-terminal domain contains eight transmembrane helices, two of which are directly involved in proton transport. Although there can be multiple isoforms of several V-ATPase subunits, the a-subunit is encoded by the largest number of isoforms in most organisms. For example, the human genome encodes four a-subunit isoforms that exhibit a tissue- and organelle-specific distribution. In the yeast S. cerevisiae, the two a-subunit isoforms, Golgi-enriched Stv1 and vacuolar Vph1, are the only V-ATPase subunit isoforms. Current structural information indicates that a-subunit isoforms adopt a similar backbone structure but sequence variations allow for specific interactions during trafficking and in response to cellular signals. V-ATPases are subject to several types of environmental regulation that serve to tune their activity to their cellular location and environmental demands. The position of the aNT domain in the complex makes it an ideal target for modulating V1-Vo interactions and regulating enzyme activity. The yeast a-subunit isoforms have served as a paradigm for dissecting interactions of regulatory inputs with subunit isoforms. Importantly, structures of yeast V-ATPases containing each a-subunit isoform are available. Chimeric a-subunits combining elements of Stv1NT and Vph1NT have provided insights into how regulatory inputs can be integrated to allow V-ATPases to support cell growth under different stress conditions. Although the function and distribution of the four mammalian a-subunit isoforms present additional complexity, it is clear that the aNT domains of these isoforms are also subject to multiple regulatory interactions. Regulatory mechanisms that target mammalian a-subunit isoforms, and specifically the aNT domains, will be described. Altered V-ATPase function is associated with multiple diseases in humans. The possibility of regulating V-ATPase subpopulations via their isoform-specific regulatory interactions are discussed.
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Affiliation(s)
| | - Patricia M. Kane
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States
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Wang H, Rubinstein JL. CryoEM of V-ATPases: Assembly, disassembly, and inhibition. Curr Opin Struct Biol 2023; 80:102592. [PMID: 37272327 DOI: 10.1016/j.sbi.2023.102592] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 06/06/2023]
Abstract
Vacuolar-type ATPases (V-ATPases) are responsible for the acidification of intracellular compartments in almost all eukaryotic cells, while in some specialized cells they acidify the extracellular environment. As ubiquitous proton pumps, these large membrane-embedded enzymes are involved in many fundamental cellular processes that require tight control of pH. Consequently, V-ATPase malfunction or aberrant activity has been linked to numerous diseases. In the past ten years, electron cryomicroscopy (cryoEM) of yeast V-ATPases has revealed the architecture and rotary catalytic mechanism of these macromolecular machines. More recently, studies have revealed the structures of V-ATPases in animals and plants, uncovered aspects of how V-ATPases are assembled and regulated by reversible dissociation, and shown how V-ATPase activity can be modulated by proteins and small molecule inhibitors. In this review, we highlight these recent developments.
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Affiliation(s)
- Hanlin Wang
- Molecular Medicine Program, The Hospital for Sick Children, M5G 0A4, Toronto, Canada; Department of Biochemistry, The University of Toronto, M5G 1L7, Toronto, Canada
| | - John L Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, M5G 0A4, Toronto, Canada; Department of Biochemistry, The University of Toronto, M5G 1L7, Toronto, Canada; Department of Medical Biophysics, The University of Toronto, M5S 1A8, Toronto, Canada.
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Mitra C, Kane PM. Human V-ATPase a-subunit isoforms bind specifically to distinct phosphoinositide phospholipids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538068. [PMID: 37162989 PMCID: PMC10168244 DOI: 10.1101/2023.04.24.538068] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
V-ATPases are highly conserved multi-subunit enzymes that maintain the distinct pH of eukaryotic organelles. The integral membrane a-subunit is encoded by tissue and organelle specific isoforms, and its cytosolic N-terminal domain (aNT) modulates organelle specific regulation and targeting of V-ATPases. Organelle membranes have specific phosphatidylinositol phosphate (PIP) lipid enrichment linked to maintenance of organelle pH. In yeast, the aNT domains of the two a-subunit isoforms bind PIP lipids enriched in the organelle membranes where they reside; these interactions affect activity and regulatory properties of the V-ATPases containing each isoform. Humans have four a-subunit isoforms. We hypothesize that the aNT domains of the human isoforms will also bind to specific PIP lipids. The a1 and a2 isoforms of human V-ATPase a-subunits are localized to endolysosomes and Golgi, respectively. Bacterially expressed Hua1NT and Hua2NT bind specifically to endolysosomal PIP lipids PI(3)P and PI(3,5)P2 and Golgi enriched PI(4)P, respectively. Despite the lack of canonical PIP binding sites, potential binding sites in the HuaNT domains were identified by sequence comparisons and existing subunit structures and models. Mutations at a similar location in the distal loops of both HuaNT isoforms compromise binding to their cognate PIP lipids, suggesting that these loops encode PIP specificity of the a-subunit isoforms. These data also suggest a mechanism through which PIP lipid binding could stabilize and activate V-ATPases in distinct organelles.
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Affiliation(s)
- Connie Mitra
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY
| | - Patricia M Kane
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY
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15
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Tuli F, Kane PM. Chimeric a-subunit isoforms generate functional yeast V-ATPases with altered regulatory properties in vitro and in vivo. Mol Biol Cell 2023; 34:ar14. [PMID: 36598799 PMCID: PMC10011726 DOI: 10.1091/mbc.e22-07-0265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
V-ATPases are highly regulated proton pumps that acidify organelles. The V-ATPase a-subunit is a two-domain protein containing a C-terminal transmembrane domain responsible for proton transport and an N-terminal cytosolic domain (aNT) that is a regulatory hub, integrating environmental inputs to regulate assembly, localization, and V-ATPase activity. The yeast Saccharomyces cerevisiae encodes only two organelle-specific a-isoforms, Stv1 in the Golgi and Vph1 in the vacuole. On the basis of recent structures, we designed chimeric yeast aNTs in which the globular proximal and distal ends are exchanged. The Vph1 proximal-Stv1 distal (VPSD) aNT chimera binds to the glucose-responsive RAVE assembly factor in vitro but exhibits little binding to PI(3,5)P2. The Stv1 proximal-Vph1 distal (SPVD) aNT lacks RAVE binding but binds more tightly to phosphoinositides than Vph1 or Stv1. When attached to the Vph1 C-terminal domain in vivo, both chimeras complement growth defects of a vph1∆ mutant, but only the SPVD chimera exhibits wild-type V-ATPase activity. Cells containing the SPVD chimera adapt more slowly to a poor carbon source than wild-type cells but grow more rapidly than wild-type cells after a shift to alkaline pH. This is the first example of a "redesigned" V-ATPase with altered regulatory properties and adaptation to specific stresses.
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Affiliation(s)
- Farzana Tuli
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210
| | - Patricia M Kane
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210
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Lévêque C, Maulet Y, Wang Q, Rame M, Rodriguez L, Mochida S, Sangiardi M, Youssouf F, Iborra C, Seagar M, Vitale N, El Far O. A Role for the V0 Sector of the V-ATPase in Neuroexocytosis: Exogenous V0d Blocks Complexin and SNARE Interactions with V0c. Cells 2023; 12:cells12050750. [PMID: 36899886 PMCID: PMC10001230 DOI: 10.3390/cells12050750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/03/2023] Open
Abstract
V-ATPase is an important factor in synaptic vesicle acidification and is implicated in synaptic transmission. Rotation in the extra-membranous V1 sector drives proton transfer through the membrane-embedded multi-subunit V0 sector of the V-ATPase. Intra-vesicular protons are then used to drive neurotransmitter uptake by synaptic vesicles. V0a and V0c, two membrane subunits of the V0 sector, have been shown to interact with SNARE proteins, and their photo-inactivation rapidly impairs synaptic transmission. V0d, a soluble subunit of the V0 sector strongly interacts with its membrane-embedded subunits and is crucial for the canonic proton transfer activity of the V-ATPase. Our investigations show that the loop 1.2 of V0c interacts with complexin, a major partner of the SNARE machinery and that V0d1 binding to V0c inhibits this interaction, as well as V0c association with SNARE complex. The injection of recombinant V0d1 in rat superior cervical ganglion neurons rapidly reduced neurotransmission. In chromaffin cells, V0d1 overexpression and V0c silencing modified in a comparable manner several parameters of unitary exocytotic events. Our data suggest that V0c subunit promotes exocytosis via interactions with complexin and SNAREs and that this activity can be antagonized by exogenous V0d.
