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Krah A, Ragunathan P, Bond PJ, Grüber G. Variations of the Mycobacterium abscessus F-ATP synthase subunit a-c interface alter binding and potency of the anti-TB drug bedaquiline. Biochem Biophys Res Commun 2024; 690:149249. [PMID: 38000294 DOI: 10.1016/j.bbrc.2023.149249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023]
Abstract
The anti-tuberculosis therapeutic bedaquiline (BDQ) is used against Mycobacterium abscessus. In M. abscessus BDQ is only bacteriostatic and less potent compared to M. tuberculosis or M. smegmatis. Here we demonstrate its reduced ATP synthesis inhibition against M. abscessus inside-out vesicles, including the F1FO-ATP synthase. Molecular dynamics simulations and binding free energy calculations highlight the differences in drug-binding of the M. abscessus and M. smegmatis FO-domain at the lagging site, where the drug deploys its mechanistic action, inhibiting ATP synthesis. These data pave the way for improved anti-M. abscessus BDQ analogs.
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Affiliation(s)
- Alexander Krah
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, 138671, Singapore.
| | - Priya Ragunathan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Peter J Bond
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, 138671, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore.
| | - Gerhard Grüber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, 138671, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.
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2
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Ragunathan P, Shuyi Ng P, Singh S, Poh WH, Litty D, Kalia NP, Larsson S, Harikishore A, Rice SA, Ingham PW, Müller V, Moraski G, Miller MJ, Dick T, Pethe K, Grüber G. GaMF1.39's antibiotic efficacy and its enhanced antitubercular activity in combination with clofazimine, Telacebec, ND-011992, or TBAJ-876. Microbiol Spectr 2023; 11:e0228223. [PMID: 37982630 PMCID: PMC10715162 DOI: 10.1128/spectrum.02282-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 10/12/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE New drugs are needed to combat multidrug-resistant tuberculosis. The electron transport chain (ETC) maintains the electrochemical potential across the cytoplasmic membrane and allows the production of ATP, the energy currency of any living cell. The mycobacterial engine F-ATP synthase catalyzes the formation of ATP and has come into focus as an attractive and rich drug target. Recent deep insights into these mycobacterial F1FO-ATP synthase elements opened the door for a renaissance of structure-based target identification and inhibitor design. In this study, we present the GaMF1.39 antimycobacterial compound, targeting the rotary subunit γ of the biological engine. The compound is bactericidal, inhibits infection ex vivo, and displays enhanced anti-tuberculosis activity in combination with ETC inhibitors, which promises new strategies to shorten tuberculosis chemotherapy.
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Affiliation(s)
- Priya Ragunathan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Pearly Shuyi Ng
- Experimental Drug Development Centre, Agency for Science, Technology and Research, Singapore, Singapore
| | - Samsher Singh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building, Singapore, Singapore
| | - Wee Han Poh
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Dennis Litty
- Molecular Microbiology and Bioenergetics, Institute for Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Frankfurt, Germany
| | - Nitin Pal Kalia
- Department of Biological Sciences (Pharmacology & Toxicology), National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Simon Larsson
- Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building, Singapore, Singapore
| | - Amaravadhi Harikishore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
| | - Scott A. Rice
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Philip W. Ingham
- Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building, Singapore, Singapore
| | - Volker Müller
- Molecular Microbiology and Bioenergetics, Institute for Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Frankfurt, Germany
| | - Garrett Moraski
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Marvin J. Miller
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
- Department of Microbiology and Immunology, Georgetown University, Washington, DC, USA
| | - Kevin Pethe
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building, Singapore, Singapore
- National Centre for Infectious Diseases (NCID), Jalan Tan Tock Seng, Singapore, Singapore
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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3
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Nikiforova AB, Baburina YL, Borisova MP, Surin AK, Kharechkina ES, Krestinina OV, Suvorina MY, Kruglova SA, Kruglov AG. Mitochondrial F-ATP Synthase Co-Migrating Proteins and Ca 2+-Dependent Formation of Large Channels. Cells 2023; 12:2414. [PMID: 37830628 PMCID: PMC10572550 DOI: 10.3390/cells12192414] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/18/2023] [Accepted: 10/02/2023] [Indexed: 10/14/2023] Open
Abstract
Monomers, dimers, and individual FOF1-ATP synthase subunits are, presumably, involved in the formation of the mitochondrial permeability transition pore (PTP), whose molecular structure, however, is still unknown. We hypothesized that, during the Ca2+-dependent assembly of a PTP complex, the F-ATP synthase (subunits) recruits mitochondrial proteins that do not interact or weakly interact with the F-ATP synthase under normal conditions. Therefore, we examined whether the PTP opening in mitochondria before the separation of supercomplexes via BN-PAGE will increase the channel stability and channel-forming capacity of isolated F-ATP synthase dimers and monomers in planar lipid membranes. Additionally, we studied the specific activity and the protein composition of F-ATP synthase dimers and monomers from rat liver and heart mitochondria before and after PTP opening. Against our expectations, preliminary PTP opening dramatically suppressed the high-conductance channel activity of F-ATP synthase dimers and monomers and decreased their specific "in-gel" activity. The decline in the channel-forming activity correlated with the reduced levels of as few as two proteins in the bands: methylmalonate-semialdehyde dehydrogenase and prohibitin 2. These results indicate that proteins co-migrating with the F-ATP synthase may be important players in PTP formation and stabilization.
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Affiliation(s)
- Anna B. Nikiforova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Institutskaya 3, 142290 Pushchino, Russia; (A.B.N.); (Y.L.B.); (M.P.B.); (E.S.K.); (O.V.K.)
| | - Yulia L. Baburina
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Institutskaya 3, 142290 Pushchino, Russia; (A.B.N.); (Y.L.B.); (M.P.B.); (E.S.K.); (O.V.K.)
| | - Marina P. Borisova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Institutskaya 3, 142290 Pushchino, Russia; (A.B.N.); (Y.L.B.); (M.P.B.); (E.S.K.); (O.V.K.)
| | - Alexey K. Surin
- Branch of the Shemyakin—Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Prospekt Nauki 6, 142290 Pushchino, Russia;
- State Research Centre for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290 Pushchino, Russia;
| | - Ekaterina S. Kharechkina
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Institutskaya 3, 142290 Pushchino, Russia; (A.B.N.); (Y.L.B.); (M.P.B.); (E.S.K.); (O.V.K.)
| | - Olga V. Krestinina
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Institutskaya 3, 142290 Pushchino, Russia; (A.B.N.); (Y.L.B.); (M.P.B.); (E.S.K.); (O.V.K.)
| | - Maria Y. Suvorina
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290 Pushchino, Russia;
| | - Svetlana A. Kruglova
- Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya 2, 142290 Pushchino, Russia;
| | - Alexey G. Kruglov
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Institutskaya 3, 142290 Pushchino, Russia; (A.B.N.); (Y.L.B.); (M.P.B.); (E.S.K.); (O.V.K.)
