101
|
Novel vertebrate- and brain-specific driver of neuronal outgrowth. Prog Neurobiol 2021; 202:102069. [PMID: 33933532 DOI: 10.1016/j.pneurobio.2021.102069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 03/31/2021] [Accepted: 04/21/2021] [Indexed: 12/30/2022]
Abstract
During the process of neuronal outgrowth, developing neurons produce new projections, neurites, that are essential for brain wiring. Here, we discover a relatively late-evolved protein that we denote Ac45-related protein (Ac45RP) and that, surprisingly, drives neuronal outgrowth. Ac45RP is a paralog of the Ac45 protein that is a component of the vacuolar proton ATPase (V-ATPase), the main pH regulator in eukaryotic cells. Ac45RP mRNA expression is brain specific and coincides with the peak of neurogenesis and the onset of synaptogenesis. Furthermore, Ac45RP physically interacts with the V-ATPase V0-sector and colocalizes with V0 in unconventional, but not synaptic, secretory vesicles of extending neurites. Excess Ac45RP enhances the expression of V0-subunits, causes a more elaborate Golgi, and increases the number of cytoplasmic vesicular structures, plasma membrane formation and outgrowth of actin-containing neurites devoid of synaptic markers. CRISPR-cas9n-mediated Ac45RP knockdown reduces neurite outgrowth. We conclude that the novel vertebrate- and brain-specific Ac45RP is a V0-interacting constituent of unconventional vesicular structures that drives membrane expansion during neurite outgrowth and as such may furnish a tool for future neuroregenerative treatment strategies.
Collapse
|
102
|
Murray JB, Mikhael C, Han G, de Faria LP, Rody WJ, Holliday LS. Activation of (pro)renin by (pro)renin receptor in extracellular vesicles from osteoclasts. Sci Rep 2021; 11:9214. [PMID: 33911158 PMCID: PMC8080643 DOI: 10.1038/s41598-021-88665-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/12/2021] [Indexed: 12/13/2022] Open
Abstract
The (pro)renin receptor (PRR) is a multifunctional integral membrane protein that serves as a component of the vacuolar H+-ATPase (V-ATPase) and also activates (pro)renin. We recently showed that full-length PRR, found as part of a V-ATPase sub-complex, is abundant in extracellular vesicles shed by osteoclasts. Here, we tested whether these extracellular vesicles stimulate (pro)renin. Extracellular vesicles isolated from the conditioned media of RAW 264.7 osteoclast-like cells or primary osteoclasts were characterized and counted by nanoparticle tracking. Immunoblotting confirmed that full-length PRR was present. Extracellular vesicles from osteoclasts dose-dependently stimulated (pro)renin activity, while extracellular vesicles from 4T1 cancer cells, in which we did not detect PRR, did not activate (pro)renin. To confirm that the ability of extracellular vesicles from osteoclasts to stimulate (pro)renin activity was due to the PRR, the "handle region peptide" from the PRR, a competitive inhibitor of PRR activity, was tested. It dose-dependently blocked the ability of extracellular vesicles to stimulate the enzymatic activity of (pro)renin. In summary, the PRR, an abundant component of extracellular vesicles shed by osteoclasts, stimulates (pro)renin activity. This represents a novel mechanism by which extracellular vesicles can function in intercellular regulation, with direct implications for bone biology.
Collapse
Affiliation(s)
- Jonathan B Murray
- Department of Orthodontics, University of Florida College of Dentistry, Gainesville, FL, 32610, USA
| | - Christy Mikhael
- Department of Orthodontics, University of Florida College of Dentistry, Gainesville, FL, 32610, USA
| | - Guanghong Han
- Department of Oral Geriatrics, Hospital of Stomatology, Jilin University, Changchun, 130021, People's Republic of China
| | - Lorraine Perciliano de Faria
- Department of Biomaterials and Oral Biology, School of Dentistry, University of São Paulo, São Paulo, 01000, Brazil
| | - Wellington J Rody
- Department of Orthodontics and Pediatric Dentistry, Stony Brook University School of Dental Medicine, Stony Brook, NY, 11794, USA
| | - L Shannon Holliday
- Department of Orthodontics, University of Florida College of Dentistry, Gainesville, FL, 32610, USA.
- Department of Anatomy & Cell Biology, University of Florida College of Medicine, Gainesville, FL, 23610, USA.
- Department of Orthodontics, University of Florida College of Dentistry, 1600 SW Archer Road, CB 1000444, Gainesville, FL, 23610, USA.
| |
Collapse
|
103
|
Agasid MT, Robinson CV. Probing membrane protein-lipid interactions. Curr Opin Struct Biol 2021; 69:78-85. [PMID: 33930613 DOI: 10.1016/j.sbi.2021.03.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/08/2021] [Accepted: 03/21/2021] [Indexed: 12/15/2022]
Abstract
Structure determination of membrane proteins has highlighted the many roles played by lipids in influencing overall protein architecture. It is now widely accepted that lipids surrounding membrane proteins play crucial roles by modulating their conformational, structural, and functional properties. Capturing often transient lipid interactions and defining their chemical identity, however, remains challenging. Recent advances in mass spectrometry have resolved questions concerning lipid interactions by providing the molecular composition of intact complexes in association with lipids. Together with other biophysical tools, a picture is emerging of the dynamic nature of lipid-mediated interactions and their effects on conformation, interactions, and signaling.
Collapse
Affiliation(s)
- Mark T Agasid
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| |
Collapse
|
104
|
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: 67] [Impact Index Per Article: 22.3] [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.
