1
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Lei Y, Yang Y, Zhang Z, Zhang R, Song X, Malek SN, Tang D, Klionsky DJ. Big1 is a newly identified autophagy regulator that is critical for a fully functional V-ATPase. Mol Biol Cell 2024; 35:br20. [PMID: 39259764 DOI: 10.1091/mbc.e24-04-0189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024] Open
Abstract
The vacuolar-type H+-translocating ATPase (V-ATPase) is the major proton pump for intraorganellar acidification. Therefore, the integrity of the V-ATPase is closely associated with cellular homeostasis, and mutations in genes encoding V-ATPase components and assembly factors have been reported in certain types of diseases. For instance, the recurrent mutations of ATP6AP1, a gene encoding a V-ATPase accessory protein, have been associated with cancers and immunodeficiency. With the aim of studying V-ATPase-related mutations using the yeast model system, we report that Big1 is another homologue of ATP6AP1 in yeast cells, and we characterize the role of Big1 in maintaining a fully functional V-ATPase. In addition to its role in acidifying the vacuole or lysosome, our data support the concept that the V-ATPase may function as part of a signaling pathway to regulate macroautophagy/autophagy through a mechanism that is independent from Tor/MTOR.
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Affiliation(s)
- Yuchen Lei
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-2216
| | - Ying Yang
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-2216
| | - Zhihai Zhang
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-2216
| | - Ruoxi Zhang
- Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Xinxin Song
- Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Sami N Malek
- Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI 48109-0936
| | - Daolin Tang
- Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Daniel J Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-2216
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2
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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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3
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Khan MM, Wilkens S. Molecular mechanism of Oxr1p mediated disassembly of yeast V-ATPase. EMBO Rep 2024; 25:2323-2347. [PMID: 38565737 PMCID: PMC11094088 DOI: 10.1038/s44319-024-00126-5] [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: 12/03/2023] [Revised: 03/07/2024] [Accepted: 03/09/2024] [Indexed: 04/04/2024] Open
Abstract
The eukaryotic vacuolar H+-ATPase (V-ATPase) is regulated by reversible disassembly into autoinhibited V1-ATPase and Vo proton channel subcomplexes. We recently reported that the TLDc protein Oxr1p induces V-ATPase disassembly in vitro. Whether and how Oxr1p is involved in enzyme disassembly in vivo, however, is not known. Here, using yeast genetics and fluorescence microscopy, we show that Oxr1p is essential for efficient V-ATPase disassembly in the cell. Supporting biochemical and biophysical in vitro experiments show that whereas Oxr1p-driven holoenzyme disassembly can occur in the absence of nucleotides, the presence of ATP greatly accelerates the process. ATP hydrolysis is needed, however, for subsequent release of Oxr1p so that the free V1 can adopt the autoinhibited conformation. Overall, our study unravels the molecular mechanism of Oxr1p-induced disassembly that occurs in vivo as part of the canonical V-ATPase regulation by reversible disassembly.
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Affiliation(s)
- Md Murad Khan
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Stephan Wilkens
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
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4
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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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5
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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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6
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Indrawinata K, Argiropoulos P, Sugita S. Structural and functional understanding of disease-associated mutations in V-ATPase subunit a1 and other isoforms. Front Mol Neurosci 2023; 16:1135015. [PMID: 37465367 PMCID: PMC10352029 DOI: 10.3389/fnmol.2023.1135015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/09/2023] [Indexed: 07/20/2023] Open
Abstract
The vacuolar-type ATPase (V-ATPase) is a multisubunit protein composed of the cytosolic adenosine triphosphate (ATP) hydrolysis catalyzing V1 complex, and the integral membrane complex, Vo, responsible for proton translocation. The largest subunit of the Vo complex, subunit a, enables proton translocation upon ATP hydrolysis, mediated by the cytosolic V1 complex. Four known subunit a isoforms (a1-a4) are expressed in different cellular locations. Subunit a1 (also known as Voa1), the neural isoform, is strongly expressed in neurons and is encoded by the ATP6V0A1 gene. Global knockout of this gene in mice causes embryonic lethality, whereas pyramidal neuron-specific knockout resulted in neuronal cell death with impaired spatial and learning memory. Recently reported, de novo and biallelic mutations of the human ATP6V0A1 impair autophagic and lysosomal activities, contributing to neuronal cell death in developmental and epileptic encephalopathies (DEE) and early onset progressive myoclonus epilepsy (PME). The de novo heterozygous R740Q mutation is the most recurrent variant reported in cases of DEE. Homology studies suggest R740 deprotonates protons from specific glutamic acid residues in subunit c, highlighting its importance to the overall V-ATPase function. In this paper, we discuss the structure and mechanism of the V-ATPase, emphasizing how mutations in subunit a1 can lead to lysosomal and autophagic dysfunction in neurodevelopmental disorders, and how mutations to the non-neural isoforms, a2-a4, can also lead to various genetic diseases. Given the growing discovery of disease-causing variants of V-ATPase subunit a and its function as a pump-based regulator of intracellular organelle pH, this multiprotein complex warrants further investigation.
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Affiliation(s)
- Karen Indrawinata
- Division of Translational and Experimental Neuroscience, Krembil Brain Institute, University Health Network, Toronto, ON, Canada
| | - Peter Argiropoulos
- Division of Translational and Experimental Neuroscience, Krembil Brain Institute, University Health Network, Toronto, ON, Canada
| | - Shuzo Sugita
- Division of Translational and Experimental Neuroscience, Krembil Brain Institute, University Health Network, Toronto, ON, Canada
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
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7
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Wilkens S, Khan MM, Knight K, Oot R. Tender love and disassembly: How a TLDc domain protein breaks the V-ATPase. Bioessays 2023; 45:e2200251. [PMID: 37183929 PMCID: PMC10392918 DOI: 10.1002/bies.202200251] [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: 12/31/2022] [Revised: 04/13/2023] [Accepted: 05/03/2023] [Indexed: 05/16/2023]
Abstract
Vacuolar ATPases (V-ATPases, V1 Vo -ATPases) are rotary motor proton pumps that acidify intracellular compartments, and, when localized to the plasma membrane, the extracellular space. V-ATPase is regulated by a unique process referred to as reversible disassembly, wherein V1 -ATPase disengages from Vo proton channel in response to diverse environmental signals. Whereas the disassembly step of this process is ATP dependent, the (re)assembly step is not, but requires the action of a heterotrimeric chaperone referred to as the RAVE complex. Recently, an alternative pathway of holoenzyme disassembly was discovered that involves binding of Oxidation Resistance 1 (Oxr1p), a poorly characterized protein implicated in oxidative stress response. Unlike conventional reversible disassembly, which depends on enzyme activity, Oxr1p induced dissociation can occur in absence of ATP. Yeast Oxr1p belongs to the family of TLDc domain containing proteins that are conserved from yeast to mammals, and have been implicated in V-ATPase function in a variety of tissues. This brief perspective summarizes what we know about the molecular mechanisms governing both reversible (ATP dependent) and Oxr1p driven (ATP independent) V-ATPase dissociation into autoinhibited V1 and Vo subcomplexes.
