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Duport C, Armengaud J, Schmitt C, Morin D, Lacapère JJ. Elucidating the pivotal role of TSPO in porphyrin-related cellular processes, in Bacillus cereus. Biochimie 2024:S0300-9084(24)00046-4. [PMID: 38423451 DOI: 10.1016/j.biochi.2024.02.008] [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: 01/11/2024] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
A structural homolog of the mammalian TSPO has been identified in the human pathogen Bacillus cereus. BcTSPO, in its recombinant form, has previously been shown to bind and degrade porphyrins. In this study, we generated a ΔtspO mutant strain in B. cereus ATCC 14579 and assessed the impact of the absence of BcTSPO on cellular proteomics and physiological characteristics. The proteomic analysis revealed correlations between the lack of BcTSPO and the observed growth defects, increased oxygen consumption, ATP deficiency, heightened tryptophan catabolism, reduced motility, and impaired biofilm formation in the ΔtspO mutant strain. Our results also suggested that BcTSPO plays a crucial role in regulating intracellular levels of metabolites from the coproporphyrin-dependent branch of the heme biosynthetic pathway. This regulation potentially underlies alterations in the metabolic landscape, emphasizing the pivotal role of BcTSPO in B. cereus aerobic metabolism. Notably, our study unveils, for the first time, the involvement of TSPO in tryptophan metabolism. These findings underscore the multifaceted role of TSPO, not only in metabolic pathways but also potentially in the microorganism's virulence mechanisms.
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Affiliation(s)
| | - Jean Armengaud
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200, Bagnols-sur-Cèze, France
| | - Caroline Schmitt
- Assistance Publique Hôpitaux de Paris (AP-HP), Centre Français des Porphyries, Hôpital Louis Mourier, 92700, Colombes, France; INSERM U1149, Center for Research on Inflammation (CRI), Université de Paris, 75018, Paris, France
| | - Didier Morin
- INSERM, U955, équipe 3, Faculté de Médecine, Université Paris Est, 94010, Creteil, France
| | - Jean-Jacques Lacapère
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS UMR 7203, Laboratoire des BioMolécules (LBM), 4 place Jussieu, F-75005, Paris, France
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Mendoza-Hoffmann F, Yang L, Buratto D, Brito-Sánchez J, Garduño-Javier G, Salinas-López E, Uribe-Álvarez C, Ortega R, Sotelo-Serrano O, Cevallos MÁ, Ramírez-Silva L, Uribe-Carvajal S, Pérez-Hernández G, Celis-Sandoval H, García-Trejo JJ. Inhibitory to non-inhibitory evolution of the ζ subunit of the F 1F O-ATPase of Paracoccus denitrificans and α-proteobacteria as related to mitochondrial endosymbiosis. Front Mol Biosci 2023; 10:1184200. [PMID: 37664184 PMCID: PMC10469736 DOI: 10.3389/fmolb.2023.1184200] [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: 03/11/2023] [Accepted: 08/01/2023] [Indexed: 09/05/2023] Open
Abstract
Introduction: The ζ subunit is a potent inhibitor of the F1FO-ATPase of Paracoccus denitrificans (PdF1FO-ATPase) and related α-proteobacteria different from the other two canonical inhibitors of bacterial (ε) and mitochondrial (IF1) F1FO-ATPases. ζ mimics mitochondrial IF1 in its inhibitory N-terminus, blocking the PdF1FO-ATPase activity as a unidirectional pawl-ratchet and allowing the PdF1FO-ATP synthase turnover. ζ is essential for the respiratory growth of P. denitrificans, as we showed by a Δζ knockout. Given the vital role of ζ in the physiology of P. denitrificans, here, we assessed the evolution of ζ across the α-proteobacteria class. Methods: Through bioinformatic, biochemical, molecular biology, functional, and structural analyses of several ζ subunits, we confirmed the conservation of the inhibitory N-terminus of ζ and its divergence toward its C-terminus. We reconstituted homologously or heterologously the recombinant ζ subunits from several α-proteobacteria into the respective F-ATPases, including free-living photosynthetic, facultative symbiont, and intracellular facultative or obligate parasitic α-proteobacteria. Results and discussion: The results show that ζ evolved, preserving its inhibitory function in free-living α-proteobacteria exposed to broad environmental changes that could compromise the cellular ATP pools. However, the ζ inhibitory function was diminished or lost in some symbiotic α-proteobacteria where ζ is non-essential given the possible exchange of nutrients and ATP from hosts. Accordingly, the ζ gene is absent in some strictly parasitic pathogenic Rickettsiales, which may obtain ATP from the parasitized hosts. We also resolved the NMR structure of the ζ subunit of Sinorhizobium meliloti (Sm-ζ) and compared it with its structure modeled in AlphaFold. We found a transition from a compact ordered non-inhibitory conformation into an extended α-helical inhibitory N-terminus conformation, thus explaining why the Sm-ζ cannot exert homologous inhibition. However, it is still able to inhibit the PdF1FO-ATPase heterologously. Together with the loss of the inhibitory function of α-proteobacterial ε, the data confirm that the primary inhibitory function of the α-proteobacterial F1FO-ATPase was transferred from ε to ζ and that ζ, ε, and IF1 evolved by convergent evolution. Some key evolutionary implications on the endosymbiotic origin of mitochondria, as most likely derived from α-proteobacteria, are also discussed.
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Affiliation(s)
- Francisco Mendoza-Hoffmann
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Lingyun Yang
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Damiano Buratto
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Jorge Brito-Sánchez
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - Gilberto Garduño-Javier
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - Emiliano Salinas-López
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - Cristina Uribe-Álvarez
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - Raquel Ortega
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - Oliver Sotelo-Serrano
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - Miguel Ángel Cevallos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - Leticia Ramírez-Silva
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - Salvador Uribe-Carvajal
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - Gerardo Pérez-Hernández
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Ciudad de México, México
| | - Heliodoro Celis-Sandoval
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - José J. García-Trejo
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
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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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Zharova TV, Kozlovsky VS, Grivennikova VG. Interaction of Venturicidin and F o·F 1-ATPase/ATP Synthase of Tightly Coupled Subbacterial Particles of Paracoccus denitrificans in Energized Membranes. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:742-751. [PMID: 36171655 DOI: 10.1134/s0006297922080065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 06/16/2023]
Abstract
Proton-translocating Fo×F1-ATPase/synthase that catalyzes synthesis and hydrolysis of ATP is commonly considered to be a reversibly functioning complex. We have previously shown that venturicidin, a specific Fo-directed inhibitor, blocks the synthesis and hydrolysis of ATP with a significant difference in the affinity [Zharova, T. V. and Vinogradov, A. D. (2017) Biochim. Biophys. Acta, 1858, 939-944]. In this paper, we have studied in detail inhibition of Fo×F1-ATPase/synthase by venturicidin in tightly coupled membranes of Paracoccus denitrificans under conditions of membrane potential generation. ATP hydrolysis was followed by the ATP-dependent succinate-supported NAD+ reduction (potential-dependent reverse electron transfer) catalyzed by the respiratory chain complex I. It has been demonstrated that membrane energization did not affect the affinity of Fo×F1-ATPase/synthase for venturicidin. The dependence of the residual ATP synthase activity on the concentration of venturicidin approximated a linear function, whereas the dependence of ATP hydrolysis was sigmoidal: at low inhibitor concentrations venturicidin strongly inhibited ATP synthesis without decrease in the rate of ATP hydrolysis. A model is proposed suggesting that ATP synthesis and ATP hydrolysis are catalyzed by two different forms of Fo×F1.
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Affiliation(s)
- Tatyana V Zharova
- Department of Biochemistry, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Vladimir S Kozlovsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Vera G Grivennikova
- Department of Biochemistry, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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Lapashina AS, Kashko ND, Zubareva VM, Galkina KV, Markova OV, Knorre DA, Feniouk BA. Attenuated ADP-inhibition of F OF 1 ATPase mitigates manifestations of mitochondrial dysfunction in yeast. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148544. [PMID: 35331734 DOI: 10.1016/j.bbabio.2022.148544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 03/01/2022] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Proton-translocating FOF1 ATP synthase (F-ATPase) couples ATP synthesis or hydrolysis to transmembrane proton transport in bacteria, chloroplasts, and mitochondria. The primary function of the mitochondrial FOF1 is ATP synthesis driven by protonmotive force (pmf) generated by the respiratory chain. However, when pmf is low or absent (e.g. during anoxia), FOF1 consumes ATP and functions as a proton-pumping ATPase. Several regulatory mechanisms suppress the ATPase activity of FOF1 at low pmf. In yeast mitochondria they include special inhibitory proteins Inh1p and Stf1p, and non-competitive inhibition of ATP hydrolysis by MgADP (ADP-inhibition). Presumably, these mechanisms help the cell to preserve the ATP pool upon membrane de-energization. However, no direct evidence was presented to support this hypothesis so far. Here we report that a point mutation Q263L in subunit beta of Saccharomyces cerevisiae ATP synthase significantly attenuated ADP-inhibition of the enzyme without major effect on the rate of ATP production by mitochondria. The mutation also decreased the sensitivity of the enzyme ATPase activity to azide. Similar effects of the corresponding mutations were observed in earlier studies in bacterial enzymes. This observation indicates that the molecular mechanism of ADP-inhibition is probably the same in mitochondrial and in bacterial FOF1. The mutant yeast strain had lower growth rate and had a longer lag period preceding exponential growth phase when starved cells were transferred to fresh growth medium. However, upon the loss of mitochondrial DNA (ρ0) the βQ263L mutation effect was reversed: the βQ263L ρ0 mutant grew faster than the wild-type ρ0 yeast. The results suggest that ADP-inhibition might play a role in prevention of wasteful ATP hydrolysis in the mitochondrial matrix.