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4
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Saw WG, Le KCM, Shin J, Kwek JHM, Wong CF, Ragunathan P, Fong TC, Müller V, Grüber G. Atomic insights of an up and down conformation of the Acinetobacter baumannii F 1 -ATPase subunit ε and deciphering the residues critical for ATP hydrolysis inhibition and ATP synthesis. FASEB J 2023; 37:e23040. [PMID: 37318822 DOI: 10.1096/fj.202300175rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/23/2023] [Accepted: 06/05/2023] [Indexed: 06/16/2023]
Abstract
The Acinetobacter baumannii F1 FO -ATP synthase (α3 :β3 :γ:δ:ε:a:b2 :c10 ), which is essential for this strictly respiratory opportunistic human pathogen, is incapable of ATP-driven proton translocation due to its latent ATPase activity. Here, we generated and purified the first recombinant A. baumannii F1 -ATPase (AbF1 -ATPase) composed of subunits α3 :β3 :γ:ε, showing latent ATP hydrolysis. A 3.0 Å cryo-electron microscopy structure visualizes the architecture and regulatory element of this enzyme, in which the C-terminal domain of subunit ε (Abε) is present in an extended position. An ε-free AbF1 -ɑβγ complex generated showed a 21.5-fold ATP hydrolysis increase, demonstrating that Abε is the major regulator of AbF1 -ATPase's latent ATP hydrolysis. The recombinant system enabled mutational studies of single amino acid substitutions within Abε or its interacting subunits β and γ, respectively, as well as C-terminal truncated mutants of Abε, providing a detailed picture of Abε's main element for the self-inhibition mechanism of ATP hydrolysis. Using a heterologous expression system, the importance of Abε's C-terminus in ATP synthesis of inverted membrane vesicles, including AbF1 FO -ATP synthases, has been explored. In addition, we are presenting the first NMR solution structure of the compact form of Abε, revealing interaction of its N-terminal β-barrel and C-terminal ɑ-hairpin domain. A double mutant of Abε highlights critical residues for Abε's domain-domain formation which is important also for AbF1 -ATPase's stability. Abε does not bind MgATP, which is described to regulate the up and down movements in other bacterial counterparts. The data are compared to regulatory elements of F1 -ATPases in bacteria, chloroplasts, and mitochondria to prevent wasting of ATP.
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Affiliation(s)
- Wuan-Geok Saw
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Khoa Cong Minh Le
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Joon Shin
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jes Hui Min Kwek
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Chui Fann Wong
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Priya Ragunathan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Tuck Choy Fong
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Volker Müller
- Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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5
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Marchetti M, Puglisi R, Cellini B, Dindo M, Marchesani F. Editorial: The role of cofactors in protein stability and homeostasis: Focus on human metabolism. Front Mol Biosci 2023; 10:1147451. [PMID: 36762209 PMCID: PMC9907023 DOI: 10.3389/fmolb.2023.1147451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Affiliation(s)
- Marialaura Marchetti
- Department of Medicine and Surgery, University of Parma, Parma, Italy,*Correspondence: Marialaura Marchetti,
| | - Rita Puglisi
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, United Kingdom
| | - Barbara Cellini
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Mirco Dindo
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
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6
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Feng X, Cheng XT, Zheng P, Li Y, Hakim J, Zhang SQ, Anderson SM, Linask K, Prestil R, Zou J, Sheng ZH, Blackstone C. Ligand-free mitochondria-localized mutant AR-induced cytotoxicity in spinal bulbar muscular atrophy. Brain 2023; 146:278-294. [PMID: 35867854 DOI: 10.1093/brain/awac269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 06/12/2022] [Accepted: 07/03/2022] [Indexed: 01/11/2023] Open
Abstract
Spinal bulbar muscular atrophy (SBMA), the first identified CAG-repeat expansion disorder, is an X-linked neuromuscular disorder involving CAG-repeat-expansion mutations in the androgen receptor (AR) gene. We utilized CRISPR-Cas9 gene editing to engineer novel isogenic human induced pluripotent stem cell (hiPSC) models, consisting of isogenic AR knockout, control and disease lines expressing mutant AR with distinct repeat lengths, as well as control and disease lines expressing FLAG-tagged wild-type and mutant AR, respectively. Adapting a small-molecule cocktail-directed approach, we differentiate the isogenic hiPSC models into motor neuron-like cells with a highly enriched population to uncover cell-type-specific mechanisms underlying SBMA and to distinguish gain- from loss-of-function properties of mutant AR in disease motor neurons. We demonstrate that ligand-free mutant AR causes drastic mitochondrial dysfunction in neurites of differentiated disease motor neurons due to gain-of-function mechanisms and such cytotoxicity can be amplified upon ligand (androgens) treatment. We further show that aberrant interaction between ligand-free, mitochondria-localized mutant AR and F-ATP synthase is associated with compromised mitochondrial respiration and multiple other mitochondrial impairments. These findings counter the established notion that androgens are requisite for mutant AR-induced cytotoxicity in SBMA, reveal a compelling mechanistic link between ligand-free mutant AR, F-ATP synthase and mitochondrial dysfunction, and provide innovative insights into motor neuron-specific therapeutic interventions for SBMA.
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Affiliation(s)
- Xia Feng
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Cell Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.,Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Xiu-Tang Cheng
- Synaptic Function Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Pengli Zheng
- Cell Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Yan Li
- Protein/Peptide Sequencing Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Jill Hakim
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | | | - Stacie M Anderson
- Flow Cytometry Core, National Human Genome Research Institute, National Institute of Health, Bethesda, MD, USA
| | - Kaari Linask
- iPSC Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ryan Prestil
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Jizhong Zou
- iPSC Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zu-Hang Sheng
- Synaptic Function Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Craig Blackstone
- Cell Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.,MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
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7
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Wong CF, Saw WG, Basak S, Sano M, Ueno H, Kerk HW, Litty D, Ragunathan P, Dick T, Müller V, Noji H, Grüber G. Structural Elements Involved in ATP Hydrolysis Inhibition and ATP Synthesis of Tuberculosis and Nontuberculous Mycobacterial F-ATP Synthase Decipher New Targets for Inhibitors. Antimicrob Agents Chemother 2022; 66:e0105622. [PMID: 36445139 DOI: 10.1128/aac.01056-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The F1FO-ATP synthase is required for the viability of tuberculosis (TB) and nontuberculous mycobacteria (NTM) and has been validated as a drug target. Here, we present the cryo-EM structures of the Mycobacterium smegmatis F1-ATPase and the F1FO-ATP synthase with different nucleotide occupation within the catalytic sites and visualize critical elements for latent ATP hydrolysis and efficient ATP synthesis. Mutational studies reveal that the extended C-terminal domain (αCTD) of subunit α is the main element for the self-inhibition mechanism of ATP hydrolysis for TB and NTM bacteria. Rotational studies indicate that the transition between the inhibition state by the αCTD and the active state is a rapid process. We demonstrate that the unique mycobacterial γ-loop and subunit δ are critical elements required for ATP formation. The data underline that these mycobacterium-specific elements of α, γ, and δ are attractive targets, providing a platform for the discovery of species-specific inhibitors.
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8
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Shin J, Harikishore A, Wong CF, Ragunathan P, Thomas D, Grüber G. Atomic solution structure of Mycobacterium abscessus F-ATP synthase subunit ε and identification of Ep1MabF1 as a targeted inhibitor. FEBS J 2022; 289:6308-6323. [PMID: 35612822 PMCID: PMC10609657 DOI: 10.1111/febs.16536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 04/27/2022] [Accepted: 05/24/2022] [Indexed: 11/30/2022]
Abstract
Mycobacterium abscessus (Mab) is a nontuberculous mycobacterium of increasing clinical relevance. The rapidly growing opportunistic pathogen is intrinsically multi-drug-resistant and causes difficult-to-cure lung disease. Adenosine triphosphate, generated by the essential F1 FO ATP synthase, is the major energy currency of the pathogen, bringing this enzyme complex into focus for the discovery of novel antimycobacterial compounds. Coupling of proton translocation through the membrane-embedded FO sector and ATP formation in the F1 headpiece of the bipartite F1 FO ATP synthase occurs via the central stalk subunits γ and ε. Here, we used solution NMR spectroscopy to resolve the first atomic structure of the Mab subunit ε (Mabε), showing that it consists of an N-terminal β-barrel domain (NTD) and a helix-loop-helix motif in its C-terminal domain (CTD). NMR relaxation measurements of Mabε shed light on dynamic epitopes and amino acids relevant for coupling processes within the protein. We describe structural differences between other mycobacterial ε subunits and Mabε's lack of ATP binding. Based on the structural insights, we conducted an in silico inhibitor screen. One hit, Ep1MabF1, was shown to inhibit the growth of Mab and bacterial ATP synthesis. NMR titration experiments and docking studies described the binding epitopes of Ep1MabF1 on Mabε. Together, our data demonstrate the potential to develop inhibitors targeting the ε subunit of Mab F1 FO ATP synthase to interrupt the coupling process.
