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Koshak AE, Elfaky MA, Albadawi DAI, Abdallah HM, Mohamed GA, Ibrahim SRM, Alzain AA, Khafagy ES, Elsayed EM, Hegazy WAH. Piceatannol: a renaissance in antibacterial innovation unveiling synergistic potency and virulence disruption against serious pathogens. Int Microbiol 2024:10.1007/s10123-024-00532-8. [PMID: 38767683 DOI: 10.1007/s10123-024-00532-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/27/2024] [Accepted: 05/09/2024] [Indexed: 05/22/2024]
Abstract
In the relentless battle against multi-drug resistant Gram-negative bacteria, piceatannol emerges as a beacon of hope, showcasing unparalleled antibacterial efficacy and a unique ability to disrupt virulence factors. Our study illuminates the multifaceted prowess of piceatannol against prominent pathogens-Proteus mirabilis, Pseudomonas aeruginosa, Acinetobacter baumannii, and Klebsiella pneumoniae. Notably, piceatannol demonstrated a remarkable ability to inhibit biofilm formation, reduce bacterial mobility, and diminish extracellular enzyme synthesis.Mechanistic insights into piceatannol's activity unraveled its impact on membrane potential, proton motive force, and ATP production. Furthermore, our study delved into piceatannol's anti-quorum sensing (QS) activity, showcasing its potential to downregulate QS-encoding genes and affirming its affinity to critical QS receptors through molecular docking. Crucially, piceatannol exhibited a low propensity for resistance development, positioning it as a promising candidate for combating antibiotic-resistant strains. Its mild effect on red blood cells (RBCs) suggests safety even at higher concentrations, reinforcing its potential translational value. In an in vivo setting, piceatannol demonstrated protective capabilities, significantly reducing pathogenesis in mice infected with P. aeruginosa and P. mirabilis. This comprehensive analysis positions piceatannol as a renaissance in antibacterial innovation, offering a versatile and effective strategy to confront the evolving challenges posed by resilient Gram-negative pathogens.
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Affiliation(s)
- Abdulrahman E Koshak
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Mahmoud A Elfaky
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Centre for Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Dina A I Albadawi
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Hossam M Abdallah
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
| | - Gamal A Mohamed
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Sabrin R M Ibrahim
- Department of Chemistry, Batterjee Medical College, Preparatory Year Program, Jeddah, 21442, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut, 71526, Egypt
| | - Abdulrahim A Alzain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Wad Madani, 21111, Sudan
| | - El-Sayed Khafagy
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Suez Canal University, Ismailia, 41522, Egypt
| | - Eslam M Elsayed
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, 35043, Germany
- Department of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig, 44519, Egypt
| | - Wael A H Hegazy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig, 44519, Egypt
- Pharmacy Program, Department of Pharmaceutical Sciences, Oman College of Health Sciences, Muscat, 113, Oman
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2
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F1·Fo ATP Synthase/ATPase: Contemporary View on Unidirectional Catalysis. Int J Mol Sci 2023; 24:ijms24065417. [PMID: 36982498 PMCID: PMC10049701 DOI: 10.3390/ijms24065417] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/05/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
F1·Fo-ATP synthases/ATPases (F1·Fo) are molecular machines that couple either ATP synthesis from ADP and phosphate or ATP hydrolysis to the consumption or production of a transmembrane electrochemical gradient of protons. Currently, in view of the spread of drug-resistant disease-causing strains, there is an increasing interest in F1·Fo as new targets for antimicrobial drugs, in particular, anti-tuberculosis drugs, and inhibitors of these membrane proteins are being considered in this capacity. However, the specific drug search is hampered by the complex mechanism of regulation of F1·Fo in bacteria, in particular, in mycobacteria: the enzyme efficiently synthesizes ATP, but is not capable of ATP hydrolysis. In this review, we consider the current state of the problem of “unidirectional” F1·Fo catalysis found in a wide range of bacterial F1·Fo and enzymes from other organisms, the understanding of which will be useful for developing a strategy for the search for new drugs that selectively disrupt the energy production of bacterial cells.
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3
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Krah A, Vogelaar T, de Jong SI, Claridge JK, Bond PJ, McMillan DGG. ATP binding by an F 1F o ATP synthase ε subunit is pH dependent, suggesting a diversity of ε subunit functional regulation in bacteria. Front Mol Biosci 2023; 10:1059673. [PMID: 36923639 PMCID: PMC10010621 DOI: 10.3389/fmolb.2023.1059673] [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: 10/17/2022] [Accepted: 01/03/2023] [Indexed: 03/03/2023] Open
Abstract
It is a conjecture that the ε subunit regulates ATP hydrolytic function of the F1Fo ATP synthase in bacteria. This has been proposed by the ε subunit taking an extended conformation, with a terminal helix probing into the central architecture of the hexameric catalytic domain, preventing ATP hydrolysis. The ε subunit takes a contracted conformation when bound to ATP, thus would not interfere with catalysis. A recent crystallographic study has disputed this; the Caldalkalibacillus thermarum TA2.A1 F1Fo ATP synthase cannot natively hydrolyse ATP, yet studies have demonstrated that the loss of the ε subunit terminal helix results in an ATP synthase capable of ATP hydrolysis, supporting ε subunit function. Analysis of sequence and crystallographic data of the C. thermarum F1Fo ATP synthase revealed two unique histidine residues. Molecular dynamics simulations suggested that the protonation state of these residues may influence ATP binding site stability. Yet these residues lie outside the ATP/Mg2+ binding site of the ε subunit. We then probed the effect of pH on the ATP binding affinity of the ε subunit from the C. thermarum F1Fo ATP synthase at various physiologically relevant pH values. We show that binding affinity changes 5.9 fold between pH 7.0, where binding is weakest, to pH 8.5 where it is strongest. Since the C. thermarum cytoplasm is pH 8.0 when it grows optimally, this correlates to the ε subunit being down due to ATP/Mg2+ affinity, and not being involved in blocking ATP hydrolysis. Here, we have experimentally correlated that the pH of the bacterial cytoplasm is of critical importance for ε subunit ATP affinity regulated by second-shell residues thus the function of the ε subunit changes with growth conditions.
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Affiliation(s)
- Alexander Krah
- Korea Institute for Advanced Study, School of Computational Sciences, Seoul, South Korea.,Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Timothy Vogelaar
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Sam I de Jong
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Jolyon K Claridge
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Peter J Bond
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Duncan G G McMillan
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands.,School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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4
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Yang Q, Olaifa K, Andrew FP, Ajibade PA, Ajunwa OM, Marsili E. Assessment of physiological and electrochemical effects of a repurposed zinc dithiocarbamate complex on Acinetobacter baumannii biofilms. Sci Rep 2022; 12:11701. [PMID: 35810245 PMCID: PMC9271062 DOI: 10.1038/s41598-022-16047-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/04/2022] [Indexed: 11/09/2022] Open
Abstract
Acinetobacter baumannii is an infectious agent of global proportion and concern, partly due to its proficiency in development of antibiotic resistance phenotypes and biofilm formation. Dithiocarbamates (DTC) have been identified as possible alternatives to the current antimicrobials. We report here the evaluation of several DTC-metal complexes against A. baumannii planktonic cells and biofilms. Among the DTC-metal complexes and DTCs tested, ZnL1 (N-methyl-1-phenyldithiocarbamato-S,S' Zn(II)), originally designed as an antitumor agent, is effective against biofilm forming A. baumannii. A MIC value of 12.5 µM, comparable to that of Gentamicin (5 µM) was measured for planktonic cells in tryptic soy broth. Spectroscopy, microscopy and biochemical analyses reveal cell membrane degradation and leakage after treatment with ZnL1. Bioelectrochemical analyses show that ZnL1 reduces biofilm formation and decreases extracellular respiration of pre-formed biofilms, as corroborated by microscopic analyses. Due to the affinity of Zn to cells and the metal chelating nature of L1 ligand, we hypothesize ZnL1 could alter metalloprotein functions in the membranes of A. baumannii cells, leading to altered redox balance. Results indicate that the DTC-Zn metal complex is an effective antimicrobial agent against early A. baumannii biofilms under laboratory conditions.
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Affiliation(s)
- Qing Yang
- Biofilm Laboratory, Department of Chemical and Materials Engineering, School of Engineering and Digital Sciences, Nazarbayev University, 53 Kabanbay Batyr Avenue, Nur-Sultan, 01000, Kazakhstan
| | - Kayode Olaifa
- Biofilm Laboratory, Department of Chemical and Materials Engineering, School of Engineering and Digital Sciences, Nazarbayev University, 53 Kabanbay Batyr Avenue, Nur-Sultan, 01000, Kazakhstan
| | - Fartisincha P Andrew
- Department of Science Laboratory Technology, Modibbo Adama University, Yola, Nigeria
| | - Peter A Ajibade
- School of Chemistry and Physics, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
| | - Obinna M Ajunwa
- Biofilm Laboratory, Department of Chemical and Materials Engineering, School of Engineering and Digital Sciences, Nazarbayev University, 53 Kabanbay Batyr Avenue, Nur-Sultan, 01000, Kazakhstan.,Department of Microbiology, Modibbo Adama University, Yola, Nigeria
| | - Enrico Marsili
- Biofilm Laboratory, Department of Chemical and Materials Engineering, School of Engineering and Digital Sciences, Nazarbayev University, 53 Kabanbay Batyr Avenue, Nur-Sultan, 01000, Kazakhstan.
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5
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Ranjbarvaziri S, Kooiker KB, Ellenberger M, Fajardo G, Zhao M, Vander Roest AS, Woldeyes RA, Koyano TT, Fong R, Ma N, Tian L, Traber GM, Chan F, Perrino J, Reddy S, Chiu W, Wu JC, Woo JY, Ruppel KM, Spudich JA, Snyder MP, Contrepois K, Bernstein D. Altered Cardiac Energetics and Mitochondrial Dysfunction in Hypertrophic Cardiomyopathy. Circulation 2021; 144:1714-1731. [PMID: 34672721 PMCID: PMC8608736 DOI: 10.1161/circulationaha.121.053575] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Hypertrophic cardiomyopathy (HCM) is a complex disease partly explained by the effects of individual gene variants on sarcomeric protein biomechanics. At the cellular level, HCM mutations most commonly enhance force production, leading to higher energy demands. Despite significant advances in elucidating sarcomeric structure-function relationships, there is still much to be learned about the mechanisms that link altered cardiac energetics to HCM phenotypes. In this work, we test the hypothesis that changes in cardiac energetics represent a common pathophysiologic pathway in HCM. METHODS We performed a comprehensive multiomics profile of the molecular (transcripts, metabolites, and complex lipids), ultrastructural, and functional components of HCM energetics using myocardial samples from 27 HCM patients and 13 normal controls (donor hearts). RESULTS Integrated omics analysis revealed alterations in a wide array of biochemical pathways with major dysregulation in fatty acid metabolism, reduction of acylcarnitines, and accumulation of free fatty acids. HCM hearts showed evidence of global energetic decompensation manifested by a decrease in high energy phosphate metabolites (ATP, ADP, and phosphocreatine) and a reduction in mitochondrial genes involved in creatine kinase and ATP synthesis. Accompanying these metabolic derangements, electron microscopy showed an increased fraction of severely damaged mitochondria with reduced cristae density, coinciding with reduced citrate synthase activity and mitochondrial oxidative respiration. These mitochondrial abnormalities were associated with elevated reactive oxygen species and reduced antioxidant defenses. However, despite significant mitochondrial injury, HCM hearts failed to upregulate mitophagic clearance. CONCLUSIONS Overall, our findings suggest that perturbed metabolic signaling and mitochondrial dysfunction are common pathogenic mechanisms in patients with HCM. These results highlight potential new drug targets for attenuation of the clinical disease through improving metabolic function and reducing mitochondrial injury.