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Affiliation(s)
- Anna S Lapashina
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia; Sechenov First Moscow State Medical University, Department of Biological Chemistry, Moscow, Russia
| | - Nataliia D Kashko
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Valeria M Zubareva
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Kseniia V Galkina
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Olga V Markova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry A Knorre
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Boris A Feniouk
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.
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Covian R, Edwards L, He Y, Kim G, Houghton C, Levine RL, Balaban RS. Energy homeostasis is a conserved process: Evidence from Paracoccus denitrificans' response to acute changes in energy demand. PLoS One 2021; 16:e0259636. [PMID: 34748578 PMCID: PMC8575270 DOI: 10.1371/journal.pone.0259636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 10/24/2021] [Indexed: 11/19/2022] Open
Abstract
Paracoccus denitrificans is a model organism for the study of oxidative phosphorylation. We demonstrate a very high respiratory capacity compared to mitochondria when normalizing to cytochrome aa3 content even in the absence of alternative terminal oxidases. To gain insight into conserved mechanisms of energy homeostasis, we characterized the metabolic response to K+ reintroduction. A rapid 3-4-fold increase in respiration occurred before substantial cellular K+ accumulation followed by a sustained increase of up to 6-fold that persisted after net K+ uptake stopped. Proton motive force (Δp) was slightly higher upon addition of K+ with ΔpH increasing and compensating for membrane potential (ΔΨ) depolarization. Blocking the F0F1-ATP synthase (Complex V) with venturicidin revealed that the initial K+-dependent respiratory activation was primarily due to K+ influx. However, the ability to sustain an increased respiration rate was partially dependent on Complex V activity. The 6-fold stimulation of respiration by K+ resulted in a small net reduction of most cytochromes, different from the pattern observed with chemical uncoupling and consistent with balanced input and utilization of reducing equivalents. Metabolomics showed increases in glycolytic and TCA cycle intermediates together with a decrease in basic amino acids, suggesting an increased nitrogen mobilization upon K+ replenishment. ATP and GTP concentrations increased after K+ addition, indicating a net increase in cellular potential energy. Thus, K+ stimulates energy generation and utilization resulting in an almost constant Δp and increased high-energy phosphates during large acute and steady state changes in respiration. The specific energy consuming processes and signaling events associated with this simultaneous activation of work and metabolism in P. denitrificans remain unknown. Nevertheless, this homeostatic behavior is very similar to that observed in mitochondria in tissues when cellular energy requirements increase. We conclude that the regulation of energy generation and utilization to maintain homeostasis is conserved across the prokaryote/eukaryote boundary.
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Affiliation(s)
- Raul Covian
- Laboratory of Cardiac Energetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Lanelle Edwards
- Laboratory of Cardiac Energetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Yi He
- Fermentation Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Geumsoo Kim
- Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Carly Houghton
- Laboratory of Cardiac Energetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Rodney L. Levine
- Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Robert S. Balaban
- Laboratory of Cardiac Energetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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Lucero RA, Mercedes EP, Thorsten L, Giovanni GC, Michael F, Guadalupe Z, Pablo PJ, Federico M, Oscar FH. Deletion of the natural inhibitory protein Inh1 in Ustilago maydis has no effect on the dimeric state of the F 1F O-ATP synthase but increases the ATPase activity and reduces the stability. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148429. [PMID: 33862003 DOI: 10.1016/j.bbabio.2021.148429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/28/2021] [Accepted: 04/07/2021] [Indexed: 10/21/2022]
Abstract
Transduction of electrochemical proton gradient into ATP synthesis is performed by F1FO-ATP synthase. The reverse reaction is prevented by the regulatory subunit Inh1. Knockout of the inh1 gene in the basidiomycete Ustilago maydis was generated in order to study the function of this protein in the mitochondrial metabolism and cristae architecture. Deletion of inh1 gen did not affect cell growth, glucose consumption, and biomass production. Ultrastructure and fluorescence analyzes showed that size, cristae shape, network, and distribution of mitochondria was similar to wild strain. Membrane potential, ATP synthesis, and oxygen consumption in wild type and mutant strains had similar values. Kinetic analysis of ATPase activity of complex V in permeabilized mitochondria showed similar values of Vmax and KM for both strains, and no effect of pH was observed. Interestingly, the dimeric state of complex V occurs in the mutant strain, indicating that this subunit is not essential for dimerization. ATPase activity of the isolated monomeric and dimeric forms of complex V indicated Vmax values 4-times higher for the mutant strain than for the WT strain, suggesting that the absence of Inh1 subunit increased ATPase activity, and supporting a regulatory role for this protein; however, no effect of pH was observed. ATPase activity of WT oligomers was stimulated several times by dodecyl-maltoside (DDM), probably by removal of ADP from F1 sector, while DDM induced an inactive form of the mutant oligomers.
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Affiliation(s)
- Romero-Aguilar Lucero
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Apartado Postal 70-159, Coyoacán 04510, México, Mexico
| | - Esparza-Perusquía Mercedes
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Apartado Postal 70-159, Coyoacán 04510, México, Mexico
| | - Langner Thorsten
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Department of Biology, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - García-Cruz Giovanni
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Apartado Postal 70-159, Coyoacán 04510, México, Mexico
| | - Feldbrügge Michael
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Department of Biology, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Zavala Guadalupe
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001 Chamilpa, 62210, Cuernavaca, Morelos, Mexico
| | - Pardo Juan Pablo
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Apartado Postal 70-159, Coyoacán 04510, México, Mexico
| | - Martínez Federico
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Apartado Postal 70-159, Coyoacán 04510, México, Mexico
| | - Flores-Herrera Oscar
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Apartado Postal 70-159, Coyoacán 04510, México, Mexico.
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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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9
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The 3 × 120° rotary mechanism of Paracoccus denitrificans F 1-ATPase is different from that of the bacterial and mitochondrial F 1-ATPases. Proc Natl Acad Sci U S A 2020; 117:29647-29657. [PMID: 33168750 PMCID: PMC7703542 DOI: 10.1073/pnas.2003163117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The rotation of Paracoccus denitrificans F1-ATPase (PdF1) was studied using single-molecule microscopy. At all concentrations of adenosine triphosphate (ATP) or a slowly hydrolyzable ATP analog (ATPγS), above or below K m, PdF1 showed three dwells per turn, each separated by 120°. Analysis of dwell time between steps showed that PdF1 executes binding, hydrolysis, and probably product release at the same dwell. The comparison of ATP binding and catalytic pauses in single PdF1 molecules suggested that PdF1 executes both elementary events at the same rotary position. This point was confirmed in an inhibition experiment with a nonhydrolyzable ATP analog (AMP-PNP). Rotation assays in the presence of adenosine diphosphate (ADP) or inorganic phosphate at physiological concentrations did not reveal any obvious substeps. Although the possibility of the existence of substeps remains, all of the datasets show that PdF1 is principally a three-stepping motor similar to bacterial vacuolar (V1)-ATPase from Thermus thermophilus This contrasts with all other known F1-ATPases that show six or nine dwells per turn, conducting ATP binding and hydrolysis at different dwells. Pauses by persistent Mg-ADP inhibition or the inhibitory ζ-subunit were also found at the same angular position of the rotation dwell, supporting the simplified chemomechanical scheme of PdF1 Comprehensive analysis of rotary catalysis of F1 from different species, including PdF1, suggests a clear trend in the correlation between the numbers of rotary steps of F1 and Fo domains of F-ATP synthase. F1 motors with more distinctive steps are coupled with proton-conducting Fo rings with fewer proteolipid subunits, giving insight into the design principle the F1Fo of ATP synthase.
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Vinogradov AD. New Perspective on the Reversibility of ATP Synthesis and Hydrolysis by F o×F 1-ATP Synthase (Hydrolase). BIOCHEMISTRY (MOSCOW) 2019; 84:1247-1255. [PMID: 31760915 DOI: 10.1134/s0006297919110038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Fo×F1-ATPases of mitochondria, chloroplasts, and microorganisms catalyze transformation of proton motive force (the difference between the electrochemical potentials of hydrogen ion across a coupling membrane) to the free energy of ATP phosphoryl potential. It is often stated that Fo×F1-ATPases operate as reversible chemo-mechano-electrical molecular machines that provide either ATP synthesis or hydrolysis depending on particular physiological demands of an organism; the microreversibility principle of the enzyme catalysis is usually taken as a dogma. Since 1980, the author has upheld the view that the mechanisms of ATP synthesis and hydrolysis by the Fo×F1 complex are different (Vinogradov, A. D. (2000) J. Exp. Biol., 203, 41-49). In this paper, the author proposes a new model considering the existence in coupling membranes of two non-equilibrium isoforms of Fo×F1 unidirectionally catalyzing synthesis and/or hydrolysis of ATP.
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Affiliation(s)
- A D Vinogradov
- Lomonosov Moscow State University, School of Biology, Department of Biochemistry, Moscow, 119234, Russia.