Collapse
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.
| |
Collapse
|
105
|
Grishin A, Voth K, Gagarinova A, Cygler M. Structural biology of the invasion arsenal of Gram-negative bacterial pathogens. FEBS J 2021; 289:1385-1427. [PMID: 33650300 DOI: 10.1111/febs.15794] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 02/11/2021] [Accepted: 02/26/2021] [Indexed: 12/20/2022]
Abstract
In the last several years, there has been a tremendous progress in the understanding of host-pathogen interactions and the mechanisms by which bacterial pathogens modulate behavior of the host cell. Pathogens use secretion systems to inject a set of proteins, called effectors, into the cytosol of the host cell. These effectors are secreted in a highly regulated, temporal manner and interact with host proteins to modify a multitude of cellular processes. The number of effectors varies between pathogens from ~ 30 to as many as ~ 350. The functional redundancy of effectors encoded by each pathogen makes it difficult to determine the cellular effects or function of individual effectors, since their individual knockouts frequently produce no easily detectable phenotypes. Structural biology of effector proteins and their interactions with host proteins, in conjunction with cell biology approaches, has provided invaluable information about the cellular function of effectors and underlying molecular mechanisms of their modes of action. Many bacterial effectors are functionally equivalent to host proteins while being structurally divergent from them. Other effector proteins display new, previously unobserved functionalities. Here, we summarize the contribution of the structural characterization of effectors and effector-host protein complexes to our understanding of host subversion mechanisms used by the most commonly investigated Gram-negative bacterial pathogens. We describe in some detail the enzymatic activities discovered among effector proteins and how they affect various cellular processes.
Collapse
Affiliation(s)
- Andrey Grishin
- Department of Biochemistry, Microbiology, & Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Kevin Voth
- Department of Biochemistry, Microbiology, & Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Alla Gagarinova
- Department of Biochemistry, Microbiology, & Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Miroslaw Cygler
- Department of Biochemistry, Microbiology, & Immunology, University of Saskatchewan, Saskatoon, Canada
| |
Collapse
|
106
|
Wittig S, Ganzella M, Barth M, Kostmann S, Riedel D, Pérez-Lara Á, Jahn R, Schmidt C. Cross-linking mass spectrometry uncovers protein interactions and functional assemblies in synaptic vesicle membranes. Nat Commun 2021; 12:858. [PMID: 33558502 PMCID: PMC7870876 DOI: 10.1038/s41467-021-21102-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 12/18/2020] [Indexed: 02/08/2023] Open
Abstract
Synaptic vesicles are storage organelles for neurotransmitters. They pass through a trafficking cycle and fuse with the pre-synaptic membrane when an action potential arrives at the nerve terminal. While molecular components and biophysical parameters of synaptic vesicles have been determined, our knowledge on the protein interactions in their membranes is limited. Here, we apply cross-linking mass spectrometry to study interactions of synaptic vesicle proteins in an unbiased approach without the need for specific antibodies or detergent-solubilisation. Our large-scale analysis delivers a protein network of vesicle sub-populations and functional assemblies including an active and an inactive conformation of the vesicular ATPase complex as well as non-conventional arrangements of the luminal loops of SV2A, Synaptophysin and structurally related proteins. Based on this network, we specifically target Synaptobrevin-2, which connects with many proteins, in different approaches. Our results allow distinction of interactions caused by 'crowding' in the vesicle membrane from stable interaction modules.
Collapse
Affiliation(s)
- Sabine Wittig
- Interdisciplinary Research Centre HALOmem, Charles Tanford Protein Centre, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Marcelo Ganzella
- Department for Neurobiology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Marie Barth
- Interdisciplinary Research Centre HALOmem, Charles Tanford Protein Centre, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Susann Kostmann
- Interdisciplinary Research Centre HALOmem, Charles Tanford Protein Centre, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Dietmar Riedel
- Department for Neurobiology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ángel Pérez-Lara
- Department for Neurobiology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- Department of Physical Chemistry, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Reinhard Jahn
- Department for Neurobiology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Carla Schmidt
- Interdisciplinary Research Centre HALOmem, Charles Tanford Protein Centre, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany.
| |
Collapse
|
107
|
Brouwers B, Coppola I, Vints K, Dislich B, Jouvet N, Van Lommel L, Segers C, Gounko NV, Thorrez L, Schuit F, Lichtenthaler SF, Estall JL, Declercq J, Ramos-Molina B, Creemers JWM. Loss of Furin in β-Cells Induces an mTORC1-ATF4 Anabolic Pathway That Leads to β-Cell Dysfunction. Diabetes 2021; 70:492-503. [PMID: 33277337 DOI: 10.2337/db20-0474] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 11/19/2020] [Indexed: 11/13/2022]
Abstract
FURIN is a proprotein convertase (PC) responsible for proteolytic activation of a wide array of precursor proteins within the secretory pathway. It maps to the PRC1 locus, a type 2 diabetes susceptibility locus, but its specific role in pancreatic β-cells is largely unknown. The aim of this study was to determine the role of FURIN in glucose homeostasis. We show that FURIN is highly expressed in human islets, whereas PCs that potentially could provide redundancy are expressed at considerably lower levels. β-cell-specific Furin knockout (βFurKO) mice are glucose intolerant as a result of smaller islets with lower insulin content and abnormal dense-core secretory granule morphology. mRNA expression analysis and differential proteomics on βFurKO islets revealed activation of activating transcription factor 4 (ATF4), which was mediated by mammalian target of rapamycin C1 (mTORC1). βFurKO cells show impaired cleavage or shedding of vacuolar-type ATPase (V-ATPase) subunits Ac45 and prorenin receptor, respectively, and impaired lysosomal acidification. Blocking V-ATPase pharmacologically in β-cells increased mTORC1 activity, suggesting involvement of the V-ATPase proton pump in the phenotype. Taken together, these results suggest a model of mTORC1-ATF4 hyperactivation and impaired lysosomal acidification in β-cells lacking Furin, causing β-cell dysfunction.