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Affiliation(s)
- Stephan Wilkens
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY
| | - Md. Murad Khan
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY
| | - Kassidy Knight
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY
| | - Rebecca Oot
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY
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8
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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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9
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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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10
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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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11
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Yokoyama K. Rotary mechanism of V/A-ATPases-how is ATP hydrolysis converted into a mechanical step rotation in rotary ATPases? Front Mol Biosci 2023; 10:1176114. [PMID: 37168257 PMCID: PMC10166205 DOI: 10.3389/fmolb.2023.1176114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/13/2023] [Indexed: 05/13/2023] Open
Abstract
V/A-ATPase is a rotary molecular motor protein that produces ATP through the rotation of its central rotor. The soluble part of this protein, the V1 domain, rotates upon ATP hydrolysis. However, the mechanism by which ATP hydrolysis in the V1 domain couples with the mechanical rotation of the rotor is still unclear. Cryo-EM snapshot analysis of V/A-ATPase indicated that three independent and simultaneous catalytic events occurred at the three catalytic dimers (ABopen, ABsemi, and ABclosed), leading to a 120° rotation of the central rotor. Besides the closing motion caused by ATP bound to ABopen, the hydrolysis of ATP bound to ABsemi drives the 120° step. Our recent time-resolved cryo-EM snapshot analysis provides further evidence for this model. This review aimed to provide a comprehensive overview of the structure and function of V/A-ATPase from a thermophilic bacterium, one of the most well-studied rotary ATPases to date.
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Affiliation(s)
- Ken Yokoyama
- Department of Molecular Biosciences, Kyoto Sangyo University, Kyoto, Japan
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12
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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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13
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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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14
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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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15
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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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16
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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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17
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Tao T, Liu Y, Zhang J, Lai W, Long H. NGF-Induced Upregulation of CGRP in Orofacial Pain Induced by Tooth Movement Is Dependent on Atp6v0a1 and Vesicle Release. Int J Mol Sci 2022; 23:ijms231911440. [PMID: 36232740 PMCID: PMC9569904 DOI: 10.3390/ijms231911440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
The nerve growth factor (NGF) and calcitonin gene-related peptide (CGRP) play a crucial role in the regulation of orofacial pain. It has been demonstrated that CGRP increases orofacial pain induced by NGF. V-type proton ATPase subunit an isoform 1 (Atp6v0a1) is involved in the exocytosis pathway, especially in vesicular transport in neurons. The objective was to examine the role of Atp6v0a1 in NGF-induced upregulation of CGRP in orofacial pain induced by experimental tooth movement. Orofacial pain was elicited by ligating closed-coil springs between incisors and molars in Sprague–Dawley rats. Gene and protein expression levels were determined through real-time polymerase chain reaction, immunostaining, and fluorescence in situ hybridization. Lentivirus vectors carrying Atp6v0a1 shRNA were used to knockdown the expression of Atp6v0a1 in TG and SH-SY5Y neurons. The release of vesicles in SH-SY5Y neurons was observed by using fluorescence dye FM1-43, and the release of CGRP was detected by Enzyme-Linked Immunosorbent Assy. Orofacial pain was evaluated through the rat grimace scale. Our results revealed that intraganglionic administration of NGF and Atp6v0a1 shRNA upregulated and downregulated CGRP in trigeminal ganglia (TG) and trigeminal subnucleus caudalis (Vc), respectively, and the orofacial pain was also exacerbated and alleviated, respectively, following administration of NGF and Atp6v0a1 shRNA. Besides, intraganglionic administration of NGF simultaneously caused the downregulation of Atp6v0a1 in TG. Moreover, the release of vesicles and CGRP in SH-SY5Y neurons was interfered by NGF and Atp6v0a1 shRNA. In conclusion, in the orofacial pain induced by experimental tooth movement, NGF induced the upregulation of CGRP in TG and Vc, and this process is dependent on Atp6v0a1 and vesicle release, suggesting that they are involved in the transmission of nociceptive information in orofacial pain.
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Affiliation(s)
| | | | | | | | - Hu Long
- Correspondence: (W.L.); (H.L.)
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18
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Gomes AS, Passos LS, Rocha Aride PH, Chisté B, Gomes LC, Boldrini-França J. Gene expression changes in Epinephelus marginatus (Teleostei, Serranidae) liver reveals candidate molecular biomarker of iron ore contamination. CHEMOSPHERE 2022; 303:134899. [PMID: 35561782 DOI: 10.1016/j.chemosphere.2022.134899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
Wastes from iron ore mining activities are potentially damaging to adjacent aquatic ecosystems. We aimed to determine biomarkers of environmental exposure to this xenobiotic in the dusky grouper Epinephelus marginatus by differential gene expression analysis. For this, fish were exposed to iron ore (15.2 mg/L) and gene expression in liver was assessed by RNA-Seq and compared to the control group. A total of 124 differentially expressed genes were identified, from which 52 were upregulated and 72 were downregulated in response to iron ore. From these, ferritin (medium subunit), cytochrome b reductase and epoxide hydrolase genes were selected for validation by RT-qPCR that confirmed the upregulation of epoxide hydrolase in fish exposed to iron ore.
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Affiliation(s)
- Aline Silva Gomes
- Universidade Vila Velha, Rua Comissário José Dantas Melo, 21, 29102-770, Vila Velha ES, Brazil
| | - Larissa Souza Passos
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Av. Professor Lineu Prestes, 580, 05508-000, São Paulo SP, Brazil
| | | | - Bárbara Chisté
- Universidade Vila Velha, Rua Comissário José Dantas Melo, 21, 29102-770, Vila Velha ES, Brazil
| | - Levy Carvalho Gomes
- Universidade Vila Velha, Rua Comissário José Dantas Melo, 21, 29102-770, Vila Velha ES, Brazil
| | - Johara Boldrini-França
- Universidade Vila Velha, Rua Comissário José Dantas Melo, 21, 29102-770, Vila Velha ES, Brazil; School of Biochemistry, Biomedical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom.
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19
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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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20
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Marshansky V. Discovery and Study of Transmembrane Rotary Ion-Translocating Nano-Motors: F-ATPase/Synthase of Mitochondria/Bacteria and V-ATPase of Eukaryotic Cells. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:702-719. [PMID: 36171652 DOI: 10.1134/s000629792208003x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 06/16/2023]
Abstract
This review discusses the history of discovery and study of the operation of the two rotary ion-translocating ATPase nano-motors: (i) F-ATPase/synthase (holocomplex F1FO) of mitochondria/bacteria and (ii) eukaryotic V-ATPase (holocomplex V1VO). Vacuolar adenosine triphosphatase (V-ATPase) is a transmembrane multisubunit complex found in all eukaryotes from yeast to humans. It is structurally and functionally similar to the F-ATPase/synthase of mitochondria/bacteria and the A-ATPase/synthase of archaebacteria, which indicates a common evolutionary origin of the rotary ion-translocating nano-motors built into cell membranes and invented by Nature billions of years ago. Previously we have published several reviews on this topic with appropriate citations of our original research. This review is focused on the historical analysis of the discovery and study of transmembrane rotary ion-translocating ATPase nano-motors functioning in bacteria, eukaryotic cells and mitochondria of animals.