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11
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Zhang XM, Li Y, Gu YX, Zhang CN, Lai HC, Shi JY. Ta-Coated Titanium Surface With Superior Bacteriostasis And Osseointegration. Int J Nanomedicine 2019; 14:8693-8706. [PMID: 31806965 PMCID: PMC6842742 DOI: 10.2147/ijn.s218640] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 10/04/2019] [Indexed: 12/13/2022] Open
Abstract
Background Although tantalum (Ta)-based coatings have been proven to have good antibacterial activity, the underlying mechanism and in vivo biological performance remain unclear, which are essential for the clinical application of Ta-coated biomaterials as dental implants. Purpose The main objective of this study is to investigate the antibacterial activity of Ta-modified titanium (Ti) implants against peri-implantitis-related microbes and the potential molecular mechanisms. Methods Fusobacterium nucleatum and Porphyromonas gingivalis were selected to evaluate the antibacterial activity and potential antibacterial mechanism of Ta modification. The in vivo biocompatibility of Ta-modified implants was also evaluated. Results The results showed that Ta-modified surface performed excellent antimicrobial activity against Fusobacterium nucleatum and Porphyromonas gingivalis. Micro galvanic might be formed between the incorporated Ta and the Ti base, which could consume the protons and result in decreased ATP synthesis and increased ROS generation. The gene expression of bacterial virulence factors associated with cellular attachment, invasion and viability as the target of ROS was downregulated. Importantly, in vivo biological studies showed that Ta modification significantly promoted the osseointegration of implants by stimulating the expression of bone-forming proteins. Conclusion This study may provide some insights into clinical applications of Ta-coated Ti implants, especially in possibly infected situations.
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Affiliation(s)
- Xiao-Meng Zhang
- Department of Implant Dentistry, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, People's Republic of China
| | - Yuan Li
- Department of Implant Dentistry, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, People's Republic of China
| | - Ying-Xin Gu
- Department of Implant Dentistry, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, People's Republic of China
| | - Chu-Nan Zhang
- Department of Implant Dentistry, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, People's Republic of China
| | - Hong-Chang Lai
- Department of Implant Dentistry, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, People's Republic of China
| | - Jun-Yu Shi
- Department of Implant Dentistry, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, People's Republic of China
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12
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Antimicrobial activities of biologically synthesized metal nanoparticles: an insight into the mechanism of action. J Biol Inorg Chem 2019; 24:929-941. [PMID: 31515623 DOI: 10.1007/s00775-019-01717-7] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 08/28/2019] [Indexed: 12/16/2022]
Abstract
Increasing antimicrobial resistance is a clinical crisis worldwide. Recent progress in the field of green synthesis has fascinated scientists and researchers to explore its potentials against pathogenic microbes. Bioinspired-metal-based nanoparticles (silver, copper, gold, zinc, etc.) have been reported to be tested against both Gram-positive and Gram-negative bacteria such as B. subtilis, E. coli, Staphylococcus aureus, etc., as well as some pathogenic fungi including A. niger, F. oxysporum, A. fumigatus, etc., and are testified to exhibit inhibitory effects against pathogenic microbes. The possible modes of action of these metal nanoparticles include: (a) excess production of reactive oxygen species inside microbes; (b) disruption of vital enzymes in respiratory chain via damaging microbial plasma membranes; (c) accumulation of metal ions in microbial membranes; (d) electrostatic attraction between metal nanoparticles and microbial cells which disrupt metabolic activities; and (e) inhibition of microbial proteins/enzymes by increased production of H2O2. Although these pathways are interconnected, information on potential mechanism of most of these biogenic nanoparticles is still limited. Further exploration of these mechanisms could help in tackling the burning issue of antibiotics resistance.
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13
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Lapashina AS, Shugaeva TE, Berezina KM, Kholina TD, Feniouk BA. Amino Acid Residues β139, β189, and β319 Modulate ADP-Inhibition in Escherichia coli H+-F OF 1-ATP Synthase. BIOCHEMISTRY (MOSCOW) 2019; 84:407-415. [PMID: 31228932 DOI: 10.1134/s0006297919040084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Proton-translocating FOF1-ATP synthase (F-type ATPase, F-ATPase or FOF1) performs ATP synthesis/hydrolysis coupled to proton transport across the membrane in mitochondria, chloroplasts, and most eubacteria. The ATPase activity of the enzyme is suppressed in the absence of protonmotive force by several regulatory mechanisms. The most conserved of these mechanisms is noncompetitive inhibition of ATP hydrolysis by the MgADP complex (ADP-inhibition) which has been found in all the enzymes studied. When MgADP binds without phosphate in the catalytic site, the enzyme enters an inactive state, and MgADP gets locked in the catalytic site and does not exchange with the medium. The degree of ADP-inhibition varies in FOF1 enzymes from different organisms. In the Escherichia coli enzyme, ADP-inhibition is relatively weak and, in contrast to other organisms, is enhanced rather than suppressed by phosphate. In this study, we used site-directed mutagenesis to investigate the role of amino acid residues β139, β158, β189, and β319 of E. coli FOF1-ATP synthase in the mechanism of ADP-inhibition and its modulation by the protonmotive force. The amino acid residues in these positions differ in the enzymes from beta- and gammaproteobacteria (including E. coli) and FOF1-ATP synthases from other eubacteria, mitochondria, and chloroplasts. The βN158L substitution produced no effect on the enzyme activity, while substitutions βF139Y, βF189L, and βV319T only slightly affected ATP (1 mM) hydrolysis. However, in a mixture of ATP and ADP, the activity of the mutants was less suppressed than that of the wild-type enzyme. In addition, mutations βF189L and βV319T weakened the ATPase activity inhibition by phosphate in the presence of ADP. We suggest that residues β139, β189, and β319 are involved in the mechanism of ADP-inhibition and its modulation 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
| | - T E Shugaeva
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia
| | - K M Berezina
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia
| | - T D Kholina
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, 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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14
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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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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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Mendoza-Hoffmann F, Pérez-Oseguera Á, Cevallos MÁ, Zarco-Zavala M, Ortega R, Peña-Segura C, Espinoza-Simón E, Uribe-Carvajal S, García-Trejo JJ. The Biological Role of the ζ Subunit as Unidirectional Inhibitor of the F 1F O-ATPase of Paracoccus denitrificans. Cell Rep 2018; 22:1067-1078. [PMID: 29386127 DOI: 10.1016/j.celrep.2017.12.106] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 09/09/2017] [Accepted: 12/28/2017] [Indexed: 11/16/2022] Open
Abstract
The biological roles of the three natural F1FO-ATPase inhibitors, ε, ζ, and IF1, on cell physiology remain controversial. The ζ subunit is a useful model for deletion studies since it mimics mitochondrial IF1, but in the F1FO-ATPase of Paracoccus denitrificans (PdF1FO), it is a monogenic and supernumerary subunit. Here, we constructed a P. denitrificans 1222 derivative (PdΔζ) with a deleted ζ gene to determine its role in cell growth and bioenergetics. The results show that the lack of ζ in vivo strongly restricts respiratory P. denitrificans growth, and this is restored by complementation in trans with an exogenous ζ gene. Removal of ζ increased the coupled PdF1FO-ATPase activity without affecting the PdF1FO-ATP synthase turnover, and the latter was not affected at all by ζ reconstitution in vitro. Therefore, ζ works as a unidirectional pawl-ratchet inhibitor of the PdF1FO-ATPase nanomotor favoring the ATP synthase turnover to improve respiratory cell growth and bioenergetics.
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Affiliation(s)
- Francisco Mendoza-Hoffmann
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Delegación Coyoacán, Ciudad de México (CDMX) 04510, México
| | - Ángeles Pérez-Oseguera
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, U.N.A.M., Cuernavaca, Morelos, México
| | - Miguel Ángel Cevallos
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, U.N.A.M., Cuernavaca, Morelos, México
| | | | - Raquel Ortega
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Delegación Coyoacán, Ciudad de México (CDMX) 04510, México
| | | | | | | | - José J García-Trejo
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Delegación Coyoacán, Ciudad de México (CDMX) 04510, México.
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19
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Varghese F, Blaza JN, Jones AJY, Jarman OD, Hirst J. Deleting the IF 1-like ζ subunit from Paracoccus denitrificans ATP synthase is not sufficient to activate ATP hydrolysis. Open Biol 2018; 8:170206. [PMID: 29367351 PMCID: PMC5795051 DOI: 10.1098/rsob.170206] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/26/2017] [Indexed: 11/12/2022] Open
Abstract
In oxidative phosphorylation, ATP synthases interconvert two forms of free energy: they are driven by the proton-motive force across an energy-transducing membrane to synthesize ATP and displace the ADP/ATP ratio from equilibrium. For thermodynamically efficient energy conversion they must be reversible catalysts. However, in many species ATP synthases are unidirectional catalysts (their rates of ATP hydrolysis are negligible), and in others mechanisms have evolved to regulate or minimize hydrolysis. Unidirectional catalysis by Paracoccus denitrificans ATP synthase has been attributed to its unique ζ subunit, which is structurally analogous to the mammalian inhibitor protein IF1 Here, we used homologous recombination to delete the ζ subunit from the P. denitrificans genome, and compared ATP synthesis and hydrolysis by the wild-type and knockout enzymes in inverted membrane vesicles and the F1-ATPase subcomplex. ATP synthesis was not affected by loss of the ζ subunit, and the rate of ATP hydrolysis increased by less than twofold, remaining negligible in comparison with the rates of the Escherichia coli and mammalian enzymes. Therefore, deleting the P. denitrificans ζ subunit is not sufficient to activate ATP hydrolysis. We close by considering our conclusions in the light of reversible catalysis and regulation in ATP synthase enzymes.