Collapse
Affiliation(s)
- Bas Brouwers
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
- Metabolic Research Laboratories, Wellcome Trust Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, U.K
| | - Ilaria Coppola
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Katlijn Vints
- Electron Microscopy Platform and Vlaams Instituut voor Biotechnologie (VIB) Bioimaging Core, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
- Leuven Brain Institute, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Bastian Dislich
- German Center for Neurodegenerative Diseases, Munich, Germany
- Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Nathalie Jouvet
- Institut de recherches cliniques de Montréal, Montréal, Quebec, Canada
| | - Leentje Van Lommel
- Gene Expression Unit, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Charlotte Segers
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
- Interdisciplinary Biosciences Group, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Natalia V Gounko
- Electron Microscopy Platform and Vlaams Instituut voor Biotechnologie (VIB) Bioimaging Core, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
- Leuven Brain Institute, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Lieven Thorrez
- Department of Development and Regeneration, Campus Kulak, KU Leuven, Kortrijk, Belgium
| | - Frans Schuit
- Gene Expression Unit, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Stefan F Lichtenthaler
- German Center for Neurodegenerative Diseases, Munich, Germany
- Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Jennifer L Estall
- Institut de recherches cliniques de Montréal, Montréal, Quebec, Canada
| | - Jeroen Declercq
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
- German Center for Neurodegenerative Diseases, Munich, Germany
| | - Bruno Ramos-Molina
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
- Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain
| | - John W M Creemers
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| |
Collapse
|
108
|
Wang M, Li A, Sekiya M, Beckmann ND, Quan X, Schrode N, Fernando MB, Yu A, Zhu L, Cao J, Lyu L, Horgusluoglu E, Wang Q, Guo L, Wang YS, Neff R, Song WM, Wang E, Shen Q, Zhou X, Ming C, Ho SM, Vatansever S, Kaniskan HÜ, Jin J, Zhou MM, Ando K, Ho L, Slesinger PA, Yue Z, Zhu J, Katsel P, Gandy S, Ehrlich ME, Fossati V, Noggle S, Cai D, Haroutunian V, Iijima KM, Schadt E, Brennand KJ, Zhang B. Transformative Network Modeling of Multi-omics Data Reveals Detailed Circuits, Key Regulators, and Potential Therapeutics for Alzheimer's Disease. Neuron 2021; 109:257-272.e14. [PMID: 33238137 PMCID: PMC7855384 DOI: 10.1016/j.neuron.2020.11.002] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 09/16/2020] [Accepted: 10/30/2020] [Indexed: 01/11/2023]
Abstract
To identify the molecular mechanisms and novel therapeutic targets of late-onset Alzheimer's Disease (LOAD), we performed an integrative network analysis of multi-omics profiling of four cortical areas across 364 donors with varying cognitive and neuropathological phenotypes. Our analyses revealed thousands of molecular changes and uncovered neuronal gene subnetworks as the most dysregulated in LOAD. ATP6V1A was identified as a key regulator of a top-ranked neuronal subnetwork, and its role in disease-related processes was evaluated through CRISPR-based manipulation in human induced pluripotent stem cell-derived neurons and RNAi-based knockdown in Drosophila models. Neuronal impairment and neurodegeneration caused by ATP6V1A deficit were improved by a repositioned compound, NCH-51. This study provides not only a global landscape but also detailed signaling circuits of complex molecular interactions in key brain regions affected by LOAD, and the resulting network models will serve as a blueprint for developing next-generation therapeutic agents against LOAD.
Collapse
Affiliation(s)
- Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,These authors contributed equally
| | - Aiqun Li
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,These authors contributed equally
| | - Michiko Sekiya
- Department of Alzheimer’s Disease Research, Center for Development of Advanced Medicine for Dementia, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan 474-8511,Department of Experimental Gerontology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan 467-8603,These authors contributed equally
| | - Noam D. Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,These authors contributed equally
| | - Xiuming Quan
- Department of Alzheimer’s Disease Research, Center for Development of Advanced Medicine for Dementia, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan 474-8511,These authors contributed equally
| | - Nadine Schrode
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Michael B. Fernando
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Alex Yu
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Li Zhu
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York NY 10029,Alzheimer’s Disease Research Center, Icahn School of Medicine at Mount Sinai, New York NY 10029,The New York Stem Cell Foundation Research Institute, New York, NY 10019
| | - Jiqing Cao
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York NY 10029,Alzheimer’s Disease Research Center, Icahn School of Medicine at Mount Sinai, New York NY 10029,The New York Stem Cell Foundation Research Institute, New York, NY 10019
| | - Liwei Lyu
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Emrin Horgusluoglu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Qian Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Lei Guo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Yuan-shuo Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Ryan Neff
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Won-min Song
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Erming Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Qi Shen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Chen Ming
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Seok-Man Ho
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Sezen Vatansever
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - H. Ümit Kaniskan
- Department of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY10029, United States
| | - Jian Jin
- Department of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY10029, United States.,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY10029, United States
| | - Ming-Ming Zhou
- Department of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Kanae Ando
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan 192-0397
| | - Lap Ho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Paul A. Slesinger
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Zhenyu Yue
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York NY 10029
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Pavel Katsel
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Psychiatry, JJ Peters VA Medical Center, 130 West Kingsbridge Road, Bronx, NY 10468, USA
| | - Sam Gandy
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Department of Neurology, Icahn School of Medicine at Mount Sinai, New York NY 10029,Alzheimer’s Disease Research Center, Icahn School of Medicine at Mount Sinai, New York NY 10029
| | - Michelle E. Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York NY 10029,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York NY 10029
| | - Valentina Fossati
- The New York Stem Cell Foundation Research Institute, New York, NY 10019
| | - Scott Noggle
- The New York Stem Cell Foundation Research Institute, New York, NY 10019
| | - Dongming Cai
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York NY 10029,Alzheimer’s Disease Research Center, Icahn School of Medicine at Mount Sinai, New York NY 10029,Neurology, JJ Peters VA Medical Center, 130 West Kingsbridge Road, Bronx, NY 10468, USA
| | - Vahram Haroutunian
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Alzheimer’s Disease Research Center, Icahn School of Medicine at Mount Sinai, New York NY 10029,Psychiatry, JJ Peters VA Medical Center, 130 West Kingsbridge Road, Bronx, NY 10468, USA
| | - Koichi M. Iijima
- Department of Alzheimer’s Disease Research, Center for Development of Advanced Medicine for Dementia, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan 474-8511,Department of Experimental Gerontology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan 467-8603,Senior author
| | - Eric Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Senior author
| | - Kristen J. Brennand
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Senior author
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Senior author,Lead Contact,Correspondence: (B.Z.)