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Affiliation(s)
- Christian Lévêque
- INSERM UMR_S 1072, 13015 Marseille, France
- Aix-Marseille Université, 13015 Marseille, France
| | - Yves Maulet
- INSERM UMR_S 1072, 13015 Marseille, France
- Aix-Marseille Université, 13015 Marseille, France
| | - Qili Wang
- Institut des Neurosciences Cellulaires et Intégratives, Centre National de la Recherche Scientifique, Université de Strasbourg, 67000 Strasbourg, France
| | - Marion Rame
- Institut des Neurosciences Cellulaires et Intégratives, Centre National de la Recherche Scientifique, Université de Strasbourg, 67000 Strasbourg, France
| | - Léa Rodriguez
- INSERM UMR_S 1072, 13015 Marseille, France
- Aix-Marseille Université, 13015 Marseille, France
| | - Sumiko Mochida
- Department of Physiology, Tokyo Medical University, Tokyo 160-8402, Japan
| | - Marion Sangiardi
- INSERM UMR_S 1072, 13015 Marseille, France
- Aix-Marseille Université, 13015 Marseille, France
| | - Fahamoe Youssouf
- INSERM UMR_S 1072, 13015 Marseille, France
- Aix-Marseille Université, 13015 Marseille, France
| | - Cécile Iborra
- INSERM UMR_S 1072, 13015 Marseille, France
- Aix-Marseille Université, 13015 Marseille, France
| | - Michael Seagar
- INSERM UMR_S 1072, 13015 Marseille, France
- Aix-Marseille Université, 13015 Marseille, France
| | - Nicolas Vitale
- Institut des Neurosciences Cellulaires et Intégratives, Centre National de la Recherche Scientifique, Université de Strasbourg, 67000 Strasbourg, France
- Correspondence: (N.V.); or (O.E.F.); Tel.: +33-(0)3-8845-6712 (N.V.); +33-(0)4-9169-8860 (O.E.F.)
| | - Oussama El Far
- INSERM UMR_S 1072, 13015 Marseille, France
- Aix-Marseille Université, 13015 Marseille, France
- Correspondence: (N.V.); or (O.E.F.); Tel.: +33-(0)3-8845-6712 (N.V.); +33-(0)4-9169-8860 (O.E.F.)
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Structural and Functional Diversity of Two ATP-Driven Plant Proton Pumps. Int J Mol Sci 2023; 24:ijms24054512. [PMID: 36901943 PMCID: PMC10003446 DOI: 10.3390/ijms24054512] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/09/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Two ATP-dependent proton pumps function in plant cells. Plasma membrane H+-ATPase (PM H+-ATPase) transfers protons from the cytoplasm to the apoplast, while vacuolar H+-ATPase (V-ATPase), located in tonoplasts and other endomembranes, is responsible for proton pumping into the organelle lumen. Both enzymes belong to two different families of proteins and, therefore, differ significantly in their structure and mechanism of action. The plasma membrane H+-ATPase is a member of the P-ATPases that undergo conformational changes, associated with two distinct E1 and E2 states, and autophosphorylation during the catalytic cycle. The vacuolar H+-ATPase represents rotary enzymes functioning as a molecular motor. The plant V-ATPase consists of thirteen different subunits organized into two subcomplexes, the peripheral V1 and the membrane-embedded V0, in which the stator and rotor parts have been distinguished. In contrast, the plant plasma membrane proton pump is a functional single polypeptide chain. However, when the enzyme is active, it transforms into a large twelve-protein complex of six H+-ATPase molecules and six 14-3-3 proteins. Despite these differences, both proton pumps can be regulated by the same mechanisms (such as reversible phosphorylation) and, in some processes, such as cytosolic pH regulation, may act in a coordinated way.
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Zhu S, Wen H, Wang W, Chen Y, Han F, Cai W. Anti-hepatitis B virus activity of lithospermic acid, a polyphenol from Salvia miltiorrhiza, in vitro and in vivo by autophagy regulation. JOURNAL OF ETHNOPHARMACOLOGY 2023; 302:115896. [PMID: 36334815 DOI: 10.1016/j.jep.2022.115896] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/15/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Salvia miltiorrhiza (the roots of S. miltiorrhiza Bunge, Danshen in Chinese), a traditional Chinese medicine, has been clinically used to prevent and treat various diseases, such as cardiovascular and cerebrovascular diseases, diabetes, and hepatitis B, in China and some other Asian countries. Lithospermic acid (LA), a polyphenol derived from S. miltiorrhiza, has been reported to exhibit multiple pharmacological properties, such as anti-inflammatory, anti-HIV, and anti-carbon tetrachloride-induced liver injury activities. However, little is known about the anti-hepatitis B virus (HBV) activity of LA. AIM OF THE STUDY The study was projected to investigate the anti-HBV activity of LA in vitro (HepG2.2.15 and pHBV1.3-transfected HepG2 cells) and in vivo (pAAV-HBV1.2 hydrodynamic injection [HBV-HDI] mice) and explore the potential mechanism as well. MATERIALS AND METHODS Hepatitis B surface antigen (HBsAg) and hepatitis B e antigen (HBeAg) contents were detected by ELISA kits. HBV DNA and hepatitis B core antigen (HBcAg) levels were evaluated by quantitative real-time polymerase chain reaction and immunohistochemistry assay, respectively. The proteins in autophagy process, lysosomal acidic function, and autophagy-related signaling pathways were examined by Western blot. Transmission electron microscopy was used to observe the number of autophagosomes and autolysosomes. Confocal microscopy was applied to analyze the autophagic flux and lysosomal acidification, using mCherry-enhanced green fluorescent protein (EGFP)-microtubule-associated protein light chain (LC)3 and lysosomal probes, respectively. RESULTS LA exhibited anti-HBV activity by inhibiting HBV DNA replication in HepG2.2.15 and pHBV-transfected HepG2 cells in dose- and time-dependent manners and hampering HBsAg and HBeAg levels in HepG2.2.15 cells to a certain extent. LA reduced HBV DNA, HBsAg/HBeAg, and HBcAg levels in the serum/liver tissues of HBV-HDI C57BL/6 mice during the 3-week treatment and suppressed the withdrawal rebound of HBV DNA and HBsAg in the mice serum. LA increased LC3-II protein expression and the number of autolysosomes/autophagosomes and promoted the degradation of sequestosome 1(p62) protein in vitro and in vivo. LA enhanced the co-localization of LC3 protein with autolysosomes, further confirming the ability of LA to induce a complete autophagy. Knockdown of autophagy-related gene (Atg) 7 or 5 in vitro and administration of 3-methyladenine (an autophagic inhibitor) in vivo disabled the inhibitory efficacy of LA on HBV DNA replication, suggesting that the anti-HBV efficacy of LA depended on its ability of inducing autophagy. LA could enhance lysosomal acidification and improve the function of lysosomes by promoting the protein expression of lysosomal-associated membrane protein (LAMP)-1, LAMP-2, and mature cathepsin D, which may contribute to the autophagic induction of LA. LA inhibited the activation of AKT and mammalian target of rapamycin (mTOR) induced by HBV, which was reversed by IGF-1 (an agonist of the PI3K/AKT/mTOR signaling pathway), indicating that LA elicited autophagy through hampering the PI3K/AKT/mTOR signaling pathway. CONCLUSION We revealed the anti-HBV activity and mechanism of LA in vitro and in vivo. This study facilitates a new understanding of the anti-HBV potent components of S. miltiorrhiza and sheds light on LA for further development as an active constituent or candidate used in the therapy against HBV infection.
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Affiliation(s)
- Shiqi Zhu
- Hubei Province Key Laboratory of Biotechnology of Chinese Traditional Medicine, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Haimei Wen
- Hubei Province Key Laboratory of Biotechnology of Chinese Traditional Medicine, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Wenling Wang
- Hubei Province Key Laboratory of Biotechnology of Chinese Traditional Medicine, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Yong Chen
- Hubei Province Key Laboratory of Biotechnology of Chinese Traditional Medicine, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Fengmei Han
- Hubei Province Key Laboratory of Biotechnology of Chinese Traditional Medicine, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China.
| | - Wentao Cai
- Hubei Province Key Laboratory of Biotechnology of Chinese Traditional Medicine, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China.
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Structural basis of V-ATPase V O region assembly by Vma12p, 21p, and 22p. Proc Natl Acad Sci U S A 2023; 120:e2217181120. [PMID: 36724250 PMCID: PMC9963935 DOI: 10.1073/pnas.2217181120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Vacuolar-type adenosine triphosphatases (V-ATPases) are rotary proton pumps that acidify specific intracellular compartments in almost all eukaryotic cells. These multi-subunit enzymes consist of a soluble catalytic V1 region and a membrane-embedded proton-translocating VO region. VO is assembled in the endoplasmic reticulum (ER) membrane, and V1 is assembled in the cytosol. However, V1 binds VO only after VO is transported to the Golgi membrane, thereby preventing acidification of the ER. We isolated VO complexes and subcomplexes from Saccharomyces cerevisiae bound to V-ATPase assembly factors Vma12p, Vma21p, and Vma22p. Electron cryomicroscopy shows how the Vma12-22p complex recruits subunits a, e, and f to the rotor ring of VO while blocking premature binding of V1. Vma21p, which contains an ER-retrieval motif, binds the VO:Vma12-22p complex, "mature" VO, and a complex that appears to contain a ring of loosely packed rotor subunits and the proteins YAR027W and YAR028W. The structures suggest that Vma21p binds assembly intermediates that contain a rotor ring and that activation of proton pumping following assembly of V1 with VO removes Vma21p, allowing V-ATPase to remain in the Golgi. Together, these structures show how Vma12-22p and Vma21p function in V-ATPase assembly and quality control, ensuring the enzyme acidifies only its intended cellular targets.