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Affiliation(s)
- Febin Varghese
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - James N Blaza
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Andrew J Y Jones
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Owen D Jarman
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Judy Hirst
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
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20
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Zharova TV, Vinogradov AD. Functional heterogeneity of F o·F 1H +-ATPase/synthase in coupled Paracoccus denitrificans plasma membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:939-944. [PMID: 28803911 DOI: 10.1016/j.bbabio.2017.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/10/2017] [Accepted: 08/09/2017] [Indexed: 11/16/2022]
Abstract
Fo·F1H+-ATPase/synthase in coupled plasma membrane vesicles of Paracoccus denitrificans catalyzes ATP hydrolysis and/or ATP synthesis with comparable enzyme turnover. Significant difference in pH-profile of these alternative activities is seen: decreasing pH from 8.0 to 7.0 results in reversible inhibition of hydrolytic activity, whereas ATP synthesis activity is not changed. The inhibition of ATPase activity upon acidification results from neither change in ADP(Mg2+)-induced deactivation nor the energy-dependent enzyme activation. Vmax, not apparent KmATP is affected by lowering the pH. Venturicidin noncompetitively inhibits ATP synthesis and coupled ATP hydrolysis, showing significant difference in the affinity to its inhibitory site depending on the direction of the catalysis. This difference cannot be attributed to variations of the substrate-enzyme intermediates for steady-state forward and back reactions or to possible equilibrium between ATP hydrolase and ATP synthase Fo·F1 modes of the opposite directions of catalysis. The data are interpreted as to suggest that distinct non-equilibrated molecular isoforms of Fo·F1 ATP synthase and ATP hydrolase exist in coupled energy-transducing membranes.
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Affiliation(s)
- Tatyana V Zharova
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119234, Russian Federation
| | - Andrei D Vinogradov
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119234, Russian Federation.
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21
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Gutiérrez-Estrada A, Ramírez-Santos J, Gómez-Eichelmann MDC. Role of chaperones and ATP synthase in DNA gyrase reactivation in Escherichia coli stationary-phase cells after nutrient addition. SPRINGERPLUS 2014; 3:656. [PMID: 25485196 PMCID: PMC4230433 DOI: 10.1186/2193-1801-3-656] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 10/29/2014] [Indexed: 12/03/2022]
Abstract
Escherichia coli stationary-phase (SP) cells contain relaxed DNA molecules and recover DNA supercoiling once nutrients become available. In these cells, the reactivation of DNA gyrase, which is a DNA topoisomerase type IIA enzyme, is responsible for the recovery of DNA supercoiling. The results presented in this study show that DNA gyrase reactivation does not require cellular chaperones or polyphosphate. Glucose addition to SP cells induced a slow recovery of DNA supercoiling, whereas resveratrol, which is an inhibitor of ATP synthase, inhibited the enzyme reactivation. These results suggest that DNA gyrase, which is an ATP-dependent enzyme, remains soluble in SP cells, and that its reactivation occurs primarily due to a rapid increase in the cellular ATP concentration.
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Affiliation(s)
- Alejandra Gutiérrez-Estrada
- Department of Molecular Biology and Biotechnology, Institute of Biomedical Research, National Autonomous University of México, P.O. Box 70228, México City, 04510 México
| | - Jesús Ramírez-Santos
- Department of Molecular Biology and Biotechnology, Institute of Biomedical Research, National Autonomous University of México, P.O. Box 70228, México City, 04510 México
| | - María Del Carmen Gómez-Eichelmann
- Department of Molecular Biology and Biotechnology, Institute of Biomedical Research, National Autonomous University of México, P.O. Box 70228, México City, 04510 México
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Malyan AN. Noncatalytic nucleotide binding sites: properties and mechanism of involvement in ATP synthase activity regulation. BIOCHEMISTRY (MOSCOW) 2014; 78:1512-23. [PMID: 24490737 DOI: 10.1134/s0006297913130099] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
ATP synthases (FoF1-ATPases) of chloroplasts, mitochondria, and bacteria catalyze ATP synthesis or hydrolysis coupled with the transmembrane transfer of protons or sodium ions. Their activity is regulated through their reversible inactivation resulting from a decreased transmembrane potential difference. The inactivation is believed to conserve ATP previously synthesized under conditions of sufficient energy supply against unproductive hydrolysis. This review is focused on the mechanism of nucleotide-dependent regulation of the ATP synthase activity where the so-called noncatalytic nucleotide binding sites are involved. Properties of these sites varying upon free enzyme transition to its membrane-bound form, their dependence on membrane energization, and putative mechanisms of noncatalytic site-mediated regulation of the ATP synthase activity are discussed.
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Affiliation(s)
- A N Malyan
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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23
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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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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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Zarco-Zavala M, Morales-Ríos E, Mendoza-Hernández G, Ramírez-Silva L, Pérez-Hernández G, García-Trejo JJ. The ζ subunit of the F1FO-ATP synthase of α-proteobacteria controls rotation of the nanomotor with a different structure. FASEB J 2014; 28:2146-57. [PMID: 24522203 DOI: 10.1096/fj.13-241430] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The ζ subunit is a novel natural inhibitor of the α-proteobacterial F1FO-ATPase described originally in Paracoccus denitrificans. To characterize the mechanism by which this subunit inhibits the F1FO nanomotor, the ζ subunit of Paracoccus denitrificans (Pd-ζ) was analyzed by the combination of kinetic, biochemical, bioinformatic, proteomic, and structural approaches. The ζ subunit causes full inhibition of the sulfite-activated PdF1-ATPase with an apparent IC50 of 270 nM by a mechanism independent of the ε subunit. The inhibitory region of the ζ subunit resides in the first 14 N-terminal residues of the protein, which protrude from the 4-α-helix bundle structure of the isolated ζ subunit, as resolved by NMR. Cross-linking experiments show that the ζ subunit interacts with rotor (γ) and stator (α, β) subunits of the F1-ATPase, indicating that the ζ subunit hinders rotation of the central stalk. In addition, a putatively regulatory nucleotide-binding site was found in the ζ subunit by isothermal titration calorimetry. Together, the data show that the ζ subunit controls the rotation of F1FO-ATPase by a mechanism reminiscent of, but different from, those described for mitochondrial IF1 and bacterial ε subunits where the 4-α-helix bundle of ζ seems to work as an anchoring domain that orients the N-terminal inhibitory domain to hinder rotation of the central stalk.
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Affiliation(s)
- Mariel Zarco-Zavala
- 1Universidad Nacional Autónoma de México (UNAM), Facultad de Química, Departamento de Biología, Circuito Escolar, s/n, Laboratorio 206, Edificio F, Ciudad Universitaria, Coyoacán, CP 04510, México, DF.
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Biuković G, Basak S, Manimekalai MSS, Rishikesan S, Roessle M, Dick T, Rao SPS, Hunke C, Grüber G. Variations of subunit {varepsilon} of the Mycobacterium tuberculosis F1Fo ATP synthase and a novel model for mechanism of action of the tuberculosis drug TMC207. Antimicrob Agents Chemother 2013; 57:168-76. [PMID: 23089752 PMCID: PMC3535943 DOI: 10.1128/aac.01039-12] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2012] [Accepted: 10/11/2012] [Indexed: 11/20/2022] Open
Abstract
The subunit ε of bacterial F(1)F(O) ATP synthases plays an important regulatory role in coupling and catalysis via conformational transitions of its C-terminal domain. Here we present the first low-resolution solution structure of ε of Mycobacterium tuberculosis (Mtε) F(1)F(O) ATP synthase and the nuclear magnetic resonance (NMR) structure of its C-terminal segment (Mtε(103-120)). Mtε is significantly shorter (61.6 Å) than forms of the subunit in other bacteria, reflecting a shorter C-terminal sequence, proposed to be important in coupling processes via the catalytic β subunit. The C-terminal segment displays an α-helical structure and a highly positive surface charge due to the presence of arginine residues. Using NMR spectroscopy, fluorescence spectroscopy, and mutagenesis, we demonstrate that the new tuberculosis (TB) drug candidate TMC207, proposed to bind to the proton translocating c-ring, also binds to Mtε. A model for the interaction of TMC207 with both ε and the c-ring is presented, suggesting that TMC207 forms a wedge between the two rotating subunits by interacting with the residues W15 and F50 of ε and the c-ring, respectively. T19 and R37 of ε provide the necessary polar interactions with the drug molecule. This new model of the mechanism of TMC207 provides the basis for the design of new drugs targeting the F(1)F(O) ATP synthase in M. tuberculosis.