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21
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Structure of the Human BK Ion Channel in Lipid Environment. MEMBRANES 2022; 12:membranes12080758. [PMID: 36005673 PMCID: PMC9414842 DOI: 10.3390/membranes12080758] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/27/2022] [Accepted: 07/30/2022] [Indexed: 02/04/2023]
Abstract
Voltage-gated and ligand-modulated ion channels play critical roles in excitable cells. To understand the interplay among voltage sensing, ligand binding, and channel opening, the structures of ion channels in various functional states and in lipid membrane environments need to be determined. Here, the random spherically constrained (RSC) single-particle cryo-EM method was employed to study human large conductance voltage- and calcium-activated potassium (hBK or hSlo1) channels reconstituted into liposomes. The hBK structure was determined at 3.5 Å resolution in the absence of Ca2+. Instead of the common fourfold symmetry observed in ligand-modulated ion channels, a twofold symmetry was observed in hBK in liposomes. Compared with the structure of isolated hSlo1 Ca2+ sensing gating rings, two opposing subunits in hBK unfurled, resulting in a wider opening towards the transmembrane region of hBK. In the pore gate domain, two opposing subunits also moved downwards relative to the two other subunits.
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22
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Gerle C, Kishikawa JI, Yamaguchi T, Nakanishi A, Çoruh O, Makino F, Miyata T, Kawamoto A, Yokoyama K, Namba K, Kurisu G, Kato T. Structures of Multisubunit Membrane Complexes With the CRYO ARM 200. Microscopy (Oxf) 2022; 71:249-261. [PMID: 35861182 PMCID: PMC9535789 DOI: 10.1093/jmicro/dfac037] [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: 04/25/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 11/18/2022] Open
Abstract
Progress in structural membrane biology has been significantly accelerated by the ongoing ‘Resolution Revolution’ in cryo-electron microscopy (cryo-EM). In particular, structure determination by single-particle analysis has evolved into the most powerful method for atomic model building of multisubunit membrane protein complexes. This has created an ever-increasing demand in cryo-EM machine time, which to satisfy is in need of new and affordable cryo-electron microscopes. Here, we review our experience in using the JEOL CRYO ARM 200 prototype for the structure determination by single-particle analysis of three different multisubunit membrane complexes: the Thermus thermophilus V-type ATPase VO complex, the Thermosynechococcus elongatus photosystem I monomer and the flagellar motor lipopolysaccharide peptidoglycan ring (LP ring) from Salmonella enterica.
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Affiliation(s)
- Christoph Gerle
- Institute for Protein Research, Osaka University, 3-2 Yamada Oka, Suita, Osaka 565-0871, Japan.,RIKEN SPring-8 Center, Life Science Research Infrastructure Group, Sayo-gun, Hyogo 679-5148, Japan
| | - Jun-Ichi Kishikawa
- Institute for Protein Research, Osaka University, 3-2 Yamada Oka, Suita, Osaka 565-0871, Japan
| | - Tomoko Yamaguchi
- Graduate School of Frontier Biosciences, 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, Ibaraki, Osaka 567-0047, Japan
| | - Orkun Çoruh
- Institute for Protein Research, Osaka University, 3-2 Yamada Oka, Suita, Osaka 565-0871, Japan.,Institute of Science and Technology Austria, Klosterneuburg, 3400 Austria
| | - Fumiaki Makino
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,JEOL Ltd., Akishima, Tokyo, Japan
| | - Tomoko Miyata
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Akihiro Kawamoto
- Institute for Protein Research, Osaka University, 3-2 Yamada Oka, Suita, Osaka 565-0871, Japan
| | - Ken Yokoyama
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan.,JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka, Japan
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, 3-2 Yamada Oka, Suita, Osaka 565-0871, Japan
| | - Takayuki Kato
- Institute for Protein Research, Osaka University, 3-2 Yamada Oka, Suita, Osaka 565-0871, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
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23
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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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24
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Wang R, Qin Y, Xie XS, Li X. Molecular basis of mEAK7-mediated human V-ATPase regulation. Nat Commun 2022; 13:3272. [PMID: 35672408 PMCID: PMC9174246 DOI: 10.1038/s41467-022-30899-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/24/2022] [Indexed: 11/09/2022] Open
Abstract
The activity of V-ATPase is well-known to be regulated by reversible dissociation of its V1 and Vo domains in response to growth factor stimulation, nutrient sensing, and cellular differentiation. The molecular basis of its regulation by an endogenous modulator without affecting V-ATPase assembly remains unclear. Here, we discover that a lysosome-anchored protein termed (mammalian Enhancer-of-Akt-1-7 (mEAK7)) binds to intact V-ATPase. We determine cryo-EM structure of human mEAK7 in complex with human V-ATPase in native lipid-containing nanodiscs. The structure reveals that the TLDc domain of mEAK7 engages with subunits A, B, and E, while its C-terminal domain binds to subunit D, presumably blocking V1-Vo torque transmission. Our functional studies suggest that mEAK7, which may act as a V-ATPase inhibitor, does not affect the activity of V-ATPase in vitro. However, overexpression of mEAK7 in HCT116 cells that stably express subunit a4 of V-ATPase represses the phosphorylation of ribosomal protein S6. Thus, this finding suggests that mEAK7 potentially links mTOR signaling with V-ATPase activity.
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Affiliation(s)
- Rong Wang
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Yu Qin
- 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.
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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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Zeng J, Kang WN, Jin L, Anjum AA, Li GQ. Vacuolar ATPase subunit F is critical for larval survival in Henosepilachna vigintioctopunctata. INSECT MOLECULAR BIOLOGY 2022; 31:177-189. [PMID: 34787941 DOI: 10.1111/imb.12749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 11/02/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
Vacuolar ATPase (vATPase) is an important proton pump in insect tissues including gut and Malpighian tubule. Subunit F, one of the 16 subunits of the vATPase holoenzyme, is not well characterized. Here, we found that two HvvATPaseF isoforms were highly expressed in the hindgut and Malpighian tubules (MT) in the 28-spotted lady-beetle Henosepilachna vigintioctopunctata, an agricultural pest that feeds on Solanaceae and Cucurbitaceae. Knockdown of both HvvATPaseF variants by RNA interference (RNAi) delayed larval growth and negatively affected ecdysis and adult emergence. In the midgut, RNAi treatment resulted in the disappearance of peritrophic membrane, the reduction in the size and the impaired integrity of the gut, which was associated with sparse principle cells and an increase in TUNEL- and EdU-positive cells. Whereas the MT were opaque and the tubule lumens were full of urine in dsegfp-fed larvae, the tubules were clear and the tubule lumens were empty in the dsvATPaseF-fed larvae. HvvATPaseF knockdown was also associated with a decrease in the abundance of the fat body and the levels of glucose, trehalose, triglyceride, total soluble amino acids and proteins, and an increase in glycogen. Consistent with the known effects of sugars on chitin formation, both the expression level of a chitin biosynthesis gene and the thickness of the head capsule cuticle were reduced in the HvvATPaseF-depleted beetles. Our results demonstrated that subunit F plays an essential role in H. vigintioctopunctata development.