| |
Collapse
|
109
|
Festa BP, Berquez M, Nieri D, Luciani A. Endolysosomal Disorders Affecting the Proximal Tubule of the Kidney: New Mechanistic Insights and Therapeutics. Rev Physiol Biochem Pharmacol 2021; 185:233-257. [PMID: 33649992 DOI: 10.1007/112_2020_57] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Epithelial cells that line the proximal tubule of the kidney rely on an intertwined ecosystem of vesicular membrane trafficking pathways to ensure the reabsorption of essential nutrients. To function effectively and to achieve homeostasis, these specialized cells require the sorting and recycling of a wide array of cell surface proteins within the endolysosomal network, including signaling receptors, nutrient transporters, ion channels, and polarity markers. The dysregulation of the endolysosomal system can lead to a generalized proximal tubule dysfunction, ultimately causing severe metabolic complications and kidney disease.In this chapter, we highlight the biological functions of the genes that code endolysosomal proteins from the perspective of understanding - and potentially reversing - the pathophysiology of endolysosomal disorders affecting the proximal tubule of the kidney. These insights might ultimately lead to potential treatments for currently intractable diseases and transform our ability to regulate kidney homeostasis and health.
Collapse
Affiliation(s)
- Beatrice Paola Festa
- Institute of Physiology, Mechanisms of Inherited Kidney Disorders Group, University of Zurich, Zurich, Switzerland
| | - Marine Berquez
- Institute of Physiology, Mechanisms of Inherited Kidney Disorders Group, University of Zurich, Zurich, Switzerland
| | - Daniela Nieri
- Institute of Physiology, Mechanisms of Inherited Kidney Disorders Group, University of Zurich, Zurich, Switzerland
| | - Alessandro Luciani
- Institute of Physiology, Mechanisms of Inherited Kidney Disorders Group, University of Zurich, Zurich, Switzerland.
| |
Collapse
|
110
|
Papke DJ, Hornick JL. Recent developments in gastroesophageal mesenchymal tumours. Histopathology 2020; 78:171-186. [PMID: 33382494 DOI: 10.1111/his.14164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 12/19/2022]
Abstract
The pathologist's approach to gastroesophageal mesenchymal tumours has changed dramatically during the last 25 years. In particular, gastrointestinal stromal tumour (GIST) has evolved from a wastebasket mesenchymal tumour category to a precisely defined entity with an increasingly detailed genetic subclassification. This subclassification has brought gastrointestinal mesenchymal neoplasia into the realm of precision medicine, with specific treatments optimised for particular genetic subtypes. Molecular genetic data have also greatly improved our understanding of oesophageal mesenchymal tumours, including the discovery that so-called 'giant fibrovascular polyps' in fact represent a clinically distinctive presentation of well-differentiated liposarcoma. Here, we will focus on gastroesophageal mesenchymal tumours for which there have been recent developments in classification, molecular genetics or tumour biology: granular cell tumour, 'giant fibrovascular polyp'/well-differentiated liposarcoma, plexiform fibromyxoma, gastroblastoma and, of course, GIST.
Collapse
Affiliation(s)
- David J Papke
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| |
Collapse
|
111
|
Carro SD, Cherry S. Beyond the Surface: Endocytosis of Mosquito-Borne Flaviviruses. Viruses 2020; 13:E13. [PMID: 33374822 PMCID: PMC7824540 DOI: 10.3390/v13010013] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/16/2020] [Accepted: 12/19/2020] [Indexed: 02/06/2023] Open
Abstract
Flaviviruses are a group of positive-sense RNA viruses that are primarily transmitted through arthropod vectors and are capable of causing a broad spectrum of diseases. Many of the flaviviruses that are pathogenic in humans are transmitted specifically through mosquito vectors. Over the past century, many mosquito-borne flavivirus infections have emerged and re-emerged, and are of global importance with hundreds of millions of infections occurring yearly. There is a need for novel, effective, and accessible vaccines and antivirals capable of inhibiting flavivirus infection and ameliorating disease. The development of therapeutics targeting viral entry has long been a goal of antiviral research, but most efforts are hindered by the lack of broad-spectrum potency or toxicities associated with on-target effects, since many host proteins necessary for viral entry are also essential for host cell biology. Mosquito-borne flaviviruses generally enter cells by clathrin-mediated endocytosis (CME), and recent studies suggest that a subset of these viruses can be internalized through a specialized form of CME that has additional dependencies distinct from canonical CME pathways, and antivirals targeting this pathway have been discovered. In this review, we discuss the role and contribution of endocytosis to mosquito-borne flavivirus entry as well as consider past and future efforts to target endocytosis for therapeutic interventions.
Collapse
Affiliation(s)
| | - Sara Cherry
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| |
Collapse
|
112
|
Davies JP, Almasy KM, McDonald EF, Plate L. Comparative Multiplexed Interactomics of SARS-CoV-2 and Homologous Coronavirus Nonstructural Proteins Identifies Unique and Shared Host-Cell Dependencies. ACS Infect Dis 2020; 6:3174-3189. [PMID: 33263384 PMCID: PMC7724760 DOI: 10.1021/acsinfecdis.0c00500] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Indexed: 12/15/2022]
Abstract
Human coronaviruses (hCoVs) have become a threat to global health and society, as evident from the SARS outbreak in 2002 caused by SARS-CoV-1 and the most recent COVID-19 pandemic caused by SARS-CoV-2. Despite a high sequence similarity between SARS-CoV-1 and -2, each strain has a distinctive virulence. A better understanding of the basic molecular mechanisms mediating changes in virulence is needed. Here, we profile the virus-host protein-protein interactions of two hCoV nonstructural proteins (nsps) that are critical for virus replication. We use tandem mass tag-multiplexed quantitative proteomics to sensitively compare and contrast the interactomes of nsp2 and nsp4 from three betacoronavirus strains: SARS-CoV-1, SARS-CoV-2, and hCoV-OC43-an endemic strain associated with the common cold. This approach enables the identification of both unique and shared host cell protein binding partners and the ability to further compare the enrichment of common interactions across homologues from related strains. We identify common nsp2 interactors involved in endoplasmic reticulum (ER) Ca2+ signaling and mitochondria biogenesis. We also identify nsp4 interactors unique to each strain, such as E3 ubiquitin ligase complexes for SARS-CoV-1 and ER homeostasis factors for SARS-CoV-2. Common nsp4 interactors include N-linked glycosylation machinery, unfolded protein response associated proteins, and antiviral innate immune signaling factors. Both nsp2 and nsp4 interactors are strongly enriched in proteins localized at mitochondria-associated ER membranes suggesting a new functional role for modulating host processes, such as calcium homeostasis, at these organelle contact sites. Our results shed light on the role these hCoV proteins play in the infection cycle, as well as host factors that may mediate the divergent pathogenesis of OC43 from SARS strains. Our mass spectrometry workflow enables rapid and robust comparisons of multiple bait proteins, which can be applied to additional viral proteins. Furthermore, the identified common interactions may present new targets for exploration by host-directed antiviral therapeutics.