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Affiliation(s)
- Goran Biuković
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
| | - Sandip Basak
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
| | | | | | - Manfred Roessle
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, Hamburg, Germany
| | - Thomas Dick
- National University of Singapore, Yong Loo Lin School of Medicine, Department of Microbiology, Singapore, Republic of Singapore
| | - Srinivasa P. S. Rao
- Novartis Institute for Tropical Diseases Pte. Ltd., Singapore, Republic of Singapore
| | - Cornelia Hunke
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
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Cui Y, Zhao Y, Tian Y, Zhang W, Lü X, Jiang X. The molecular mechanism of action of bactericidal gold nanoparticles on Escherichia coli. Biomaterials 2011; 33:2327-33. [PMID: 22182745 DOI: 10.1016/j.biomaterials.2011.11.057] [Citation(s) in RCA: 429] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 11/22/2011] [Indexed: 11/17/2022]
Abstract
This work examines the molecular mechanism of action of a class of bactericidal gold nanoparticles (NPs) which show potent antibacterial activities against multidrug-resistant Gram-negative bacteria by transcriptomic and proteomic approaches. Gold NPs exert their antibacterial activities mainly by two ways: one is to collapse membrane potential, inhibiting ATPase activities to decrease the ATP level; the other is to inhibit the subunit of ribosome from binding tRNA. Gold NPs enhance chemotaxis in the early-phase reaction. The action of gold NPs did not include reactive oxygen species (ROS)-related mechanism, the cause for cellular death induced by most bactericidal antibiotics and nanomaterials. Our investigation would allow the development of antibacterial agents that target the energy-metabolism and transcription of bacteria without triggering the ROS reaction, which may be at the same time harmful for the host when killing bacteria.
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Affiliation(s)
- Yan Cui
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 2 Si Pailou, Nanjing 210096, China
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Ahmad Z, Okafor F, Laughlin TF. Role of Charged Residues in the Catalytic Sites of Escherichia coli ATP Synthase. JOURNAL OF AMINO ACIDS 2011; 2011:785741. [PMID: 22312470 PMCID: PMC3268026 DOI: 10.4061/2011/785741] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 04/21/2011] [Indexed: 11/21/2022]
Abstract
Here we describe the role of charged amino acids at the catalytic sites of Escherichia coli ATP synthase. There are four positively charged and four negatively charged residues in the vicinity of of E. coli ATP synthase catalytic sites. Positive charges are contributed by three arginine and one lysine, while negative charges are contributed by two aspartic acid and two glutamic acid residues. Replacement of arginine with a neutral amino acid has been shown to abrogate phosphate binding, while restoration of phosphate binding has been accomplished by insertion of arginine at the same or a nearby location. The number and position of positive charges plays a critical role in the proper and efficient binding of phosphate. However, a cluster of many positive charges inhibits phosphate binding. Moreover, the presence of negatively charged residues seems a requisite for the proper orientation and functioning of positively charged residues in the catalytic sites. This implies that electrostatic interactions between amino acids are an important constituent of initial phosphate binding in the catalytic sites. Significant loss of function in growth and ATPase activity assays in mutants generated through charge modulations has demonstrated that precise location and stereochemical interactions are of paramount importance.
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Affiliation(s)
- Zulfiqar Ahmad
- Department of Biology, Alabama A&M University, P.O. Box 610, Normal, AL 35762, USA
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Kegyarikova KA, Zharova TV, Vinogradov AD. Paracoccus denitrificans proton-translocating ATPase: kinetics of oxidative phosphorylation. BIOCHEMISTRY (MOSCOW) 2011; 75:1264-71. [PMID: 21166644 DOI: 10.1134/s0006297910100081] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The initial rates of ATP synthesis catalyzed by tightly coupled Paracoccus denitrificans plasma membrane were measured. The reaction rate was hyperbolically dependent on the substrates, ADP and inorganic phosphate (P(i)). Apparent K(m) values for ADP and P(i) were 7-11 and 60-120 µM, respectively, at saturating concentration of the second substrate (pH 8.0, saturating Mg²(+)). These values were dependent on coupling efficiency. The substrate binding in the ATP synthesis reaction proceeds randomly: K(m) value for a given substrate was independent of the concentration of the other one. A decrease of electrochemical proton gradient by the addition of malonate (when succinate served as the respiratory substrate) or by a decrease of steady-state level of NADH (when NADH served as the respiratory substrate) resulted in a proportional decrease of the maximal rates and apparent K(m) values for ADP and P(i) (double substitution, ping-pong mechanism). The kinetic scheme for ATP synthesis was compared with that described previously for the proton-translocating ATP hydrolysis catalyzed by the same enzyme preparation (T. V. Zharova and A. D. Vinogradov (2006) Biochemistry, 45, 14552-14558).
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Affiliation(s)
- K A Kegyarikova
- Department of Biochemistry, Lomonosov Moscow State University, Russia
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Haagsma AC, Driessen NN, Hahn MM, Lill H, Bald D. ATP synthase in slow- and fast-growing mycobacteria is active in ATP synthesis and blocked in ATP hydrolysis direction. FEMS Microbiol Lett 2010; 313:68-74. [PMID: 21039782 DOI: 10.1111/j.1574-6968.2010.02123.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
ATP synthase is a validated drug target for the treatment of tuberculosis, and ATP synthase inhibitors are promising candidate drugs for the treatment of infections caused by other slow-growing mycobacteria, such as Mycobacterium leprae and Mycobacterium ulcerans. ATP synthase is an essential enzyme in the energy metabolism of Mycobacterium tuberculosis; however, no biochemical data are available to characterize the role of ATP synthase in slow-growing mycobacterial strains. Here, we show that inverted membrane vesicles from the slow-growing model strain Mycobacterium bovis BCG are active in ATP synthesis, but ATP synthase displays no detectable ATP hydrolysis activity and does not set up a proton-motive force (PMF) using ATP as a substrate. Treatment with methanol as well as PMF activation unmasked the ATP hydrolysis activity, indicating that the intrinsic subunit ɛ and inhibitory ADP are responsible for the suppression of hydrolytic activity. These results suggest that the enzyme is needed for the synthesis of ATP, not for the maintenance of the PMF. For the development of new antimycobacterial drugs acting on ATP synthase, screening for ATP synthesis inhibitors, but not for ATP hydrolysis blockers, can be regarded as a promising strategy.
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Affiliation(s)
- Anna C Haagsma
- Department of Molecular Cell Biology, Faculty of Earth and Life Sciences, VU University Amsterdam, Amsterdam, The Netherlands
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ATP hydrolysis in ATP synthases can be differently coupled to proton transport and modulated by ADP and phosphate: a structure based model of the mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:755-62. [PMID: 20230778 DOI: 10.1016/j.bbabio.2010.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2009] [Revised: 03/02/2010] [Accepted: 03/02/2010] [Indexed: 11/20/2022]
Abstract
In the ATP synthases of Escherichia coli ADP and phosphate exert an apparent regulatory role on the efficiency of proton transport coupled to the hydrolysis of ATP. Both molecules induce clearly biphasic effects on hydrolysis and proton transfer. At intermediate concentrations (approximately 0.5-1 microM and higher) ADP inhibits hydrolysis and proton transfer; a quantitative analysis of the fluxes however proves that the coupling efficiency remains constant in this concentration range. On the other hand at nanomolar concentrations of ADP (a level obtainable only using an enzymatic ATP regenerating system) the efficiency of proton transport drops progressively, while the rate of hydrolysis remains high. Phosphate, at concentrations>or=0.1 mM, inhibits hydrolysis only if ADP is present at sufficiently high concentrations, keeping the coupling efficiency constant. At lower ADP levels phosphate is, however, necessary for an efficiently coupled catalytic cycle. We present a model for a catalytic cycle of ATP hydrolysis uncoupled from the transport of protons. The model is based on the available structures of bovine and yeast F1 and on the known binding affinities for ADP and Pi of the catalytic sites in their different functional states. The binding site related to the inhibitory effects of Pi (in association with ADP) is identified as the alphaHCbetaHC site, the pre-release site for the hydrolysis products. We suggest, moreover, that the high affinity site, associated with the operation of an efficient proton transport, could coincide with a conformational state intermediate between the alphaTPbetaTP and the alphaDPbetaDP (similar to the transition state of the hydrolysis/synthesis reaction) that does not strongly bind the ligands and can exchange them rather freely with the external medium. The emptying of this site can lead to an unproductive hydrolysis cycle that occurs without a net rotation of the central stalk and, consequently, does not translocate protons.
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F1F0-ATP synthases of alkaliphilic bacteria: lessons from their adaptations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1362-77. [PMID: 20193659 DOI: 10.1016/j.bbabio.2010.02.028] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 02/22/2010] [Accepted: 02/23/2010] [Indexed: 12/14/2022]
Abstract
This review focuses on the ATP synthases of alkaliphilic bacteria and, in particular, those that successfully overcome the bioenergetic challenges of achieving robust H+-coupled ATP synthesis at external pH values>10. At such pH values the protonmotive force, which is posited to provide the energetic driving force for ATP synthesis, is too low to account for the ATP synthesis observed. The protonmotive force is lowered at a very high pH by the need to maintain a cytoplasmic pH well below the pH outside, which results in an energetically adverse pH gradient. Several anticipated solutions to this bioenergetic conundrum have been ruled out. Although the transmembrane sodium motive force is high under alkaline conditions, respiratory alkaliphilic bacteria do not use Na+- instead of H+-coupled ATP synthases. Nor do they offset the adverse pH gradient with a compensatory increase in the transmembrane electrical potential component of the protonmotive force. Moreover, studies of ATP synthase rotors indicate that alkaliphiles cannot fully resolve the energetic problem by using an ATP synthase with a large number of c-subunits in the synthase rotor ring. Increased attention now focuses on delocalized gradients near the membrane surface and H+ transfers to ATP synthases via membrane-associated microcircuits between the H+ pumping complexes and synthases. Microcircuits likely depend upon proximity of pumps and synthases, specific membrane properties and specific adaptations of the participating enzyme complexes. ATP synthesis in alkaliphiles depends upon alkaliphile-specific adaptations of the ATP synthase and there is also evidence for alkaliphile-specific adaptations of respiratory chain components.