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Affiliation(s)
- Sara Ranjbarvaziri
- Department of Pediatrics (S.Ranjbarvaziri, G.F., M.Z., A.S.V.R., S.Reddy, K.M.R., D.B.), Stanford University School of Medicine, CA
- Cardiovascular Research Institute (S.Ranjbarvaziri, G.F., M.Z., A.S.V.R., N.M., L.T., S.Reddy, J.C.W., D.B.), Stanford University School of Medicine, CA
| | - Kristina B Kooiker
- Department of Medicine, Division of Cardiology, University of Washington, Seattle (K.B.K.)
| | - Mathew Ellenberger
- Department of Genetics (M.E., G.M.T., M.P.S., K.C.), Stanford University School of Medicine, CA
| | - Giovanni Fajardo
- Department of Pediatrics (S.Ranjbarvaziri, G.F., M.Z., A.S.V.R., S.Reddy, K.M.R., D.B.), Stanford University School of Medicine, CA
- Cardiovascular Research Institute (S.Ranjbarvaziri, G.F., M.Z., A.S.V.R., N.M., L.T., S.Reddy, J.C.W., D.B.), Stanford University School of Medicine, CA
| | - Mingming Zhao
- Department of Pediatrics (S.Ranjbarvaziri, G.F., M.Z., A.S.V.R., S.Reddy, K.M.R., D.B.), Stanford University School of Medicine, CA
- Cardiovascular Research Institute (S.Ranjbarvaziri, G.F., M.Z., A.S.V.R., N.M., L.T., S.Reddy, J.C.W., D.B.), Stanford University School of Medicine, CA
| | - Alison Schroer Vander Roest
- Department of Pediatrics (S.Ranjbarvaziri, G.F., M.Z., A.S.V.R., S.Reddy, K.M.R., D.B.), Stanford University School of Medicine, CA
- Cardiovascular Research Institute (S.Ranjbarvaziri, G.F., M.Z., A.S.V.R., N.M., L.T., S.Reddy, J.C.W., D.B.), Stanford University School of Medicine, CA
| | - Rahel A Woldeyes
- Department of Bioengineering (R.A.W., W.C.), Stanford University, CA
| | - Tiffany T Koyano
- Department of Cardiothoracic Surgery (T.T.K., R.F., J.Y.W.), Stanford University, CA
| | - Robyn Fong
- Department of Cardiothoracic Surgery (T.T.K., R.F., J.Y.W.), Stanford University, CA
| | - Ning Ma
- Cardiovascular Research Institute (S.Ranjbarvaziri, G.F., M.Z., A.S.V.R., N.M., L.T., S.Reddy, J.C.W., D.B.), Stanford University School of Medicine, CA
- Department of Medicine, Division of Cardiology (N.M., L.T., J.C.W.), Stanford University, CA
| | - Lei Tian
- Cardiovascular Research Institute (S.Ranjbarvaziri, G.F., M.Z., A.S.V.R., N.M., L.T., S.Reddy, J.C.W., D.B.), Stanford University School of Medicine, CA
- Department of Medicine, Division of Cardiology (N.M., L.T., J.C.W.), Stanford University, CA
| | - Gavin M Traber
- Department of Genetics (M.E., G.M.T., M.P.S., K.C.), Stanford University School of Medicine, CA
| | - Frandics Chan
- Department of Radiology (F.C.), Stanford University, CA
| | - John Perrino
- Cell Sciences Imaging Facility (J.P.), Stanford University, CA
| | - Sushma Reddy
- Department of Pediatrics (S.Ranjbarvaziri, G.F., M.Z., A.S.V.R., S.Reddy, K.M.R., D.B.), Stanford University School of Medicine, CA
- Cardiovascular Research Institute (S.Ranjbarvaziri, G.F., M.Z., A.S.V.R., N.M., L.T., S.Reddy, J.C.W., D.B.), Stanford University School of Medicine, CA
| | - Wah Chiu
- Department of Bioengineering (R.A.W., W.C.), Stanford University, CA
- Division of Cryo-Electron Microscopy and Bioimaging, SLAC National Accelerator Laboratory (W.C.), Stanford University, CA
| | - Joseph C Wu
- Cardiovascular Research Institute (S.Ranjbarvaziri, G.F., M.Z., A.S.V.R., N.M., L.T., S.Reddy, J.C.W., D.B.), Stanford University School of Medicine, CA
- Department of Medicine, Division of Cardiology (N.M., L.T., J.C.W.), Stanford University, CA
| | - Joseph Y Woo
- Department of Cardiothoracic Surgery (T.T.K., R.F., J.Y.W.), Stanford University, CA
| | - Kathleen M Ruppel
- Department of Pediatrics (S.Ranjbarvaziri, G.F., M.Z., A.S.V.R., S.Reddy, K.M.R., D.B.), Stanford University School of Medicine, CA
- Department of Biochemistry (K.M.R.), Stanford University School of Medicine, CA
| | | | - Michael P Snyder
- Department of Genetics (M.E., G.M.T., M.P.S., K.C.), Stanford University School of Medicine, CA
| | - Kévin Contrepois
- Department of Genetics (M.E., G.M.T., M.P.S., K.C.), Stanford University School of Medicine, CA
| | - Daniel Bernstein
- Department of Pediatrics (S.Ranjbarvaziri, G.F., M.Z., A.S.V.R., S.Reddy, K.M.R., D.B.), Stanford University School of Medicine, CA
- Cardiovascular Research Institute (S.Ranjbarvaziri, G.F., M.Z., A.S.V.R., N.M., L.T., S.Reddy, J.C.W., D.B.), Stanford University School of Medicine, CA
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6
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Jarman OD, Biner O, Hirst J. Regulation of ATP hydrolysis by the ε subunit, ζ subunit and Mg-ADP in the ATP synthase of Paracoccus denitrificans. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148355. [PMID: 33321110 PMCID: PMC8039183 DOI: 10.1016/j.bbabio.2020.148355] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 11/27/2020] [Accepted: 12/08/2020] [Indexed: 12/17/2022]
Abstract
F1FO-ATP synthase is a crucial metabolic enzyme that uses the proton motive force from respiration to regenerate ATP. For maximum thermodynamic efficiency ATP synthesis should be fully reversible, but the enzyme from Paracoccus denitrificans catalyzes ATP hydrolysis at far lower rates than it catalyzes ATP synthesis, an effect often attributed to its unique ζ subunit. Recently, we showed that deleting ζ increases hydrolysis only marginally, indicating that other common inhibitory mechanisms such as inhibition by the C-terminal domain of the ε subunit (ε-CTD) or Mg-ADP may be more important. Here, we created mutants lacking the ε-CTD, and double mutants lacking both the ε-CTD and ζ subunit. No substantial activation of ATP hydrolysis was observed in any of these strains. Instead, hydrolysis in even the double mutant strains could only be activated by oxyanions, the detergent lauryldimethylamine oxide, or a proton motive force, which are all considered to release Mg-ADP inhibition. Our results establish that P. denitrificans ATP synthase is regulated by a combination of the ε and ζ subunits and Mg-ADP inhibition.
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Affiliation(s)
- Owen D Jarman
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Olivier Biner
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Judy Hirst
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.
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7
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Krah A, Huber RG, McMillan DGG, Bond PJ. The Molecular Basis for Purine Binding Selectivity in the Bacterial ATP Synthase ϵ Subunit. Chembiochem 2020; 21:3249-3254. [PMID: 32608105 DOI: 10.1002/cbic.202000291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/30/2020] [Indexed: 12/21/2022]
Abstract
The ϵ subunit of ATP synthases has been proposed to regulate ATP hydrolysis in bacteria. Prevailing evidence supports the notion that when the ATP concentration falls below a certain threshold, the ϵ subunit changes its conformation from a non-inhibitory down-state to an extended up-state that then inhibits enzymatic ATP hydrolysis by binding to the catalytic domain. It has been demonstrated that the ϵ subunit from Bacillus PS3 is selective for ATP over other nucleotides, including GTP. In this study, the purine triphosphate selectivity is rationalized by using results from MD simulations and free energy calculations for the R103A/R115A mutant of the ϵ subunit from Bacillus PS3, which binds ATP more strongly than the wild-type protein. Our results are in good agreement with experimental data, and the elucidated molecular basis for selectivity could help to guide the design of novel GTP sensors.
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Affiliation(s)
- Alexander Krah
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Str. #07-01 Matrix, Singapore, 138671, Singapore.,Korea Institute for Advanced Study, School of Computational Sciences, 85 Hoegiro, Dongdaemun-gu, Seoul, 02455, Republic of Korea
| | - Roland G Huber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Str. #07-01 Matrix, Singapore, 138671, Singapore
| | - Duncan G G McMillan
- Delft University of Technology, Department of Biotechnology, Van der Maasweg 9, Delft, 2629HZ, The Netherlands
| | - Peter J Bond
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Str. #07-01 Matrix, Singapore, 138671, Singapore.,National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore, 117543, Singapore
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8
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Milgrom YM, Duncan TM. F-ATP-ase of Escherichia coli membranes: The ubiquitous MgADP-inhibited state and the inhibited state induced by the ε-subunit's C-terminal domain are mutually exclusive. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148189. [PMID: 32194063 DOI: 10.1016/j.bbabio.2020.148189] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/10/2020] [Accepted: 03/13/2020] [Indexed: 12/21/2022]
Abstract
ATP synthases are important energy-coupling, rotary motor enzymes in all kingdoms of life. In all F-type ATP synthases, the central rotor of the catalytic F1 complex is composed of the γ subunit and the N-terminal domain (NTD) of the ε subunit. In the enzymes of diverse bacteria, the C-terminal domain of ε (εCTD) can undergo a dramatic conformational change to trap the enzyme in a transiently inactive state. This inhibitory mechanism is absent in the mitochondrial enzyme, so the εCTD could provide a means to selectively target ATP synthases of pathogenic bacteria for antibiotic development. For Escherichia coli and other bacterial model systems, it has been difficult to dissect the relationship between ε inhibition and a MgADP-inhibited state that is ubiquitous for FOF1 from bacteria and eukaryotes. A prior study with the isolated catalytic complex from E. coli, EcF1, showed that these two modes of inhibition are mutually exclusive, but it has long been known that interactions of F1 with the membrane-embedded FO complex modulate inhibition by the εCTD. Here, we study membranes containing EcFOF1 with wild-type ε, ε lacking the full εCTD, or ε with a small deletion at the C-terminus. By using compounds with distinct activating effects on F-ATP-ase activity, we confirm that εCTD inhibition and ubiquitous MgADP inhibition are mutually exclusive for membrane-bound E. coli F-ATP-ase. We determine that most of the enzyme complexes in wild-type membranes are in the ε-inhibited state (>50%) or in the MgADP-inhibited state (30%).
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Affiliation(s)
- Yakov M Milgrom
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, 750 E Adams St, Syracuse, NY 13210, USA.
| | - Thomas M Duncan
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, 750 E Adams St, Syracuse, NY 13210, USA.
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9
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Zhou L, Sazanov LA. Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase. Science 2020; 365:365/6455/eaaw9144. [PMID: 31439765 DOI: 10.1126/science.aaw9144] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 07/10/2019] [Indexed: 12/21/2022]
Abstract
V (vacuolar)/A (archaeal)-type adenosine triphosphatases (ATPases), found in archaea and eubacteria, couple ATP hydrolysis or synthesis to proton translocation across the plasma membrane using the rotary-catalysis mechanism. They belong to the V-type ATPase family, which differs from the mitochondrial/chloroplast F-type ATP synthases in overall architecture. We solved cryo-electron microscopy structures of the intact Thermus thermophilus V/A-ATPase, reconstituted into lipid nanodiscs, in three rotational states and two substates. These structures indicate substantial flexibility between V1 and Vo in a working enzyme, which results from mechanical competition between central shaft rotation and resistance from the peripheral stalks. We also describe details of adenosine diphosphate inhibition release, V1-Vo torque transmission, and proton translocation, which are relevant for the entire V-type ATPase family.