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Affiliation(s)
- Joon Shin
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Amaravadhi Harikishore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Chui Fann Wong
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Priya Ragunathan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Dick Thomas
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, 123 Metro Boulevard, Nutley, NJ 07110, USA
- Department of Microbiology and Immunology, Georgetown University, 3900 Reservoir Road NW Medical-Dental Building, Washington, DC 20007, USA
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
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9
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Ragunathan P, Dick T, Grüber G. Anti-Mycobacterium abscessus Activity of Tuberculosis F-ATP Synthase Inhibitor GaMF1. Antimicrob Agents Chemother 2022; 66:e0001822. [PMID: 35481752 DOI: 10.1128/aac.00018-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
New drug targets and molecules with bactericidal activity are needed against the respiratory mycobacterial pathogen Mycobacterium abscessus. Employing a lead repurposing strategy, the antituberculosis compound GaMF1 was tested against M. abscessus. Whole-cell and ATP synthesis assays demonstrated that GaMF1 inhibits growth and kills M. abscessus by targeting the F-ATP synthase. GaMF1's anti-M. abscessus activity increased in combination with clofazimine, rifabutin, or amikacin. The study expands the repertoire of anti-M. abscessus compounds targeting oxidative phosphorylation.
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10
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Harikishore A, Wong CF, Ragunathan P, Litty D, Müller V, Grüber G. Targeting Mycobacterial F-ATP Synthase C-Terminal α Subunit Interaction Motif on Rotary Subunit γ. Antibiotics (Basel) 2021; 10:1456. [PMID: 34943667 DOI: 10.3390/antibiotics10121456] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 12/03/2022] Open
Abstract
Mycobacteria regulate their energy (ATP) levels to sustain their survival even in stringent living conditions. Recent studies have shown that mycobacteria not only slow down their respiratory rate but also block ATP hydrolysis of the F-ATP synthase (α3:β3:γ:δ:ε:a:b:b’:c9) to maintain ATP homeostasis in situations not amenable for growth. The mycobacteria-specific α C-terminus (α533-545) has unraveled to be the major regulative of latent ATP hydrolysis. Its deletion stimulates ATPase activity while reducing ATP synthesis. In one of the six rotational states of F-ATP synthase, α533-545 has been visualized to dock deep into subunit γ, thereby blocking rotation of γ within the engine. The functional role(s) of this C-terminus in the other rotational states are not clarified yet and are being still pursued in structural studies. Based on the interaction pattern of the docked α533-545 region with subunit γ, we attempted to study the druggability of the α533-545 motif. In this direction, our computational work has led to the development of an eight-featured α533-545 peptide pharmacophore, followed by database screening, molecular docking, and pose selection, resulting in eleven hit molecules. ATP synthesis inhibition assays using recombinant ATP synthase as well as mycobacterial inverted membrane vesicles show that one of the hits, AlMF1, inhibited the mycobacterial F-ATP synthase in a micromolar range. The successful targeting of the α533-545-γ interaction motif demonstrates the potential to develop inhibitors targeting the α site to interrupt rotary coupling with ATP synthesis.
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11
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Carrer A, Laquatra C, Tommasin L, Carraro M. Modulation and Pharmacology of the Mitochondrial Permeability Transition: A Journey from F-ATP Synthase to ANT. Molecules 2021; 26:molecules26216463. [PMID: 34770872 PMCID: PMC8587538 DOI: 10.3390/molecules26216463] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/21/2021] [Accepted: 10/23/2021] [Indexed: 12/22/2022] Open
Abstract
The permeability transition (PT) is an increased permeation of the inner mitochondrial membrane due to the opening of the PT pore (PTP), a Ca2+-activated high conductance channel involved in Ca2+ homeostasis and cell death. Alterations of the PTP have been associated with many pathological conditions and its targeting represents an incessant challenge in the field. Although the modulation of the PTP has been extensively explored, the lack of a clear picture of its molecular nature increases the degree of complexity for any target-based approach. Recent advances suggest the existence of at least two mitochondrial permeability pathways mediated by the F-ATP synthase and the ANT, although the exact molecular mechanism leading to channel formation remains elusive for both. A full comprehension of this to-pore conversion will help to assist in drug design and to develop pharmacological treatments for a fine-tuned PT regulation. Here, we will focus on regulatory mechanisms that impinge on the PTP and discuss the relevant literature of PTP targeting compounds with particular attention to F-ATP synthase and ANT.
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12
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Angeli S, Foulger A, Chamoli M, Peiris TH, Gerencser A, Shahmirzadi AA, Andersen J, Lithgow G. The mitochondrial permeability transition pore activates the mitochondrial unfolded protein response and promotes aging. eLife 2021; 10:63453. [PMID: 34467850 PMCID: PMC8410078 DOI: 10.7554/elife.63453] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 08/15/2021] [Indexed: 02/06/2023] Open
Abstract
Mitochondrial activity determines aging rate and the onset of chronic diseases. The mitochondrial permeability transition pore (mPTP) is a pathological pore in the inner mitochondrial membrane thought to be composed of the F-ATP synthase (complex V). OSCP, a subunit of F-ATP synthase, helps protect against mPTP formation. How the destabilization of OSCP may contribute to aging, however, is unclear. We have found that loss OSCP in the nematode Caenorhabditis elegans initiates the mPTP and shortens lifespan specifically during adulthood, in part via initiation of the mitochondrial unfolded protein response (UPRmt). Pharmacological or genetic inhibition of the mPTP inhibits the UPRmt and restores normal lifespan. Loss of the putative pore-forming component of F-ATP synthase extends adult lifespan, suggesting that the mPTP normally promotes aging. Our findings reveal how an mPTP/UPRmt nexus may contribute to aging and age-related diseases and how inhibition of the UPRmt may be protective under certain conditions.
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Affiliation(s)
- Suzanne Angeli
- Buck Institute for Research on Aging, Novato, United States
| | - Anna Foulger
- Buck Institute for Research on Aging, Novato, United States
| | - Manish Chamoli
- Buck Institute for Research on Aging, Novato, United States
| | | | - Akos Gerencser
- Buck Institute for Research on Aging, Novato, United States
| | - Azar Asadi Shahmirzadi
- Buck Institute for Research on Aging, Novato, United States.,USC Leonard Davis School of Gerontology, University of Southern California, Los Angeles, United States
| | - Julie Andersen
- Buck Institute for Research on Aging, Novato, United States.,USC Leonard Davis School of Gerontology, University of Southern California, Los Angeles, United States
| | - Gordon Lithgow
- Buck Institute for Research on Aging, Novato, United States.,USC Leonard Davis School of Gerontology, University of Southern California, Los Angeles, United States
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13
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Guo L. Mitochondria and the permeability transition pore in cancer metabolic reprogramming. Biochem Pharmacol 2021; 188:114537. [PMID: 33811907 DOI: 10.1016/j.bcp.2021.114537] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 02/07/2023]
Abstract
Mitochondria are a major source of ATP provision as well as cellular suicidal weapon store. Accumulating evidences demonstrate that mitochondrial bioenergetics, biosynthesis and signaling are important mediators of tumorigenesis. Metabolic plasticity enables cancer cell reprogramming to cope with cellular and environmental alterations, a process requires mitochondria biology. Mitochondrial metabolism emerges to be a promising arena for cancer therapeutic targets. The permeability transition pore (PTP) participates in physiological Ca2+ and ROS homeostasis as well as cell death depending on the open state. The hypothesis that PTP forms from F-ATP synthase provides clues to the potential collaborative role of mitochondrial respiration and PTP in regulating cancer cell fate and metabolic reprogramming.
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Affiliation(s)
- Lishu Guo
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, China.
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14
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Wong CF, Grüber G. The Unique C-Terminal Extension of Mycobacterial F-ATP Synthase Subunit α Is the Major Contributor to Its Latent ATP Hydrolysis Activity. Antimicrob Agents Chemother 2020; 64:e01568-20. [PMID: 32988828 DOI: 10.1128/AAC.01568-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/16/2020] [Indexed: 01/03/2023] Open
Abstract
Mycobacterial F1Fo-ATP synthases (α3:β3:γ:δ:ε:a:b:b':c9 ) are incapable of ATP-driven proton translocation due to their latent ATPase activity. This prevents wasting of ATP and altering of the proton motive force, whose dissipation is lethal to mycobacteria. We demonstrate that the mycobacterial C-terminal extension of nucleotide-binding subunit α contributes mainly to the suppression of ATPase activity in the recombinant mycobacterial F1-ATPase. Using C-terminal deletion mutants, the regions responsible for the enzyme's latency were mapped, providing a new compound epitope.