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Kim M, Song E. Iron transport by proteoliposomes containing mitochondrial F(1)F(0) ATP synthase isolated from rat heart. Biochimie 2010; 92:333-42. [PMID: 20100539 DOI: 10.1016/j.biochi.2010.01.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2009] [Accepted: 01/17/2010] [Indexed: 01/18/2023]
Abstract
In this work, we present evidence of Fe(2+) transport by rat heart mitochondrial F(1)F(0) ATP synthase. Iron uptake by the vesicles containing the enzyme was concentration- and temperature-dependent, with an optimum temperature of 37 degrees C. Both ATP and ADP stimulated iron uptake in a concentration-dependent manner, whereas AMP, AMPPCP, and mADP did not. Inhibitors of the enzyme, oligomycin, and resveratrol similarly blocked iron transport. The iron uptake was confirmed by inhibition using specific antibodies against the alpha, beta, and c subunits of the enzyme. Interestingly, slight transport of common divalent and trivalent metal ions such as Mg(+2), Ca(+2), Mn(+2), Zn(+2), Cu(+2), Fe(+3), and Al(+3) was observed. Moreover, Cu(+2), even in the nM range, inhibited iron uptake and attained maximum inhibition of approximately 56%. Inorganic phosphate (Pi) in the medium exerted an opposite effect depending on the type of adenosine nucleotide, which was suppressed with ATP, but enhanced with ADP. A similarly stimulating effect of ATP and ADP with an inverse effect of Pi suggests that the activity of ATPase and ATP synthase may be associated with iron uptake in a different manner, probably via antiport of H(+).
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Affiliation(s)
- Misun Kim
- Department of Biological Science, College of Natural Sciences, Sookmyung Women's University, Seoul, Republic of Korea
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Proton Translocation and ATP Synthesis by the FoF1-ATPase of Purple Bacteria. THE PURPLE PHOTOTROPHIC BACTERIA 2009. [DOI: 10.1007/978-1-4020-8815-5_24] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Nakano M, Imamura H, Toei M, Tamakoshi M, Yoshida M, Yokoyama K. ATP hydrolysis and synthesis of a rotary motor V-ATPase from Thermus thermophilus. J Biol Chem 2008; 283:20789-96. [PMID: 18492667 DOI: 10.1074/jbc.m801276200] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Vacuolar-type H(+)-ATPase (V-ATPase) catalyzes ATP synthesis and hydrolysis coupled with proton translocation across membranes via a rotary motor mechanism. Here we report biochemical and biophysical catalytic properties of V-ATPase from Thermus thermophilus. ATP hydrolysis of V-ATPase was severely inhibited by entrapment of Mg-ADP in the catalytic site. In contrast, the enzyme was very active for ATP synthesis (approximately 70 s(-1)) with the K(m) values for ADP and phosphate being 4.7 +/- 0.5 and 460 +/- 30 microm, respectively. Single molecule observation showed V-ATPase rotated in a 120 degrees stepwise manner, and analysis of dwelling time allowed the binding rate constant k(on) for ATP to be estimated ( approximately 1.1 x 10(6) m(-1) s(-1)), which was much lower than the k(on) (= V(max)/K(m)) for ADP ( approximately 1.4 x 10(7) m(-1) s(-1)). The slower k(on)(ATP) than k(on)(ADP) and strong Mg-ADP inhibition may contribute to prevent wasteful consumption of ATP under in vivo conditions when the proton motive force collapses.
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Affiliation(s)
- Masahiro Nakano
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Japan
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Regulatory mechanisms of proton-translocating F(O)F (1)-ATP synthase. Results Probl Cell Differ 2007; 45:279-308. [PMID: 18026702 DOI: 10.1007/400_2007_043] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
H(+)-F(O)F(1)-ATP synthase catalyzes synthesis of ATP from ADP and inorganic phosphate using the energy of transmembrane electrochemical potential difference of proton (deltamu(H)(+). The enzyme can also generate this potential difference by working as an ATP-driven proton pump. Several regulatory mechanisms are known to suppress the ATPase activity of F(O)F(1): 1. Non-competitive inhibition by MgADP, a feature shared by F(O)F(1) from bacteria, chloroplasts and mitochondria 2. Inhibition by subunit epsilon in chloroplast and bacterial enzyme 3. Inhibition upon oxidation of two cysteines in subunit gamma in chloroplast F(O)F(1) 4. Inhibition by an additional regulatory protein (IF(1)) in mitochondrial enzyme In this review we summarize the information available on these regulatory mechanisms and discuss possible interplay between them.
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Gledhill JR, Montgomery MG, Leslie AGW, Walker JE. How the regulatory protein, IF(1), inhibits F(1)-ATPase from bovine mitochondria. Proc Natl Acad Sci U S A 2007; 104:15671-6. [PMID: 17895376 PMCID: PMC1994141 DOI: 10.1073/pnas.0707326104] [Citation(s) in RCA: 154] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2007] [Indexed: 11/18/2022] Open
Abstract
The structure of bovine F(1)-ATPase inhibited by a monomeric form of the inhibitor protein, IF(1), known as I1-60His, lacking most of the dimerization region, has been determined at 2.1-A resolution. The resolved region of the inhibitor from residues 8-50 consists of an extended structure from residues 8-13, followed by two alpha-helices from residues 14-18 and residues 21-50 linked by a turn. The binding site in the beta(DP)-alpha(DP) catalytic interface is complex with contributions from five different subunits of F(1)-ATPase. The longer helix extends from the external surface of F(1) via a deep groove made from helices and loops in the C-terminal domains of subunits beta(DP), alpha(DP), beta(TP), and alpha(TP) to the internal cavity surrounding the central stalk. The linker and shorter helix interact with the gamma-subunit in the central stalk, and the N-terminal region extends across the central cavity to interact with the nucleotide binding domain of the alpha(E) subunit. To form these complex interactions and penetrate into the core of the enzyme, it is likely that the initial interaction of the inhibitor with F(1) forms via the open conformation of the beta(E) subunit. Then, as two ATP molecules are hydrolyzed, the beta(E)-alpha(E) interface converts to the beta(DP)-alpha(DP) interface via the beta(TP)-alpha(TP) interface, trapping the inhibitor progressively in its binding site and a nucleotide in the catalytic site of subunit beta(DP). The inhibition probably arises by IF(1) imposing the structure and properties of the beta(TP)-alpha(TP) interface on the beta(DP)-alpha(DP) interface, thereby preventing it from hydrolyzing the bound ATP.
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Affiliation(s)
- Jonathan R. Gledhill
- *Medical Research Council Dunn Human Nutrition Unit, Cambridge CB2 0XY, United Kingdom; and
| | - Martin G. Montgomery
- *Medical Research Council Dunn Human Nutrition Unit, Cambridge CB2 0XY, United Kingdom; and
| | - Andrew G. W. Leslie
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - John E. Walker
- *Medical Research Council Dunn Human Nutrition Unit, Cambridge CB2 0XY, United Kingdom; and
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Feniouk BA, Rebecchi A, Giovannini D, Anefors S, Mulkidjanian AY, Junge W, Turina P, Melandri BA. Met23Lys mutation in subunit gamma of F(O)F(1)-ATP synthase from Rhodobacter capsulatus impairs the activation of ATP hydrolysis by protonmotive force. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1767:1319-30. [PMID: 17904517 DOI: 10.1016/j.bbabio.2007.07.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Revised: 07/18/2007] [Accepted: 07/19/2007] [Indexed: 11/26/2022]
Abstract
H(+)-F(O)F(1)-ATP synthase couples proton flow through its membrane portion, F(O), to the synthesis of ATP in its headpiece, F(1). Upon reversal of the reaction the enzyme functions as a proton pumping ATPase. Even in the simplest bacterial enzyme the ATPase activity is regulated by several mechanisms, involving inhibition by MgADP, conformational transitions of the epsilon subunit, and activation by protonmotive force. Here we report that the Met23Lys mutation in the gamma subunit of the Rhodobacter capsulatus ATP synthase significantly impaired the activation of ATP hydrolysis by protonmotive force. The impairment in the mutant was due to faster enzyme deactivation that was particularly evident at low ATP/ADP ratio. We suggest that the electrostatic interaction of the introduced gammaLys23 with the DELSEED region of subunit beta stabilized the ADP-inhibited state of the enzyme by hindering the rotation of subunit gamma rotation which is necessary for the activation.
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Affiliation(s)
- Boris A Feniouk
- Division of Biophysics, School of Biology/Chemistry, University of Osnabrück, D-49069, Osnabrück, Germany.