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Affiliation(s)
- Long Zhou
- Institute of Science and Technology Austria, Klosterneuberg 3400, Austria
| | - Leonid A Sazanov
- Institute of Science and Technology Austria, Klosterneuberg 3400, Austria.
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10
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Functional importance of αAsp-350 in the catalytic sites of Escherichia coli ATP synthase. Arch Biochem Biophys 2019; 672:108050. [PMID: 31330132 DOI: 10.1016/j.abb.2019.07.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 07/10/2019] [Accepted: 07/18/2019] [Indexed: 12/21/2022]
Abstract
Negatively charged residue αAsp-350 of the highly conserved VISIT-DG sequence is required for Pi binding and maintenance of the phosphate-binding subdomain in the catalytic sites of Escherichia coli F1Fo ATP synthase. αAsp-350 is situated in close proximity, 2.88 Å and 3.5 Å, to the conserved known phosphate-binding residues αR376 and βR182. αD350 is also in close proximity, 1.3 Å, to another functionally important residue αG351. Mutation of αAsp-350 to Ala, Gln, or Arg resulted in substantial loss of oxidative phosphorylation and reduction in ATPase activity by 6- to 16-fold. The loss of the acidic side chain in the form of αD350A, αD350Q, and αD350R caused loss of Pi binding. While removal of Arg in the form of αR376D resulted in the loss of Pi binding, the addition of Arg in the form of αG351R did not affect Pi binding. Our data demonstrates that αD350R helps in the proper orientation of αR376 and βR182 for Pi binding. Fluoroaluminate, fluoroscandium, and sodium azide caused almost complete inhibition of wild type enzyme and caused variable inhibition of αD350 mutant enzymes. NBD-Cl (4-chloro-7-nitrobenzo-2-oxa-1, 3-diazole) caused complete inhibition of wild type enzyme while some residual activity was left in mutant enzymes. Inhibition characteristics supported the conclusion that NBD-Cl reacts in βE (empty) catalytic sites. Phosphate protected against NBD-Cl inhibition of wild type and αG351R mutant enzymes but not inhibition of αD350A, αD350Q, αD350R, or αR376D mutant enzymes. These results demonstrate that αAsp-350 is an essential residue required for phosphate binding, through its interaction with αR376 and βR182, for normal function of phosphate binding subdomain and for transition state stabilization in ATP synthase catalytic sites.
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11
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Petri J, Nakatani Y, Montgomery MG, Ferguson SA, Aragão D, Leslie AGW, Heikal A, Walker JE, Cook GM. Structure of F 1-ATPase from the obligate anaerobe Fusobacterium nucleatum. Open Biol 2019; 9:190066. [PMID: 31238823 PMCID: PMC6597759 DOI: 10.1098/rsob.190066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The crystal structure of the F1-catalytic domain of the adenosine triphosphate (ATP) synthase has been determined from the pathogenic anaerobic bacterium Fusobacterium nucleatum. The enzyme can hydrolyse ATP but is partially inhibited. The structure is similar to those of the F1-ATPases from Caldalkalibacillus thermarum, which is more strongly inhibited in ATP hydrolysis, and in Mycobacterium smegmatis, which has a very low ATP hydrolytic activity. The βE-subunits in all three enzymes are in the conventional ‘open’ state, and in the case of C. thermarum and M. smegmatis, they are occupied by an ADP and phosphate (or sulfate), but in F. nucleatum, the occupancy by ADP appears to be partial. It is likely that the hydrolytic activity of the F. nucleatum enzyme is regulated by the concentration of ADP, as in mitochondria.
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Affiliation(s)
- Jessica Petri
- 1 Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago , Dunedin 9054 , New Zealand
| | - Yoshio Nakatani
- 1 Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago , Dunedin 9054 , New Zealand.,2 Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland , Private Bag 92019, Auckland 1042 , New Zealand
| | - Martin G Montgomery
- 3 Medical Research Council Mitochondrial Biology Unit , Cambridge Biomedical Campus, Cambridge CB2 0XY , UK
| | - Scott A Ferguson
- 1 Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago , Dunedin 9054 , New Zealand
| | - David Aragão
- 4 Australian Synchrotron , 800 Blackburn Road, Clayton, Victoria 3168 , Australia
| | - Andrew G W Leslie
- 5 Medical Research Council Laboratory of Molecular Biology , Cambridge Biomedical Campus, Cambridge CB2 0QH , UK
| | - Adam Heikal
- 1 Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago , Dunedin 9054 , New Zealand.,2 Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland , Private Bag 92019, Auckland 1042 , New Zealand
| | - John E Walker
- 3 Medical Research Council Mitochondrial Biology Unit , Cambridge Biomedical Campus, Cambridge CB2 0XY , UK
| | - Gregory M Cook
- 1 Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago , Dunedin 9054 , New Zealand.,2 Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland , Private Bag 92019, Auckland 1042 , New Zealand
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12
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Krasnoselska GO, Meier T. Purification and Reconstitution of Ilyobacter tartaricus ATP Synthase. Methods Mol Biol 2019; 1805:51-71. [PMID: 29971712 DOI: 10.1007/978-1-4939-8556-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
F-type adenosine triphosphate (ATP) synthase is a membrane-bound macromolecular complex, which is responsible for the synthesis of ATP, the universal energy source in living cells. This enzyme uses the proton- or sodium-motive force to power ATP synthesis by a unique rotary mechanism and can also operate in reverse, ATP hydrolysis, to generate ion gradients across membranes. The F1Fo-ATP synthases from bacteria consist of eight different structural subunits, forming a complex of ∼550 kDa in size. In the bacterium Ilyobacter tartaricus the ATP synthase has the stoichiometry α3β3γδεab2c11. This chapter describes a wet-lab working protocol for the purification of several tens of milligrams of pure, heterologously (E. coli-)produced I. tartaricus Na+-driven F1Fo-ATP synthase and its subsequent efficient reconstitution into proteoliposomes. The methods are useful for a broad range of subsequent biochemical and biotechnological applications.
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Affiliation(s)
- Ganna O Krasnoselska
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Thomas Meier
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
- Department of Life Sciences, Imperial College London, London, UK.
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13
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Meyrat A, von Ballmoos C. ATP synthesis at physiological nucleotide concentrations. Sci Rep 2019; 9:3070. [PMID: 30816129 PMCID: PMC6395684 DOI: 10.1038/s41598-019-38564-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 12/31/2018] [Indexed: 12/23/2022] Open
Abstract
Synthesis of ATP by the F1F0 ATP synthase in mitochondria and most bacteria is energized by the proton motive force (pmf) established and maintained by respiratory chain enzymes. Conversely, in the presence of ATP and in the absence of a pmf, the enzyme works as an ATP-driven proton pump. Here, we investigate how high concentrations of ATP affect the enzymatic activity of the F1F0 ATP synthase under high pmf conditions, which is the typical situation in mitochondria or growing bacteria. Using the ATP analogue adenosine 5′-O-(1-thiotriphosphate) (ATPαS), we have developed a modified luminescence-based assay to measure ATP synthesis in the presence of millimolar ATP concentrations, replacing an assay using radioactive nucleotides. In inverted membrane vesicles of E. coli, we found that under saturating pmf conditions, ATP synthesis was reduced to ~10% at 5 mM ATPαS. This reduction was reversed by ADP, but not Pi, indicating that the ATP/ADP ratio controls the ATP synthesis rate. Our data suggests that the ATP/ADP ratio ~30 in growing E. coli limits the ATP synthesis rate to ~20% of the maximal rate possible at the applied pmf and that the rate reduction occurs via product inhibition rather than an increased ATP hydrolysis rate.
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Affiliation(s)
- Axel Meyrat
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Christoph von Ballmoos
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland.
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14
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The structure of the catalytic domain of the ATP synthase from Mycobacterium smegmatis is a target for developing antitubercular drugs. Proc Natl Acad Sci U S A 2019; 116:4206-4211. [PMID: 30683723 DOI: 10.1073/pnas.1817615116] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The crystal structure of the F1-catalytic domain of the adenosine triphosphate (ATP) synthase has been determined from Mycobacterium smegmatis which hydrolyzes ATP very poorly. The structure of the α3β3-component of the catalytic domain is similar to those in active F1-ATPases in Escherichia coli and Geobacillus stearothermophilus However, its ε-subunit differs from those in these two active bacterial F1-ATPases as an ATP molecule is not bound to the two α-helices forming its C-terminal domain, probably because they are shorter than those in active enzymes and they lack an amino acid that contributes to the ATP binding site in active enzymes. In E. coli and G. stearothermophilus, the α-helices adopt an "up" state where the α-helices enter the α3β3-domain and prevent the rotor from turning. The mycobacterial F1-ATPase is most similar to the F1-ATPase from Caldalkalibacillus thermarum, which also hydrolyzes ATP poorly. The βE-subunits in both enzymes are in the usual "open" conformation but appear to be occupied uniquely by the combination of an adenosine 5'-diphosphate molecule with no magnesium ion plus phosphate. This occupation is consistent with the finding that their rotors have been arrested at the same point in their rotary catalytic cycles. These bound hydrolytic products are probably the basis of the inhibition of ATP hydrolysis. It can be envisaged that specific as yet unidentified small molecules might bind to the F1 domain in Mycobacterium tuberculosis, prevent ATP synthesis, and inhibit the growth of the pathogen.
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15
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Mutation Q259L in subunit beta in Bacillus subtilis ATP synthase attenuates ADP-inhibition and decreases fitness in mixed cultures. Biochem Biophys Res Commun 2018; 509:102-107. [PMID: 30580998 DOI: 10.1016/j.bbrc.2018.12.075] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 12/11/2018] [Indexed: 11/23/2022]
Abstract
The ATPase activity of H+-FOF1-ATP synthase (FOF1) is down-regulated by several mechanisms. The most universal of them found in bacterial, chloroplast and mitochondrial enzymes is non-competitive inhibition by MgADP (ADP-inhibition). When MgADP binds in a catalytic site in the absence of phosphate, the nucleotide might be trapped instead of being released and replaced by new MgATP. In this case the enzyme becomes inactivated, and MgADP release is required for re-activation. The degree of ADP-inhibition varies between different organisms: it is strong in mitochondrial and chloroplast FOF1 and in enzymes of some bacteria (including Bacillus PS3 sp., and Bacillus subtilis), but in FOF1 of Escherichia coli it is much weaker. It was shown that mutation betaGln259Leu in Bacillus PS3 FOF1 noticeably relieves its strong ADP-inhibition. In this work, we introduced the same mutation in FOF1 from B. subtilis. ADP-inhibition in the mutant FOF1 was also attenuated in comparison to the wild-type enzyme. The ATPase activity in membrane preparations was 3 fold higher in the mutant. Mutant enzyme was capable of ATP-driven proton pumping, and its ATPase activity was stimulated by dissipation of the protonmotive force, implying that the coupling efficiency between ATP hydrolysis and proton transport was not impaired by the mutation. We observed no effect of mutation on the growth rate of B. subtilis in pure cultures. However, in competition growth experiments when the wild type and the mutant strains were cultivated together in mixed cultures, the wild type strain always crowded out the mutant. To our knowledge, this is the first demonstration of the negative effect of FOF1 ADP-inhibition attenuation in vivo.
