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Wilkens S, Khan MM, Knight K, Oot RA. Tender love and disassembly: How a TLDc domain protein breaks the V-ATPase. Bioessays 2023: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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [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, New York, USA
| | - Md Murad Khan
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Kassidy Knight
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Rebecca A Oot
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
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2
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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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Mazhab-Jafari MT, Rubinstein JL. Cryo-EM studies of the structure and dynamics of vacuolar-type ATPases. SCIENCE ADVANCES 2016; 2:e1600725. [PMID: 27532044 PMCID: PMC4985227 DOI: 10.1126/sciadv.1600725] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/15/2016] [Indexed: 06/06/2023]
Abstract
Electron cryomicroscopy (cryo-EM) has significantly advanced our understanding of molecular structure in biology. Recent innovations in both hardware and software have made cryo-EM a viable alternative for targets that are not amenable to x-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. Cryo-EM has even become the method of choice in some situations where x-ray crystallography and NMR spectroscopy are possible but where cryo-EM can determine structures at higher resolution or with less time or effort. Rotary adenosine triphosphatases (ATPases) are crucial to the maintenance of cellular homeostasis. These enzymes couple the synthesis or hydrolysis of adenosine triphosphate to the use or production of a transmembrane electrochemical ion gradient, respectively. However, the membrane-embedded nature and conformational heterogeneity of intact rotary ATPases have prevented their high-resolution structural analysis to date. Recent application of cryo-EM methods to the different types of rotary ATPase has led to sudden advances in understanding the structure and function of these enzymes, revealing significant conformational heterogeneity and characteristic transmembrane α helices that are highly tilted with respect to the membrane. In this Review, we will discuss what has been learned recently about rotary ATPase structure and function, with a particular focus on the vacuolar-type ATPases.
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Affiliation(s)
- Mohammad T. Mazhab-Jafari
- Molecular Structure and Function Program, The Hospital for Sick Children Research Institute, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada
| | - John L. Rubinstein
- Molecular Structure and Function Program, The Hospital for Sick Children Research Institute, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada
- Department of Biochemistry, The University of Toronto, 1 King’s College Circle, Toronto, Ontario M5S 1A8, Canada
- Department of Medical Biophysics, The University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
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Singh D, Sielaff H, Sundararaman L, Bhushan S, Grüber G. The stimulating role of subunit F in ATPase activity inside the A1-complex of the Methanosarcina mazei Gö1 A1AO ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:177-187. [PMID: 26682760 DOI: 10.1016/j.bbabio.2015.12.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 11/19/2015] [Accepted: 12/03/2015] [Indexed: 10/22/2022]
Abstract
A1AO ATP synthases couple ion-transport of the AO sector and ATP synthesis/hydrolysis of the A3B3-headpiece via their stalk subunits D and F. Here, we produced and purified stable A3B3D- and A3B3DF-complexes of the Methanosarcina mazei Gö1 A-ATP synthase as confirmed by electron microscopy. Enzymatic studies with these complexes showed that the M. mazei Gö1 A-ATP synthase subunit F is an ATPase activating subunit. The maximum ATP hydrolysis rates (Vmax) of A3B3D and A3B3DF were determined by substrate-dependent ATP hydrolysis experiments resulting in a Vmax of 7.9 s(-1) and 30.4 s(-1), respectively, while the KM is the same for both. Deletions of the N- or C-termini of subunit F abolished the effect of ATP hydrolysis activation. We generated subunit F mutant proteins with single amino acid substitutions and demonstrated that the subunit F residues S84 and R88 are important in stimulating ATP hydrolysis. Hybrid formation of the A3B3D-complex with subunit F of the related eukaryotic V-ATPase of Saccharomyces cerevisiae or subunit ε of the F-ATP synthase from Mycobacterium tuberculosis showed that subunit F of the archaea and eukaryotic enzymes are important in ATP hydrolysis.
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Affiliation(s)
- Dhirendra Singh
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Hendrik Sielaff
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Lavanya Sundararaman
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Shashi Bhushan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore.
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Balakrishna AM, Manimekalai MSS, Grüber G. Protein-protein interactions within the ensemble, eukaryotic V-ATPase, and its concerted interactions with cellular machineries. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:84-93. [PMID: 26033199 DOI: 10.1016/j.pbiomolbio.2015.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 05/27/2015] [Accepted: 05/28/2015] [Indexed: 11/27/2022]
Abstract
The V1VO-ATPase (V-ATPase) is the important proton-pump in eukaryotic cells, responsible for pH-homeostasis, pH-sensing and amino acid sensing, and therefore essential for cell growths and metabolism. ATP-cleavage in the catalytic A3B3-hexamer of V1 has to be communicated via several so-called central and peripheral stalk units to the proton-pumping VO-part, which is membrane-embedded. A unique feature of V1VO-ATPase regulation is its reversible disassembly of the V1 and VO domain. Actin provides a network to hold the V1 in proximity to the VO, enabling effective V1VO-assembly to occur. Besides binding to actin, the 14-subunit V-ATPase interacts with multi-subunit machineries to form cellular sensors, which regulate the pH in cellular compartments or amino acid signaling in lysosomes. Here we describe a variety of subunit-subunit interactions within the V-ATPase enzyme during catalysis and its protein-protein assembling with key cellular machineries, essential for cellular function.