Collapse
Affiliation(s)
- Jonathan P. Davies
- Department of Biological Sciences, Immunology and Inflammation, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN, USA
| | - Katherine M. Almasy
- Department of Chemistry, Vanderbilt University, Immunology and Inflammation, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN, USA
| | - Eli F. McDonald
- Department of Chemistry, Vanderbilt University, Immunology and Inflammation, Nashville, TN, USA
| | - Lars Plate
- Department of Biological Sciences, Immunology and Inflammation, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Immunology and Inflammation, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN, USA
| |
Collapse
|
113
|
Chorev DS, Robinson CV. The importance of the membrane for biophysical measurements. Nat Chem Biol 2020; 16:1285-1292. [PMID: 33199903 PMCID: PMC7116504 DOI: 10.1038/s41589-020-0574-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 05/22/2020] [Indexed: 11/09/2022]
Abstract
Within cell membranes numerous protein assemblies reside. Among their many functions, these assemblies regulate the movement of molecules between membranes, facilitate signaling into and out of cells, allow movement of cells by cell-matrix attachment, and regulate the electric potential of the membrane. With such critical roles, membrane protein complexes are of considerable interest for human health, yet they pose an enduring challenge for structural biologists because it is difficult to study these protein structures at atomic resolution in in situ environments. To advance structural and functional insights for these protein assemblies, membrane mimetics are typically employed to recapitulate some of the physical and chemical properties of the lipid bilayer membrane. However, extraction from native membranes can sometimes change the structure and lipid-binding properties of these complexes, leading to conflicting results and fueling a drive to study complexes directly from native membranes. Here we consider the co-development of membrane mimetics with technological breakthroughs in both cryo-electron microscopy (cryo-EM) and native mass spectrometry (nMS). Together, these developments are leading to a plethora of high-resolution protein structures, as well as new knowledge of their lipid interactions, from different membrane-like environments.
Collapse
Affiliation(s)
- Dror S Chorev
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK.
| |
Collapse
|
114
|
Kozlova MI, Bushmakin IM, Belyaeva JD, Shalaeva DN, Dibrova DV, Cherepanov DA, Mulkidjanian AY. Expansion of the "Sodium World" through Evolutionary Time and Taxonomic Space. BIOCHEMISTRY. BIOKHIMIIA 2020; 85:1518-1542. [PMID: 33705291 DOI: 10.1134/s0006297920120056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In 1986, Vladimir Skulachev and his colleagues coined the term "Sodium World" for the group of diverse organisms with sodium (Na)-based bioenergetics. Albeit only few such organisms had been discovered by that time, the authors insightfully noted that "the great taxonomic variety of organisms employing the Na-cycle points to the ubiquitous distribution of this novel type of membrane-linked energy transductions". Here we used tools of bioinformatics to follow expansion of the Sodium World through the evolutionary time and taxonomic space. We searched for those membrane protein families in prokaryotic genomes that correlate with the use of the Na-potential for ATP synthesis by different organisms. In addition to the known Na-translocators, we found a plethora of uncharacterized protein families; most of them show no homology with studied proteins. In addition, we traced the presence of Na-based energetics in many novel archaeal and bacterial clades, which were recently identified by metagenomic techniques. The data obtained support the view that the Na-based energetics preceded the proton-dependent energetics in evolution and prevailed during the first two billion years of the Earth history before the oxygenation of atmosphere. Hence, the full capacity of Na-based energetics in prokaryotes remains largely unexplored. The Sodium World expanded owing to the acquisition of new functions by Na-translocating systems. Specifically, most classes of G-protein-coupled receptors (GPCRs), which are targeted by almost half of the known drugs, appear to evolve from the Na-translocating microbial rhodopsins. Thereby the GPCRs of class A, with 700 representatives in human genome, retained the Na-binding site in the center of the transmembrane heptahelical bundle together with the capacity of Na-translocation. Mathematical modeling showed that the class A GPCRs could use the energy of transmembrane Na-potential for increasing both their sensitivity and selectivity. Thus, GPCRs, the largest protein family coded by human genome, stem from the Sodium World, which encourages exploration of other Na-dependent enzymes of eukaryotes.
Collapse
Affiliation(s)
- M I Kozlova
- School of Physics, Osnabrueck University, Osnabrueck, 49069, Germany. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - I M Bushmakin
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - J D Belyaeva
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - D N Shalaeva
- School of Physics, Osnabrueck University, Osnabrueck, 49069, Germany.
| | - D V Dibrova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - D A Cherepanov
- Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia.