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16
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Lapashina AS, Feniouk BA. ADP-Inhibition of H+-F OF 1-ATP Synthase. BIOCHEMISTRY (MOSCOW) 2018; 83:1141-1160. [PMID: 30472953 DOI: 10.1134/s0006297918100012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
H+-FOF1-ATP synthase (F-ATPase, F-type ATPase, FOF1 complex) catalyzes ATP synthesis from ADP and inorganic phosphate in eubacteria, mitochondria, chloroplasts, and some archaea. ATP synthesis is powered by the transmembrane proton transport driven by the proton motive force (PMF) generated by the respiratory or photosynthetic electron transport chains. When the PMF is decreased or absent, ATP synthase catalyzes the reverse reaction, working as an ATP-dependent proton pump. The ATPase activity of the enzyme is regulated by several mechanisms, of which the most conserved is the non-competitive inhibition by the MgADP complex (ADP-inhibition). When ADP binds to the catalytic site without phosphate, the enzyme may undergo conformational changes that lock bound ADP, resulting in enzyme inactivation. PMF can induce release of inhibitory ADP and reactivate ATP synthase; the threshold PMF value required for enzyme reactivation might exceed the PMF for ATP synthesis. Moreover, membrane energization increases the catalytic site affinity to phosphate, thereby reducing the probability of ADP binding without phosphate and preventing enzyme transition to the ADP-inhibited state. Besides phosphate, oxyanions (e.g., sulfite and bicarbonate), alcohols, lauryldimethylamine oxide, and a number of other detergents can weaken ADP-inhibition and increase ATPase activity of the enzyme. In this paper, we review the data on ADP-inhibition of ATP synthases from different organisms and discuss the in vivo role of this phenomenon and its relationship with other regulatory mechanisms, such as ATPase activity inhibition by subunit ε and nucleotide binding in the noncatalytic sites of the enzyme. It should be noted that in Escherichia coli enzyme, ADP-inhibition is relatively weak and rather enhanced than prevented by phosphate.
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Affiliation(s)
- A S Lapashina
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - B A Feniouk
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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17
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Lapashina AS, Prikhodko AS, Shugaeva TE, Feniouk BA. Residue 249 in subunit beta regulates ADP inhibition and its phosphate modulation in Escherichia coli ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1860:181-188. [PMID: 30528692 DOI: 10.1016/j.bbabio.2018.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/06/2018] [Accepted: 12/07/2018] [Indexed: 11/29/2022]
Abstract
ATPase activity of proton-translocating FOF1-ATP synthase (F-type ATPase or F-ATPase) is suppressed in the absence of protonmotive force by several regulatory mechanisms. The most conservative of these mechanisms found in all enzymes studied so far is allosteric inhibition of ATP hydrolysis by MgADP (ADP-inhibition). When MgADP is bound without phosphate in the catalytic site, the enzyme lapses into an inactive state with MgADP trapped. In chloroplasts and mitochondria, as well as in most bacteria, phosphate prevents MgADP inhibition. However, in Escherichia coli ATP synthase ADP-inhibition is relatively weak and phosphate does not prevent it but seems to enhance it. We found that a single amino acid residue in subunit β is responsible for these features of E. coli enzyme. Mutation βL249Q significantly enhanced ADP-inhibition in E. coli ATP synthase, increased the extent of ATP hydrolysis stimulation by sulfite, and rendered the ADP-inhibition sensitive to phosphate in the same manner as observed in FOF1 from mitochondria, chloroplasts, and most aerobic\photosynthetic bacteria.
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Affiliation(s)
- Anna S Lapashina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Anastasia S Prikhodko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Tatiana E Shugaeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Boris A Feniouk
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia.
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18
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19
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Machado D, Girardini M, Viveiros M, Pieroni M. Challenging the Drug-Likeness Dogma for New Drug Discovery in Tuberculosis. Front Microbiol 2018; 9:1367. [PMID: 30018597 PMCID: PMC6037898 DOI: 10.3389/fmicb.2018.01367] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/06/2018] [Indexed: 01/28/2023] Open
Abstract
The emergence of multi- and extensively drug resistant tuberculosis worldwide poses a great threat to human health and highlight the need to discover and develop new, effective and inexpensive antituberculosis agents. High-throughput screening assays against well-validated drug targets and structure based drug design have been employed to discover new lead compounds. However, the great majority fail to demonstrate any antimycobacterial activity when tested against Mycobacterium tuberculosis in whole-cell screening assays. This is mainly due to some of the intrinsic properties of the bacilli, such as the extremely low permeability of its cell wall, slow growth, drug resistance, drug tolerance, and persistence. In this sense, understanding the pathways involved in M. tuberculosis drug tolerance, persistence, and pathogenesis, may reveal new approaches for drug development. Moreover, the need for compounds presenting a novel mode of action is of utmost importance due to the emergence of resistance not only to the currently used antituberculosis agents, but also to those in the pipeline. Cheminformatics studies have shown that drugs endowed with antituberculosis activity have the peculiarity of being more lipophilic than many other antibacterials, likely because this leads to improved cell penetration through the extremely waxy mycobacterial cell wall. Moreover, the interaction of the lipophilic moiety with the membrane alters its stability and functional integrity due to the disruption of the proton motive force, resulting in cell death. When a ligand-based medicinal chemistry campaign is ongoing, it is always difficult to predict whether a chemical modification or a functional group would be suitable for improving the activity. Nevertheless, in the “instruction manual” of medicinal chemists, certain functional groups or certain physicochemical characteristics (i.e., high lipophilicity) are considered red flags to look out for in order to safeguard drug-likeness and avoid attritions in the drug discovery process. In this review, we describe how antituberculosis compounds challenge established rules such as the Lipinski's “rule of five” and how medicinal chemistry for antituberculosis compounds must be thought beyond such dogmatic schemes.
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Affiliation(s)
- Diana Machado
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisbon, Portugal
| | - Miriam Girardini
- P4T Group, Department of Food and Drug, University of Parma, Parma, Italy
| | - Miguel Viveiros
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisbon, Portugal
| | - Marco Pieroni
- P4T Group, Department of Food and Drug, University of Parma, Parma, Italy
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20
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Sielaff H, Duncan TM, Börsch M. The regulatory subunit ε in Escherichia coli F OF 1-ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:775-788. [PMID: 29932911 DOI: 10.1016/j.bbabio.2018.06.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 06/13/2018] [Accepted: 06/14/2018] [Indexed: 11/16/2022]
Abstract
F-type ATP synthases are extraordinary multisubunit proteins that operate as nanomotors. The Escherichia coli (E. coli) enzyme uses the proton motive force (pmf) across the bacterial plasma membrane to drive rotation of the central rotor subunits within a stator subunit complex. Through this mechanical rotation, the rotor coordinates three nucleotide binding sites that sequentially catalyze the synthesis of ATP. Moreover, the enzyme can hydrolyze ATP to turn the rotor in the opposite direction and generate pmf. The direction of net catalysis, i.e. synthesis or hydrolysis of ATP, depends on the cell's bioenergetic conditions. Different control mechanisms have been found for ATP synthases in mitochondria, chloroplasts and bacteria. This review discusses the auto-inhibitory behavior of subunit ε found in FOF1-ATP synthases of many bacteria. We focus on E. coli FOF1-ATP synthase, with insights into the regulatory mechanism of subunit ε arising from structural and biochemical studies complemented by single-molecule microscopy experiments.
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Affiliation(s)
- Hendrik Sielaff
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Thomas M Duncan
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany.
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21
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Shepherd DL, Hathaway QA, Nichols CE, Durr AJ, Pinti MV, Hughes KM, Kunovac A, Stine SM, Hollander JM. Mitochondrial proteome disruption in the diabetic heart through targeted epigenetic regulation at the mitochondrial heat shock protein 70 (mtHsp70) nuclear locus. J Mol Cell Cardiol 2018; 119:104-115. [PMID: 29733819 DOI: 10.1016/j.yjmcc.2018.04.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 04/26/2018] [Accepted: 04/28/2018] [Indexed: 01/17/2023]
Abstract
>99% of the mitochondrial proteome is nuclear-encoded. The mitochondrion relies on a coordinated multi-complex process for nuclear genome-encoded mitochondrial protein import. Mitochondrial heat shock protein 70 (mtHsp70) is a key component of this process and a central constituent of the protein import motor. Type 2 diabetes mellitus (T2DM) disrupts mitochondrial proteomic signature which is associated with decreased protein import efficiency. The goal of this study was to manipulate the mitochondrial protein import process through targeted restoration of mtHsp70, in an effort to restore proteomic signature and mitochondrial function in the T2DM heart. A novel line of cardiac-specific mtHsp70 transgenic mice on the db/db background were generated and cardiac mitochondrial subpopulations were isolated with proteomic evaluation and mitochondrial function assessed. MicroRNA and epigenetic regulation of the mtHsp70 gene during T2DM were also evaluated. MtHsp70 overexpression restored cardiac function and nuclear-encoded mitochondrial protein import, contributing to a beneficial impact on proteome signature and enhanced mitochondrial function during T2DM. Further, transcriptional repression at the mtHsp70 genomic locus through increased localization of H3K27me3 during T2DM insult was observed. Our results suggest that restoration of a key protein import constituent, mtHsp70, provides therapeutic benefit through attenuation of mitochondrial and contractile dysfunction in T2DM.
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Affiliation(s)
- Danielle L Shepherd
- Division of Exercise Physiology, Mitochondrial, Metabolism and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV 26505, United States
| | - Quincy A Hathaway
- Division of Exercise Physiology, Mitochondrial, Metabolism and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV 26505, United States
| | - Cody E Nichols
- Division of Exercise Physiology, Mitochondrial, Metabolism and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV 26505, United States
| | - Andrya J Durr
- Division of Exercise Physiology, Mitochondrial, Metabolism and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV 26505, United States
| | - Mark V Pinti
- Division of Exercise Physiology, Mitochondrial, Metabolism and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV 26505, United States
| | - Kristen M Hughes
- Division of Exercise Physiology, Mitochondrial, Metabolism and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV 26505, United States
| | - Amina Kunovac
- Division of Exercise Physiology, Mitochondrial, Metabolism and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV 26505, United States
| | - Seth M Stine
- Division of Exercise Physiology, Mitochondrial, Metabolism and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV 26505, United States
| | - John M Hollander
- Division of Exercise Physiology, Mitochondrial, Metabolism and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV 26505, United States.
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Krah A, Zarco-Zavala M, McMillan DGG. Insights into the regulatory function of the ɛ subunit from bacterial F-type ATP synthases: a comparison of structural, biochemical and biophysical data. Open Biol 2018; 8:170275. [PMID: 29769322 PMCID: PMC5990651 DOI: 10.1098/rsob.170275] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 04/24/2018] [Indexed: 01/07/2023] Open
Abstract
ATP synthases catalyse the formation of ATP, the most common chemical energy storage unit found in living cells. These enzymes are driven by an electrochemical ion gradient, which allows the catalytic evolution of ATP by a binding change mechanism. Most ATP synthases are capable of catalysing ATP hydrolysis to varying degrees, and to prevent wasteful ATP hydrolysis, bacteria and mitochondria have regulatory mechanisms such as ADP inhibition. Additionally, ɛ subunit inhibition has also been described in three bacterial systems, Escherichia coli, Bacillus PS3 and Caldalkalibacillus thermarum TA2.A1. Previous studies suggest that the ɛ subunit is capable of undergoing an ATP-dependent conformational change from the ATP hydrolytic inhibitory 'extended' conformation to the ATP-induced non-inhibitory 'hairpin' conformation. A recently published crystal structure of the F1 domain of the C. thermarum TA2.A1 F1Fo ATP synthase revealed a mutant ɛ subunit lacking the ability to bind ATP in a hairpin conformation. This is a surprising observation considering it is an organism that performs no ATP hydrolysis in vivo, and appears to challenge the current dogma on the regulatory role of the ɛ subunit. This has prompted a re-examination of present knowledge of the ɛ subunits role in different organisms. Here, we compare published biochemical, biophysical and structural data involving ɛ subunit-mediated ATP hydrolysis regulation in a variety of organisms, concluding that the ɛ subunit from the bacterial F-type ATP synthases is indeed capable of regulating ATP hydrolysis activity in a wide variety of bacteria, making it a potentially valuable drug target, but its exact role is still under debate.