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Affiliation(s)
- Jie Zeng
- Agriculture Ministry Key Laboratory of Integrated Pest Management on Crops in East China/State and Local Joint Engineering Research Center of Green Pesticide Invention and Application, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Wei-Nan Kang
- Agriculture Ministry Key Laboratory of Integrated Pest Management on Crops in East China/State and Local Joint Engineering Research Center of Green Pesticide Invention and Application, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Lin Jin
- Agriculture Ministry Key Laboratory of Integrated Pest Management on Crops in East China/State and Local Joint Engineering Research Center of Green Pesticide Invention and Application, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ahmad Ali Anjum
- Agriculture Ministry Key Laboratory of Integrated Pest Management on Crops in East China/State and Local Joint Engineering Research Center of Green Pesticide Invention and Application, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Guo-Qing Li
- Agriculture Ministry Key Laboratory of Integrated Pest Management on Crops in East China/State and Local Joint Engineering Research Center of Green Pesticide Invention and Application, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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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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Khan MM, Lee S, Couoh‐Cardel S, Oot RA, Kim H, Wilkens S, Roh S. Oxidative stress protein Oxr1 promotes V-ATPase holoenzyme disassembly in catalytic activity-independent manner. EMBO J 2022; 41:e109360. [PMID: 34918374 PMCID: PMC8804929 DOI: 10.15252/embj.2021109360] [Citation(s) in RCA: 5] [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: 08/03/2021] [Revised: 10/30/2021] [Accepted: 11/15/2021] [Indexed: 11/09/2022] Open
Abstract
The vacuolar ATPase (V-ATPase) is a rotary motor proton pump that is regulated by an assembly equilibrium between active holoenzyme and autoinhibited V1 -ATPase and Vo proton channel subcomplexes. Here, we report cryo-EM structures of yeast V-ATPase assembled in vitro from lipid nanodisc reconstituted Vo and mutant V1 . Our analysis identified holoenzymes in three active rotary states, indicating that binding of V1 to Vo provides sufficient free energy to overcome Vo autoinhibition. Moreover, the structures suggest that the unequal spacing of Vo 's proton-carrying glutamic acid residues serves to alleviate the symmetry mismatch between V1 and Vo motors, a notion that is supported by mutagenesis experiments. We also uncover a structure of free V1 bound to Oxr1, a conserved but poorly characterized factor involved in the oxidative stress response. Biochemical experiments show that Oxr1 inhibits V1 -ATPase and causes disassembly of the holoenzyme, suggesting that Oxr1 plays a direct role in V-ATPase regulation.
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Affiliation(s)
- Md. Murad Khan
- Department of Biochemistry and Molecular BiologySUNY Upstate Medical UniversitySyracuseNYUSA
| | - Seowon Lee
- School of Biological ScienceInstitute of Molecular Biology and GeneticsSeoul National UniversitySeoulSouth Korea
| | - Sergio Couoh‐Cardel
- Department of Biochemistry and Molecular BiologySUNY Upstate Medical UniversitySyracuseNYUSA
- Present address:
Department of Molecular and Cellular PhysiologyStanford UniversityStanfordCAUSA
| | - Rebecca A Oot
- Department of Biochemistry and Molecular BiologySUNY Upstate Medical UniversitySyracuseNYUSA
| | - Hyunmin Kim
- School of Biological ScienceInstitute of Molecular Biology and GeneticsSeoul National UniversitySeoulSouth Korea
| | - Stephan Wilkens
- Department of Biochemistry and Molecular BiologySUNY Upstate Medical UniversitySyracuseNYUSA
| | - Soung‐Hun Roh
- School of Biological ScienceInstitute of Molecular Biology and GeneticsSeoul National UniversitySeoulSouth Korea
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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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Chojnowski G, Simpkin AJ, Leonardo DA, Seifert-Davila W, Vivas-Ruiz DE, Keegan RM, Rigden DJ. findMySequence: a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM. IUCRJ 2022; 9:86-97. [PMID: 35059213 PMCID: PMC8733886 DOI: 10.1107/s2052252521011088] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 10/22/2021] [Indexed: 05/15/2023]
Abstract
Although experimental protein-structure determination usually targets known proteins, chains of unknown sequence are often encountered. They can be purified from natural sources, appear as an unexpected fragment of a well characterized protein or appear as a contaminant. Regardless of the source of the problem, the unknown protein always requires characterization. Here, an automated pipeline is presented for the identification of protein sequences from cryo-EM reconstructions and crystallographic data. The method's application to characterize the crystal structure of an unknown protein purified from a snake venom is presented. It is also shown that the approach can be successfully applied to the identification of protein sequences and validation of sequence assignments in cryo-EM protein structures.
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Affiliation(s)
- Grzegorz Chojnowski
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Adam J. Simpkin
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Diego A. Leonardo
- São Carlos Institute of Physics, University of São Paulo, Avenida João Dagnone 1100, São Carlos, SP 13563-120, Brazil
| | | | - Dan E. Vivas-Ruiz
- Laboratorio de Biología Molecular, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Avenida Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima, Peru
| | - Ronan M. Keegan
- Rutherford Appleton Laboratory, Research Complex at Harwell, UKRI-STFC, Didcot OX11 0FA, United Kingdom
| | - Daniel J. Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
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Wang C, Xiang Y, Qian D. Current progress in plant V-ATPase: From biochemical properties to physiological functions. JOURNAL OF PLANT PHYSIOLOGY 2021; 266:153525. [PMID: 34560396 DOI: 10.1016/j.jplph.2021.153525] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/12/2021] [Accepted: 09/12/2021] [Indexed: 06/13/2023]
Abstract
Vacuolar-type adenosine triphosphatase (V-ATPase, VHA) is a highly conserved, ATP-driven multisubunit proton pump that is widely distributed in all eukaryotic cells. V-ATPase consists of two domains formed by at least 13 different subunits, the membrane peripheral V1 domain responsible for ATP hydrolysis, and the membrane-integral V0 domain responsible for proton translocation. V-ATPase plays an essential role in energizing secondary active transport and is indispensable to plants. In addition to multiple stress responses, plant V-ATPase is also implicated in physiological processes such as growth, development, and morphogenesis. Based on the identification of distinct V-ATPase mutants and advances in luminal pH measurements in vivo, it has been revealed that this holoenzyme complex plays a pivotal role in pH homeostasis of the plant endomembrane system and endocytic and secretory trafficking. Here, we review recent progress in comprehending the biochemical properties and physiological functions of plant V-ATPase and explore the topics that require further elucidation.