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20
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Tolani B, Celli A, Yao Y, Tan YZ, Fetter R, Liem CR, de Smith AJ, Vasanthakumar T, Bisignano P, Cotton AD, Seiple IB, Rubinstein JL, Jost M, Weissman JS. Ras-mutant cancers are sensitive to small molecule inhibition of V-type ATPases in mice. Nat Biotechnol 2022; 40:1834-1844. [PMID: 35879364 PMCID: PMC9750872 DOI: 10.1038/s41587-022-01386-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 06/03/2022] [Indexed: 01/14/2023]
Abstract
Mutations in Ras family proteins are implicated in 33% of human cancers, but direct pharmacological inhibition of Ras mutants remains challenging. As an alternative to direct inhibition, we screened for sensitivities in Ras-mutant cells and discovered 249C as a Ras-mutant selective cytotoxic agent with nanomolar potency against a spectrum of Ras-mutant cancers. 249C binds to vacuolar (V)-ATPase with nanomolar affinity and inhibits its activity, preventing lysosomal acidification and inhibiting autophagy and macropinocytosis pathways that several Ras-driven cancers rely on for survival. Unexpectedly, potency of 249C varies with the identity of the Ras driver mutation, with the highest potency for KRASG13D and G12V both in vitro and in vivo, highlighting a mutant-specific dependence on macropinocytosis and lysosomal pH. Indeed, 249C potently inhibits tumor growth without adverse side effects in mouse xenografts of KRAS-driven lung and colon cancers. A comparison of isogenic SW48 xenografts with different KRAS mutations confirmed that KRASG13D/+ (followed by G12V/+) mutations are especially sensitive to 249C treatment. These data establish proof-of-concept for targeting V-ATPase in cancers driven by specific KRAS mutations such as KRASG13D and G12V.
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Affiliation(s)
- Bhairavi Tolani
- Thoracic Oncology Program, Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.
| | - Anna Celli
- Laboratory for Cell Analysis Core Facility, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Yanmin Yao
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Yong Zi Tan
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Disease Intervention Technology Laboratory, Agency for Science, Technology and Research, Singapore, Singapore
| | - Richard Fetter
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA, USA
| | - Christina R Liem
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Thamiya Vasanthakumar
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Biochemistry, The University of Toronto, Toronto, ON, Canada
| | - Paola Bisignano
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Adam D Cotton
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Ian B Seiple
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - John L Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Biochemistry, The University of Toronto, Toronto, ON, Canada
- Department of Medical Biophysics, The University of Toronto, Toronto, ON, Canada
| | - Marco Jost
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
- Department of Microbiology & Immunology, University of California, San Francisco, CA, USA.
- Department of Microbiology, Harvard Medical School, Boston, MA, USA.
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
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21
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Tan YZ, Abbas YM, Wu JZ, Wu D, Keon KA, Hesketh GG, Bueler SA, Gingras AC, Robinson CV, Grinstein S, Rubinstein JL. CryoEM of endogenous mammalian V-ATPase interacting with the TLDc protein mEAK-7. Life Sci Alliance 2022; 5:e202201527. [PMID: 35794005 PMCID: PMC9263379 DOI: 10.26508/lsa.202201527] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 12/18/2022] Open
Abstract
V-ATPases are rotary proton pumps that serve as signaling hubs with numerous protein binding partners. CryoEM with exhaustive focused classification allowed detection of endogenous proteins associated with porcine kidney V-ATPase. An extra C subunit was found in ∼3% of complexes, whereas ∼1.6% of complexes bound mEAK-7, a protein with proposed roles in dauer formation in nematodes and mTOR signaling in mammals. High-resolution cryoEM of porcine kidney V-ATPase with recombinant mEAK-7 showed that mEAK-7's TLDc domain interacts with V-ATPase's stator, whereas its C-terminal α helix binds V-ATPase's rotor. This crosslink would be expected to inhibit rotary catalysis. However, unlike the yeast TLDc protein Oxr1p, exogenous mEAK-7 does not inhibit V-ATPase and mEAK-7 overexpression in cells does not alter lysosomal or phagosomal pH. Instead, cryoEM suggests that the mEAK-7:V-ATPase interaction is disrupted by ATP-induced rotation of the rotor. Comparison of Oxr1p and mEAK-7 binding explains this difference. These results show that V-ATPase binding by TLDc domain proteins can lead to effects ranging from strong inhibition to formation of labile interactions that are sensitive to the enzyme's activity.
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Affiliation(s)
- Yong Zi Tan
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada
| | - Yazan M Abbas
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada
| | - Jing Ze Wu
- Program in Cell Biology, The Hospital for Sick Children, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Di Wu
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Kristine A Keon
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada
| | - Geoffrey G Hesketh
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | - Stephanie A Bueler
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Sergio Grinstein
- Program in Cell Biology, The Hospital for Sick Children, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
| | - John L Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
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22
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Otomo A, Iida T, Okuni Y, Ueno H, Murata T, Iino R. Direct observation of stepping rotation of V-ATPase reveals rigid component in coupling between V o and V 1 motors. Proc Natl Acad Sci U S A 2022; 119:e2210204119. [PMID: 36215468 PMCID: PMC9586324 DOI: 10.1073/pnas.2210204119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/13/2022] [Indexed: 11/30/2022] Open
Abstract
V-ATPases are rotary motor proteins that convert the chemical energy of ATP into the electrochemical potential of ions across cell membranes. V-ATPases consist of two rotary motors, Vo and V1, and Enterococcus hirae V-ATPase (EhVoV1) actively transports Na+ in Vo (EhVo) by using torque generated by ATP hydrolysis in V1 (EhV1). Here, we observed ATP-driven stepping rotation of detergent-solubilized EhVoV1 wild-type, aE634A, and BR350K mutants under various Na+ and ATP concentrations ([Na+] and [ATP], respectively) by using a 40-nm gold nanoparticle as a low-load probe. When [Na+] was low and [ATP] was high, under the condition that only Na+ binding to EhVo is rate limiting, wild-type and aE634A exhibited 10 pausing positions reflecting 10-fold symmetry of the EhVo rotor and almost no backward steps. Duration time before the forward steps was inversely proportional to [Na+], confirming that Na+ binding triggers the steps. When both [ATP] and [Na+] were low, under the condition that both Na+ and ATP bindings are rate limiting, aE634A exhibited 13 pausing positions reflecting 10- and 3-fold symmetries of EhVo and EhV1, respectively. The distribution of duration time before the forward step was fitted well by the sum of two exponential decay functions with distinct time constants. Furthermore, occasional backward steps smaller than 36° were observed. Small backward steps were also observed during three long ATP cleavage pauses of BR350K. These results indicate that EhVo and EhV1 do not share pausing positions, Na+ and ATP bindings occur at different angles, and the coupling between EhVo and EhV1 has a rigid component.
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Affiliation(s)
- Akihiro Otomo
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
- Department of Functional Molecular Science, School of Physical Sciences, Graduate University for Advanced Studies, Hayama 240-0193, Japan
| | - Tatsuya Iida
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
- Department of Functional Molecular Science, School of Physical Sciences, Graduate University for Advanced Studies, Hayama 240-0193, Japan
| | - Yasuko Okuni
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
| | - Hiroshi Ueno
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba 263-8522, Japan
| | - Ryota Iino
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
- Department of Functional Molecular Science, School of Physical Sciences, Graduate University for Advanced Studies, Hayama 240-0193, Japan
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23
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Structure of V-ATPase from citrus fruit. Structure 2022; 30:1403-1410.e4. [PMID: 36041457 DOI: 10.1016/j.str.2022.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/14/2022] [Accepted: 07/18/2022] [Indexed: 11/23/2022]
Abstract
We used the Legionella pneumophila effector SidK to affinity purify the endogenous vacuolar-type ATPases (V-ATPases) from lemon fruit. The preparation was sufficient for cryoelectron microscopy, allowing structure determination of the enzyme in two rotational states. The structure defines the ATP:H+ ratio of the enzyme, demonstrating that it can establish a maximum ΔpH of ∼3, which is insufficient to maintain the low pH observed in the vacuoles of juice sac cells in lemons and other citrus fruit. Compared with yeast and mammalian enzymes, the membrane region of the plant V-ATPase lacks subunit f and possesses an unusual configuration of transmembrane α helices. Subunit H, which inhibits ATP hydrolysis in the isolated catalytic region of V-ATPase, adopts two different conformations in the intact complex, hinting at a role in modulating activity in the intact enzyme.