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Affiliation(s)
- Alexander Krah
- School of Computational Sciences, Korea Institute for Advanced Study, 85 Hoegiro Dongdaemun-gu, Seoul 02455, Republic of Korea
| | - Mariel Zarco-Zavala
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Duncan G G McMillan
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, Delft 2629 HZ, The Netherlands
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Tkachenko AG. Stress Responses of Bacterial Cells as Mechanism of Development of Antibiotic Tolerance (Review). APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683818020114] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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24
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Singh D, Grüber G. Crystallographic and enzymatic insights into the mechanisms of Mg-ADP inhibition in the A 1 complex of the A 1A O ATP synthase. J Struct Biol 2017; 201:26-35. [PMID: 29074108 DOI: 10.1016/j.jsb.2017.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 10/19/2017] [Accepted: 10/21/2017] [Indexed: 01/02/2023]
Abstract
F-ATP synthases are described to have mechanisms which regulate the unnecessary depletion of ATP pool during an energy limited state of the cell. Mg-ADP inhibition is one of the regulatory features where Mg-ADP gets entrapped in the catalytic site, preventing the binding of ATP and further inhibiting ATP hydrolysis. Knowledge about the existence and regulation of the related archaeal-type A1AO ATP synthases (A3B3CDE2FG2ac) is limited. We demonstrate MgADP inhibition of the enzymatically active A3B3D- and A3B3DF complexes of Methanosarcina mazei Gö1 A-ATP synthase and reveal the importance of the amino acids P235 and S238 inside the P-loop (GPFGSGKTV) of the catalytic A subunit. Substituting these two residues by the respective P-loop residues alanine and cysteine (GAFGCGKTV) of the related eukaryotic V-ATPase increases significantly the ATPase activity of the enzyme variant and abolishes MgADP inhibition. The atomic structure of the P235A, S238C double mutant of subunit A of the Pyrococcus horikoshii OT3 A-ATP synthase provides details of how these critical residues affect nucleotide-binding and ATP hydrolysis in this molecular engine. The qualitative data are confirmed by quantitative results derived from fluorescence correlation spectroscopy experiments.
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Affiliation(s)
- Dhirendra Singh
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Gerhard Grüber
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore.
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25
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Shepherd DL, Hathaway QA, Pinti MV, Nichols CE, Durr AJ, Sreekumar S, Hughes KM, Stine SM, Martinez I, Hollander JM. Exploring the mitochondrial microRNA import pathway through Polynucleotide Phosphorylase (PNPase). J Mol Cell Cardiol 2017; 110:15-25. [PMID: 28709769 PMCID: PMC5854179 DOI: 10.1016/j.yjmcc.2017.06.012] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 06/20/2017] [Accepted: 06/27/2017] [Indexed: 01/01/2023]
Abstract
Cardiovascular disease is the primary cause of mortality for individuals with type 2 diabetes mellitus. During the diabetic condition, cardiovascular dysfunction can be partially attributed to molecular changes in the tissue, including alterations in microRNA (miRNA) interactions. MiRNAs have been reported in the mitochondrion and their presence may influence cellular bioenergetics, creating decrements in functional capacity. In this study, we examined the roles of Argonaute 2 (Ago2), a protein associated with cytosolic and mitochondrial miRNAs, and Polynucleotide Phosphorylase (PNPase), a protein found in the inner membrane space of the mitochondrion, to determine their role in mitochondrial miRNA import. In cardiac tissue from human and mouse models of type 2 diabetes mellitus, Ago2 protein levels were unchanged while PNPase protein expression levels were increased; also, there was an increase in the association between both proteins in the diabetic state. MiRNA-378 was found to be significantly increased in db/db mice, leading to decrements in ATP6 levels and ATP synthase activity, which was also exhibited when overexpressing PNPase in HL-1 cardiomyocytes and in HL-1 cells with stable miRNA-378 overexpression (HL-1-378). To assess potential therapeutic interventions, flow cytometry evaluated the capacity for targeting miRNA-378 species in mitochondria through antimiR treatment, revealing miRNA-378 level-dependent inhibition. Our study establishes PNPase as a contributor to mitochondrial miRNA import through the transport of miRNA-378, which may regulate bioenergetics during type 2 diabetes mellitus. Further, our data provide evidence that manipulation of PNPase levels may enhance the delivery of antimiR therapeutics to mitochondria in physiological and pathological conditions.
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Affiliation(s)
- Danielle L Shepherd
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV 26506, United States; Mitochondria, Metabolism & Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV 26506, United States
| | - Quincy A Hathaway
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV 26506, United States; Mitochondria, Metabolism & Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV 26506, United States
| | - Mark V Pinti
- Mitochondria, Metabolism & Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV 26506, United States
| | - Cody E Nichols
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV 26506, United States
| | - Andrya J Durr
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV 26506, United States; Mitochondria, Metabolism & Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV 26506, United States
| | - Shruthi Sreekumar
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV 26506, United States
| | - Kristen M Hughes
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV 26506, United States
| | - Seth M Stine
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV 26506, United States
| | - Ivan Martinez
- Cancer Cell Biology, West Virginia University School of Medicine, Morgantown, WV 26506, United States
| | - John M Hollander
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV 26506, United States; Mitochondria, Metabolism & Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV 26506, United States.
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26
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Corbin DR, Rehg JE, Shepherd DL, Stoilov P, Percifield RJ, Horner L, Frase S, Zhang YM, Rock CO, Hollander JM, Jackowski S, Leonardi R. Excess coenzyme A reduces skeletal muscle performance and strength in mice overexpressing human PANK2. Mol Genet Metab 2017; 120:350-362. [PMID: 28189602 PMCID: PMC5382100 DOI: 10.1016/j.ymgme.2017.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 02/01/2017] [Indexed: 11/23/2022]
Abstract
Coenzyme A (CoA) is a cofactor that is central to energy metabolism and CoA synthesis is controlled by the enzyme pantothenate kinase (PanK). A transgenic mouse strain expressing human PANK2 was derived to determine the physiological impact of PANK overexpression and elevated CoA levels. The Tg(PANK2) mice expressed high levels of the transgene in skeletal muscle and heart; however, CoA was substantially elevated only in skeletal muscle, possibly associated with the comparatively low endogenous levels of acetyl-CoA, a potent feedback inhibitor of PANK2. Tg(PANK2) mice were smaller, had less skeletal muscle mass and displayed significantly impaired exercise tolerance and grip strength. Skeletal myofibers were characterized by centralized nuclei and aberrant mitochondria. Both the content of fully assembled complex I of the electron transport chain and ATP levels were reduced, while markers of oxidative stress were elevated in Tg(PANK2) skeletal muscle. These abnormalities were not detected in the Tg(PANK2) heart muscle, with the exception of spotty loss of cristae organization in the mitochondria. The data demonstrate that excessively high CoA may be detrimental to skeletal muscle function.
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Affiliation(s)
- Deborah R Corbin
- Department of Biochemistry, West Virginia University, Morgantown, WV 26506, USA
| | - Jerold E Rehg
- Department Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Danielle L Shepherd
- Department of Exercise Physiology, West Virginia University, Morgantown, WV 26506, USA
| | - Peter Stoilov
- Department of Biochemistry, West Virginia University, Morgantown, WV 26506, USA
| | - Ryan J Percifield
- Department of Biology, West Virginia University, Morgantown, WV 26506, USA
| | - Linda Horner
- Cell and Tissue Imaging-Electron Microscopy Shared Resource, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Sharon Frase
- Cell and Tissue Imaging-Electron Microscopy Shared Resource, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yong-Mei Zhang
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - John M Hollander
- Department of Exercise Physiology, West Virginia University, Morgantown, WV 26506, USA
| | - Suzanne Jackowski
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Roberta Leonardi
- Department of Biochemistry, West Virginia University, Morgantown, WV 26506, USA.
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27
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Koh HY, Park H, Lee JH, Han SJ, Sohn YC, Lee SG. Proteomic and transcriptomic investigations on cold-responsive properties of the psychrophilic Antarctic bacterium Psychrobacter sp. PAMC 21119 at subzero temperatures. Environ Microbiol 2016; 19:628-644. [PMID: 27750393 DOI: 10.1111/1462-2920.13578] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 10/12/2016] [Indexed: 11/28/2022]
Abstract
Psychrobacter sp. PAMC 21119, isolated from Antarctic permafrost soil, grows and proliferates at subzero temperatures. However, its major mechanism of cold adaptation regulation remains poorly understood. We investigated the transcriptomic and proteomic responses of this species to cold temperatures by comparing profiles at -5°C and 20°C to understand how extreme microorganisms survive under subzero conditions. We found a total of 2,906 transcripts and 584 differentially expressed genes (≥ twofold, P <0.005) by RNA-seq. Genes for translation, ribosomal structure and biogenesis were upregulated, and lipid transport and metabolism was downregulated at low temperatures. A total of 60 protein spots (≥ 1.8 fold, P < 0.005) showed differential expression on two-dimensional gel electrophoresis and the proteins were identified by mass spectrometry. The most prominent upregulated proteins in response to cold were involved in metabolite transport, protein folding and membrane fluidity. Proteins involved in energy production and conversion, and heme protein synthesis were downregulated. Moreover, isoform exchange of cold-shock proteins was detected at both temperatures. Interestingly, pathways for acetyl-CoA metabolism, putrescine synthesis and amino acid metabolism were upregulated. This study highlights some of the strategies and different physiological states that Psychrobacter sp. PAMC 21119 has developed to adapt to the cold environment in Antarctica.
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Affiliation(s)
- Hye Yeon Koh
- Unit of Polar Genomics Korea Polar Research Institute, Incheon, South Korea.,Department of Marine Molecular Biotechnology, Gangneung-Wonju National University, Gangneung, South Korea
| | - Hyun Park
- Unit of Polar Genomics Korea Polar Research Institute, Incheon, South Korea.,Department of Polar Sciences, University of Science and Technology, Incheon, South Korea
| | - Jun Hyuck Lee
- Unit of Polar Genomics Korea Polar Research Institute, Incheon, South Korea.,Department of Polar Sciences, University of Science and Technology, Incheon, South Korea
| | - Se Jong Han
- Unit of Polar Genomics Korea Polar Research Institute, Incheon, South Korea.,Department of Polar Sciences, University of Science and Technology, Incheon, South Korea
| | - Young Chang Sohn
- Department of Marine Molecular Biotechnology, Gangneung-Wonju National University, Gangneung, South Korea
| | - Sung Gu Lee
- Unit of Polar Genomics Korea Polar Research Institute, Incheon, South Korea.,Department of Polar Sciences, University of Science and Technology, Incheon, South Korea
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28
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Ballmann C, Tang Y, Bush Z, Rowe GC. Adult expression of PGC-1α and -1β in skeletal muscle is not required for endurance exercise-induced enhancement of exercise capacity. Am J Physiol Endocrinol Metab 2016; 311:E928-E938. [PMID: 27780821 PMCID: PMC5183883 DOI: 10.1152/ajpendo.00209.2016] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 09/30/2016] [Accepted: 10/17/2016] [Indexed: 12/17/2022]
Abstract
Exercise has been shown to be the best intervention in the treatment of many diseases. Many of the benefits of exercise are mediated by adaptions induced in skeletal muscle. The peroxisome proliferator-activated receptor gamma coactivator-1 (PGC-1) family of transcriptional coactivators has emerged as being key mediators of the exercise response and is considered to be essential for many of the adaptions seen in skeletal muscle. However, the contribution of the PGC-1s in skeletal muscle has been evaluated by the use of either whole body or congenital skeletal muscle-specific deletion. In these models, PGC-1s were never present, thereby opening the possibility to developmental compensation. Therefore, we generated an inducible muscle-specific deletion of PGC-1α and -1β (iMyo-PGC-1DKO), in which both PGC-1α and -β can be deleted specifically in adult skeletal muscle. These iMyo-PGC-1DKO animals were used to assess the role of both PGC-1α and -1β in adult skeletal muscle and their contribution to the exercise training response. Untrained iMyo-PGC-1DKO animals exhibited a time-dependent decrease in exercise performance 8 wk postdeletion, similar to what was observed in the congenital muscle-specific PGC-1DKOs. However, after 4 wk of voluntary training, the iMyo-PGC-1DKOs exhibited an increase in exercise performance with a similar adaptive response compared with control animals. This increase was associated with an increase in electron transport complex (ETC) expression and activity in the absence of PGC-1α and -1β expression. Taken together these data suggest that PGC-1α and -1β expression are not required for training-induced exercise performance, highlighting the contribution of PGC-1-independent mechanisms.