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Affiliation(s)
- Chao Wang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yun Xiang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Dong Qian
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
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Bott LC, Forouhan M, Lieto M, Sala AJ, Ellerington R, Johnson JO, Speciale AA, Criscuolo C, Filla A, Chitayat D, Alkhunaizi E, Shannon P, Nemeth AH, Angelucci F, Lim WF, Striano P, Zara F, Helbig I, Muona M, Courage C, Lehesjoki AE, Berkovic SF, Fischbeck KH, Brancati F, Morimoto RI, Wood MJA, Rinaldi C. Variants in ATP6V0A1 cause progressive myoclonus epilepsy and developmental and epileptic encephalopathy. Brain Commun 2021; 3:fcab245. [PMID: 34909687 PMCID: PMC8665645 DOI: 10.1093/braincomms/fcab245] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/05/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
The vacuolar H+-ATPase is a large multi-subunit proton pump, composed of an integral membrane V0 domain, involved in proton translocation, and a peripheral V1 domain, catalysing ATP hydrolysis. This complex is widely distributed on the membrane of various subcellular organelles, such as endosomes and lysosomes, and plays a critical role in cellular processes ranging from autophagy to protein trafficking and endocytosis. Variants in ATP6V0A1, the brain-enriched isoform in the V0 domain, have been recently associated with developmental delay and epilepsy in four individuals. Here, we identified 17 individuals from 14 unrelated families with both with new and previously characterized variants in this gene, representing the largest cohort to date. Five affected subjects with biallelic variants in this gene presented with a phenotype of early-onset progressive myoclonus epilepsy with ataxia, while 12 individuals carried de novo missense variants and showed severe developmental and epileptic encephalopathy. The R740Q mutation, which alone accounts for almost 50% of the mutations identified among our cases, leads to failure of lysosomal hydrolysis by directly impairing acidification of the endolysosomal compartment, causing autophagic dysfunction and severe developmental defect in Caenorhabditis elegans. Altogether, our findings further expand the neurological phenotype associated with variants in this gene and provide a direct link with endolysosomal acidification in the pathophysiology of ATP6V0A1-related conditions.
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Affiliation(s)
- Laura C Bott
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL 60208, USA
| | - Mitra Forouhan
- Department of Paediatrics, University of Oxford, Oxford OX1 3QX, UK
| | - Maria Lieto
- Department of Physiology, Anatomy and Genetics, Oxford OX1 3QX, UK
- Department of Neurosciences, Reproductive and Odontostomatological Sciences, Federico II University, Naples 80121, Italy
| | - Ambre J Sala
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL 60208, USA
| | - Ruth Ellerington
- Department of Paediatrics, University of Oxford, Oxford OX1 3QX, UK
| | - Janel O Johnson
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Chiara Criscuolo
- Department of Neurosciences, Reproductive and Odontostomatological Sciences, Federico II University, Naples 80121, Italy
| | - Alessandro Filla
- Department of Neurosciences, Reproductive and Odontostomatological Sciences, Federico II University, Naples 80121, Italy
| | - David Chitayat
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario M5G 1X8, Canada
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario M5G 1X5, Canada
| | - Ebba Alkhunaizi
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario M5G 1X8, Canada
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario M5G 1X5, Canada
| | - Patrick Shannon
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, University of Toronto, Toronto, Ontario M5G 1X5, Canada
| | - Andrea H Nemeth
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Francesco Angelucci
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 Coppito, L'Aquila, Italy
| | - Wooi Fang Lim
- Department of Paediatrics, University of Oxford, Oxford OX1 3QX, UK
| | - Pasquale Striano
- Institute for Research, Hospitalization and Health Care (IRCCS) "G. Gaslini" Institute, Genova 16147, Italy
| | - Federico Zara
- Institute for Research, Hospitalization and Health Care (IRCCS) "G. Gaslini" Institute, Genova 16147, Italy
| | - Ingo Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Mikko Muona
- Blueprint Genetics, 02150 Espoo, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, 00290, Finland
| | - Carolina Courage
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, 00290, Finland
| | - Anna-Elina Lehesjoki
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, 00290, Finland
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, Victoria 3010, Australia
| | - Kenneth H Fischbeck
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, MD 20892, USA
| | - Francesco Brancati
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 Coppito, L'Aquila, Italy
- IRCCS San Raffaele Pisana, 00163 Roma, Italy
| | - Richard I Morimoto
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL 60208, USA
| | - Matthew J A Wood
- Department of Paediatrics, University of Oxford, Oxford OX1 3QX, UK
- Oxford Harrington Rare Disease Centre, University of Oxford, Oxford OX1 3QX, UK
| | - Carlo Rinaldi
- Department of Paediatrics, University of Oxford, Oxford OX1 3QX, UK
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Knockdown of Vacuolar ATPase Subunit G Gene Affects Larval Survival and Impaired Pupation and Adult Emergence in Henosepilachna vigintioctopunctata. INSECTS 2021; 12:insects12100935. [PMID: 34680704 PMCID: PMC8538789 DOI: 10.3390/insects12100935] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 09/30/2021] [Accepted: 10/03/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary Vacuolar ATPase (vATPase), a proton pump driven by ATP hydrolysis, acts as a membrane energizer to motivate the movement of ions and nutrients across the cellular membrane in insect guts and Malpighian tubules, among others. The vATPase holoenzyme contains 16 subunits. Out of these subunits, mammalian G subunit includes three isoforms (G1-G3) which are encoded by three distinctive genes. The physiological role of a specific G isoform can be compensated by others. Thus, current experimental evidence on the in vivo function of G is rather limited among eight V1 subunits. In the present paper, particular attention was paid to an insect model, Henosepilachna vigintioctopunctata ladybird, a serious defoliator of Solanaceae and Cucurbitaceae plants in many Asian countries. Given that the beetle is sensitive to RNA interference (RNAi), HvvATPaseG gene was knocked down by ingestion of its corresponding dsRNA at the fourth-instar larval stage. Silence of HvvATPaseG affected larval growth and survival, impaired pupation and adult emergence. Our results provide a basis for further functional research on the vATPase G subunit in insects and suggest new ideas for the management of H. vigintioctopunctata. Abstract The vATPase holoenzyme consists of two functional subcomplexes, the cytoplasmic (peripheral) V1 and the membrane-embedded V0. Both V1 and V0 sectors contain eight subunits, with stoichiometry of A3B3CDE3FG3H in V1 and ac8c’c”def(Voa1p) in V0 respectively. However, the function of G subunit has not been characterized in any non-Drosophilid insect species. In the present paper, we uncovered that HvvATPaseG was actively transcribed from embryo to adult in a Coleopteran pest Henosepilachna vigintioctopunctata. Its mRNA levels peaked in larval hindgut and Malpighian tubules. RNA interference (RNAi)-mediated knockdown of HvvATPaseG significantly reduced larval feeding, affected chitin biosynthesis, destroyed midgut integrity, damaged midgut peritrophic membrane, and retarded larval growth. The function of Malpighian tubules was damaged, the contents of glucose, trehalose, lipid, total soluble amino acids and protein were lowered and the fat bodies were lessened in the HvvATPaseG RNAi larvae, compared with those in the PBS- and dsegfp-fed beetles. In contrast, the amount of glycogen was dramatically increased in the HvvATPaseG depletion ladybirds. As a result, the development was arrested, pupation was inhibited and adult emergence was impaired in the HvvATPaseG hypomorphs. Our results demonstrated that G subunit plays a critical role during larval development in H. vigintioctopunctata.