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15
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Wong CF, Lau AM, Harikishore A, Saw WG, Shin J, Ragunathan P, Bhushan S, Ngan SFC, Sze SK, Bates RW, Dick T, Grüber G. A systematic assessment of mycobacterial F 1 -ATPase subunit ε's role in latent ATPase hydrolysis. FEBS J 2020; 288:818-836. [PMID: 32525613 DOI: 10.1111/febs.15440] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 05/05/2020] [Accepted: 06/03/2020] [Indexed: 12/20/2022]
Abstract
In contrast to most bacteria, the mycobacterial F1 FO -ATP synthase (α3 :β3 :γ:δ:ε:a:b:b':c9 ) does not perform ATP hydrolysis-driven proton translocation. Although subunits α, γ and ε of the catalytic F1 -ATPase component α3 :β3 :γ:ε have all been implicated in the suppression of the enzyme's ATPase activity, the mechanism remains poorly defined. Here, we brought the central stalk subunit ε into focus by generating the recombinant Mycobacterium smegmatis F1 -ATPase (MsF1 -ATPase), whose 3D low-resolution structure is presented, and its ε-free form MsF1 αβγ, which showed an eightfold ATP hydrolysis increase and provided a defined system to systematically study the segments of mycobacterial ε's suppression of ATPase activity. Deletion of four amino acids at ε's N terminus, mutant MsF1 αβγεΔ2-5 , revealed similar ATP hydrolysis as MsF1 αβγ. Together with biochemical and NMR solution studies of a single, double, triple and quadruple N-terminal ε-mutants, the importance of the first N-terminal residues of mycobacterial ε in structure stability and latency is described. Engineering ε's C-terminal mutant MsF1 αβγεΔ121 and MsF1 αβγεΔ103-121 with deletion of the C-terminal residue D121 and the two C-terminal ɑ-helices, respectively, revealed the requirement of the very C terminus for communication with the catalytic α3 β3 -headpiece and its function in ATP hydrolysis inhibition. Finally, we applied the tools developed during the study for an in silico screen to identify a novel subunit ε-targeting F-ATP synthase inhibitor.
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Affiliation(s)
- Chui-Fann Wong
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Aik-Meng Lau
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Amaravadhi Harikishore
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Wuan-Geok Saw
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Joon Shin
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Priya Ragunathan
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Shashi Bhushan
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore City, Singapore
| | - So-Fong Cam Ngan
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Roderick W Bates
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore City, Singapore.,Department of Medical Sciences, Hackensack Meridian School of Medicine at Seton Hall University, Nutley, NJ, USA
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
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16
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Kamariah N, Huber RG, Bond PJ, Müller V, Grüber G. 3D reconstruction and flexibility of the hybrid engine Acetobacterium woodii F-ATP synthase. Biochem Biophys Res Commun 2020; 527:518-524. [PMID: 32423799 DOI: 10.1016/j.bbrc.2020.04.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 11/16/2022]
Abstract
The Na+-translocating F1FO ATP synthase from Acetobacterium woodii (AwF-ATP synthase) with a subunit stoichiometry of α3:β3:γ:δ:ε:a:b2:(c2/3)9:c1 represents an evolutionary path between ATP-synthases and vacuolar ATPases, by containing a heteromeric rotor c-ring, composed of subunits c1, c2 and c3, and an extra loop (γ195-211) within the rotary γ subunit. Here, the recombinant AwF-ATP synthase was subjected to negative stain electron microscopy and single particle analysis. The reference free 2D class averages revealed high flexibility of the enzyme, wherein the F1 and FO domains distinctively bended to adopt multiple conformations. Moreover, both the F1 and FO domains tilted relative to each other to a maximum extent of 28° and 30°, respectively. The first 3D reconstruction of the AwF-ATP synthase was determined which accommodates well the modelled structure of the AwF-ATP synthase as well as the γ195-211-loop. Molecular simulations of the enzyme underlined the bending features and flexibility observed in the electron micrographs, and enabled assessment of the dynamics of the extra γ195-211-loop.
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Affiliation(s)
- Neelagandan Kamariah
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
| | - Roland G Huber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A∗STAR), #07-01 Matrix, 30 Biopolis Street, Singapore, 38671
| | - Peter J Bond
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A∗STAR), #07-01 Matrix, 30 Biopolis Street, Singapore, 38671; Department of Biological Sciences (DBS), National University of Singapore (NUS), 14 Science Drive 4, Singapore, 117543
| | - Volker Müller
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Gerhard Grüber
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore; Bioinformatics Institute (BII), Agency for Science, Technology and Research (A∗STAR), #07-01 Matrix, 30 Biopolis Street, Singapore, 38671.
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17
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Sarathy JP, Gruber G, Dick T. Re-Understanding the Mechanisms of Action of the Anti-Mycobacterial Drug Bedaquiline. Antibiotics (Basel) 2019; 8:E261. [PMID: 31835707 DOI: 10.3390/antibiotics8040261] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 12/07/2019] [Indexed: 12/14/2022] Open
Abstract
Bedaquiline (BDQ) inhibits ATP generation in Mycobacterium tuberculosis by interfering with the F-ATP synthase activity. Two mechanisms of action of BDQ are broadly accepted. A direct mechanism involves BDQ binding to the enzyme’s c-ring to block its rotation, thus inhibiting ATP synthesis in the enzyme’s catalytic α3β3-headpiece. An indirect mechanism involves BDQ uncoupling electron transport in the electron transport chain from ATP synthesis at the F-ATP synthase. In a recently uncovered second direct mechanism, BDQ binds to the enzyme’s ε-subunit to disrupt its ability to link c-ring rotation to ATP synthesis at the α3β3-headpiece. However, this mechanism is controversial as the drug’s binding affinity for the isolated ε-subunit protein is moderate and spontaneous resistance mutants in the ε-subunit cannot be isolated. Recently, the new, structurally distinct BDQ analogue TBAJ-876 was utilized as a chemical probe to revisit BDQ’s mechanisms of action. In this review, we first summarize discoveries on BDQ’s mechanisms of action and then describe the new insights derived from the studies of TBAJ-876. The TBAJ-876 investigations confirm the c-ring as a target, while also supporting a functional role for targeting the ε-subunit. Surprisingly, the new findings suggest that the uncoupler mechanism does not play a key role in BDQ’s anti-mycobacterial activity.
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18
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Saw WG, Wong CF, Dick T, Grüber G. Overexpression, purification, enzymatic and microscopic characterization of recombinant mycobacterial F-ATP synthase. Biochem Biophys Res Commun 2019; 522:374-380. [PMID: 31761325 DOI: 10.1016/j.bbrc.2019.11.098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 11/15/2019] [Indexed: 01/16/2023]
Abstract
The F-ATP synthase is an essential enzyme in mycobacteria, including the pathogenic Mycobacterium tuberculosis. Several new compounds in the TB-drug pipeline target the F-ATP synthase. In light of the importance and pharmacological attractiveness of this novel antibiotic target, tools have to be developed to generate a recombinant mycobacterial F1FO ATP synthase to achieve atomic insight and mutants for mechanistic and regulatory understanding as well as structure-based drug design. Here, we report the first genetically engineered, purified and enzymatically active recombinant M. smegmatis F1FO ATP synthase. The projected 2D- and 3D structures of the recombinant enzyme derived from negatively stained electron micrographs are presented. Furthermore, the first 2D projections from cryo-electron images are revealed, paving the way for an atomic resolution structure determination.
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Affiliation(s)
- Wuan-Geok Saw
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
| | - Chui-Fann Wong
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Gerhard Grüber
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.