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Affiliation(s)
- Christopher Ballmann
- Division of Cardiovascular Disease, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama; and
| | - Yawen Tang
- Division of Cardiovascular Disease, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama; and
- Department of Biomedical Engineering, School of Engineering, University of Alabama at Birmingham, Birmingham, Alabama
| | - Zachary Bush
- Division of Cardiovascular Disease, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama; and
| | - Glenn C Rowe
- Division of Cardiovascular Disease, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama; and
- Department of Biomedical Engineering, School of Engineering, University of Alabama at Birmingham, Birmingham, Alabama
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29
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D'Alessandro M, Turina P, Melandri BA, Dunn SD. Modulation of coupling in the Escherichia coli ATP synthase by ADP and P i: Role of the ε subunit C-terminal domain. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1858:34-44. [PMID: 27751906 DOI: 10.1016/j.bbabio.2016.10.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 08/06/2016] [Accepted: 10/13/2016] [Indexed: 01/28/2023]
Abstract
The ε-subunit of ATP-synthase is an endogenous inhibitor of the hydrolysis activity of the complex and its α-helical C-terminal domain (εCTD) undergoes drastic changes among at least two different conformations. Even though this domain is not essential for ATP synthesis activity, there is evidence for its involvement in the coupling mechanism of the pump. Recently, it was proposed that coupling of the ATP synthase can vary as a function of ADP and Pi concentration. In the present work, we have explored the possible role of the εCTD in this ADP- and Pi-dependent coupling, by examining an εCTD-lacking mutant of Escherichia coli. We show that the loss of Pi-dependent coupling can be observed also in the εCTD-less mutant, but the effects of Pi on both proton pumping and ATP hydrolysis were much weaker in the mutant than in the wild-type. We also show that the εCTD strongly influences the binding of ADP to a very tight binding site (half-maximal effect≈1nM); binding at this site induces higher coupling in EFOF1 and increases responses to Pi. It is proposed that one physiological role of the εCTD is to regulate the kinetics and affinity of ADP/Pi binding, promoting ADP/Pi-dependent coupling.
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Affiliation(s)
- M D'Alessandro
- Department of Biology, Laboratory of Biochemistry and Biophysics, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy
| | - P Turina
- Department of Biology, Laboratory of Biochemistry and Biophysics, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy.
| | - B A Melandri
- Department of Biology, Laboratory of Biochemistry and Biophysics, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy
| | - S D Dunn
- Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
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30
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Shao WH, Chen JJ, Fan SH, Lei Y, Xu HB, Zhou J, Cheng PF, Yang YT, Rao CL, Wu B, Liu HP, Xie P. Combined Metabolomics and Proteomics Analysis of Major Depression in an Animal Model: Perturbed Energy Metabolism in the Chronic Mild Stressed Rat Cerebellum. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 19:383-92. [PMID: 26134254 DOI: 10.1089/omi.2014.0164] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Major depressive disorder (MDD) is a highly prevalent, debilitating mental illness of importance for global health. However, its molecular pathophysiology remains poorly understood. Combined proteomics and metabolomics approaches should provide a comprehensive understanding of MDD's etiology. The present study reports novel "-omics" insights from a rodent model of MDD. Cerebellar samples from chronic mild stressed (CMS)-treated depressed rats and controls were compared with a focus on the differentially expressed proteins and metabolites using isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomics and gas chromotography/mass spectrometry (GC-MS) metabolomics techniques, respectively. The combined analyses found significant alterations associated with cerebellar energy metabolism, as indicated by (1) abnormal amino acid metabolism accompanied by corresponding metabolic enzymatic alterations and disturbed protein turnover, (2) increased glycolytic and tricarboxylic acid (TCA) cycle enzyme levels paralleled by changes in the concentrations of associated metabolites, and (3) perturbation of ATP biosynthesis through adenosine accompanied by perturbation of the mitochondrial respiratory chain. To the best of our knowledge, this study is the first to integrate proteomics and metabolomics analyses to examine the pathophysiological mechanism(s) underlying MDD in a CMS rodent model of depression. These results can offer important insights into the pathogenesis of MDD.
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Affiliation(s)
- Wei-hua Shao
- 1 Department of Respiratory Medicine, First Affiliated Hospital of Chongqing Medical University , Chongqing, China .,3 Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University , Chongqing, China .,4 Chongqing Key Laboratory of Neurobiology , Chongqing, China
| | - Jian-jun Chen
- 3 Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University , Chongqing, China .,4 Chongqing Key Laboratory of Neurobiology , Chongqing, China
| | - Song-hua Fan
- 2 Department of Neurology, First Affiliated Hospital of Chongqing Medical University , Chongqing, China .,3 Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University , Chongqing, China .,4 Chongqing Key Laboratory of Neurobiology , Chongqing, China
| | - Yang Lei
- 2 Department of Neurology, First Affiliated Hospital of Chongqing Medical University , Chongqing, China .,3 Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University , Chongqing, China .,4 Chongqing Key Laboratory of Neurobiology , Chongqing, China
| | - Hong-bo Xu
- 2 Department of Neurology, First Affiliated Hospital of Chongqing Medical University , Chongqing, China .,3 Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University , Chongqing, China .,4 Chongqing Key Laboratory of Neurobiology , Chongqing, China
| | - Jian Zhou
- 3 Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University , Chongqing, China .,4 Chongqing Key Laboratory of Neurobiology , Chongqing, China
| | - Peng-fei Cheng
- 2 Department of Neurology, First Affiliated Hospital of Chongqing Medical University , Chongqing, China .,3 Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University , Chongqing, China .,4 Chongqing Key Laboratory of Neurobiology , Chongqing, China
| | - Yong-tao Yang
- 2 Department of Neurology, First Affiliated Hospital of Chongqing Medical University , Chongqing, China .,3 Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University , Chongqing, China .,4 Chongqing Key Laboratory of Neurobiology , Chongqing, China
| | - Cheng-long Rao
- 3 Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University , Chongqing, China .,4 Chongqing Key Laboratory of Neurobiology , Chongqing, China
| | - Bo Wu
- 3 Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University , Chongqing, China .,4 Chongqing Key Laboratory of Neurobiology , Chongqing, China
| | - Hai-peng Liu
- 2 Department of Neurology, First Affiliated Hospital of Chongqing Medical University , Chongqing, China .,3 Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University , Chongqing, China .,4 Chongqing Key Laboratory of Neurobiology , Chongqing, China
| | - Peng Xie
- 2 Department of Neurology, First Affiliated Hospital of Chongqing Medical University , Chongqing, China .,3 Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University , Chongqing, China .,4 Chongqing Key Laboratory of Neurobiology , Chongqing, China
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31
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On the ATP binding site of the ε subunit from bacterial F-type ATP synthases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:332-40. [PMID: 26780667 DOI: 10.1016/j.bbabio.2016.01.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 12/11/2015] [Accepted: 01/14/2016] [Indexed: 11/20/2022]
Abstract
F-type ATP synthases are reversible machinery that not only synthesize adenosine triphosphate (ATP) using an electrochemical gradient across the membrane, but also can hydrolyze ATP to pump ions under certain conditions. To prevent wasteful ATP hydrolysis, subunit ε in bacterial ATP synthases changes its conformation from the non-inhibitory down- to the inhibitory up-state at a low cellular ATP concentration. Recently, a crystal structure of the ε subunit in complex with ATP was solved in a non-biologically relevant dimeric form. Here, to derive the functional ATP binding site motif, we carried out molecular dynamics simulations and free energy calculations. Our results suggest that the ATP binding site markedly differs from the experimental resolved one; we observe a reorientation of several residues, which bind to ATP in the crystal structure. In addition we find that an Mg(2+) ion is coordinated by ATP, replacing interactions of the second chain in the crystal structure. Thus we demonstrate more generally the influence of crystallization effects on ligand binding sites and their respective binding modes. Furthermore, we propose a role for two highly conserved residues to control the ATP binding/unbinding event, which have not been considered before. Additionally our results provide the basis for the rational development of new biosensors based on subunit ε, as shown previously for novel sensors measuring the ATP concentration in cells.
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32
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Abstract
The F1F0-ATP synthase (EC 3.6.1.34) is a remarkable enzyme that functions as a rotary motor. It is found in the inner membranes of Escherichia coli and is responsible for the synthesis of ATP in response to an electrochemical proton gradient. Under some conditions, the enzyme functions reversibly and uses the energy of ATP hydrolysis to generate the gradient. The ATP synthase is composed of eight different polypeptide subunits in a stoichiometry of α3β3γδεab2c10. Traditionally they were divided into two physically separable units: an F1 that catalyzes ATP hydrolysis (α3β3γδε) and a membrane-bound F0 sector that transports protons (ab2c10). In terms of rotary function, the subunits can be divided into rotor subunits (γεc10) and stator subunits (α3β3δab2). The stator subunits include six nucleotide binding sites, three catalytic and three noncatalytic, formed primarily by the β and α subunits, respectively. The stator also includes a peripheral stalk composed of δ and b subunits, and part of the proton channel in subunit a. Among the rotor subunits, the c subunits form a ring in the membrane, and interact with subunit a to form the proton channel. Subunits γ and ε bind to the c-ring subunits, and also communicate with the catalytic sites through interactions with α and β subunits. The eight subunits are expressed from a single operon, and posttranscriptional processing and translational regulation ensure that the polypeptides are made at the proper stoichiometry. Recent studies, including those of other species, have elucidated many structural and rotary properties of this enzyme.
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33
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Linking structural features from mitochondrial and bacterial F-type ATP synthases to their distinct mechanisms of ATPase inhibition. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:94-102. [DOI: 10.1016/j.pbiomolbio.2015.06.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 06/25/2015] [Accepted: 06/26/2015] [Indexed: 01/11/2023]
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34
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On the Mg2+ binding site of the ε subunit from bacterial F-type ATP synthases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1101-12. [DOI: 10.1016/j.bbabio.2015.05.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 05/20/2015] [Accepted: 05/22/2015] [Indexed: 11/19/2022]
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35
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Simple mechanism whereby the F1-ATPase motor rotates with near-perfect chemomechanical energy conversion. Proc Natl Acad Sci U S A 2015. [PMID: 26195785 DOI: 10.1073/pnas.1422885112] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
F1-ATPase is a motor enzyme in which a central shaft γ subunit rotates 120° per ATP in the cylinder made of α3β3 subunits. During rotation, the chemical energy of ATP hydrolysis (ΔGATP) is converted almost entirely into mechanical work by an elusive mechanism. We measured the force for rotation (torque) under various ΔGATP conditions as a function of rotation angles of the γ subunit with quasi-static, single-molecule manipulation and estimated mechanical work (torque × traveled angle) from the area of the function. The torque functions show three sawtooth-like repeats of a steep jump and linear descent in one catalytic turnover, indicating a simple physical model in which the motor is driven by three springs aligned along a 120° rotation angle. Although the second spring is unaffected by ΔGATP, activation of the first spring (timing of the torque jump) delays at low [ATP] (or high [ADP]) and activation of the third spring delays at high [Pi]. These shifts decrease the size and area of the sawtooth (magnitude of the work). Thus, F1-ATPase responds to the change of ΔGATP by shifting the torque jump timing and uses ΔGATP for the mechanical work with near-perfect efficiency.