| | - A Y Mulkidjanian
- School of Physics, Osnabrueck University, Osnabrueck, 49069, Germany. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.,School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia
| |
Collapse
|
115
|
Olinares PDB, Kang JY, Llewellyn E, Chiu C, Chen J, Malone B, Saecker RM, Campbell EA, Darst SA, Chait BT. Native Mass Spectrometry-Based Screening for Optimal Sample Preparation in Single-Particle Cryo-EM. Structure 2020; 29:186-195.e6. [PMID: 33217329 PMCID: PMC7867593 DOI: 10.1016/j.str.2020.11.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/26/2020] [Accepted: 11/02/2020] [Indexed: 01/19/2023]
Abstract
Recent advances in single-particle cryogenic electron microscopy (cryo-EM) have enabled the structural determination of numerous protein assemblies at high resolution, yielding unprecedented insights into their function. However, despite its extraordinary capabilities, cryo-EM remains time-consuming and resource-intensive. It is therefore beneficial to have a means for rapidly assessing and optimizing the quality of samples prior to lengthy cryo-EM analyses. To do this, we have developed a native mass spectrometry (nMS) platform that provides rapid feedback on sample quality and highly streamlined biochemical screening. Because nMS enables accurate mass analysis of protein complexes, it is well suited to routine evaluation of the composition, integrity, and homogeneity of samples prior to their plunge-freezing on EM grids. We demonstrate the utility of our nMS-based platform for facilitating cryo-EM studies using structural characterizations of exemplar bacterial transcription complexes as well as the replication-transcription assembly from the SARS-CoV-2 virus that is responsible for the COVID-19 pandemic.
Collapse
Affiliation(s)
- Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA.
| | - Jin Young Kang
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Eliza Llewellyn
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Courtney Chiu
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - James Chen
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Brandon Malone
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Ruth M Saecker
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA.
| |
Collapse
|
116
|
A "Sugar-Coated" Proton Pump Comes into Focus: High-Resolution Structure of a Human V-ATPase. Mol Cell 2020; 80:379-380. [PMID: 33157012 DOI: 10.1016/j.molcel.2020.10.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In this issue of Molecular Cell, Wang et al. (2020a) present near-atomic resolution cryoEM structures of a proton-pumping vacuolar ATPase from human cells, illuminating the glycosylation of integral subunits and identifying a novel and conserved glycolipid ligand.
Collapse
|
117
|
Arai S, Maruyama S, Shiroishi M, Yamato I, Murata T. An affinity change model to elucidate the rotation mechanism of V 1-ATPase. Biochem Biophys Res Commun 2020; 533:1413-1418. [PMID: 33097182 DOI: 10.1016/j.bbrc.2020.10.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 10/13/2020] [Indexed: 10/23/2022]
Abstract
V-ATPases are ubiquitous proton-transporting ATPases of eukaryotic and prokaryotic membranes that utilize energy from ATP hydrolysis. The hydrophilic catalytic part called V1-ATPase is composed of a ring-shaped hexametric A3B3 complex and a central DF shaft. We previously proposed a rotation mechanism of the Enterococcus hirae V1-ATPase based on the crystal structures of the V1 and A3B3 complexes. However, the driving force that induces the conformational changes of A3B3 and rotation of the DF shaft remains unclear. In this study, we investigated the binding affinity changes between subunits of V1-ATPase by surface plasmon resonance analysis. The binding of ATP to subunit A was found to considerably increase the affinity between the A and B subunits, and thereby ATP binding contributes to forming the A1B1 tight conformation. Furthermore, the DF shaft bound to the reconstituted A1B1 complex with high affinity, suggesting that the tight A1B1 complex is a major binding unit of the shaft in the A3B3 ring complex. Based on these results, we propose that rotation of the V1-ATPase is driven by affinity changes between each subunit via thermal fluctuations.
Collapse
Affiliation(s)
- Satoshi Arai
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku Katsushika-ku, Tokyo 125-8585, Japan; Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho Inage, Chiba, 263-8522, Japan
| | - Shintaro Maruyama
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho Inage, Chiba, 263-8522, Japan
| | - Mitsunori Shiroishi
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku Katsushika-ku, Tokyo 125-8585, Japan
| | - Ichiro Yamato
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku Katsushika-ku, Tokyo 125-8585, Japan; Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho Inage, Chiba, 263-8522, Japan.
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho Inage, Chiba, 263-8522, Japan; Molecular Chirality Research, Chiba University, 1-33 Yayoi-cho Inage, Chiba, 263-8522, Japan.
| |
Collapse
|
118
|
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.
Collapse
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.
| |
Collapse
|
119
|
Tinker RJ, Burghel GJ, Garg S, Steggall M, Cuvertino S, Banka S. Haploinsufficiency of ATP6V0C possibly underlies 16p13.3 deletions that cause microcephaly, seizures, and neurodevelopmental disorder. Am J Med Genet A 2020; 185:196-202. [PMID: 33090716 DOI: 10.1002/ajmg.a.61905] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/15/2020] [Accepted: 09/19/2020] [Indexed: 12/11/2022]
Abstract
We recently contributed to the description of eight individuals with a novel condition caused by 16p13.3 microdeletions encompassing TBC1D24, ATP6V0C, and PDPK1 and resulting in epilepsy, microcephaly and neurodevelopmental problems. The phenotypic spectrum, the minimum overlapping region and the underlying disease mechanism for this disorder remain to be clarified. Here we report a 3.5-year-old male, with microcephaly, autism spectrum disorder and a de novo 16p13.3 microdeletion. We performed detailed in silico analysis to show that the minimum overlapping region for the condition is ~80Kb encompassing five protein coding genes. Analysis of loss of function constraint metrics, transcript-aware evaluation of the population variants, GeVIR scores, analysis of reported pathogenic point variants, detailed review of the known functions of gene products and their animal models showed that the haploinsufficiency of ATP6V0C likely underlies the phenotype of this condition. Protein-protein interaction network, gene phenology and analysis of topologically associating domain showed that it was unlikely that the disorder has an epistatic or regulatory basis. 16p13.3 deletions encompassing ATP6V0C cause a neurodevelopmental disorder. Our results broaden the phenotypic spectrum of this disorder and clarify the likely underlying disease mechanism for the condition.