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24
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Seidel T. The Plant V-ATPase. FRONTIERS IN PLANT SCIENCE 2022; 13:931777. [PMID: 35845650 PMCID: PMC9280200 DOI: 10.3389/fpls.2022.931777] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/03/2022] [Indexed: 05/25/2023]
Abstract
V-ATPase is the dominant proton pump in plant cells. It contributes to cytosolic pH homeostasis and energizes transport processes across endomembranes of the secretory pathway. Its localization in the trans Golgi network/early endosomes is essential for vesicle transport, for instance for the delivery of cell wall components. Furthermore, it is crucial for response to abiotic and biotic stresses. The V-ATPase's rather complex structure and multiple subunit isoforms enable high structural flexibility with respect to requirements for different organs, developmental stages, and organelles. This complexity further demands a sophisticated assembly machinery and transport routes in cells, a process that is still not fully understood. Regulation of V-ATPase is a target of phosphorylation and redox-modifications but also involves interactions with regulatory proteins like 14-3-3 proteins and the lipid environment. Regulation by reversible assembly, as reported for yeast and the mammalian enzyme, has not be proven in plants but seems to be absent in autotrophic cells. Addressing the regulation of V-ATPase is a promising approach to adjust its activity for improved stress resistance or higher crop yield.
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25
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Vasanthakumar T, Keon KA, Bueler SA, Jaskolka MC, Rubinstein JL. Coordinated conformational changes in the V 1 complex during V-ATPase reversible dissociation. Nat Struct Mol Biol 2022; 29:430-439. [PMID: 35469063 DOI: 10.1038/s41594-022-00757-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/03/2022] [Indexed: 11/10/2022]
Abstract
Vacuolar-type ATPases (V-ATPases) are rotary enzymes that acidify intracellular compartments in eukaryotic cells. These multi-subunit complexes consist of a cytoplasmic V1 region that hydrolyzes ATP and a membrane-embedded VO region that transports protons. V-ATPase activity is regulated by reversible dissociation of the two regions, with the isolated V1 and VO complexes becoming autoinhibited on disassembly and subunit C subsequently detaching from V1. In yeast, assembly of the V1 and VO regions is mediated by the regulator of the ATPase of vacuoles and endosomes (RAVE) complex through an unknown mechanism. We used cryogenic-electron microscopy of yeast V-ATPase to determine structures of the intact enzyme, the dissociated but complete V1 complex and the V1 complex lacking subunit C. On separation, V1 undergoes a dramatic conformational rearrangement, with its rotational state becoming incompatible for reassembly with VO. Loss of subunit C allows V1 to match the rotational state of VO, suggesting how RAVE could reassemble V1 and VO by recruiting subunit C.
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Affiliation(s)
- Thamiya Vasanthakumar
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Biochemistry, The University of Toronto, Toronto, Ontario, Canada
| | - Kristine A Keon
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Medical Biophysics, The University of Toronto, Toronto, Ontario, Canada
| | - Stephanie A Bueler
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael C Jaskolka
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - John L Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada. .,Department of Biochemistry, The University of Toronto, Toronto, Ontario, Canada. .,Department of Medical Biophysics, The University of Toronto, Toronto, Ontario, Canada.
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26
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Keon KA, Benlekbir S, Kirsch SH, Müller R, Rubinstein JL. Cryo-EM of the Yeast V O Complex Reveals Distinct Binding Sites for Macrolide V-ATPase Inhibitors. ACS Chem Biol 2022; 17:619-628. [PMID: 35148071 DOI: 10.1021/acschembio.1c00894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Vacuolar-type adenosine triphosphatases (V-ATPases) are proton pumps found in almost all eukaryotic cells. These enzymes consist of a soluble catalytic V1 region that hydrolyzes ATP and a membrane-embedded VO region responsible for proton translocation. V-ATPase activity leads to acidification of endosomes, phagosomes, lysosomes, secretory vesicles, and the trans-Golgi network, with extracellular acidification occurring in some specialized cells. Small-molecule inhibitors of V-ATPase have played a crucial role in elucidating numerous aspects of cell biology by blocking acidification of intracellular compartments, while therapeutic use of V-ATPase inhibitors has been proposed for the treatment of cancer, osteoporosis, and some infections. Here, we determine structures of the isolated VO complex from Saccharomyces cerevisiae bound to two well-known macrolide inhibitors: bafilomycin A1 and archazolid A. The structures reveal different binding sites for the inhibitors on the surface of the proton-carrying c ring, with only a small amount of overlap between the two sites. Binding of both inhibitors is mediated primarily through van der Waals interactions in shallow pockets and suggests that the inhibitors block rotation of the ring. Together, these structures indicate the existence of a large chemical space available for V-ATPase inhibitors that block acidification by binding the c ring.
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Affiliation(s)
- Kristine A. Keon
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Canada M5G0A4
- Department of Medical Biophysics, The University of Toronto, Toronto, Canada M5G1L7
| | - Samir Benlekbir
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Canada M5G0A4
| | - Susanne H. Kirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University Campus, 66123 Saarbrücken, Germany
| | - John L. Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Canada M5G0A4
- Department of Medical Biophysics, The University of Toronto, Toronto, Canada M5G1L7
- Department of Biochemistry, The University of Toronto, Toronto, Canada M5S1A8
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27
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Maxson ME, Abbas YM, Wu JZ, Plumb JD, Grinstein S, Rubinstein JL. Detection and quantification of the vacuolar H+ATPase using the Legionella effector protein SidK. J Biophys Biochem Cytol 2022; 221:212963. [PMID: 35024770 PMCID: PMC8763849 DOI: 10.1083/jcb.202107174] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/14/2021] [Accepted: 12/21/2021] [Indexed: 12/11/2022] Open
Abstract
Acidification of secretory and endocytic organelles is required for proper receptor recycling, membrane traffic, protein degradation, and solute transport. Proton-pumping vacuolar H+ ATPases (V-ATPases) are responsible for this luminal acidification, which increases progressively as secretory and endocytic vesicles mature. An increasing density of V-ATPase complexes is thought to account for the gradual decrease in pH, but available reagents have not been sufficiently sensitive or specific to test this hypothesis. We introduce a new probe to localize and quantify V-ATPases. The probe is derived from SidK, a Legionella pneumophila effector protein that binds to the V-ATPase A subunit. We generated plasmids encoding fluorescent chimeras of SidK1-278, and labeled recombinant SidK1-278 with Alexa Fluor 568 to visualize and quantify V-ATPases with high specificity in live and fixed cells, respectively. We show that V-ATPases are acquired progressively during phagosome maturation, that they distribute in discrete membrane subdomains, and that their density in lysosomes depends on their subcellular localization.
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Affiliation(s)
- Michelle E Maxson
- Program in Cell Biology, The Hospital for Sick Children, Toronto, Canada
| | - Yazan M Abbas
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, Canada
| | - Jing Ze Wu
- Program in Cell Biology, The Hospital for Sick Children, Toronto, Canada.,Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Jonathan D Plumb
- Program in Cell Biology, The Hospital for Sick Children, Toronto, Canada
| | - Sergio Grinstein
- Program in Cell Biology, The Hospital for Sick Children, Toronto, Canada.,Department of Biochemistry, University of Toronto, Toronto, Canada
| | - John L Rubinstein
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Department of Biochemistry, University of Toronto, Toronto, Canada
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28
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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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29
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Sun Y, Li X. Cholesterol efflux mechanism revealed by structural analysis of human ABCA1 conformational states. NATURE CARDIOVASCULAR RESEARCH 2022; 1:238-245. [PMID: 37181814 PMCID: PMC10181854 DOI: 10.1038/s44161-022-00022-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
ATP-binding cassette transporter A1 (ABCA1) utilizes energy derived from ATP hydrolysis to export cholesterol and phospholipids from macrophages. ABCA1 plays a central role in the biosynthesis of high-density lipoprotein (HDL), which mediates reverse cholesterol transport and prevents detrimental lipid deposition. Mutations in ABCA1 cause Tangier disease characterized by a remarkable reduction in the amount of HDL in blood. Here we present cryo-electron microscopy structures of human ABCA1 in ATP-bound and nucleotide-free states. Structural comparison reveals that ATP molecules pull the nucleotide-binding domains together, inducing movements of transmembrane helices 1, 2, 7 and 8 through a series of salt-bridge interactions. Subsequently, extracellular domains (ECDs) undergo a rotation and introduce conformational changes in the ECD-transmembrane interface. In addition, while we observe a sterol-like molecule in ECDs, no such density was observed in the structure of an HDL-deficiency mutant ABCA1Y482C, demonstrating the physiological importance of ECDs and a putative interaction mode between ABCA1 and its lipid acceptors. Thus, these structures, along with cholesterol efflux assays, advance the understanding ABCA1-mediated reverse cholesterol transport.
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Affiliation(s)
- Yingyuan Sun
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaochun Li
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Correspondence and requests for materials should be addressed to Xiaochun Li.