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36
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Kinetic and hysteretic behavior of ATP hydrolysis of the highly stable dimeric ATP synthase of Polytomella sp. Arch Biochem Biophys 2015; 575:30-7. [PMID: 25843420 DOI: 10.1016/j.abb.2015.03.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 03/20/2015] [Accepted: 03/21/2015] [Indexed: 11/21/2022]
Abstract
The F1FO-ATP synthase of the colorless alga Polytomella sp. exhibits a robust peripheral arm constituted by nine atypical subunits only present in chlorophycean algae. The isolated dimeric enzyme exhibits a latent ATP hydrolytic activity which can be activated by some detergents. To date, the kinetic behavior of the algal ATPase has not been studied. Here we show that while the soluble F1 sector exhibits Michaelis-Menten kinetics, the dimer exhibits a more complex behavior. The kinetic parameters (Vmax and Km) were obtained for both the F1 sector and the dimeric enzyme as isolated or activated by detergent, and this activation was also seen on the enzyme reconstituted in liposomes. Unlike other ATP synthases, the algal dimer hydrolyzes ATP on a wide range of pH and temperature. The enzyme was inhibited by oligomycin, DCCD and Mg-ADP, although oligomycin induced a peculiar inhibition pattern that can be attributed to structural differences in the algal subunit-c. The hydrolytic activity was temperature-dependent and exhibited activation energy of 4 kcal/mol. The enzyme also exhibited a hysteretic behavior with a lag phase strongly dependent on temperature but not on pH, that may be related to a possible regulatory role in vivo.
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Thapa D, Nichols CE, Lewis SE, Shepherd DL, Jagannathan R, Croston TL, Tveter KJ, Holden AA, Baseler WA, Hollander JM. Transgenic overexpression of mitofilin attenuates diabetes mellitus-associated cardiac and mitochondria dysfunction. J Mol Cell Cardiol 2015; 79:212-23. [PMID: 25463274 PMCID: PMC4302057 DOI: 10.1016/j.yjmcc.2014.11.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 10/23/2014] [Accepted: 11/07/2014] [Indexed: 11/20/2022]
Abstract
Mitofilin, also known as heart muscle protein, is an inner mitochondrial membrane structural protein that plays a central role in maintaining cristae morphology and structure. It is a critical component of the mitochondrial contact site and cristae organizing system (MICOS) complex which is important for mitochondrial architecture and cristae morphology. Our laboratory has previously reported alterations in mitochondrial morphology and proteomic make-up during type 1 diabetes mellitus, with mitofilin being significantly down-regulated in interfibrillar mitochondria (IFM). The goal of this study was to investigate whether overexpression of mitofilin can limit mitochondrial disruption associated with the diabetic heart through restoration of mitochondrial morphology and function. A transgenic mouse line overexpressing mitofilin was generated and mice injected intraperitoneally with streptozotocin using a multi low-dose approach. Five weeks following diabetes mellitus onset, cardiac contractile function was assessed. Restoration of ejection fraction and fractional shortening was observed in mitofilin diabetic mice as compared to wild-type controls (P<0.05 for both). Decrements observed in electron transport chain (ETC) complex I, III, IV and V activities, state 3 respiration, lipid peroxidation as well as mitochondria membrane potential in type 1 diabetic IFM were restored in mitofilin diabetic mice (P<0.05 for all). Qualitative analyses of electron micrographs revealed restoration of mitochondrial cristae structure in mitofilin diabetic mice as compared to wild-type controls. Furthermore, measurement of mitochondrial internal complexity using flow cytometry displayed significant reduction in internal complexity in diabetic IFM which was restored in mitofilin diabetic IFM (P<0.05). Taken together these results suggest that transgenic overexpression of mitofilin preserves mitochondrial structure, leading to restoration of mitochondrial function and attenuation of cardiac contractile dysfunction in the diabetic heart.
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Affiliation(s)
- Dharendra Thapa
- West Virginia University School of Medicine, Division of Exercise Physiology, Center for Cardiovascular and Respiratory Sciences, Morgantown, WV 26506, USA
| | - Cody E Nichols
- West Virginia University School of Medicine, Division of Exercise Physiology, Center for Cardiovascular and Respiratory Sciences, Morgantown, WV 26506, USA
| | - Sara E Lewis
- West Virginia University School of Medicine, Division of Exercise Physiology, Center for Cardiovascular and Respiratory Sciences, Morgantown, WV 26506, USA
| | - Danielle L Shepherd
- West Virginia University School of Medicine, Division of Exercise Physiology, Center for Cardiovascular and Respiratory Sciences, Morgantown, WV 26506, USA
| | - Rajaganapathi Jagannathan
- West Virginia University School of Medicine, Division of Exercise Physiology, Center for Cardiovascular and Respiratory Sciences, Morgantown, WV 26506, USA
| | - Tara L Croston
- West Virginia University School of Medicine, Division of Exercise Physiology, Center for Cardiovascular and Respiratory Sciences, Morgantown, WV 26506, USA
| | - Kevin J Tveter
- West Virginia University School of Medicine, Department of Surgery, Morgantown, WV 26506, USA
| | - Anthony A Holden
- West Virginia University School of Medicine, Department of Surgery, Morgantown, WV 26506, USA
| | - Walter A Baseler
- West Virginia University School of Medicine, Division of Exercise Physiology, Center for Cardiovascular and Respiratory Sciences, Morgantown, WV 26506, USA
| | - John M Hollander
- West Virginia University School of Medicine, Division of Exercise Physiology, Center for Cardiovascular and Respiratory Sciences, Morgantown, WV 26506, USA.
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Zharova TV, Vinogradov AD. Oxidative phosphorylation and respiratory control phenomenon in Paracoccus denitrificans plasma membrane. BIOCHEMISTRY (MOSCOW) 2014; 77:1000-7. [PMID: 23157259 DOI: 10.1134/s0006297912090064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Changes in respiratory activity, transmembrane electric potential, and ATP synthesis as induced by additions of limited amounts of ADP and P(i) to tightly coupled inverted (inside-out) Paracoccus denitrificans plasma membrane vesicles were traced. The pattern of the changes was qualitatively the same as those observed for coupled mitochondria during the classical State 4-State 3-State 4 transition. Bacterial vesicles devoid of energy-dependent permeability barriers for the substrates of oxidation and phosphorylation were used as a simple experimental model to investigate two possible mechanisms of respiratory control: (i) in State 4 phosphoryl transfer potential (ATP/ADP × P(i)) is equilibrated with proton-motive force by reversibly operating F(1)·F(o)-ATPase (thermodynamic control); (ii) in State 4 apparent "equilibrium" is reached by unidirectional operation of proton motive force-activated F(1)·F(o)-ATP synthase. The data support the kinetic mechanism of the respiratory control phenomenon.
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Affiliation(s)
- T V Zharova
- Department of Biochemistry, Faculty of Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
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Black PA, Warren RM, Louw GE, van Helden PD, Victor TC, Kana BD. Energy metabolism and drug efflux in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2014; 58:2491-503. [PMID: 24614376 PMCID: PMC3993223 DOI: 10.1128/aac.02293-13] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The inherent drug susceptibility of microorganisms is determined by multiple factors, including growth state, the rate of drug diffusion into and out of the cell, and the intrinsic vulnerability of drug targets with regard to the corresponding antimicrobial agent. Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), remains a significant source of global morbidity and mortality, further exacerbated by its ability to readily evolve drug resistance. It is well accepted that drug resistance in M. tuberculosis is driven by the acquisition of chromosomal mutations in genes encoding drug targets/promoter regions; however, a comprehensive description of the molecular mechanisms that fuel drug resistance in the clinical setting is currently lacking. In this context, there is a growing body of evidence suggesting that active extrusion of drugs from the cell is critical for drug tolerance. M. tuberculosis encodes representatives of a diverse range of multidrug transporters, many of which are dependent on the proton motive force (PMF) or the availability of ATP. This suggests that energy metabolism and ATP production through the PMF, which is established by the electron transport chain (ETC), are critical in determining the drug susceptibility of M. tuberculosis. In this review, we detail advances in the study of the mycobacterial ETC and highlight drugs that target various components of the ETC. We provide an overview of some of the efflux pumps present in M. tuberculosis and their association, if any, with drug transport and concomitant effects on drug resistance. The implications of inhibiting drug extrusion, through the use of efflux pump inhibitors, are also discussed.
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Affiliation(s)
- Philippa A. Black
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - Robin M. Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - Gail E. Louw
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - Paul D. van Helden
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - Thomas C. Victor
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - Bavesh D. Kana
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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40
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ATPase/synthase activity of Paracoccus denitrificans Fo·F1 as related to the respiratory control phenomenon. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1322-9. [PMID: 24732246 DOI: 10.1016/j.bbabio.2014.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 03/21/2014] [Accepted: 04/01/2014] [Indexed: 02/04/2023]
Abstract
The time course of ATP synthesis, oxygen consumption, and change in the membrane potential in Paracoccus denitrificans inside-out plasma membrane vesicles was traced. ATP synthesis initiated by the addition of a limited amount of either ADP or inorganic phosphate proceeded up to very low residual concentrations of the limiting substrate. Accumulated ATP did not decrease the rate of its synthesis initiated by the addition of ADP. The amount of residual ADP determined at State 4 respiration was independent of ten-fold variation of Pi or the presence of ATP. The pH-dependence of Km for Pi could not be fitted to a simple phosphoric acid dissociation curve. Partial inhibition of respiration resulted in a decrease in the rate of ATP synthesis without affecting the ATP/ADP reached at State 4. At pH8.0, hydrolysis of ATP accumulated at State 4 was induced by a low concentration of an uncoupler, whereas complete uncoupling results in rapid inactivation of ATPase. At pH7.0, no reversal of the ATP synthase reaction by the uncoupler was seen. The data show that ATP/ADP×Pi ratio maintained at State 4 is not in equilibrium with respiratory-generated driving force. Possible mechanisms of kinetic control and unidirectional operation of the Fo·F1-ATP synthase are discussed.
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41
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Assembly of the Escherichia coli FoF1 ATP synthase involves distinct subcomplex formation. Biochem Soc Trans 2014; 41:1288-93. [PMID: 24059521 DOI: 10.1042/bst20130096] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The ATP synthase (FoF1) of Escherichia coli couples the translocation of protons across the cytoplasmic membrane by Fo to ATP synthesis or hydrolysis in F1. Whereas good knowledge of the nanostructure and the rotary mechanism of the ATP synthase is at hand, the assembly pathway of the 22 polypeptide chains present in a stoichiometry of ab2c10α3β3γδϵ has so far not received sufficient attention. In our studies, mutants that synthesize different sets of FoF1 subunits allowed the characterization of individually formed stable subcomplexes. Furthermore, the development of a time-delayed in vivo assembly system enabled the subsequent synthesis of particular missing subunits to allow the formation of functional ATP synthase complexes. These observations form the basis for a model that describes the assembly pathway of the E. coli ATP synthase from pre-formed subcomplexes, thereby avoiding membrane proton permeability by a concomitant assembly of the open H+-translocating unit within a coupled FoF1 complex.