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19
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Kamariah N, Ragunathan P, Shin J, Saw WG, Wong CF, Dick T, Grüber G. Unique structural and mechanistic properties of mycobacterial F-ATP synthases: Implications for drug design. Prog Biophys Mol Biol 2020; 152:64-73. [PMID: 31743686 DOI: 10.1016/j.pbiomolbio.2019.11.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/25/2019] [Accepted: 11/13/2019] [Indexed: 12/31/2022]
Abstract
The causative agent of Tuberculosis (TB) Mycobacterium tuberculosis (Mtb) encounters unfavourable environmental conditions in the lungs, including nutrient limitation, low oxygen tensions and/or low/high pH values. These harsh conditions in the host triggers Mtb to enter a dormant state in which the pathogen does not replicate and uses host-derived fatty acids instead of carbohydrates as an energy source. Independent to the energy source, the bacterium's energy currency ATP is generated by oxidative phosphorylation, in which the F1FO-ATP synthase uses the proton motive force generated by the electron transport chain. This catalyst is essential in Mtb and inhibition by the diarylquinoline class of drugs like Bedaquilline, TBAJ-587, TBAJ-876 or squaramides demonstrated that this engine is an attractive target in TB drug discovery. A special feature of the mycobacterial F-ATP synthase is its inability to establish a significant proton gradient during ATP hydrolysis, and its latent ATPase activity, to prevent energy waste and to control the membrane potential. Recently, unique epitopes of mycobacterial F1FO-ATP synthase subunits absent in their prokaryotic or mitochondrial counterparts have been identified to contribute to the regulation of the low ATPase activity. Most recent structural insights into individual subunits, the F1 domain or the entire mycobacterial enzyme added to the understanding of mechanisms, regulation and differences of the mycobacterial F1FO-ATP synthase compared to other bacterial and eukaryotic engines. These novel insights provide the basis for the design of new compounds targeting this engine and even novel regimens for multidrug resistant TB.
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20
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Sarathy JP, Ragunathan P, Shin J, Cooper CB, Upton AM, Grüber G, Dick T. TBAJ-876 Retains Bedaquiline's Activity against Subunits c and ε of Mycobacterium tuberculosis F-ATP Synthase. Antimicrob Agents Chemother 2019; 63:e01191-19. [PMID: 31358589 DOI: 10.1128/AAC.01191-19] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 07/25/2019] [Indexed: 12/18/2022] Open
Abstract
The antituberculosis drug bedaquiline (BDQ) inhibits Mycobacterium tuberculosis F-ATP synthase by interfering with two subunits. Drug binding to the c subunit stalls the rotation of the c ring, while binding to the ε subunit blocks coupling of c ring rotation to ATP synthesis at the catalytic α3:β3 headpiece. BDQ is used for the treatment of drug-resistant tuberculosis. The antituberculosis drug bedaquiline (BDQ) inhibits Mycobacterium tuberculosis F-ATP synthase by interfering with two subunits. Drug binding to the c subunit stalls the rotation of the c ring, while binding to the ε subunit blocks coupling of c ring rotation to ATP synthesis at the catalytic α3:β3 headpiece. BDQ is used for the treatment of drug-resistant tuberculosis. However, the drug is highly lipophilic, displays a long terminal half-life, and has a cardiotoxicity liability by causing QT interval prolongation. Recent medicinal chemistry campaigns have resulted in the discovery of 3,5-dialkoxypyridine analogues of BDQ that are less lipophilic, have higher clearance, and display lower cardiotoxic potential. TBAJ-876, which is a new developmental compound of this series, shows attractive antitubercular activity and efficacy in a murine tuberculosis model. Here, we asked whether TBAJ-876 and selected analogues of the compound retain BDQ’s mechanism of action. Biochemical assays showed that TBAJ-876 is a potent inhibitor of mycobacterial F-ATP synthase. Selection of spontaneous TBAJ-876-resistant mutants identified missense mutations at BDQ’s binding site on the c subunit, suggesting that TBAJ-876 retains BDQ’s targeting of the c ring. Susceptibility testing against a strain overexpressing the ε subunit and a strain harboring an engineered mutation in BDQ’s ε subunit binding site suggest that TBAJ-876 retains BDQ’s activity on the ε subunit. Nuclear magnetic resonance (NMR) titration studies confirmed that TBAJ-876 binds to the ε subunit at BDQ’s binding site. We show that TBAJ-876 retains BDQ’s antimycobacterial mode of action. The developmental compound inhibits the mycobacterial F-ATP synthase via a dual-subunit mechanism of interfering with the functions of both the enzyme’s c and ε subunits.
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21
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Affiliation(s)
- Paolo Bernardi
- Department of Biomedical Sciences, University of Padova, Padua, Italy
| | - Giovanna Lippe
- Department of Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
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22
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Bogdanović N, Trifunović D, Sielaff H, Westphal L, Bhushan S, Müller V, Grüber G. The structural features of Acetobacterium woodii F-ATP synthase reveal the importance of the unique subunit γ-loop in Na + translocation and ATP synthesis. FEBS J 2019; 286:1894-1907. [PMID: 30791207 DOI: 10.1111/febs.14793] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 01/25/2019] [Accepted: 02/18/2019] [Indexed: 12/18/2022]
Abstract
The Na+ translocating F1 FO ATP synthase from Acetobacterium woodii shows a subunit stoichiometry of α3 :β3 :γ:δ:ε:a:b2 :(c2/3 )9 :c1 and reveals an evolutionary path between synthases and pumps involving adaptations in the rotor c-ring, which is composed of F- and vacuolar-type c subunits in a stoichiometry of 9 : 1. This hybrid turbine couples rotation with Na+ translocation in the FO part and rotation of the central stalk subunits γ-ε to drive ATP synthesis in the catalytic α3 :β3 headpiece. Here, we isolated a highly pure recombinant A. woodii F-ATP synthase and present the first projected structure of this hybrid engine as determined by negative-stain electron microscopy and single-particle analysis. The uniqueness of the A. woodii F-ATP synthase is also reflected by an extra 17 amino acid residues loop (195 TSGKVKITEETKEEKSK211 ) in subunit γ. Deleting the loop-encoding DNA sequence (γΔ195-211 ) and purifying the recombinant F-ATP synthase γΔ195-211 mutant provided a platform to study its effect in enzyme stability and activity. The recombinant F-ATP synthase γΔ195-211 mutant revealed the same subunit composition as the wild-type enzyme and a minor reduction in ATP hydrolysis. When reconstituted into proteoliposomes ATP synthesis and Na+ transport were diminished, demonstrating the importance of the γ195-211 loop in both enzymatic processes. Based on a structural model, a coupling mechanism for this enzyme is proposed, highlighting the role of the γ-loop. Finally, the γ195-211 loop of A. woodii is discussed in comparison with the extra γ-loops of mycobacterial and chloroplasts F-ATP synthases described to be involved in species-specific regulatory mechanisms.
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Affiliation(s)
- Nebojša Bogdanović
- Nanyang Technological University, School of Biological Sciences, Singapore City, Singapore
| | - Dragan Trifunović
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Germany
| | - Hendrik Sielaff
- Nanyang Technological University, School of Biological Sciences, Singapore City, Singapore
| | - Lars Westphal
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Germany
| | - Shashi Bhushan
- Nanyang Technological University, School of Biological Sciences, Singapore City, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore City, Singapore
| | - Volker Müller
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Germany
| | - Gerhard Grüber
- Nanyang Technological University, School of Biological Sciences, Singapore City, Singapore
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23
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Abstract
In the presence of Ca2+, F-ATP synthase preparations eluted from Blue Native gels generate electrophysiological currents that are typical of an inner mitochondrial membrane mega-channel, the permeability transition pore. Here we describe an experimental protocol for purification of F-ATP synthase that allows to maintain the enzyme assembly and activity that are essential for catalysis and channel formation.