Collapse
Affiliation(s)
- Rory J Tinker
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University Foundation NHS Trust, Manchester, UK
| | - George J Burghel
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University Foundation NHS Trust, Manchester, UK
| | - Shruti Garg
- Division of Neuroscience & Experimental Psychology, School of Biological Sciences, University of Manchester, Manchester, UK
- Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Greater Manchester Mental Health NHS Trust, Manchester, UK
- Department of Child and Adolescent Psychiatry, Royal Manchester Children's Hospital, Manchester, UK
| | - Maggie Steggall
- Department of Paediatric Medicine, Royal Manchester Children's Hospital, Manchester, UK
| | - Sara Cuvertino
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University Foundation NHS Trust, Manchester, UK
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| |
Collapse
|
120
|
Barth M, Schmidt C. Native mass spectrometry-A valuable tool in structural biology. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4578. [PMID: 32662584 DOI: 10.1002/jms.4578] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 05/16/2023]
Abstract
Proteins and the complexes they form with their ligands are the players of cellular action. Their function is directly linked with their structure making the structural analysis of protein-ligand complexes essential. Classical techniques of structural biology include X-ray crystallography, nuclear magnetic resonance spectroscopy and recently distinguished cryo-electron microscopy. However, protein-ligand complexes are often dynamic and heterogeneous and consequently challenging for these techniques. Alternative approaches are therefore needed and gained importance during the last decades. One alternative is native mass spectrometry, which is the analysis of intact protein complexes in the gas phase. To achieve this, sample preparation and instrument conditions have to be optimised. Native mass spectrometry then reveals stoichiometry, protein interactions and topology of protein assemblies. Advanced techniques such as ion mobility and high-resolution mass spectrometry further add to the range of applications and deliver information on shape and microheterogeneity of the complexes. In this tutorial, we explain the basics of native mass spectrometry including sample requirements, instrument modifications and interpretation of native mass spectra. We further discuss the developments of native mass spectrometry and provide example spectra and applications.
Collapse
Affiliation(s)
- Marie Barth
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| |
Collapse
|
121
|
Chen Y, Xu C. The interaction partners of (pro)renin receptor in the distal nephron. FASEB J 2020; 34:14136-14149. [PMID: 32975331 DOI: 10.1096/fj.202001711r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 11/11/2022]
Abstract
The (pro)renin receptor (PRR), a key regulator of intrarenal renin-angiotensin system (RAS), is predominantly presented in podocytes, proximal tubules, distal convoluted tubules, and the apical membrane of collecting duct A-type intercalated cells, and plays a crucial role in hypertension, cardiovascular disease, kidney disease, and fluid homeostasis. In addition to its well-known renin-regulatory function, increasing evidence suggests PRR can also act in a variety of intracellular signaling cascades independently of RAS in the renal medulla, including Wnt/β-catenin signaling, cyclooxygenase-2 (COX-2)/prostaglandin E2 (PGE2 ) signaling, and the apelinergic system, and work as a component of the vacuolar H+ -ATPase. PRR and these pathways regulate the expression/activity of each other that controlling blood pressure and renal functions. In this review, we highlight recent findings regarding the antagonistic interaction between PRR and ELABELA/apelin, the mutually stimulatory relationship between PRR and COX-2/PGE2 or Wnt/β-catenin signaling in the renal medulla, and their involvement in the regulation of intrarenal RAS thereby control blood pressure, renal injury, and urine concentrating ability in health and patho-physiological conditions. We also highlight the latest progress in the involvement of PRR for the vacuolar H+ -ATPase activity.
Collapse
Affiliation(s)
- Yanting Chen
- Institute of Hypertension, Sun Yat-sen University School of Medicine, Guangzhou, China.,Internal Medicine, Division of Nephrology and Hypertension, University of Utah and Veterans Affairs Medical Center, Salt Lake City, UT, USA
| | - Chuanming Xu
- Internal Medicine, Division of Nephrology and Hypertension, University of Utah and Veterans Affairs Medical Center, Salt Lake City, UT, USA.,Center for Translational Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| |
Collapse
|
122
|
Beauregard-Lacroix E, Pacheco-Cuellar G, Ajeawung NF, Tardif J, Dieterich K, Dabir T, Vind-Kezunovic D, White SM, Zadori D, Castiglioni C, Tranebjærg L, Tørring PM, Blair E, Wisniewska M, Camurri MV, van Bever Y, Molidperee S, Taylor J, Dionne-Laporte A, Sisodiya SM, Hennekam RCM, Campeau PM. DOORS syndrome and a recurrent truncating ATP6V1B2 variant. Genet Med 2020; 23:149-154. [PMID: 32873933 DOI: 10.1038/s41436-020-00950-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 08/12/2020] [Accepted: 08/12/2020] [Indexed: 12/31/2022] Open
Abstract
PURPOSE Biallelic variants in TBC1D24, which encodes a protein that regulates vesicular transport, are frequently identified in patients with DOORS (deafness, onychodystrophy, osteodystrophy, intellectual disability [previously referred to as mental retardation], and seizures) syndrome. The aim of the study was to identify a genetic cause in families with DOORS syndrome and without a TBC1D24 variant. METHODS Exome or Sanger sequencing was performed in individuals with a clinical diagnosis of DOORS syndrome without TBC1D24 variants. RESULTS We identified the same truncating variant in ATP6V1B2 (NM_001693.4:c.1516C>T; p.Arg506*) in nine individuals from eight unrelated families with DOORS syndrome. This variant was already reported in individuals with dominant deafness onychodystrophy (DDOD) syndrome. Deafness was present in all individuals, along with onychodystrophy and abnormal fingers and/or toes. All families but one had developmental delay or intellectual disability and five individuals had epilepsy. We also describe two additional families with DDOD syndrome in whom the same variant was found. CONCLUSION We expand the phenotype associated with ATP6V1B2 and propose another causal gene for DOORS syndrome. This finding suggests that DDOD and DOORS syndromes might lie on a spectrum of clinically and molecularly related conditions.