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30
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31
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Chen F, Kang R, Liu J, Tang D. The V-ATPases in cancer and cell death. Cancer Gene Ther 2022; 29:1529-1541. [PMID: 35504950 PMCID: PMC9063253 DOI: 10.1038/s41417-022-00477-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/07/2022] [Accepted: 04/21/2022] [Indexed: 02/04/2023]
Abstract
Transmembrane ATPases are membrane-bound enzyme complexes and ion transporters that can be divided into F-, V-, and A-ATPases according to their structure. The V-ATPases, also known as H+-ATPases, are large multi-subunit protein complexes composed of a peripheral domain (V1) responsible for the hydrolysis of ATP and a membrane-integrated domain (V0) that transports protons across plasma membrane or organelle membrane. V-ATPases play a fundamental role in maintaining pH homeostasis through lysosomal acidification and are involved in modulating various physiological and pathological processes, such as macropinocytosis, autophagy, cell invasion, and cell death (e.g., apoptosis, anoikis, alkaliptosis, ferroptosis, and lysosome-dependent cell death). In addition to participating in embryonic development, V-ATPase pathways, when dysfunctional, are implicated in human diseases, such as neurodegenerative diseases, osteopetrosis, distal renal tubular acidosis, and cancer. In this review, we summarize the structure and regulation of isoforms of V-ATPase subunits and discuss their context-dependent roles in cancer biology and cell death. Updated knowledge about V-ATPases may enable us to design new anticancer drugs or strategies.
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Affiliation(s)
- Fangquan Chen
- grid.417009.b0000 0004 1758 4591DAMP Laboratory, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120 China
| | - Rui Kang
- grid.267313.20000 0000 9482 7121Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Jiao Liu
- grid.417009.b0000 0004 1758 4591DAMP Laboratory, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120 China
| | - Daolin Tang
- grid.267313.20000 0000 9482 7121Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
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32
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The Role of Sch9 and the V-ATPase in the Adaptation Response to Acetic Acid and the Consequences for Growth and Chronological Lifespan. Microorganisms 2021; 9:microorganisms9091871. [PMID: 34576766 PMCID: PMC8472237 DOI: 10.3390/microorganisms9091871] [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: 07/23/2021] [Revised: 08/20/2021] [Accepted: 08/30/2021] [Indexed: 11/17/2022] Open
Abstract
Studies with Saccharomyces cerevisiae indicated that non-physiologically high levels of acetic acid promote cellular acidification, chronological aging, and programmed cell death. In the current study, we compared the cellular lipid composition, acetic acid uptake, intracellular pH, growth, and chronological lifespan of wild-type cells and mutants lacking the protein kinase Sch9 and/or a functional V-ATPase when grown in medium supplemented with different acetic acid concentrations. Our data show that strains lacking the V-ATPase are especially more susceptible to growth arrest in the presence of high acetic acid concentrations, which is due to a slower adaptation to the acid stress. These V-ATPase mutants also displayed changes in lipid homeostasis, including alterations in their membrane lipid composition that influences the acetic acid diffusion rate and changes in sphingolipid metabolism and the sphingolipid rheostat, which is known to regulate stress tolerance and longevity of yeast cells. However, we provide evidence that the supplementation of 20 mM acetic acid has a cytoprotective and presumable hormesis effect that extends the longevity of all strains tested, including the V-ATPase compromised mutants. We also demonstrate that the long-lived sch9Δ strain itself secretes significant amounts of acetic acid during stationary phase, which in addition to its enhanced accumulation of storage lipids may underlie its increased lifespan.
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33
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Abstract
The ABCG1 homodimer (G1) and ABCG5-ABCG8 heterodimer (G5G8), two members of the adenosine triphosphate (ATP)-binding cassette (ABC) transporter G family, are required for maintenance of cellular cholesterol levels. G5G8 mediates secretion of neutral sterols into bile and the gut lumen, whereas G1 transports cholesterol from macrophages to high-density lipoproteins (HDLs). The mechanisms used by G5G8 and G1 to recognize and export sterols remain unclear. Here, we report cryoelectron microscopy (cryo-EM) structures of human G5G8 in sterol-bound and human G1 in cholesterol- and ATP-bound states. Both transporters have a sterol-binding site that is accessible from the cytosolic leaflet. A second site is present midway through the transmembrane domains of G5G8. The Walker A motif of G8 adopts a unique conformation that accounts for the marked asymmetry in ATPase activities between the two nucleotide-binding sites of G5G8. These structures, along with functional validation studies, provide a mechanistic framework for understanding cholesterol efflux via ABC transporters.
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34
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Oot RA, Yao Y, Manolson MF, Wilkens S. Purification of active human vacuolar H +-ATPase in native lipid-containing nanodiscs. J Biol Chem 2021; 297:100964. [PMID: 34270960 PMCID: PMC8353480 DOI: 10.1016/j.jbc.2021.100964] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/07/2021] [Accepted: 07/12/2021] [Indexed: 12/26/2022] Open
Abstract
Vacuolar H+-ATPases (V-ATPases) are large, multisubunit proton pumps that acidify the lumen of organelles in virtually every eukaryotic cell and in specialized acid-secreting animal cells, the enzyme pumps protons into the extracellular space. In higher organisms, most of the subunits are expressed as multiple isoforms, with some enriched in specific compartments or tissues and others expressed ubiquitously. In mammals, subunit a is expressed as four isoforms (a1-4) that target the enzyme to distinct biological membranes. Mutations in a isoforms are known to give rise to tissue-specific disease, and some a isoforms are upregulated and mislocalized to the plasma membrane in invasive cancers. However, isoform complexity and low abundance greatly complicate purification of active human V-ATPase, a prerequisite for developing isoform-specific therapeutics. Here, we report the purification of an active human V-ATPase in native lipid nanodiscs from a cell line stably expressing affinity-tagged a isoform 4 (a4). We find that exogenous expression of this single subunit in HEK293F cells permits assembly of a functional V-ATPase by incorporation of endogenous subunits. The ATPase activity of the preparation is >95% sensitive to concanamycin A, indicating that the lipid nanodisc-reconstituted enzyme is functionally coupled. Moreover, this strategy permits purification of the enzyme's isolated membrane subcomplex together with biosynthetic assembly factors coiled-coil domain-containing protein 115, transmembrane protein 199, and vacuolar H+-ATPase assembly integral membrane protein 21. Our work thus lays the groundwork for biochemical characterization of active human V-ATPase in an a subunit isoform-specific manner and establishes a platform for the study of the assembly and regulation of the human holoenzyme.
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Affiliation(s)
- Rebecca A Oot
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Yeqi Yao
- Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Morris F Manolson
- Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Stephan Wilkens
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA.
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35
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The milk-derived lactoferrin inhibits V-ATPase activity by targeting its V1 domain. Int J Biol Macromol 2021; 186:54-70. [PMID: 34237360 DOI: 10.1016/j.ijbiomac.2021.06.200] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/20/2021] [Accepted: 06/29/2021] [Indexed: 11/20/2022]
Abstract
Lactoferrin (Lf), a bioactive milk protein, exhibits strong anticancer and antifungal activities. The search for Lf targets and mechanisms of action is of utmost importance to enhance its effective applications. A common feature among Lf-treated cancer and fungal cells is the inhibition of a proton pump called V-ATPase. Lf-driven V-ATPase inhibition leads to cytosolic acidification, ultimately causing cell death of cancer and fungal cells. Given that a detailed elucidation of how Lf and V-ATPase interact is still missing, herein we aimed to fill this gap by employing a five-stage computational approach. Molecular dynamics simulations of both proteins were performed to obtain a robust sampling of their conformational landscape, followed by clustering, which allowed retrieving representative structures, to then perform protein-protein docking. Subsequently, molecular dynamics simulations of the docked complexes and free binding energy calculations were carried out to evaluate the dynamic binding process and build a final ranking based on the binding affinities. Detailed atomist analysis of the top ranked complexes clearly indicates that Lf binds to the V1 cytosolic domain of V-ATPase. Particularly, our data suggest that Lf binds to the interfaces between A/B subunits, where the ATP hydrolysis occurs, thus inhibiting this process. The free energy decomposition analysis further identified key binding residues that will certainly aid in the rational design of follow-up experimental studies, hence bridging computational and experimental biochemistry.
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Chu A, Zirngibl RA, Manolson MF. The V-ATPase a3 Subunit: Structure, Function and Therapeutic Potential of an Essential Biomolecule in Osteoclastic Bone Resorption. Int J Mol Sci 2021; 22:ijms22136934. [PMID: 34203247 PMCID: PMC8269383 DOI: 10.3390/ijms22136934] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 12/29/2022] Open
Abstract
This review focuses on one of the 16 proteins composing the V-ATPase complex responsible for resorbing bone: the a3 subunit. The rationale for focusing on this biomolecule is that mutations in this one protein account for over 50% of osteopetrosis cases, highlighting its critical role in bone physiology. Despite its essential role in bone remodeling and its involvement in bone diseases, little is known about the way in which this subunit is targeted and regulated within osteoclasts. To this end, this review is broadened to include the three other mammalian paralogues (a1, a2 and a4) and the two yeast orthologs (Vph1p and Stv1p). By examining the literature on all of the paralogues/orthologs of the V-ATPase a subunit, we hope to provide insight into the molecular mechanisms and future research directions specific to a3. This review starts with an overview on bone, highlighting the role of V-ATPases in osteoclastic bone resorption. We then cover V-ATPases in other location/functions, highlighting the roles which the four mammalian a subunit paralogues might play in differential targeting and/or regulation. We review the ways in which the energy of ATP hydrolysis is converted into proton translocation, and go in depth into the diverse role of the a subunit, not only in proton translocation but also in lipid binding, cell signaling and human diseases. Finally, the therapeutic implication of targeting a3 specifically for bone diseases and cancer is discussed, with concluding remarks on future directions.