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Poor Person's pH Simulation of Membrane Proteins. Methods Mol Biol 2021. [PMID: 34302678 DOI: 10.1007/978-1-0716-1468-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
pH conditions are central to the functioning of all biomolecules. However, implications of pH changes are nontrivial on a molecular scale. Though a rigorous microscopic definition of pH exists, its implementation in classical molecular dynamics (MD) simulations is cumbersome, and more so in large integral membrane systems. In this chapter, an integrative pipeline is described that combines Multi-Conformation Continuum Electrostatics (MCCE) computations with MD simulations to capture the effect of transient protonation states on the coupled conformational changes in transmembrane proteins. The core methodologies are explained, and all the software required to set up this pipeline are outlined with their key parameters. All associated analyses of structure and function are provided using two case studies, namely those of bioenergetic complexes: NADH dehydrogenase (complex I) and Vo domain of V-type ATPase. The hybrid MCCE-MD pipeline has allowed the discovery of hydrogen bond networks, ligand binding pathways, and disease-causing mutations.
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Jaskolka MC, Winkley SR, Kane PM. RAVE and Rabconnectin-3 Complexes as Signal Dependent Regulators of Organelle Acidification. Front Cell Dev Biol 2021; 9:698190. [PMID: 34249946 PMCID: PMC8264551 DOI: 10.3389/fcell.2021.698190] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/28/2021] [Indexed: 12/12/2022] Open
Abstract
The yeast RAVE (Regulator of H+-ATPase of Vacuolar and Endosomal membranes) complex and Rabconnectin-3 complexes of higher eukaryotes regulate acidification of organelles such as lysosomes and endosomes by catalyzing V-ATPase assembly. V-ATPases are highly conserved proton pumps consisting of a peripheral V1 subcomplex that contains the sites of ATP hydrolysis, attached to an integral membrane Vo subcomplex that forms the transmembrane proton pore. Reversible disassembly of the V-ATPase is a conserved regulatory mechanism that occurs in response to multiple signals, serving to tune ATPase activity and compartment acidification to changing extracellular conditions. Signals such as glucose deprivation can induce release of V1 from Vo, which inhibits both ATPase activity and proton transport. Reassembly of V1 with Vo restores ATP-driven proton transport, but requires assistance of the RAVE or Rabconnectin-3 complexes. Glucose deprivation triggers V-ATPase disassembly in yeast and is accompanied by binding of RAVE to V1 subcomplexes. Upon glucose readdition, RAVE catalyzes both recruitment of V1 to the vacuolar membrane and its reassembly with Vo. The RAVE complex can be recruited to the vacuolar membrane by glucose in the absence of V1 subunits, indicating that the interaction between RAVE and the Vo membrane domain is glucose-sensitive. Yeast RAVE complexes also distinguish between organelle-specific isoforms of the Vo a-subunit and thus regulate distinct V-ATPase subpopulations. Rabconnectin-3 complexes in higher eukaryotes appear to be functionally equivalent to yeast RAVE. Originally isolated as a two-subunit complex from rat brain, the Rabconnectin-3 complex has regions of homology with yeast RAVE and was shown to interact with V-ATPase subunits and promote endosomal acidification. Current understanding of the structure and function of RAVE and Rabconnectin-3 complexes, their interactions with the V-ATPase, their role in signal-dependent modulation of organelle acidification, and their impact on downstream pathways will be discussed.
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Affiliation(s)
- Michael C Jaskolka
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Samuel R Winkley
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Patricia M Kane
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States
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Jaskolka MC, Tarsio M, Smardon AM, Khan MM, Kane PM. Defining steps in RAVE-catalyzed V-ATPase assembly using purified RAVE and V-ATPase subcomplexes. J Biol Chem 2021; 296:100703. [PMID: 33895134 PMCID: PMC8138766 DOI: 10.1016/j.jbc.2021.100703] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 12/30/2022] Open
Abstract
The vacuolar H+-ATPase (V-ATPase) is a highly conserved proton pump responsible for the acidification of intracellular organelles in virtually all eukaryotic cells. V-ATPases are regulated by the rapid and reversible disassembly of the peripheral V1 domain from the integral membrane Vo domain, accompanied by release of the V1 C subunit from both domains. Efficient reassembly of V-ATPases requires the Regulator of the H+-ATPase of Vacuoles and Endosomes (RAVE) complex in yeast. Although a number of pairwise interactions between RAVE and V-ATPase subunits have been mapped, the low endogenous levels of the RAVE complex and lethality of constitutive RAV1 overexpression have hindered biochemical characterization of the intact RAVE complex. We describe a novel inducible overexpression system that allows purification of native RAVE and RAVE–V1 complexes. Both purified RAVE and RAVE–V1 contain substoichiometric levels of subunit C. RAVE–V1 binds tightly to expressed subunit C in vitro, but binding of subunit C to RAVE alone is weak. Neither RAVE nor RAVE–V1 interacts with the N-terminal domain of Vo subunit Vph1 in vitro. RAVE–V1 complexes, like isolated V1, have no MgATPase activity, suggesting that RAVE cannot reverse V1 inhibition generated by rotation of subunit H and entrapment of MgADP that occur upon disassembly. However, purified RAVE can accelerate reassembly of V1 carrying a mutant subunit H incapable of inhibition with Vo complexes reconstituted into lipid nanodiscs, consistent with its catalytic activity in vivo. These results provide new insights into the possible order of events in V-ATPase reassembly and the roles of the RAVE complex in each event.
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Affiliation(s)
- Michael C Jaskolka
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Maureen Tarsio
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Anne M Smardon
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Md Murad Khan
- 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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Amphipathic environments for determining the structure of membrane proteins by single-particle electron cryo-microscopy. Q Rev Biophys 2021; 54:e6. [PMID: 33785082 DOI: 10.1017/s0033583521000044] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the past decade, the structural biology of membrane proteins (MPs) has taken a new turn thanks to epoch-making technical progress in single-particle electron cryo-microscopy (cryo-EM) as well as to improvements in sample preparation. The present analysis provides an overview of the extent and modes of usage of the various types of surfactants for cryo-EM studies. Digitonin, dodecylmaltoside, protein-based nanodiscs, lauryl maltoside-neopentyl glycol, glyco-diosgenin, and amphipols (APols) are the most popular surfactants at the vitrification step. Surfactant exchange is frequently used between MP purification and grid preparation, requiring extensive optimization each time the study of a new MP is undertaken. The variety of both the surfactants and experimental approaches used over the past few years bears witness to the need to continue developing innovative surfactants and optimizing conditions for sample preparation. The possibilities offered by novel APols for EM applications are discussed.
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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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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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40
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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.