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Affiliation(s)
- Chiara Galber
- Neuroscience Institute and Department of Biomedical Sciences, CNR and University of Padua, Padua, Italy
| | - Giulia Valente
- Neuroscience Institute and Department of Biomedical Sciences, CNR and University of Padua, Padua, Italy
| | - Sophia von Stockum
- Department of Biology, University of Padua, Padua, Italy
- Fondazione Ospedale San Camillo, IRCCS, Venezia, Italy
| | - Valentina Giorgio
- Neuroscience Institute and Department of Biomedical Sciences, CNR and University of Padua, Padua, Italy.
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24
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De Col V, Petrussa E, Casolo V, Braidot E, Lippe G, Filippi A, Peresson C, Patui S, Bertolini A, Giorgio V, Checchetto V, Vianello A, Bernardi P, Zancani M. Properties of the Permeability Transition of Pea Stem Mitochondria. Front Physiol 2018; 9:1626. [PMID: 30524297 PMCID: PMC6262314 DOI: 10.3389/fphys.2018.01626] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/29/2018] [Indexed: 12/17/2022] Open
Abstract
In striking analogy with Saccharomyces cerevisiae, etiolated pea stem mitochondria did not show appreciable Ca2+ uptake. Only treatment with the ionophore ETH129 (which allows electrophoretic Ca2+ equilibration) caused Ca2+ uptake followed by increased inner membrane permeability, membrane depolarization and Ca2+ release. Like the permeability transition (PT) of mammals, yeast and Drosophila, the PT of pea stem mitochondria was stimulated by diamide and phenylarsine oxide and inhibited by Mg-ADP and Mg-ATP, suggesting a common underlying mechanism; yet, the plant PT also displayed distinctive features: (i) as in mammals it was desensitized by cyclosporin A, which does not affect the PT of yeast and Drosophila; (ii) similarly to S. cerevisiae and Drosophila it was inhibited by Pi, which stimulates the PT of mammals; (iii) like in mammals and Drosophila it was sensitized by benzodiazepine 423, which is ineffective in S. cerevisiae; (iv) like what observed in Drosophila it did not mediate swelling and cytochrome c release, which is instead seen in mammals and S. cerevisiae. We find that cyclophilin D, the mitochondrial receptor for cyclosporin A, is present in pea stem mitochondria. These results indicate that the plant PT has unique features and suggest that, as in Drosophila, it may provide pea stem mitochondria with a Ca2+ release channel.
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Affiliation(s)
- Valentina De Col
- Department of Agricultural, Food, Environmental and Animal Sciences (Di4A), University of Udine, Udine, Italy
| | - Elisa Petrussa
- Department of Agricultural, Food, Environmental and Animal Sciences (Di4A), University of Udine, Udine, Italy
| | - Valentino Casolo
- Department of Agricultural, Food, Environmental and Animal Sciences (Di4A), University of Udine, Udine, Italy
| | - Enrico Braidot
- Department of Agricultural, Food, Environmental and Animal Sciences (Di4A), University of Udine, Udine, Italy
| | - Giovanna Lippe
- Department of Agricultural, Food, Environmental and Animal Sciences (Di4A), University of Udine, Udine, Italy
| | - Antonio Filippi
- Department of Agricultural, Food, Environmental and Animal Sciences (Di4A), University of Udine, Udine, Italy
| | - Carlo Peresson
- Department of Agricultural, Food, Environmental and Animal Sciences (Di4A), University of Udine, Udine, Italy
| | - Sonia Patui
- Department of Agricultural, Food, Environmental and Animal Sciences (Di4A), University of Udine, Udine, Italy
| | - Alberto Bertolini
- Department of Agricultural, Food, Environmental and Animal Sciences (Di4A), University of Udine, Udine, Italy
| | - Valentina Giorgio
- Department of Biomedical Sciences, University of Padova and CNR Neuroscience Institute, Padova, Italy
| | | | - Angelo Vianello
- Department of Agricultural, Food, Environmental and Animal Sciences (Di4A), University of Udine, Udine, Italy
| | - Paolo Bernardi
- Department of Biomedical Sciences, University of Padova and CNR Neuroscience Institute, Padova, Italy
| | - Marco Zancani
- Department of Agricultural, Food, Environmental and Animal Sciences (Di4A), University of Udine, Udine, Italy
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25
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Bogdanović N, Sundararaman L, Kamariah N, Tyagi A, Bhushan S, Ragunathan P, Shin J, Dick T, Grüber G. Structure and function of Mycobacterium-specific components of F-ATP synthase subunits α and ε. J Struct Biol 2018; 204:420-434. [PMID: 30342092 DOI: 10.1016/j.jsb.2018.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/08/2018] [Accepted: 10/16/2018] [Indexed: 01/21/2023]
Abstract
The Mycobacterium tuberculosis (Mtb) F1FO-ATP synthase (α3:β3:γ:δ:ε:a:b:b':c9) is an essential enzyme that supplies energy for both the aerobic growing and the hypoxic dormant stage of the mycobacterial life cycle. Employing the heterologous F-ATP synthase model system αchi3:β3:γ we showed previously, that transfer of the C-terminal domain (CTD) of Mtb subunit α (Mtα514-549) to a standard F-ATP synthase α subunit suppresses ATPase activity. Here we determined the 3D reconstruction from electron micrographs of the αchi3:β3:γ complex reconstituted with the Mtb subunit ε (Mtε), which has been shown to crosstalk with the CTD of Mtα. Together with the first solution shape of Mtb subunit α (Mtα), derived from solution X-ray scattering, the structural data visualize the extended C-terminal stretch of the mycobacterial subunit α. In addition, Mtε mutants MtεR62L, MtεE87A, Mtε6-121, and Mtε1-120, reconstituted with αchi3:β3:γ provided insight into their role in coupling and in trapping inhibiting MgADP. NMR solution studies of MtεE87A gave insights into how this residue contributes to stability and crosstalk between the N-terminal domain (NTD) and the CTD of Mtε. Analyses of the N-terminal mutant Mtε6-121 highlight the differences of the NTD of mycobacterial subunit ε to the well described Geobacillus stearothermophilus or Escherichia coli counterparts. These data are discussed in context of a crosstalk between the very N-terminal amino acids of Mtε and the loop region of one c subunit of the c-ring turbine for coupling of proton-translocation and ATP synthesis activity.
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Affiliation(s)
- Nebojša Bogdanović
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Lavanya Sundararaman
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Neelagandan Kamariah
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Anu Tyagi
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Shashi Bhushan
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore; NTU Institute of Structural Biology, Nanyang Technological University, Republic of Singapore
| | - Priya Ragunathan
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Joon Shin
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Thomas Dick
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Republic of Singapore; Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, 225 Warren Street, Newark, NJ 07103, USA
| | - Gerhard Grüber
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore.
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26
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Joon S, Ragunathan P, Sundararaman L, Nartey W, Kundu S, Manimekalai MSS, Bogdanović N, Dick T, Grüber G. The NMR solution structure of Mycobacterium tuberculosis F-ATP synthase subunit ε provides new insight into energy coupling inside the rotary engine. FEBS J 2018; 285:1111-1128. [PMID: 29360236 DOI: 10.1111/febs.14392] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 11/30/2017] [Accepted: 01/18/2018] [Indexed: 11/27/2022]
Abstract
Mycobacterium tuberculosis (Mt) F1 F0 ATP synthase (α3 :β3 :γ:δ:ε:a:b:b':c9 ) is essential for the viability of growing and nongrowing persister cells of the pathogen. Here, we present the first NMR solution structure of Mtε, revealing an N-terminal β-barrel domain (NTD) and a C-terminal domain (CTD) composed of a helix-loop-helix with helix 1 and -2 being shorter compared to their counterparts in other bacteria. The C-terminal amino acids are oriented toward the NTD, forming a domain-domain interface between the NTD and CTD. The Mtε structure provides a novel mechanistic model of coupling c-ring- and ε rotation via a patch of hydrophobic residues in the NTD and residues of the CTD to the bottom of the catalytic α3 β3 -headpiece. To test our model, genome site-directed mutagenesis was employed to introduce amino acid changes in these two parts of the epsilon subunit. Inverted vesicle assays show that these mutations caused an increase in ATP hydrolysis activity and a reduction in ATP synthesis. The structural and enzymatic data are discussed in light of the transition mechanism of a compact and extended state of Mtε, which provides the inhibitory effects of this coupling subunit inside the rotary engine. Finally, the employment of these data with molecular docking shed light into the second binding site of the drug Bedaquiline. DATABASE Structural data are available in the PDB under the accession number 5YIO.