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Potassium and Sodium Salt Stress Characterization in the Yeasts Saccharomyces cerevisiae, Kluyveromyces marxianus, and Rhodotorula toruloides. Appl Environ Microbiol 2021; 87:e0310020. [PMID: 33893111 DOI: 10.1128/aem.03100-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biotechnology requires efficient microbial cell factories. The budding yeast Saccharomyces cerevisiae is a vital cell factory, but more diverse cell factories are essential for the sustainable use of natural resources. Here, we benchmarked nonconventional yeasts Kluyveromyces marxianus and Rhodotorula toruloides against S. cerevisiae strains CEN.PK and W303 for their responses to potassium and sodium salt stress. We found an inverse relationship between the maximum growth rate and the median cell volume that was responsive to salt stress. The supplementation of K+ to CEN.PK cultures reduced Na+ toxicity and increased the specific growth rate 4-fold. The higher K+ and Na+ concentrations impaired ethanol and acetate metabolism in CEN.PK and acetate metabolism in W303. In R. toruloides cultures, these salt supplementations induced a trade-off between glucose utilization and cellular aggregate formation. Their combined use increased the beta-carotene yield by 60% compared with that of the reference. Neural network-based image analysis of exponential-phase cultures showed that the vacuole-to-cell volume ratio increased with increased cell volume for W303 and K. marxianus but not for CEN.PK and R. toruloides in response to salt stress. Our results provide insights into common salt stress responses in yeasts and will help design efficient bioprocesses. IMPORTANCE Characterization of microbial cell factories under industrially relevant conditions is crucial for designing efficient bioprocesses. Salt stress, typical in industrial bioprocesses, impinges upon cell volume and affects productivity. This study presents an open-source neural network-based analysis method to evaluate volumetric changes using yeast optical microscopy images. It allows quantification of cell and vacuole volumes relevant to cellular physiology. On applying salt stress in yeasts, we found that the combined use of K+ and Na+ improves the cellular fitness of Saccharomyces cerevisiae strain CEN.PK and increases the beta-carotene productivity in Rhodotorula toruloides, a commercially important antioxidant and a valuable additive in foods.
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38
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Bickers SC, Benlekbir S, Rubinstein JL, Kanelis V. Structure of Ycf1p reveals the transmembrane domain TMD0 and the regulatory region of ABCC transporters. Proc Natl Acad Sci U S A 2021; 118:e2025853118. [PMID: 34021087 PMCID: PMC8166025 DOI: 10.1073/pnas.2025853118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
ATP binding cassette (ABC) proteins typically function in active transport of solutes across membranes. The ABC core structure is composed of two transmembrane domains (TMD1 and TMD2) and two cytosolic nucleotide binding domains (NBD1 and NBD2). Some members of the C-subfamily of ABC (ABCC) proteins, including human multidrug resistance proteins (MRPs), also possess an N-terminal transmembrane domain (TMD0) that contains five transmembrane α-helices and is connected to the ABC core by the L0 linker. While TMD0 was resolved in SUR1, the atypical ABCC protein that is part of the hetero-octameric ATP-sensitive K+ channel, little is known about the structure of TMD0 in monomeric ABC transporters. Here, we present the structure of yeast cadmium factor 1 protein (Ycf1p), a homolog of human MRP1, determined by electron cryo-microscopy (cryo-EM). A comparison of Ycf1p, SUR1, and a structure of MRP1 that showed TMD0 at low resolution demonstrates that TMD0 can adopt different orientations relative to the ABC core, including a ∼145° rotation between Ycf1p and SUR1. The cryo-EM map also reveals that segments of the regulatory (R) region, which links NBD1 to TMD2 and was poorly resolved in earlier ABCC structures, interacts with the L0 linker, NBD1, and TMD2. These interactions, combined with fluorescence quenching experiments of isolated NBD1 with and without the R region, suggest how posttranslational modifications of the R region modulate ABC protein activity. Mapping known mutations from MRP2 and MRP6 onto the Ycf1p structure explains how mutations involving TMD0 and the R region of these proteins lead to disease.
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Affiliation(s)
- Sarah C Bickers
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
- Department of Chemical and Physical Sciences, University of Toronto, Mississauga, ON L5L 1C6, Canada
| | - Samir Benlekbir
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - John L Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada;
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Voula Kanelis
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada;
- Department of Chemical and Physical Sciences, University of Toronto, Mississauga, ON L5L 1C6, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
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Wang R, Wang J, Hassan A, Lee CH, Xie XS, Li X. Molecular basis of V-ATPase inhibition by bafilomycin A1. Nat Commun 2021; 12:1782. [PMID: 33741963 PMCID: PMC7979754 DOI: 10.1038/s41467-021-22111-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/05/2021] [Indexed: 12/16/2022] Open
Abstract
Pharmacological inhibition of vacuolar-type H+-ATPase (V-ATPase) by its specific inhibitor can abrogate tumor metastasis, prevent autophagy, and reduce cellular signaling responses. Bafilomycin A1, a member of macrolide antibiotics and an autophagy inhibitor, serves as a specific and potent V-ATPases inhibitor. Although there are many V-ATPase structures reported, the molecular basis of specific inhibitors on V-ATPase remains unknown. Here, we report the cryo-EM structure of bafilomycin A1 bound intact bovine V-ATPase at an overall resolution of 3.6-Å. The structure reveals six bafilomycin A1 molecules bound to the c-ring. One bafilomycin A1 molecule engages with two c subunits and disrupts the interactions between the c-ring and subunit a, thereby preventing proton translocation. Structural and sequence analyses demonstrate that the bafilomycin A1-binding residues are conserved in yeast and mammalian species and the 7'-hydroxyl group of bafilomycin A1 acts as a unique feature recognized by subunit c.
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Affiliation(s)
- Rong Wang
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jin Wang
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Abdirahman Hassan
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chia-Hsueh Lee
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiao-Song Xie
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Xiaochun Li
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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40
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Santos-Pereira C, Rodrigues LR, Côrte-Real M. Emerging insights on the role of V-ATPase in human diseases: Therapeutic challenges and opportunities. Med Res Rev 2021; 41:1927-1964. [PMID: 33483985 DOI: 10.1002/med.21782] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/05/2020] [Accepted: 01/05/2021] [Indexed: 12/13/2022]
Abstract
The control of the intracellular pH is vital for the survival of all organisms. Membrane transporters, both at the plasma and intracellular membranes, are key players in maintaining a finely tuned pH balance between intra- and extracellular spaces, and therefore in cellular homeostasis. V-ATPase is a housekeeping ATP-driven proton pump highly conserved among prokaryotes and eukaryotes. This proton pump, which exhibits a complex multisubunit structure based on cell type-specific isoforms, is essential for pH regulation and for a multitude of ubiquitous and specialized functions. Thus, it is not surprising that V-ATPase aberrant overexpression, mislocalization, and mutations in V-ATPase subunit-encoding genes have been associated with several human diseases. However, the ubiquitous expression of this transporter and the high toxicity driven by its off-target inhibition, renders V-ATPase-directed therapies very challenging and increases the need for selective strategies. Here we review emerging evidence linking V-ATPase and both inherited and acquired human diseases, explore the therapeutic challenges and opportunities envisaged from recent data, and advance future research avenues. We highlight the importance of V-ATPases with unique subunit isoform molecular signatures and disease-associated isoforms to design selective V-ATPase-directed therapies. We also discuss the rational design of drug development pipelines and cutting-edge methodological approaches toward V-ATPase-centered drug discovery. Diseases like cancer, osteoporosis, and even fungal infections can benefit from V-ATPase-directed therapies.