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41
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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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42
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Shelby M, Gilbile D, Grant T, Bauer W, Segelke B, He W, Evans A, Crespo N, Fischer P, Pakendorf T, Hennicke V, Hunter M, Batyuk A, Barthelmess M, Meents A, Kuhl T, Frank M, Coleman M. Crystallization of ApoA1 and ApoE4 nanolipoprotein particles and initial XFEL-based structural studies. CRYSTALS 2020; 10. [PMID: 35686136 PMCID: PMC9175823 DOI: 10.3390/cryst10100886] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nanolipoprotein particles (NLPs), also called “nanodiscs”, are discoidal particles with a patch of lipid bilayer corralled by apolipoproteins. NLPs have long been of interest due to both their utility as membrane-model systems into which membrane proteins can be inserted and solubilized and their physiological role in lipid and cholesterol transport via HDL and LDL maturation, which are important for human health. Serial femtosecond crystallography (SFX) at X-ray free electron lasers (XFELs) is a powerful approach for structural biology of membrane proteins, which are traditionally difficult to crystallize as large single crystals capable of producing high-quality diffraction suitable for structure determination. To facilitate understanding of the specific role of two apolipoprotein/lipid complexes, ApoA1 and ApoE4, in lipid binding and HDL/LDL particle maturation dynamics and develop new SFX methods involving NLP membrane protein encapsulation, we have prepared and crystallized homogeneous populations of ApoA1 and ApoE4 NLPs. Crystallization of empty NLPs yields semi-ordered objects that appear crystalline and give highly anisotropic and diffuse X-ray diffraction, similar in characteristics to fiber diffraction. Several unit cell parameters were approximately determined for both NLPs from these measurements. Thus, low-background, sample conservative methods of delivery are critical. Here we implemented a fixed target sample delivery scheme utilizing the Roadrunner fast-scanning system and ultra-thin polymer/graphene support films, providing a low-volume, low-background approach to membrane protein SFX. This study represents initial steps in obtaining structural information for ApoA1 and ApoE4 NLPs and developing this system as a supporting scaffold for future structural studies of membrane proteins crystalized in a native lipid environment.
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Affiliation(s)
- M.L. Shelby
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - D. Gilbile
- Department of Chemical Engineering, University of California at Davis, Davis, CA, USA
| | - T.D. Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY, USA
- Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA
| | - W.J. Bauer
- Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA
| | - B. Segelke
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - W. He
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - A.C. Evans
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Department of Chemical Engineering, University of California at Davis, Davis, CA, USA
| | - N. Crespo
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY, USA
- Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA
| | - P. Fischer
- Center for Free-Electron Laser Science, Hamburg, Germany
| | - T. Pakendorf
- Center for Free-Electron Laser Science, Hamburg, Germany
| | - V. Hennicke
- Center for Free-Electron Laser Science, Hamburg, Germany
| | - M.S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - A. Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - M. Barthelmess
- Center for Free-Electron Laser Science, Hamburg, Germany
| | - A. Meents
- Center for Free-Electron Laser Science, Hamburg, Germany
| | - T.L. Kuhl
- Department of Chemical Engineering, University of California at Davis, Davis, CA, USA
| | - M. Frank
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Department of Chemical Engineering, University of California at Davis, Davis, CA, USA
- Correspondence: ; Tel: +1-925-423-7687 or ; Tel: 1-925-423-5068
| | - M.A. Coleman
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Department of Chemical Engineering, University of California at Davis, Davis, CA, USA
- Correspondence: ; Tel: +1-925-423-7687 or ; Tel: 1-925-423-5068
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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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44
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Cryo-EM structure of the entire mammalian F-type ATP synthase. Nat Struct Mol Biol 2020; 27:1077-1085. [DOI: 10.1038/s41594-020-0503-8] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/06/2020] [Indexed: 02/07/2023]
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45
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Recurrent sequence evolution after independent gene duplication. BMC Evol Biol 2020; 20:98. [PMID: 32770961 PMCID: PMC7414715 DOI: 10.1186/s12862-020-01660-1] [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: 01/17/2020] [Accepted: 07/17/2020] [Indexed: 11/10/2022] Open
Abstract
Background Convergent and parallel evolution provide unique insights into the mechanisms of natural selection. Some of the most striking convergent and parallel (collectively recurrent) amino acid substitutions in proteins are adaptive, but there are also many that are selectively neutral. Accordingly, genome-wide assessment has shown that recurrent sequence evolution in orthologs is chiefly explained by nearly neutral evolution. For paralogs, more frequent functional change is expected because additional copies are generally not retained if they do not acquire their own niche. Yet, it is unknown to what extent recurrent sequence differentiation is discernible after independent gene duplications in different eukaryotic taxa. Results We develop a framework that detects patterns of recurrent sequence evolution in duplicated genes. This is used to analyze the genomes of 90 diverse eukaryotes. We find a remarkable number of families with a potentially predictable functional differentiation following gene duplication. In some protein families, more than ten independent duplications show a similar sequence-level differentiation between paralogs. Based on further analysis, the sequence divergence is found to be generally asymmetric. Moreover, about 6% of the recurrent sequence evolution between paralog pairs can be attributed to recurrent differentiation of subcellular localization. Finally, we reveal the specific recurrent patterns for the gene families Hint1/Hint2, Sco1/Sco2 and vma11/vma3. Conclusions The presented methodology provides a means to study the biochemical underpinning of functional differentiation between paralogs. For instance, two abundantly repeated substitutions are identified between independently derived Sco1 and Sco2 paralogs. Such identified substitutions allow direct experimental testing of the biological role of these residues for the repeated functional differentiation. We also uncover a diverse set of families with recurrent sequence evolution and reveal trends in the functional and evolutionary trajectories of this hitherto understudied phenomenon.
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46
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Krah A, Marzinek JK, Bond PJ. Characterizing the Hydration Properties of Proton Binding Sites in the ATP Synthase c-Rings of Bacillus Species. J Phys Chem B 2020; 124:7176-7183. [PMID: 32687713 DOI: 10.1021/acs.jpcb.0c03896] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The membrane-embedded domain of ATP synthases contains the c-ring, which translocates ions across the membrane, and its resultant rotation is coupled to ATP synthesis in the extramembranous domain. During rotation, the c-ring becomes accessible on both sides of the lipid bilayer to solvent via channels connected to the other membrane-embedded component, the a subunit, and thereby allows the ion to be released into the solvent environment. In recent times, many experimental structures of c-rings from different species have been solved. In some of these, a water molecule with a proposed "structural role" has been identified within the c-ring ion binding site, but in general, the requirement for high resolution to resolve specific water densities complicates their interpretation. In the present study, we use molecular dynamics (MD) simulations and rigorous free energy calculations to characterize the dynamics and energetics of a water molecule within the ion binding site of the c-ring from Bacillus pseudofirmus OF4, in its wild type (WT) and P51A mutant forms, along with the c-ring from thermophilic Bacillus PS3. Our data suggest that a water molecule stably binds to the P51A mutant, as well as helping to identify a bound water molecule in Bacillus PS3 whose presence was previously overlooked due to the limited resolution of the structural data. Sequence analysis further identifies a novel conserved sequence motif that is likely required to harbor a water molecule for stable ion coordination in the binding site of such proteins.