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Zharova TV, Vinogradov AD. Energy-linked binding of Pi is required for continuous steady-state proton-translocating ATP hydrolysis catalyzed by F0.F1 ATP synthase. Biochemistry 2007; 45:14552-8. [PMID: 17128994 DOI: 10.1021/bi061520v] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The presence of medium Pi (half-maximal concentration of 20 microM at pH 8.0) was found to be required for the prevention of the rapid decline in the rate of proton-motive force (pmf)-induced ATP hydrolysis by Fo.F1 ATP synthase in coupled vesicles derived from Paracoccus denitrificans. The initial rate of the reaction was independent of Pi. The apparent affinity of Pi for its "ATPase-protecting" site was strongly decreased with partial uncoupling of the vesicles. Pi did not reactivate ATPase when added after complete time-dependent deactivation during the enzyme turnover. Arsenate and sulfate, which was shown to compete with Pi when Fo.F1 catalyzed oxidative phosphorylation, substituted for Pi as the protectors of ATPase against the turnover-dependent deactivation. Under conditions where the enzyme turnover was not permitted (no ATP was present), Pi was not required for the pmf-induced activation of ATPase, whereas the presence of medium Pi (or sulfate) delayed the spontaneous deactivation of the enzyme which was induced by the membrane de-energization. The data are interpreted to suggest that coupled and uncoupled ATP hydrolysis catalyzed by Fo.F1 ATP synthases proceeds via different intermediates. Pi dissociates after ADP if the coupling membrane is energized (no E.ADP intermediate exists). Pi dissociates before ADP during uncoupled ATP hydrolysis, leaving the E.ADP intermediate which is transformed into the inactive ADP(Mg2+)-inhibited form of the enzyme (latent ATPase).
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Affiliation(s)
- Tatyana V Zharova
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119992, Russian Federation
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Feniouk BA, Suzuki T, Yoshida M. Regulatory interplay between proton motive force, ADP, phosphate, and subunit epsilon in bacterial ATP synthase. J Biol Chem 2006; 282:764-72. [PMID: 17092944 DOI: 10.1074/jbc.m606321200] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ATP synthase couples transmembrane proton transport, driven by the proton motive force (pmf), to the synthesis of ATP from ADP and inorganic phosphate (P(i)). In certain bacteria, the reaction is reversed and the enzyme generates pmf, working as a proton-pumping ATPase. The ATPase activity of bacterial enzymes is prone to inhibition by both ADP and the C-terminal domain of subunit epsilon. We studied the effects of ADP, P(i), pmf, and the C-terminal domain of subunit epsilon on the ATPase activity of thermophilic Bacillus PS3 and Escherichia coli ATP synthases. We found that pmf relieved ADP inhibition during steady-state ATP hydrolysis, but only in the presence of P(i). The C-terminal domain of subunit epsilon in the Bacillus PS3 enzyme enhanced ADP inhibition by counteracting the effects of pmf. It appears that these features allow the enzyme to promptly respond to changes in the ATP:ADP ratio and in pmf levels in order to avoid potentially wasteful ATP hydrolysis in vivo.
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Affiliation(s)
- Boris A Feniouk
- ATP System Project, Exploratory Research for Advanced Technology, Japan Science and Technology Corporation, Midori-ku, Yokohama 226-0026, Japan
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41
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Keis S, Stocker A, Dimroth P, Cook GM. Inhibition of ATP hydrolysis by thermoalkaliphilic F1Fo-ATP synthase is controlled by the C terminus of the epsilon subunit. J Bacteriol 2006; 188:3796-804. [PMID: 16707672 PMCID: PMC1482892 DOI: 10.1128/jb.00040-06] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The F(1)F(o)-ATP synthases of alkaliphilic bacteria exhibit latent ATPase activity, and for the thermoalkaliphile Bacillus sp. strain TA2.A1, this activity is intrinsic to the F(1) moiety. To study the mechanism of ATPase inhibition, we developed a heterologous expression system in Escherichia coli to produce TA2F(1) complexes from this thermoalkaliphile. Like the native F(1)F(o)-ATP synthase, the recombinant TA2F(1) was blocked in ATP hydrolysis activity, and this activity was stimulated by the detergent lauryldimethylamine oxide. To determine if the C-terminal domain of the epsilon subunit acts as an inhibitor of ATPase activity and if an electrostatic interaction plays a role, a TA2F(1) mutant with either a truncated epsilon subunit [i.e., TA2F(1)(epsilon(DeltaC))] or substitution of basic residues in the second alpha-helix of epsilon with nonpolar alanines [i.e., TA2F(1)(epsilon(6A))] was constructed. Both mutants showed ATP hydrolysis activity at low and high concentrations of ATP. Treatment of the purified F(1)F(o)-ATP synthase and TA2F(1)(epsilon(WT)) complex with proteases revealed that the epsilon subunit was resistant to proteolytic digestion. In contrast, the epsilon subunit of TA2F(1)(epsilon(6A)) was completely degraded by trypsin, indicating that the C-terminal arm was in a conformation where it was no longer protected from proteolytic digestion. In addition, ATPase activity was not further activated by protease treatment when compared to the untreated control, supporting the observation that epsilon was responsible for inhibition of ATPase activity. To study the effect of the alanine substitutions in the epsilon subunit in the entire holoenzyme, we reconstituted recombinant TA2F(1) complexes with F(1)-stripped native membranes of strain TA2.A1. The reconstituted TA2F(o)F(1)(epsilon(WT)) was blocked in ATP hydrolysis and exhibited low levels of ATP-driven proton pumping consistent with the F(1)F(o)-ATP synthase in native membranes. Reconstituted TA2F(o)F(1)(epsilon(6A)) exhibited ATPase activity that correlated with increased ATP-driven proton pumping, confirming that the epsilon subunit also inhibits ATPase activity of TA2F(o)F(1).
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Affiliation(s)
- Stefanie Keis
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, P.O. Box 56, Dunedin, New Zealand
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42
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Bowler MW, Montgomery MG, Leslie AGW, Walker JE. How azide inhibits ATP hydrolysis by the F-ATPases. Proc Natl Acad Sci U S A 2006; 103:8646-9. [PMID: 16728506 PMCID: PMC1469772 DOI: 10.1073/pnas.0602915103] [Citation(s) in RCA: 181] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the structure of bovine F1-ATPase determined at 1.95-A resolution with crystals grown in the presence of ADP, 5'-adenylyl-imidodiphosphate, and azide, the azide anion interacts with the beta-phosphate of ADP and with residues in the ADP-binding catalytic subunit, betaDP. It occupies a position between the catalytically essential amino acids, beta-Lys-162 in the P loop and the "arginine finger" residue, alpha-Arg-373, similar to the site occupied by the gamma-phosphate in the ATP-binding subunit, betaTP. Its presence in the betaDP-subunit tightens the binding of the side chains to the nucleotide, enhancing its affinity and thereby stabilizing the state with bound ADP. This mechanism of inhibition appears to be common to many other ATPases, including ABC transporters, SecA, and DNA topoisomerase IIalpha. It also explains the stimulatory effect of azide on ATP-sensitive potassium channels by enhancing the binding of ADP.
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Affiliation(s)
- Matthew W. Bowler
- *Dunn Human Nutrition Unit, Medical Research Council, Hills Road, Cambridge CB2 2XY, United Kingdom; and
| | - Martin G. Montgomery
- *Dunn Human Nutrition Unit, Medical Research Council, Hills Road, Cambridge CB2 2XY, United Kingdom; and
| | - Andrew G. W. Leslie
- Laboratory of Molecular Biology, Medical Research Council, Hills Road, Cambridge CB2 2QH, United Kingdom
| | - John E. Walker
- *Dunn Human Nutrition Unit, Medical Research Council, Hills Road, Cambridge CB2 2XY, United Kingdom; and
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Turina P, Rebecchi A, D'Alessandro M, Anefors S, Melandri BA. Modulation of proton pumping efficiency in bacterial ATP synthases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:320-5. [PMID: 16765908 DOI: 10.1016/j.bbabio.2006.04.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2006] [Revised: 04/19/2006] [Accepted: 04/23/2006] [Indexed: 11/18/2022]
Abstract
The ATP synthase in chromatophores of Rhodobacter caspulatus can effectively generate a transmembrane pH difference coupled to the hydrolysis of ATP. The rate of hydrolysis was rather insensitive to the depletion of ADP in the assay medium by an ATP regenerating system (phospho-enol-pyruvate (PEP) and pyruvate kinase (PK)). The steady state values of DeltapH were however drastically reduced as a consequence of ADP depletion. The clamped concentrations of ADP obtained using different PK activities in the assay medium could be calculated and an apparent Kd approximately 0.5 microM was estimated. The extent of proton uptake was also strongly dependent on the addition of phosphate to the assay medium. The Kd for this effect was about 70 microM. Analogous experiments were performed in membrane fragment from Escherichia coli. In this case, however, the hydrolysis rate was strongly inhibited by Pi, added up to 3 mM. Inhibition by Pi was nearly completely suppressed following depletion of ADP. The Kd's for the ADP and Pi were in the micromolar range and submillimolar range, respectively, and were mutually dependent from the concentration of the other ligand. Contrary to hydrolysis, the pumping of protons was rather insensitive to changes in the concentrations of the two ligands. At intermediate concentrations, proton pumping was actually stimulated, while the hydrolysis was inhibited. It is concluded that, in these two bacterial organisms, ADP and phosphate induce a functional state of the ATP synthase competent for a tightly coupled proton pumping, while the depletion of either one of these two ligands favors an inefficient (slipping) functional state. The switch between these states can probably be related to a structural change in the C-terminal alpha-helical hairpin of the epsilon-subunit, from an extended conformation, in which ATP hydrolysis is tightly coupled to proton pumping, to a retracted one, in which ATP hydrolysis and proton pumping are loosely coupled.