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Affiliation(s)
- Cátia Santos-Pereira
- Department of Biology, Centre of Molecular and Environmental Biology (CBMA), University of Minho, Braga, Portugal.,Department of Biological Engineering, Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal
| | - Lígia R Rodrigues
- Department of Biological Engineering, Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal
| | - Manuela Côrte-Real
- Department of Biology, Centre of Molecular and Environmental Biology (CBMA), University of Minho, Braga, Portugal
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41
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Structure of mycobacterial ATP synthase bound to the tuberculosis drug bedaquiline. Nature 2020; 589:143-147. [PMID: 33299175 DOI: 10.1038/s41586-020-3004-3] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/21/2020] [Indexed: 01/01/2023]
Abstract
Tuberculosis-the world's leading cause of death by infectious disease-is increasingly resistant to current first-line antibiotics1. The bacterium Mycobacterium tuberculosis (which causes tuberculosis) can survive low-energy conditions, allowing infections to remain dormant and decreasing their susceptibility to many antibiotics2. Bedaquiline was developed in 2005 from a lead compound identified in a phenotypic screen against Mycobacterium smegmatis3. This drug can sterilize even latent M. tuberculosis infections4 and has become a cornerstone of treatment for multidrug-resistant and extensively drug-resistant tuberculosis1,5,6. Bedaquiline targets the mycobacterial ATP synthase3, which is an essential enzyme in the obligate aerobic Mycobacterium genus3,7, but how it binds the intact enzyme is unknown. Here we determined cryo-electron microscopy structures of M. smegmatis ATP synthase alone and in complex with bedaquiline. The drug-free structure suggests that hook-like extensions from the α-subunits prevent the enzyme from running in reverse, inhibiting ATP hydrolysis and preserving energy in hypoxic conditions. Bedaquiline binding induces large conformational changes in the ATP synthase, creating tight binding pockets at the interface of subunits a and c that explain the potency of this drug as an antibiotic for tuberculosis.
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42
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Lupanga U, Röhrich R, Askani J, Hilmer S, Kiefer C, Krebs M, Kanazawa T, Ueda T, Schumacher K. The Arabidopsis V-ATPase is localized to the TGN/EE via a seed plant-specific motif. eLife 2020; 9:e60568. [PMID: 33236982 PMCID: PMC7717909 DOI: 10.7554/elife.60568] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/24/2020] [Indexed: 12/17/2022] Open
Abstract
The V-ATPase is a versatile proton-pump found in a range of endomembrane compartments yet the mechanisms governing its differential targeting remain to be determined. In Arabidopsis, VHA-a1 targets the V-ATPase to the TGN/EE whereas VHA-a2 and VHA-a3 are localized to the tonoplast. We report here that the VHA-a1 targeting domain serves as both an ER-exit and as a TGN/EE-retention motif and is conserved among seed plants. In contrast, Marchantia encodes a single VHA-isoform that localizes to the TGN/EE and the tonoplast in Arabidopsis. Analysis of CRISPR/Cas9 generated null alleles revealed that VHA-a1 has an essential function for male gametophyte development but acts redundantly with the tonoplast isoforms during vegetative growth. We propose that in the absence of VHA-a1, VHA-a3 is partially re-routed to the TGN/EE. Our findings contribute to understanding the evolutionary origin of V-ATPase targeting and provide a striking example that differential localization does not preclude functional redundancy.
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Affiliation(s)
- Upendo Lupanga
- Department of Cell Biology, Centre for Organismal Studies, Heidelberg UniversityHeidelbergGermany
| | - Rachel Röhrich
- Department of Cell Biology, Centre for Organismal Studies, Heidelberg UniversityHeidelbergGermany
| | - Jana Askani
- Department of Cell Biology, Centre for Organismal Studies, Heidelberg UniversityHeidelbergGermany
| | - Stefan Hilmer
- Electron Microscopy Core Facility, Heidelberg UniversityHeidelbergGermany
| | - Christiane Kiefer
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies, Heidelberg UniversityHeidelbergGermany
| | - Melanie Krebs
- Department of Cell Biology, Centre for Organismal Studies, Heidelberg UniversityHeidelbergGermany
| | - Takehiko Kanazawa
- Division of Cellular Dynamics, National Institute for Basic BiologyOkazakiAichiJapan
- The Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies)OkazakiAichiJapan
| | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic BiologyOkazakiAichiJapan
- The Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies)OkazakiAichiJapan
| | - Karin Schumacher
- Department of Cell Biology, Centre for Organismal Studies, Heidelberg UniversityHeidelbergGermany
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43
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Plasma Membrane Protein Nce102 Modulates Morphology and Function of the Yeast Vacuole. Biomolecules 2020; 10:biom10111476. [PMID: 33114062 PMCID: PMC7690685 DOI: 10.3390/biom10111476] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/15/2020] [Accepted: 10/21/2020] [Indexed: 01/02/2023] Open
Abstract
Membrane proteins are targeted not only to specific membranes in the cell architecture, but also to distinct lateral microdomains within individual membranes to properly execute their biological functions. Yeast tetraspan protein Nce102 has been shown to migrate between such microdomains within the plasma membrane in response to an acute drop in sphingolipid levels. Combining microscopy and biochemistry methods, we show that upon gradual ageing of a yeast culture, when sphingolipid demand increases, Nce102 migrates from the plasma membrane to the vacuole. Instead of being targeted for degradation it localizes to V-ATPase-poor, i.e., ergosterol-enriched, domains of the vacuolar membrane, analogous to its plasma membrane localization. We discovered that, together with its homologue Fhn1, Nce102 modulates vacuolar morphology, dynamics, and physiology. Specifically, the fusing of vacuoles, accompanying a switch of fermenting yeast culture to respiration, is retarded in the strain missing both proteins. Furthermore, the absence of either causes an enlargement of ergosterol-rich vacuolar membrane domains, while the vacuoles themselves become smaller. Our results clearly show decreased stability of the V-ATPase in the absence of either Nce102 or Fhn1, a possible result of the disruption of normal microdomain morphology of the vacuolar membrane. Therefore, the functionality of the vacuole as a whole might be compromised in these cells.
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44
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Wang L, Wu D, Robinson CV, Wu H, Fu TM. Structures of a Complete Human V-ATPase Reveal Mechanisms of Its Assembly. Mol Cell 2020; 80:501-511.e3. [PMID: 33065002 PMCID: PMC7655608 DOI: 10.1016/j.molcel.2020.09.029] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 08/21/2020] [Accepted: 08/25/2020] [Indexed: 12/22/2022]
Abstract
Vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-driven proton pumps comprised of a cytoplasmic V1 complex for ATP hydrolysis and a membrane-embedded Vo complex for proton transfer. They play important roles in acidification of intracellular vesicles, organelles, and the extracellular milieu in eukaryotes. Here, we report cryoelectron microscopy structures of human V-ATPase in three rotational states at up to 2.9-Å resolution. Aided by mass spectrometry, we build all known protein subunits with associated N-linked glycans and identify glycolipids and phospholipids in the Vo complex. We define ATP6AP1 as a structural hub for Vo complex assembly because it connects to multiple Vo subunits and phospholipids in the c-ring. The glycolipids and the glycosylated Vo subunits form a luminal glycan coat critical for V-ATPase folding, localization, and stability. This study identifies mechanisms of V-ATPase assembly and biogenesis that rely on the integrated roles of ATP6AP1, glycans, and lipids.
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Affiliation(s)
- Longfei Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
| | - Di Wu
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
| | - Tian-Min Fu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA.
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45
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Roh SH, Shekhar M, Pintilie G, Chipot C, Wilkens S, Singharoy A, Chiu W. Cryo-EM and MD infer water-mediated proton transport and autoinhibition mechanisms of V o complex. SCIENCE ADVANCES 2020; 6:6/41/eabb9605. [PMID: 33028525 PMCID: PMC7541076 DOI: 10.1126/sciadv.abb9605] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 08/17/2020] [Indexed: 05/15/2023]
Abstract
Rotary vacuolar adenosine triphosphatases (V-ATPases) drive transmembrane proton transport through a Vo proton channel subcomplex. Despite recent high-resolution structures of several rotary ATPases, the dynamic mechanism of proton pumping remains elusive. Here, we determined a 2.7-Å cryo-electron microscopy (cryo-EM) structure of yeast Vo proton channel in nanodisc that reveals the location of ordered water molecules along the proton path, details of specific protein-lipid interactions, and the architecture of the membrane scaffold protein. Moreover, we uncover a state of Vo that shows the c-ring rotated by ~14°. Molecular dynamics simulations demonstrate that the two rotary states are in thermal equilibrium and depict how the protonation state of essential glutamic acid residues couples water-mediated proton transfer with c-ring rotation. Our cryo-EM models and simulations also rationalize a mechanism for inhibition of passive proton transport as observed for free Vo that is generated as a result of V-ATPase regulation by reversible disassembly in vivo.
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Affiliation(s)
- Soung-Hun Roh
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea.
| | - Mrinal Shekhar
- Biodesign Institute, School of Molecular Sciences, Arizona State University, Tempe, AZ 85801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Grigore Pintilie
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Christophe Chipot
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Laboratoire International Associé CNRS-UIUC, UMR 7019, Université de Lorraine, 54506 Vandœuvre-lès-Nancy, France
| | - Stephan Wilkens
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA.
| | - Abhishek Singharoy
- Biodesign Institute, School of Molecular Sciences, Arizona State University, Tempe, AZ 85801, USA.
| | - Wah Chiu
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305, USA.