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Affiliation(s)
- Alexander Krah
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Jan K Marzinek
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Peter J Bond
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
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47
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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.
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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.
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48
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Krah A, Huber RG, McMillan DGG, Bond PJ. The Molecular Basis for Purine Binding Selectivity in the Bacterial ATP Synthase ϵ Subunit. Chembiochem 2020; 21:3249-3254. [PMID: 32608105 DOI: 10.1002/cbic.202000291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/30/2020] [Indexed: 12/21/2022]
Abstract
The ϵ subunit of ATP synthases has been proposed to regulate ATP hydrolysis in bacteria. Prevailing evidence supports the notion that when the ATP concentration falls below a certain threshold, the ϵ subunit changes its conformation from a non-inhibitory down-state to an extended up-state that then inhibits enzymatic ATP hydrolysis by binding to the catalytic domain. It has been demonstrated that the ϵ subunit from Bacillus PS3 is selective for ATP over other nucleotides, including GTP. In this study, the purine triphosphate selectivity is rationalized by using results from MD simulations and free energy calculations for the R103A/R115A mutant of the ϵ subunit from Bacillus PS3, which binds ATP more strongly than the wild-type protein. Our results are in good agreement with experimental data, and the elucidated molecular basis for selectivity could help to guide the design of novel GTP sensors.
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Affiliation(s)
- Alexander Krah
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Str. #07-01 Matrix, Singapore, 138671, Singapore.,Korea Institute for Advanced Study, School of Computational Sciences, 85 Hoegiro, Dongdaemun-gu, Seoul, 02455, Republic of Korea
| | - Roland G Huber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Str. #07-01 Matrix, Singapore, 138671, Singapore
| | - Duncan G G McMillan
- Delft University of Technology, Department of Biotechnology, Van der Maasweg 9, Delft, 2629HZ, The Netherlands
| | - Peter J Bond
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Str. #07-01 Matrix, Singapore, 138671, Singapore.,National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore, 117543, Singapore
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49
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Wang Y, Zhang L, Wei Y, Huang W, Li L, Wu AA, Dastur A, Greninger P, Bray WM, Zhang CS, Li M, Lian W, Hu Z, Wang X, Liu G, Yao L, Guh JH, Chen L, Wang HR, Zhou D, Lin SC, Xu Q, Shen Y, Zhang J, Jurica MS, Benes CH, Deng X. Pharmacological Targeting of Vacuolar H +-ATPase via Subunit V1G Combats Multidrug-Resistant Cancer. Cell Chem Biol 2020; 27:1359-1370.e8. [PMID: 32649904 DOI: 10.1016/j.chembiol.2020.06.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/03/2020] [Accepted: 06/15/2020] [Indexed: 12/13/2022]
Abstract
Multidrug resistance (MDR) in cancer remains a major challenge for the success of chemotherapy. Natural products have been a rich source for the discovery of drugs against MDR cancers. Here, we applied high-throughput cytotoxicity screening of an in-house natural product library against MDR SGC7901/VCR cells and identified that the cyclodepsipeptide verucopeptin demonstrated notable antitumor potency. Cytological profiling combined with click chemistry-based proteomics revealed that ATP6V1G directly interacted with verucopeptin. ATP6V1G, a subunit of the vacuolar H+-ATPase (v-ATPase) that has not been previously targeted, was essential for SGC7901/VCR cell growth. Verucopeptin exhibited strong inhibition of both v-ATPase activity and mTORC1 signaling, leading to substantial pharmacological efficacy against SGC7901/VCR cell proliferation and tumor growth in vivo. Our results demonstrate that targeting v-ATPase via its V1G subunit constitutes a unique approach for modulating v-ATPase and mTORC1 signaling with great potential for the development of therapeutics against MDR cancers.
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MESH Headings
- Animals
- Antineoplastic Agents/chemical synthesis
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacology
- Biological Products/chemical synthesis
- Biological Products/chemistry
- Biological Products/pharmacology
- Cell Line, Tumor
- Cell Proliferation/drug effects
- Cell Survival/drug effects
- Cells, Cultured
- Depsipeptides/chemical synthesis
- Depsipeptides/chemistry
- Depsipeptides/pharmacology
- Drug Resistance, Multiple/drug effects
- Drug Resistance, Neoplasm/drug effects
- Drug Screening Assays, Antitumor
- Female
- Humans
- Male
- Mechanistic Target of Rapamycin Complex 1/antagonists & inhibitors
- Mechanistic Target of Rapamycin Complex 1/metabolism
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- Neoplasms, Experimental/drug therapy
- Neoplasms, Experimental/metabolism
- Neoplasms, Experimental/pathology
- Protein Subunits/drug effects
- Proteomics
- Vacuolar Proton-Translocating ATPases/antagonists & inhibitors
- Vacuolar Proton-Translocating ATPases/metabolism
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Affiliation(s)
- Yuezhou Wang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, Xiamen University, Xiamen, Fujian 361102, China
| | - Lei Zhang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, Xiamen University, Xiamen, Fujian 361102, China
| | - Yanling Wei
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, Xiamen University, Xiamen, Fujian 361102, China
| | - Wei Huang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, Xiamen University, Xiamen, Fujian 361102, China
| | - Li Li
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, Xiamen University, Xiamen, Fujian 361102, China
| | - An-An Wu
- State Key Laboratory for Physical Chemistry of Solid Surface, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian, China
| | - Anahita Dastur
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Patricia Greninger
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Walter M Bray
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Chen-Song Zhang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, Xiamen University, Xiamen, Fujian 361102, China
| | - Mengqi Li
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, Xiamen University, Xiamen, Fujian 361102, China
| | - Wenhua Lian
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, Xiamen University, Xiamen, Fujian 361102, China
| | - Zhiyu Hu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, Xiamen University, Xiamen, Fujian 361102, China
| | - Xiaoyong Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Gang Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Luming Yao
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, Xiamen University, Xiamen, Fujian 361102, China
| | - Jih-Hwa Guh
- School of Pharmacy, National Taiwan University, Taipei, Taiwan
| | - Lanfen Chen
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, Xiamen University, Xiamen, Fujian 361102, China
| | - Hong-Rui Wang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, Xiamen University, Xiamen, Fujian 361102, China
| | - Dawang Zhou
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, Xiamen University, Xiamen, Fujian 361102, China
| | - Sheng-Cai Lin
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, Xiamen University, Xiamen, Fujian 361102, China
| | - Qingyan Xu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, Xiamen University, Xiamen, Fujian 361102, China
| | - Yuemao Shen
- School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250012, China
| | - Jianming Zhang
- National Translational Research Center Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025 China
| | - Melissa S Jurica
- Department of Molecular Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064, USA
| | - Cyril H Benes
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Xianming Deng
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, Xiamen University, Xiamen, Fujian 361102, China.
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50
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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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