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Affiliation(s)
- Paola Turina
- Department of Biology, Laboratory of Biochemistry and Biophysics, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy
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44
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Feniouk BA, Suzuki T, Yoshida M. The role of subunit epsilon in the catalysis and regulation of FOF1-ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:326-38. [PMID: 16701076 DOI: 10.1016/j.bbabio.2006.03.022] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2006] [Revised: 03/13/2006] [Accepted: 03/30/2006] [Indexed: 10/24/2022]
Abstract
The regulation of ATP synthase activity is complex and involves several distinct mechanisms. In bacteria and chloroplasts, subunit epsilon plays an important role in this regulation, (i) affecting the efficiency of coupling, (ii) influencing the catalytic pathway, and (iii) selectively inhibiting ATP hydrolysis activity. Several experimental studies indicate that the regulation is achieved through large conformational transitions of the alpha-helical C-terminal domain of subunit epsilon that occur in response to membrane energization, change in ATP/ADP ratio or addition of inhibitors. This review summarizes the experimental data obtained on different organisms that clarify some basic features as well as some molecular details of this regulatory mechanism. Multiple functions of subunit epsilon, its role in the difference between the catalytic pathways of ATP synthesis and hydrolysis and its influence on the inhibition of ATP hydrolysis by ADP are also discussed.
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Affiliation(s)
- Boris A Feniouk
- ATP System Project, Exploratory Research for Advanced Technology, Japan Science and Technology Corporation (JST), 5800-3 Nagatsuta, Midori-ku, Yokohama 226-0026, Japan.
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45
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Zharova TV, Vinogradov AD. Requirement of medium ADP for the steady-state hydrolysis of ATP by the proton-translocating Paracoccus denitrificans Fo.F1-ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:304-10. [PMID: 16730637 DOI: 10.1016/j.bbabio.2006.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2005] [Revised: 03/03/2006] [Accepted: 03/06/2006] [Indexed: 11/22/2022]
Abstract
Fo.F1-ATP synthase in inside-out coupled vesicles derived from Paracoccus denitrificans catalyzes Pi-dependent proton-translocating ATPase reaction if exposed to prior energization that relieves ADP.Mg2+ -induced inhibition (Zharova, T.V. and Vinogradov, A.D. (2004) J. Biol. Chem.,279, 12319-12324). Here we present evidence that the presence of medium ADP is required for the steady-state energetically self-sustained coupled ATP hydrolysis. The initial rapid ATPase activity is declined to a certain level if the reaction proceeds in the presence of the ADP-consuming, ATP-regenerating system (pyruvate kinase/phosphoenol pyruvate). The rate and extent of the enzyme de-activation are inversely proportional to the steady-state ADP concentration, which is altered by various amounts of pyruvate kinase at constant ATPase level. The half-maximal rate of stationary ATP hydrolysis is reached at an ADP concentration of 8 x 10(-6) M. The kinetic scheme is proposed explaining the requirement of the reaction products (ADP and Pi), the substrates of ATP synthesis, in the medium for proton-translocating ATP hydrolysis by P. denitrificans Fo.F1-ATP synthase.
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Affiliation(s)
- Tatyana V Zharova
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119992, Russian Federation
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Feniouk BA, Junge W. Regulation of the F0F1-ATP synthase: the conformation of subunit epsilon might be determined by directionality of subunit gamma rotation. FEBS Lett 2005; 579:5114-8. [PMID: 16154570 DOI: 10.1016/j.febslet.2005.08.030] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2005] [Revised: 08/16/2005] [Accepted: 08/16/2005] [Indexed: 11/22/2022]
Abstract
F(0)F(1)-ATP synthase couples ATP synthesis/hydrolysis with transmembrane proton transport. The catalytic mechanism involves rotation of the gamma epsilon c(approximately 10)-subunits complex relative to the rest of the enzyme. In the absence of protonmotive force the enzyme is inactivated by the tight binding of MgADP. Subunit epsilon also modulates the activity: its conformation can change from a contracted to extended form with C-terminus stretched towards F(1). The latter form inhibits ATP hydrolysis (but not synthesis). We propose that the directionality of the coiled-coil subunit gamma rotation determines whether subunit epsilon is in contracted or extended form. Block of rotation by MgADP presumably induces the extended conformation of subunit epsilon. This conformation might serve as a safety lock, stabilizing the ADP-inhibited state upon de-energization and preventing spontaneous re-activation and wasteful ATP hydrolysis. The hypothesis merges the known regulatory effects of ADP, protonmotive force and conformational changes of subunit epsilon into a consistent picture.
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Affiliation(s)
- Boris A Feniouk
- Division of Biophysics, Faculty of Biology/Chemistry, University of Osnabrück, D-49069 Osnabrück, Germany.
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47
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Ishmukhametov RR, Galkin MA, Vik SB. Ultrafast purification and reconstitution of His-tagged cysteine-less Escherichia coli F1Fo ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2005; 1706:110-6. [PMID: 15620371 DOI: 10.1016/j.bbabio.2004.09.012] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2004] [Revised: 09/21/2004] [Accepted: 09/24/2004] [Indexed: 11/30/2022]
Abstract
His-tagged cysteine-less F1Fo ATP synthase from Escherichia coli was purified using Ni-NTA affinity chromatography. During the purification procedure the loss of total ATPase activity did not exceed 50%, and the extent of purification was about 80-fold. The purified enzyme was essentially free of other proteins, was highly active in ATP hydrolysis (75 units/mg at pH 8 and 37 degrees C), and was sensitive to N,N'-dicyclohexylcarbodiimide (70%). Incorporation of F1Fo into soybean liposomes yielded well-coupled and highly active proteoliposomes. The entire procedure, from the disruption of cells by French press to the preparation of proteoliposomes, took only about 8 h. Some improvements in procedures for the estimation of rates of both ATP hydrolysis and ATP-dependent 9-amino-6-chloro-2-methoxyacridine (ACMA) fluorescence quenching are described.
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Affiliation(s)
- Robert R Ishmukhametov
- Department of Biological Sciences, PO Box 750376, 6501 Airline Road, Southern Methodist University, Dallas, Texas 75275-0376, USA
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48
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Hirono-Hara Y, Ishizuka K, Kinosita K, Yoshida M, Noji H. Activation of pausing F1 motor by external force. Proc Natl Acad Sci U S A 2005; 102:4288-93. [PMID: 15758075 PMCID: PMC555477 DOI: 10.1073/pnas.0406486102] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A rotary motor F(1), a catalytic part of ATP synthase, makes a 120 degrees step rotation driven by hydrolysis of one ATP, which consists of 80 degrees and 40 degrees substeps initiated by ATP binding and probably by ADP and/or P(i) dissociation, respectively. During active rotations, F(1) spontaneously fails in ADP release and pauses after a 80 degrees substep, which is called the ADP-inhibited form. In the present work, we found that, when pushed >+40 degrees with magnetic tweezers, the pausing F(1) resumes its active rotation after releasing inhibitory ADP. The rate constant of the mechanical activation exponentially increased with the pushed angle, implying that F(1) weakens the affinity of its catalytic site for ADP as the angle goes forward. This finding explains not only its unidirectional nature of rotation, but also its physiological function in ATP synthesis; it would readily bind ADP from solution when rotated backward by an F(o) motor in the ATP synthase. Furthermore, the mechanical work for the forced rotation was efficiently converted into work for expelling ADP from the catalytic site, supporting the tight coupling between the rotation and catalytic event.
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Affiliation(s)
- Yoko Hirono-Hara
- Institute of Industrial Science and Precursory Research for Embryonic Science and Technology, Japan Science and Technology Corporation, University of Tokyo, Tokyo 153-8505, Japan
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49
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Galkin M, Venard R, Vaillier J, Velours J, Haraux F. Functional transitions of F0F1-ATPase mediated by the inhibitory peptide IF1 in yeast coupled submitochondrial particles. EUROPEAN JOURNAL OF BIOCHEMISTRY 2004; 271:1963-70. [PMID: 15128305 DOI: 10.1111/j.1432-1033.2004.04108.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanism of inhibition of yeast F(0)F(1)-ATPase by its naturally occurring protein inhibitor (IF1) was investigated in submitochondrial particles by studying the IF1-mediated ATPase inhibition in the presence and absence of a protonmotive force. In the presence of protonmotive force, IF1 added during net NTP hydrolysis almost completely inhibited NTPase activity. At moderate IF1 concentration, subsequent uncoupler addition unexpectedly caused a burst of NTP hydrolysis. We propose that the protonmotive force induces the conversion of IF1-inhibited F(0)F(1)-ATPase into a new form having a lower affinity for IF1. This form remains inactive for ATP hydrolysis after IF1 release. Uncoupling simultaneously releases ATP hydrolysis and converts the latent form of IF1-free F(0)F(1)-ATPase back to the active form. The relationship between the different steps of the catalytic cycle, the mechanism of inhibition by IF1 and the interconversion process is discussed.
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Affiliation(s)
- Mikhail Galkin
- Service de Bioénergétique & CNRS-URA 2096, Gif-sur-Yvette, France
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