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
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46
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Kishikawa JI, Nakanishi A, Furuta A, Kato T, Namba K, Tamakoshi M, Mitsuoka K, Yokoyama K. Mechanical inhibition of isolated V o from V/A-ATPase for proton conductance. eLife 2020; 9:56862. [PMID: 32639230 PMCID: PMC7367684 DOI: 10.7554/elife.56862] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/07/2020] [Indexed: 12/18/2022] Open
Abstract
V-ATPase is an energy converting enzyme, coupling ATP hydrolysis/synthesis in the hydrophilic V1 domain, with proton flow through the Vo membrane domain, via rotation of the central rotor complex relative to the surrounding stator apparatus. Upon dissociation from the V1 domain, the Vo domain of the eukaryotic V-ATPase can adopt a physiologically relevant auto-inhibited form in which proton conductance through the Vo domain is prevented, however the molecular mechanism of this inhibition is not fully understood. Using cryo-electron microscopy, we determined the structure of both the holo V/A-ATPase and isolated Vo at near-atomic resolution, respectively. These structures clarify how the isolated Vo domain adopts the auto-inhibited form and how the holo complex prevents formation of the inhibited Vo form.
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Affiliation(s)
- Jun-Ichi Kishikawa
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan.,Institute for Protein Research, Osaka University, Suita, Japan
| | - Atsuko Nakanishi
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan.,Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Research Center for Ultra-High Voltage Electron Microscopy, Mihogaoka, Osaka, Japan
| | - Aya Furuta
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan
| | - Takayuki Kato
- Institute for Protein Research, Osaka University, Suita, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,RIKEN Center for Biosystems Dynamics Research and SPring-8 Center, Suita, Japan.,JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Japan
| | - Masatada Tamakoshi
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Sciences, Horinouchi, Hachioji, Tokyo, Japan
| | - Kaoru Mitsuoka
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Research Center for Ultra-High Voltage Electron Microscopy, Mihogaoka, Osaka, Japan
| | - Ken Yokoyama
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan
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47
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Banerjee S, Kane PM. Regulation of V-ATPase Activity and Organelle pH by Phosphatidylinositol Phosphate Lipids. Front Cell Dev Biol 2020; 8:510. [PMID: 32656214 PMCID: PMC7324685 DOI: 10.3389/fcell.2020.00510] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/28/2020] [Indexed: 12/14/2022] Open
Abstract
Luminal pH and the distinctive distribution of phosphatidylinositol phosphate (PIP) lipids are central identifying features of organelles in all eukaryotic cells that are also critical for organelle function. V-ATPases are conserved proton pumps that populate and acidify multiple organelles of the secretory and the endocytic pathway. Complete loss of V-ATPase activity causes embryonic lethality in higher animals and conditional lethality in yeast, while partial loss of V-ATPase function is associated with multiple disease states. On the other hand, many cancer cells increase their virulence by upregulating V-ATPase expression and activity. The pH of individual organelles is tightly controlled and essential for function, but the mechanisms for compartment-specific pH regulation are not completely understood. There is substantial evidence indicating that the PIP content of membranes influences organelle pH. We present recent evidence that PIPs interact directly with subunit isoforms of the V-ATPase to dictate localization of V-ATPase subpopulations and participate in their regulation. In yeast cells, which have only one set of organelle-specific V-ATPase subunit isoforms, the Golgi-enriched lipid PI(4)P binds to the cytosolic domain of the Golgi-enriched a-subunit isoform Stv1, and loss of PI(4)P binding results in mislocalization of Stv1-containing V-ATPases from the Golgi to the vacuole/lysosome. In contrast, levels of the vacuole/lysosome-enriched signaling lipid PI(3,5)P2 affect assembly and activity of V-ATPases containing the Vph1 a-subunit isoform. Mutations in the Vph1 isoform that disrupt the lipid interaction increase sensitivity to stress. These studies have decoded “zip codes” for PIP lipids in the cytosolic N-terminal domain of the a-subunit isoforms of the yeast V-ATPase, and similar interactions between PIP lipids and the V-ATPase subunit isoforms are emerging in higher eukaryotes. In addition to direct effects on the V-ATPase, PIP lipids are also likely to affect organelle pH indirectly, through interactions with other membrane transporters. We discuss direct and indirect effects of PIP lipids on organelle pH, and the functional consequences of the interplay between PIP lipid content and organelle pH.
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Affiliation(s)
- Subhrajit Banerjee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Patricia M Kane
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States
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48
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Peng W, Casey AK, Fernandez J, Carpinone EM, Servage KA, Chen Z, Li Y, Tomchick DR, Starai VJ, Orth K. A distinct inhibitory mechanism of the V-ATPase by Vibrio VopQ revealed by cryo-EM. Nat Struct Mol Biol 2020; 27:589-597. [PMID: 32424347 DOI: 10.1038/s41594-020-0429-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 04/01/2020] [Indexed: 12/18/2022]
Abstract
The Vibrio parahaemolyticus T3SS effector VopQ targets host-cell V-ATPase, resulting in blockage of autophagic flux and neutralization of acidic compartments. Here, we report the cryo-EM structure of VopQ bound to the Vo subcomplex of the V-ATPase. VopQ inserts into membranes and forms an unconventional pore while binding directly to subunit c of the V-ATPase membrane-embedded subcomplex Vo. We show that VopQ arrests yeast growth in vivo by targeting the immature Vo subcomplex in the endoplasmic reticulum (ER), thus providing insight into the observation that VopQ kills cells in the absence of a functional V-ATPase. VopQ is a bacterial effector that has been discovered to inhibit a host-membrane megadalton complex by coincidentally binding its target, inserting into a membrane and disrupting membrane potential. Collectively, our results reveal a mechanism by which bacterial effectors modulate host cell biology and provide an invaluable tool for future studies on V-ATPase-mediated membrane fusion and autophagy.
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Affiliation(s)
- Wei Peng
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Amanda K Casey
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jessie Fernandez
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Kelly A Servage
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Zhe Chen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yang Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Diana R Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vincent J Starai
- Department of Microbiology, University of Georgia, Athens, GA, USA
- Department of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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49
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Sobti M, Walshe JL, Wu D, Ishmukhametov R, Zeng YC, Robinson CV, Berry RM, Stewart AG. Cryo-EM structures provide insight into how E. coli F 1F o ATP synthase accommodates symmetry mismatch. Nat Commun 2020; 11:2615. [PMID: 32457314 PMCID: PMC7251095 DOI: 10.1038/s41467-020-16387-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/30/2020] [Indexed: 12/19/2022] Open
Abstract
F1Fo ATP synthase functions as a biological rotary generator that makes a major contribution to cellular energy production. It comprises two molecular motors coupled together by a central and a peripheral stalk. Proton flow through the Fo motor generates rotation of the central stalk, inducing conformational changes in the F1 motor that catalyzes ATP production. Here we present nine cryo-EM structures of E. coli ATP synthase to 3.1-3.4 Å resolution, in four discrete rotational sub-states, which provide a comprehensive structural model for this widely studied bacterial molecular machine. We observe torsional flexing of the entire complex and a rotational sub-step of Fo associated with long-range conformational changes that indicates how this flexibility accommodates the mismatch between the 3- and 10-fold symmetries of the F1 and Fo motors. We also identify density likely corresponding to lipid molecules that may contribute to the rotor/stator interaction within the Fo motor.
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Affiliation(s)
- Meghna Sobti
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia.,Faculty of Medicine, St Vincent's Clinical School, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - James L Walshe
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia
| | - Di Wu
- Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, United Kingdom
| | - Robert Ishmukhametov
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, United Kingdom
| | - Yi C Zeng
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, United Kingdom
| | - Richard M Berry
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, United Kingdom
| | - Alastair G Stewart
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia. .,Faculty of Medicine, St Vincent's Clinical School, UNSW Sydney, Kensington, NSW, 2052, Australia.
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50
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Collins MP, Forgac M. Regulation and function of V-ATPases in physiology and disease. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183341. [PMID: 32422136 DOI: 10.1016/j.bbamem.2020.183341] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/30/2020] [Accepted: 05/03/2020] [Indexed: 02/07/2023]
Abstract
The vacuolar H+-ATPases (V-ATPases) are essential, ATP-dependent proton pumps present in a variety of eukaryotic cellular membranes. Intracellularly, V-ATPase-dependent acidification functions in such processes as membrane traffic, protein degradation, autophagy and the coupled transport of small molecules. V-ATPases at the plasma membrane of certain specialized cells function in such processes as bone resorption, sperm maturation and urinary acidification. V-ATPases also function in disease processes such as pathogen entry and cancer cell invasiveness, while defects in V-ATPase genes are associated with disorders such as osteopetrosis, renal tubular acidosis and neurodegenerative diseases. This review highlights recent advances in our understanding of V-ATPase structure, mechanism, function and regulation, with an emphasis on the signaling pathways controlling V-ATPase assembly in mammalian cells. The role of V-ATPases in cancer and other human pathologies, and the prospects for therapeutic intervention, are also discussed.
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Affiliation(s)
- Michael P Collins
- Cell, Molecular and Developmental Biology, Tufts University Graduate School of Biomedical Sciences, United States of America
| | - Michael Forgac
- Cell, Molecular and Developmental Biology, Tufts University Graduate School of Biomedical Sciences, United States of America; Dept. of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, United States of America.
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