Collapse
Affiliation(s)
- Eliane Beauregard-Lacroix
- Medical Genetics Division, Department of Pediatrics, Sainte-Justine University Hospital Center, Montreal, QC, Canada
| | - Guillermo Pacheco-Cuellar
- Medical Genetics Division, Department of Pediatrics, Sainte-Justine University Hospital Center, Montreal, QC, Canada
| | - Norbert F Ajeawung
- CHU Sainte Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Jessica Tardif
- Medical Genetics Division, Department of Pediatrics, Sainte-Justine University Hospital Center, Montreal, QC, Canada
| | - Klaus Dieterich
- Univ. Grenoble Alpes, Inserm, U1216, CHU Grenoble Alpes, Grenoble Institut Neurosciences (GIN), Grenoble, France
| | - Tabib Dabir
- Department of Genetic Medicine, Belfast City Hospital, Belfast, Northern Ireland, UK
| | - Dina Vind-Kezunovic
- Department of Dermatology, Copenhagen University Hospital Bispebjerg, Copenhagen, NV, Denmark
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
| | - Denes Zadori
- Department of Neurology, Interdisciplinary Excellence Center, Faculty of Medicine, Albert Szent-Györgyi Clinical Center, University of Szeged, Szeged, Hungary
| | | | - Lisbeth Tranebjærg
- The Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.,Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - Ed Blair
- Oxford Regional Genetics Service, Oxford University Hospitals, Oxford, UK
| | - Marzena Wisniewska
- Department of Medical Genetics, Poznañ University of Medical Sciences, Poznañ, Poland
| | - Maria Vittoria Camurri
- Medical Genetics Division, Department of Pediatrics, Sainte-Justine University Hospital Center, Montreal, QC, Canada
| | - Yolande van Bever
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Sirinart Molidperee
- CHU Sainte Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Juliet Taylor
- Genetic Health Service New Zealand-Northern Hub, Auckland, New Zealand
| | - Alexandre Dionne-Laporte
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK.,Chalfont Centre for Epilepsy, Bucks, UK
| | - Raoul C M Hennekam
- Department of Pediatrics, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Philippe M Campeau
- Medical Genetics Division, Department of Pediatrics, Sainte-Justine University Hospital Center, Montreal, QC, Canada.
| |
Collapse
|
123
|
Lysosome as a Central Hub for Rewiring PH Homeostasis in Tumors. Cancers (Basel) 2020; 12:cancers12092437. [PMID: 32867178 PMCID: PMC7565471 DOI: 10.3390/cancers12092437] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/18/2020] [Accepted: 08/21/2020] [Indexed: 02/06/2023] Open
Abstract
Cancer cells generate large quantities of cytoplasmic protons as byproducts of aberrantly activated aerobic glycolysis and lactate fermentation. To avoid potentially detrimental acidification of the intracellular milieu, cancer cells activate multiple acid-removal pathways that promote cytosolic alkalization and extracellular acidification. Accumulating evidence suggests that in addition to the well-characterized ion pumps and exchangers in the plasma membrane, cancer cell lysosomes are also reprogrammed for this purpose. On the one hand, the increased expression and activity of the vacuolar-type H+-ATPase (V-ATPase) on the lysosomal limiting membrane combined with the larger volume of the lysosomal compartment increases the lysosomal proton storage capacity substantially. On the other hand, enhanced lysosome exocytosis enables the efficient release of lysosomal protons to the extracellular space. Together, these two steps dynamically drive proton flow from the cytosol to extracellular space. In this perspective, we provide mechanistic insight into how lysosomes contribute to the rewiring of pH homeostasis in cancer cells.
Collapse
|
124
|
Wang R, Long T, Hassan A, Wang J, Sun Y, Xie XS, Li X. Cryo-EM structures of intact V-ATPase from bovine brain. Nat Commun 2020; 11:3921. [PMID: 32764564 PMCID: PMC7414150 DOI: 10.1038/s41467-020-17762-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/17/2020] [Indexed: 12/12/2022] Open
Abstract
The vacuolar-type H+-ATPases (V-ATPase) hydrolyze ATP to pump protons across the plasma or intracellular membrane, secreting acids to the lumen or acidifying intracellular compartments. It has been implicated in tumor metastasis, renal tubular acidosis, and osteoporosis. Here, we report two cryo-EM structures of the intact V-ATPase from bovine brain with all the subunits including the subunit H, which is essential for ATPase activity. Two type-I transmembrane proteins, Ac45 and (pro)renin receptor, along with subunit c", constitute the core of the c-ring. Three different conformations of A/B heterodimers suggest a mechanism for ATP hydrolysis that triggers a rotation of subunits DF, inducing spinning of subunit d with respect to the entire c-ring. Moreover, many lipid molecules have been observed in the Vo domain to mediate the interactions between subunit c, c", (pro)renin receptor, and Ac45. These two structures reveal unique features of mammalian V-ATPase and suggest a mechanism of V1-Vo torque transmission.
Collapse
Affiliation(s)
- Rong Wang
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Tao Long
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Abdirahman Hassan
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jin Wang
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Yingyuan Sun
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Xiao-Song Xie
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Xiaochun Li
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA. .,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| |
Collapse
|
125
|
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.
Collapse
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
| |
Collapse
|
126
|
Shin HR, Zoncu R. The Lysosome at the Intersection of Cellular Growth and Destruction. Dev Cell 2020; 54:226-238. [PMID: 32610045 DOI: 10.1016/j.devcel.2020.06.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/01/2020] [Indexed: 12/27/2022]
Abstract
The lysosome is an essential catabolic organelle that consumes cellular biomass to regenerate basic building blocks that can fuel anabolic reactions. This simple view has evolved more recently to integrate novel functions of the lysosome as a key signaling center, which can steer the metabolic trajectory of cells in response to changes in nutrients, growth factors, and stress. Master protein kinases and transcription factors mediate the growth-promoting and catabolic activities of the lysosome and undergo a complex interplay that enables cellular adaptation to ever-changing metabolic conditions. Understanding how this coordination occurs will shed light on the fundamental logic of how the lysosome functions to control growth in the context of development, tissue homeostasis, and cancer.
Collapse
Affiliation(s)
- Hijai R Shin
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA; The Paul F. Glenn Center for Aging Research at the University of California Berkeley, Berkeley, CA 94720, USA
| | - Roberto Zoncu
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA; The Paul F. Glenn Center for Aging Research at the University of California Berkeley, Berkeley, CA 94720, USA.
| |
Collapse
|