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Zhou M, Politis A, Davies R, Liko I, Wu KJ, Stewart AG, Stock D, Robinson CV. Ion mobility-mass spectrometry of a rotary ATPase reveals ATP-induced reduction in conformational flexibility. Nat Chem 2014; 6:208-215. [PMID: 24557135 PMCID: PMC4067995 DOI: 10.1038/nchem.1868] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 01/08/2014] [Indexed: 12/20/2022]
Abstract
Rotary ATPases play fundamental roles in energy conversion as their catalytic rotation is associated with interdomain fluctuations and heterogeneity of conformational states. Using ion mobility mass spectrometry we compared the conformational dynamics of the intact ATPase from Thermus thermophilus with those of its membrane and soluble subcomplexes. Our results define regions with enhanced flexibility assigned to distinct subunits within the overall assembly. To provide a structural context for our experimental data we performed molecular dynamics simulations and observed conformational changes of the peripheral stalks that reflect their intrinsic flexibility. By isolating complexes at different phases of cell growth and manipulating nucleotides, metal ions and pH during isolation, we reveal differences that can be related to conformational changes in the Vo complex triggered by ATP binding. Together these results implicate nucleotides in modulating flexibility of the stator components and uncover mechanistic detail that underlies operation and regulation in the context of the holoenzyme.
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Affiliation(s)
- Min Zhou
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Argyris Politis
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Roberta Davies
- The Victor Chang Cardiac Research Institute, Darlinghurst NSW 2010, Australia
- The University of New South Wales, Sydney NSW 2052, Australia
| | - Idlir Liko
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Kuan-Jung Wu
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Alastair G Stewart
- The Victor Chang Cardiac Research Institute, Darlinghurst NSW 2010, Australia
- The University of New South Wales, Sydney NSW 2052, Australia
| | - Daniela Stock
- The Victor Chang Cardiac Research Institute, Darlinghurst NSW 2010, Australia
- The University of New South Wales, Sydney NSW 2052, Australia
| | - Carol V Robinson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
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43
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Proteomic analysis of the purple sulfur bacterium Candidatus “Thiodictyon syntrophicum” strain Cad16T isolated from Lake Cadagno. EUPA OPEN PROTEOMICS 2014. [DOI: 10.1016/j.euprot.2013.11.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Lu P, Lill H, Bald D. ATP synthase in mycobacteria: special features and implications for a function as drug target. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1208-18. [PMID: 24513197 DOI: 10.1016/j.bbabio.2014.01.022] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 01/28/2014] [Accepted: 01/29/2014] [Indexed: 10/25/2022]
Abstract
ATP synthase is a ubiquitous enzyme that is largely conserved across the kingdoms of life. This conservation is in accordance with its central role in chemiosmotic energy conversion, a pathway utilized by far by most living cells. On the other hand, in particular pathogenic bacteria whilst employing ATP synthase have to deal with energetically unfavorable conditions such as low oxygen tensions in the human host, e.g. Mycobacterium tuberculosis can survive in human macrophages for an extended time. It is well conceivable that such ATP synthases may carry idiosyncratic features that contribute to efficient ATP production. In this review genetic and biochemical data on mycobacterial ATP synthase are discussed in terms of rotary catalysis, stator composition, and regulation of activity. ATP synthase in mycobacteria is of particular interest as this enzyme has been validated as a target for promising new antibacterial drugs. A deeper understanding of the working of mycobacterial ATP synthase and its atypical features can provide insight in adaptations of bacterial energy metabolism. Moreover, pinpointing and understanding critical differences as compared with human ATP synthase may provide input for the design and development of selective ATP synthase inhibitors as antibacterials. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
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Affiliation(s)
- Ping Lu
- Department of Molecular Cell Biology, AIMMS, Faculty of Earth- and Life Sciences, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Holger Lill
- Department of Molecular Cell Biology, AIMMS, Faculty of Earth- and Life Sciences, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Dirk Bald
- Department of Molecular Cell Biology, AIMMS, Faculty of Earth- and Life Sciences, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
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45
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Zhao Y, Xie P, Fan H, Zhao S. Impairment of the mitochondrial oxidative phosphorylation system and oxidative stress in liver of crucian carp (Carassius auratus L.) exposed to microcystins. ENVIRONMENTAL TOXICOLOGY 2014; 29:30-39. [PMID: 21913302 DOI: 10.1002/tox.20770] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 08/11/2011] [Accepted: 08/18/2011] [Indexed: 05/31/2023]
Abstract
Hepatotoxic microcystins (MCs) are produced by cyanobacteria in diverse water bodies and the pathophysiology includes induction of reactive oxygen species and adenosine triphosphate (ATP) depletion in cells. In this study, we evaluated MCs induced changes in the oxidative phosphorylation (OXPHOS) system in mitochondria of crucian carp liver. Fish were subdivided into two groups that were intraperitoneally injected with two doses of MCs (50 and 200 MC-LReq μg/kg bw) and were sacrificed at 1, 3, 12, 24, and 48 h postinjection. The activities of five enzyme complexes of electron transport chain and mRNA expression of mitochondrial-encoded genes (cox1, cox2, cox3, and atp6) were significantly reduced in a time-dependent pattern after injection. There were also changes in mitochondrial ultrastructure, decreases in ATPase activities and reduction in antioxidant level after MCs exposure. Disorder in the OXPHOS system and decreased activities of antioxidative enzymes might contribute to bioenergy deficiency and consequent hepatocyte damage induced by MCs.
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Affiliation(s)
- Yanyan Zhao
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, People's Republic of China
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46
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Kishikawa JI, Nakanishi A, Furuike S, Tamakoshi M, Yokoyama K. Molecular basis of ADP inhibition of vacuolar (V)-type ATPase/synthase. J Biol Chem 2013; 289:403-12. [PMID: 24247239 DOI: 10.1074/jbc.m113.523498] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Reduction of ATP hydrolysis activity of vacuolar-type ATPase/synthase (V0V1) as a result of ADP inhibition occurs as part of the normal mechanism of V0V1 of Thermus thermophilus but not V0V1 of Enterococcus hirae or eukaryotes. To investigate the molecular basis for this difference, domain-swapped chimeric V1 consisting of both T. thermophilus and E. hirae enzymes were generated, and their function was analyzed. The data showed that the interaction between the nucleotide binding and C-terminal domains of the catalytic A subunit from E. hirae V1 is central to increasing binding affinity of the chimeric V1 for phosphate, resulting in reduction of the ADP inhibition. These findings together with a comparison of the crystal structures of T. thermophilus V1 with E. hirae V1 strongly suggest that the A subunit adopts a conformation in T. thermophilus V1 different from that in E. hirae V1. This key difference results in ADP inhibition of T. thermophilus V1 by abolishing the binding affinity for phosphate during ATP hydrolysis.
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Affiliation(s)
- Jun-ichi Kishikawa
- From the Department of Molecular Biosciences, Kyoto Sangyo University, Motoyama Kamigamo, Kita-ku, Kyoto 603-8555, Japan
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47
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Akopyan K, Trchounian A. Proton cycles through membranes in bacteria: Relationship between proton passive and active fluxes and their dependence on some external physico-chemical factors under fermentation. Biophysics (Nagoya-shi) 2013. [DOI: 10.1134/s0006350913050023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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48
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ε subunit of Bacillus subtilis F1-ATPase relieves MgADP inhibition. PLoS One 2013; 8:e73888. [PMID: 23967352 PMCID: PMC3742539 DOI: 10.1371/journal.pone.0073888] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 07/23/2013] [Indexed: 11/19/2022] Open
Abstract
MgADP inhibition, which is considered as a part of the regulatory system of ATP synthase, is a well-known process common to all F1-ATPases, a soluble component of ATP synthase. The entrapment of inhibitory MgADP at catalytic sites terminates catalysis. Regulation by the ε subunit is a common mechanism among F1-ATPases from bacteria and plants. The relationship between these two forms of regulatory mechanisms is obscure because it is difficult to distinguish which is active at a particular moment. Here, using F1-ATPase from Bacillus subtilis (BF1), which is strongly affected by MgADP inhibition, we can distinguish MgADP inhibition from regulation by the ε subunit. The ε subunit did not inhibit but activated BF1. We conclude that the ε subunit relieves BF1 from MgADP inhibition.
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49
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Baseler WA, Dabkowski ER, Jagannathan R, Thapa D, Nichols CE, Shepherd DL, Croston TL, Powell M, Razunguzwa TT, Lewis SE, Schnell DM, Hollander JM. Reversal of mitochondrial proteomic loss in Type 1 diabetic heart with overexpression of phospholipid hydroperoxide glutathione peroxidase. Am J Physiol Regul Integr Comp Physiol 2013; 304:R553-65. [PMID: 23408027 DOI: 10.1152/ajpregu.00249.2012] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mitochondrial dysfunction is a contributor to diabetic cardiomyopathy. Previously, we observed proteomic decrements within the inner mitochondrial membrane (IMM) and matrix of diabetic cardiac interfibrillar mitochondria (IFM) correlating with dysfunctional mitochondrial protein import. The goal of this study was to determine whether overexpression of mitochondria phospholipid hydroperoxide glutathione peroxidase 4 (mPHGPx), an antioxidant enzyme capable of scavenging membrane-associated lipid peroxides in the IMM, could reverse proteomic alterations, dysfunctional protein import, and ultimately, mitochondrial dysfunction associated with the diabetic heart. MPHGPx transgenic mice and controls were made diabetic by multiple low-dose streptozotocin injections and examined after 5 wk of hyperglycemia. Five weeks after hyperglycemia onset, in vivo analysis of cardiac contractile function revealed decreased ejection fraction and fractional shortening in diabetic hearts that was reversed with mPHGPx overexpression. MPHGPx overexpression increased electron transport chain function while attenuating hydrogen peroxide production and lipid peroxidation in diabetic mPHGPx IFM. MPHGPx overexpression lessened proteomic loss observed in diabetic IFM. Posttranslational modifications, including oxidations and deamidations, were attenuated in diabetic IFM with mPHGPx overexpression. Mitochondrial protein import dysfunction in diabetic IFM was reversed with mPHGPx overexpression correlating with protein import constituent preservation. Ingenuity Pathway Analyses indicated that oxidative phosphorylation, tricarboxylic acid cycle, and fatty acid oxidation processes most influenced in diabetic IFM were preserved by mPHGPx overexpression. Specific mitochondrial networks preserved included complex I and II, mitochondrial ultrastructure, and mitochondrial protein import. These results indicate that mPHGPx overexpression can preserve the mitochondrial proteome and provide cardioprotective benefits to the diabetic heart.
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Affiliation(s)
- Walter A Baseler
- Center for Cardiovascular and Respiratory Sciences, Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV 26506, USA
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50
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Shah NB, Hutcheon ML, Haarer BK, Duncan TM. F1-ATPase of Escherichia coli: the ε- inhibited state forms after ATP hydrolysis, is distinct from the ADP-inhibited state, and responds dynamically to catalytic site ligands. J Biol Chem 2013; 288:9383-95. [PMID: 23400782 DOI: 10.1074/jbc.m113.451583] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
F1-ATPase is the catalytic complex of rotary nanomotor ATP synthases. Bacterial ATP synthases can be autoinhibited by the C-terminal domain of subunit ε, which partially inserts into the enzyme's central rotor cavity to block functional subunit rotation. Using a kinetic, optical assay of F1·ε binding and dissociation, we show that formation of the extended, inhibitory conformation of ε (εX) initiates after ATP hydrolysis at the catalytic dwell step. Prehydrolysis conditions prevent formation of the εX state, and post-hydrolysis conditions stabilize it. We also show that ε inhibition and ADP inhibition are distinct, competing processes that can follow the catalytic dwell. We show that the N-terminal domain of ε is responsible for initial binding to F1 and provides most of the binding energy. Without the C-terminal domain, partial inhibition by the ε N-terminal domain is due to enhanced ADP inhibition. The rapid effects of catalytic site ligands on conformational changes of F1-bound ε suggest dynamic conformational and rotational mobility in F1 that is paused near the catalytic dwell position.
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Affiliation(s)
- Naman B Shah
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210, USA
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