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Affiliation(s)
- Shin Joon
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Priya Ragunathan
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Lavanya Sundararaman
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Wilson Nartey
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Subhashri Kundu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Nebojša Bogdanović
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Thomas Dick
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA
| | - Gerhard Grüber
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
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27
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Ragunathan P, Sielaff H, Sundararaman L, Biuković G, Subramanian Manimekalai MS, Singh D, Kundu S, Wohland T, Frasch W, Dick T, Grüber G. The uniqueness of subunit α of mycobacterial F-ATP synthases: An evolutionary variant for niche adaptation. J Biol Chem 2017; 292:11262-11279. [PMID: 28495884 PMCID: PMC5500794 DOI: 10.1074/jbc.m117.784959] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 05/11/2017] [Indexed: 01/30/2023] Open
Abstract
The F1F0 -ATP (F-ATP) synthase is essential for growth of Mycobacterium tuberculosis, the causative agent of tuberculosis (TB). In addition to their synthase function most F-ATP synthases possess an ATP-hydrolase activity, which is coupled to proton-pumping activity. However, the mycobacterial enzyme lacks this reverse activity, but the reason for this deficiency is unclear. Here, we report that a Mycobacterium-specific, 36-amino acid long C-terminal domain in the nucleotide-binding subunit α (Mtα) of F-ATP synthase suppresses its ATPase activity and determined the mechanism of suppression. First, we employed vesicles to show that in intact membrane-embedded mycobacterial F-ATP synthases deletion of the C-terminal domain enabled ATPase and proton-pumping activity. We then generated a heterologous F-ATP synthase model system, which demonstrated that transfer of the mycobacterial C-terminal domain to a standard F-ATP synthase α subunit suppresses ATPase activity. Single-molecule rotation assays indicated that the introduction of this Mycobacterium-specific domain decreased the angular velocity of the power-stroke after ATP binding. Solution X-ray scattering data and NMR results revealed the solution shape of Mtα and the 3D structure of the subunit α C-terminal peptide 521PDEHVEALDEDKLAKEAVKV540 of M. tubercolosis (Mtα(521-540)), respectively. Together with cross-linking studies, the solution structural data lead to a model, in which Mtα(521-540) comes in close proximity with subunit γ residues 104-109, whose interaction may influence the rotation of the camshaft-like subunit γ. Finally, we propose that the unique segment Mtα(514-549), which is accessible at the C terminus of mycobacterial subunit α, is a promising drug epitope.
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Affiliation(s)
- Priya Ragunathan
- From the Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Hendrik Sielaff
- From the Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Lavanya Sundararaman
- From the Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Goran Biuković
- the Department of Microbiology and Immunology, National University of Singapore, Yong Loo Lin School of Medicine, 14 Medical Drive, Singapore 117599, Republic of Singapore
| | | | - Dhirendra Singh
- From the Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Subhashri Kundu
- the Department of Microbiology and Immunology, National University of Singapore, Yong Loo Lin School of Medicine, 14 Medical Drive, Singapore 117599, Republic of Singapore
| | - Thorsten Wohland
- the Departments of Biological Sciences and Chemistry and NUS Centre for Bioimaging Sciences (CBIS), National University of Singapore, 14 Science Drive 4, Singapore 117557, Republic of Singapore, and
| | - Wayne Frasch
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287
| | - Thomas Dick
- the Department of Microbiology and Immunology, National University of Singapore, Yong Loo Lin School of Medicine, 14 Medical Drive, Singapore 117599, Republic of Singapore
| | - Gerhard Grüber
- From the Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore,
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28
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Giorgio V, Guo L, Bassot C, Petronilli V, Bernardi P. Calcium and regulation of the mitochondrial permeability transition. Cell Calcium 2017; 70:56-63. [PMID: 28522037 DOI: 10.1016/j.ceca.2017.05.004] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 05/05/2017] [Accepted: 05/05/2017] [Indexed: 12/11/2022]
Abstract
Recent years have seen renewed interest in the permeability transition pore, a high conductance channel responsible for permeabilization of the inner mitochondrial membrane, a process that leads to depolarization and Ca2+ release. Transient openings may be involved in physiological Ca2+ homeostasis while long-lasting openings may trigger and/or execute cell death. In this review we specifically focus (i) on the hypothesis that the PTP forms from the F-ATP synthase and (ii) on the mechanisms through which Ca2+ can reversibly switch this energy-conserving nanomachine into an energy-dissipating device.
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Affiliation(s)
- Valentina Giorgio
- Department of Biomedical Sciences and CNR Neuroscience Institute, University of Padova, Italy
| | - Lishu Guo
- Department of Biomedical Sciences and CNR Neuroscience Institute, University of Padova, Italy
| | - Claudio Bassot
- Department of Biomedical Sciences and CNR Neuroscience Institute, University of Padova, Italy
| | - Valeria Petronilli
- Department of Biomedical Sciences and CNR Neuroscience Institute, University of Padova, Italy
| | - Paolo Bernardi
- Department of Biomedical Sciences and CNR Neuroscience Institute, University of Padova, Italy.
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29
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Sielaff H, Martin J, Singh D, Biuković G, Grüber G, Frasch WD. Power Stroke Angular Velocity Profiles of Archaeal A-ATP Synthase Versus Thermophilic and Mesophilic F-ATP Synthase Molecular Motors. J Biol Chem 2016; 291:25351-25363. [PMID: 27729450 PMCID: PMC5207238 DOI: 10.1074/jbc.m116.745240] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 10/03/2016] [Indexed: 01/21/2023] Open
Abstract
The angular velocities of ATPase-dependent power strokes as a function of the rotational position for the A-type molecular motor A3B3DF, from the Methanosarcina mazei Gö1 A-ATP synthase, and the thermophilic motor α3β3γ, from Geobacillus stearothermophilus (formerly known as Bacillus PS3) F-ATP synthase, are resolved at 5 μs resolution for the first time. Unexpectedly, the angular velocity profile of the A-type was closely similar in the angular positions of accelerations and decelerations to the profiles of the evolutionarily distant F-type motors of thermophilic and mesophilic origins, and they differ only in the magnitude of their velocities. M. mazei A3B3DF power strokes occurred in 120° steps at saturating ATP concentrations like the F-type motors. However, because ATP-binding dwells did not interrupt the 120° steps at limiting ATP, ATP binding to A3B3DF must occur during the catalytic dwell. Elevated concentrations of ADP did not increase dwells occurring 40° after the catalytic dwell. In F-type motors, elevated ADP induces dwells 40° after the catalytic dwell and slows the overall velocity. The similarities in these power stroke profiles are consistent with a common rotational mechanism for A-type and F-type rotary motors, in which the angular velocity is limited by the rotary position at which ATP binding occurs and by the drag imposed on the axle as it rotates within the ring of stator subunits.