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Affiliation(s)
- Asha Manikkoth Balakrishna
- Nanyang Technological University, Division of Structural Biology and Biochemistry, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Malathy Sony Subramanian Manimekalai
- Nanyang Technological University, Division of Structural Biology and Biochemistry, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Gerhard Grüber
- Nanyang Technological University, Division of Structural Biology and Biochemistry, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore.
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Balakrishna AM, Basak S, Manimekalai MSS, Grüber G. Crystal structure of subunits D and F in complex gives insight into energy transmission of the eukaryotic V-ATPase from Saccharomyces cerevisiae. J Biol Chem 2015; 290:3183-96. [PMID: 25505269 PMCID: PMC4318993 DOI: 10.1074/jbc.m114.622688] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 11/26/2014] [Indexed: 11/06/2022] Open
Abstract
Eukaryotic V1VO-ATPases hydrolyze ATP in the V1 domain coupled to ion pumping in VO. A unique mode of regulation of V-ATPases is the reversible disassembly of V1 and VO, which reduces ATPase activity and causes silencing of ion conduction. The subunits D and F are proposed to be key in these enzymatic processes. Here, we describe the structures of two conformations of the subunit DF assembly of Saccharomyces cerevisiae (ScDF) V-ATPase at 3.1 Å resolution. Subunit D (ScD) consists of a long pair of α-helices connected by a short helix ((79)IGYQVQE(85)) as well as a β-hairpin region, which is flanked by two flexible loops. The long pair of helices is composed of the N-terminal α-helix and the C-terminal helix, showing structural alterations in the two ScDF structures. The entire subunit F (ScF) consists of an N-terminal domain of four β-strands (β1-β4) connected by four α-helices (α1-α4). α1 and β2 are connected via the loop (26)GQITPETQEK(35), which is unique in eukaryotic V-ATPases. Adjacent to the N-terminal domain is a flexible loop, followed by a C-terminal α-helix (α5). A perpendicular and extended conformation of helix α5 was observed in the two crystal structures and in solution x-ray scattering experiments, respectively. Fitted into the nucleotide-bound A3B3 structure of the related A-ATP synthase from Enterococcus hirae, the arrangements of the ScDF molecules reflect their central function in ATPase-coupled ion conduction. Furthermore, the flexibility of the terminal helices of both subunits as well as the loop (26)GQITPETQEK(35) provides information about the regulatory step of reversible V1VO disassembly.
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Affiliation(s)
- Asha Manikkoth Balakrishna
- From the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Sandip Basak
- From the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | | | - Gerhard Grüber
- From the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
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Shibata H, Tsuchikawa H, Hayashi T, Matsumori N, Murata M, Usui T. Modification of Bafilomycin Structure to Efficiently Synthesize Solid-State NMR Probes that Selectively Bind to Vacuolar-Type ATPase. Chem Asian J 2015; 10:915-24. [DOI: 10.1002/asia.201403299] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Indexed: 01/05/2023]
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Marshansky V, Rubinstein JL, Grüber G. Eukaryotic V-ATPase: novel structural findings and functional insights. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:857-79. [PMID: 24508215 DOI: 10.1016/j.bbabio.2014.01.018] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Revised: 12/25/2013] [Accepted: 01/27/2014] [Indexed: 02/06/2023]
Abstract
The eukaryotic V-type adenosine triphosphatase (V-ATPase) is a multi-subunit membrane protein complex that is evolutionarily related to F-type adenosine triphosphate (ATP) synthases and A-ATP synthases. These ATPases/ATP synthases are functionally conserved and operate as rotary proton-pumping nano-motors, invented by Nature billions of years ago. In the first part of this review we will focus on recent structural findings of eukaryotic V-ATPases and discuss the role of different subunits in the function of the V-ATPase holocomplex. Despite structural and functional similarities between rotary ATPases, the eukaryotic V-ATPases are the most complex enzymes that have acquired some unconventional cellular functions during evolution. In particular, the novel roles of V-ATPases in the regulation of cellular receptors and their trafficking via endocytotic and exocytotic pathways were recently uncovered. In the second part of this review we will discuss these unique roles of V-ATPases in modulation of function of cellular receptors, involved in the development and progression of diseases such as cancer and diabetes as well as neurodegenerative and kidney disorders. Moreover, it was recently revealed that the V-ATPase itself functions as an evolutionarily conserved pH sensor and receptor for cytohesin-2/Arf-family GTP-binding proteins. Thus, in the third part of the review we will evaluate the structural basis for and functional insights into this novel concept, followed by the analysis of the potentially essential role of V-ATPase in the regulation of this signaling pathway in health and disease. Finally, future prospects for structural and functional studies of the eukaryotic V-ATPase will be discussed.
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Affiliation(s)
- Vladimir Marshansky
- Center for Systems Biology, Program in Membrane Biology, Division of Nephrology, Simches Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA; Kadmon Pharmaceuticals Corporation, Alexandria Center for Life Science, 450 East 29th Street, New York, NY 10016, USA.
| | - John L Rubinstein
- Molecular Structure and Function Program, The Hospital for Sick Children Research Institute, University of Toronto, Toronto, ON M5G 1X8, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5G 1X8, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Gerhard Grüber
- Nanyang Technological University, Division of Structural Biology and Biochemistry, School of Biological Sciences, Singapore 637551, Republic of Singapore; Bioinformatics Institute, A(⁎)STAR, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
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