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Affiliation(s)
- Hendrik Sielaff
- the School of Biological Sciences, Nanyang Technological University, Singapore 637551, Republic of Singapore
| | - James Martin
- From the School of Life Sciences, Arizona State University, Tempe, Arizona 85287 and
| | - Dhirendra Singh
- the School of Biological Sciences, Nanyang Technological University, Singapore 637551, Republic of Singapore
| | - Goran Biuković
- the School of Biological Sciences, Nanyang Technological University, Singapore 637551, Republic of Singapore
| | - Gerhard Grüber
- the School of Biological Sciences, Nanyang Technological University, Singapore 637551, Republic of Singapore
| | - Wayne D Frasch
- From the School of Life Sciences, Arizona State University, Tempe, Arizona 85287 and
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30
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Hotra A, Suter M, Biuković G, Ragunathan P, Kundu S, Dick T, Grüber G. Deletion of a unique loop in the mycobacterial F-ATP synthase γ subunit sheds light on its inhibitory role in ATP hydrolysis-driven H(+) pumping. FEBS J 2016; 283:1947-61. [PMID: 26996828 DOI: 10.1111/febs.13715] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/29/2016] [Accepted: 03/15/2016] [Indexed: 11/28/2022]
Abstract
The F1 FO -ATP synthase is one of the enzymes that is essential to meet the energy requirement of both the proliferating aerobic and hypoxic dormant stages of the life cycle of mycobacteria. Most F-ATP synthases consume ATP in the α3 :β3 headpiece to drive the γ subunit, which couples ATP cleavage with proton pumping in the c ring of FO via the bottom of the γ subunit. ATPase-driven H(+) pumping is latent in mycobacteria. The presence of a unique 14 amino acid residue loop of the mycobacterial γ subunit has been described and aligned in close vicinity to the c-ring loop Priya R et al. (2013) J Bioenerg Biomembr 45, 121-129 Here, we used inverted membrane vesicles (IMVs) of fast-growing Mycobacterium smegmatis and a variety of covalent and non-covalent inhibitors to characterize the ATP hydrolysis activity of the F-ATP synthase inside IMVs. These vesicles formed a platform to investigate the function of the unique mycobaterial γ loop by deleting the respective loop-encoding sequence (γ166-179 ) in the genome of M. smegmatis. ATP hydrolysis-driven H(+) pumping was observed in IMVs containing the Δγ166-179 mutant protein but not for IMVs containing the wild-type F-ATP synthase. In addition, when compared to the wild-type enzyme, IMVs containing the Δγ166-179 mutant protein showed increased ATP cleavage and lower levels of ATP synthesis, demonstrating that the loop affects ATPase activity, ATPase-driven H(+) pumping and ATP synthesis. These results further indicate that the loop may affect coupling of ATP hydrolysis and synthesis in a different mode.
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Affiliation(s)
- Adam Hotra
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore.,Nanyang Institute of Technology in Health and Medicine, Interdisciplinary Graduate School, Nanyang Technological University, Singapore, Singapore
| | - Manuel Suter
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Goran Biuković
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Priya Ragunathan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Subhashri Kundu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Thomas Dick
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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31
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Carraro M, Bernardi P. Calcium and reactive oxygen species in regulation of the mitochondrial permeability transition and of programmed cell death in yeast. Cell Calcium 2016; 60:102-7. [PMID: 26995056 DOI: 10.1016/j.ceca.2016.03.005] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/07/2016] [Accepted: 03/08/2016] [Indexed: 01/28/2023]
Abstract
Mitochondria-dependent programmed cell death (PCD) in yeast shares many features with the intrinsic apoptotic pathway of mammals. With many stimuli, increased cytosolic [Ca(2+)] and ROS generation are the triggering signals that lead to mitochondrial permeabilization and release of proapoptotic factors, which initiates yeast PCD. While in mammals the permeability transition pore (PTP), a high-conductance inner membrane channel activated by increased matrix Ca(2+) and oxidative stress, is recognized as part of this signaling cascade, whether a similar process occurs in yeast is still debated. The potential role of the PTP in yeast PCD has generally been overlooked because yeast mitochondria lack the Ca(2+) uniporter, which in mammals allows rapid equilibration of cytosolic Ca(2+) with the matrix. In this short review we discuss the nature of the yeast permeability transition and reevaluate its potential role in the effector phase of yeast PCD triggered by Ca(2+) and oxidative stress.
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Affiliation(s)
- Michela Carraro
- Department of Biomedical Sciences and CNR Neuroscience Institute, University of Padova, Italy
| | - Paolo Bernardi
- Department of Biomedical Sciences and CNR Neuroscience Institute, University of Padova, Italy.
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32
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Rasola A, Bernardi P. Reprint of "The mitochondrial permeability transition pore and its adaptive responses in tumor cells". Cell Calcium 2015; 58:18-26. [PMID: 25828565 DOI: 10.1016/j.ceca.2015.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 10/06/2014] [Accepted: 10/07/2014] [Indexed: 02/07/2023]
Abstract
This review covers recent progress on the nature of the mitochondrial permeability transition pore (PTP) – a key effector in the mitochondrial pathways to cell death – and on the adaptive responses of tumor cells that desensitize the PTP to Ca(2+) and reactive oxygen species (ROS), thereby playing an important role in the resistance of tumors to cell death. The discovery that the PTP forms from dimers of F-ATP synthase; and the definition of the Ca(2+)- and ROS-dependent signaling pathways affecting the transition of the F-ATP synthase from an energy-conserving to an energy-dissipating device open new perspectives for therapeutic intervention in cancer cells.
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Affiliation(s)
- Andrea Rasola
- Department of Biomedical Sciences and CNR Neuroscience Institute, University of Padova, Italy.
| | - Paolo Bernardi
- Department of Biomedical Sciences and CNR Neuroscience Institute, University of Padova, Italy.
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33
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Rasola A, Bernardi P. The mitochondrial permeability transition pore and its adaptive responses in tumor cells. Cell Calcium 2014; 56:437-45. [PMID: 25454774 PMCID: PMC4274314 DOI: 10.1016/j.ceca.2014.10.003] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 10/06/2014] [Accepted: 10/07/2014] [Indexed: 01/12/2023]
Abstract
This review covers recent progress on the nature of the mitochondrial permeability transition pore (PTP) - a key effector in the mitochondrial pathways to cell death - and on the adaptive responses of tumor cells that desensitize the PTP to Ca(2+) and reactive oxygen species (ROS), thereby playing an important role in the resistance of tumors to cell death. The discovery that the PTP forms from dimers of F-ATP synthase; and the definition of the Ca(2+)- and ROS-dependent signaling pathways affecting the transition of the F-ATP synthase from an energy-conserving to an energy-dissipating device open new perspectives for therapeutic intervention in cancer cells.
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Affiliation(s)
- Andrea Rasola
- Department of Biomedical Sciences and CNR Neuroscience Institute, University of Padova, Italy.
| | - Paolo Bernardi
- Department of Biomedical Sciences and CNR Neuroscience Institute, University of Padova, Italy.
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34
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Balakrishna AM, Seelert H, Marx SH, Dencher NA, Grüber G. Crystallographic structure of the turbine C-ring from spinach chloroplast F-ATP synthase. Biosci Rep 2014; 34:e00102. [PMID: 27919036 PMCID: PMC3971453 DOI: 10.1042/bsr20130114] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 01/09/2014] [Accepted: 01/13/2014] [Indexed: 11/27/2022] Open
Abstract
In eukaryotic and prokaryotic cells, F-ATP synthases provide energy through the synthesis of ATP. The chloroplast F-ATP synthase (CF1FO-ATP synthase) of plants is integrated into the thylakoid membrane via its FO-domain subunits a, b, b' and c Subunit c with a stoichiometry of 14 and subunit a form the gate for H+-pumping, enabling the coupling of electrochemical energy with ATP synthesis in the F1 sector.Here we report the crystallization and structure determination of the c14-ring of subunit c of the CF1FO-ATP synthase from spinach chloroplasts. The crystals belonged to space group C2, with unit-cell parameters a=144.420, b=99.295, c=123.51 Å, and β=104.34° and diffracted to 4.5 Å resolution. Each c-ring contains 14 monomers in the asymmetric unit. The length of the c-ring is 60.32 Å, with an outer ring diameter 52.30 Å and an inner ring width of 40 Å.
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Affiliation(s)
- Asha Manikkoth Balakrishna
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Holger Seelert
- Physikalische Biochemie, Fachbereich Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str.4, D-64287 Darmstadt, Germany
| | - Sven-Hendric Marx
- Physikalische Biochemie, Fachbereich Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str.4, D-64287 Darmstadt, Germany
| | - Norbert A Dencher
- Physikalische Biochemie, Fachbereich Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str.4, D-64287 Darmstadt, Germany
| | - Gerhard Grüber
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
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