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Huang Q, Chen C, Wu X, Qin Y, Tan X, Zhang D, Liu Y, Li W, Chen Y. Overexpression of ATP Synthase Subunit Beta (Atp2) Confers Enhanced Blast Disease Resistance in Transgenic Rice. J Fungi (Basel) 2023; 10:5. [PMID: 38276021 PMCID: PMC10820023 DOI: 10.3390/jof10010005] [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: 11/06/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Previous research has shown that the pathogenicity and appressorium development of Magnaporthe oryzae can be inhibited by the ATP synthase subunit beta (Atp2) present in the photosynthetic bacterium Rhodopseudomonas palustris. In the present study, transgenic plants overexpressing the ATP2 gene were generated via genetic transformation in the Zhonghua11 (ZH11) genetic background. We compared the blast resistance and immune response of ATP2-overexpressing lines and wild-type plants. The expression of the Atp2 protein and the physiology, biochemistry, and growth traits of the mutant plants were also examined. The results showed that, compared with the wild-type plant ZH11, transgenic rice plants heterologously expressing ATP2 had no significant defects in agronomic traits, but the disease lesions caused by the rice blast fungus were significantly reduced. When infected by the rice blast fungus, the transgenic rice plants exhibited stronger antioxidant enzyme activity and a greater ratio of chlorophyll a to chlorophyll b. Furthermore, the immune response was triggered stronger in transgenic rice, especially the increase in reactive oxygen species (ROS), was more strongly triggered in plants. In summary, the expression of ATP2 as an antifungal protein in rice could improve the ability of rice to resist rice blast.
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Affiliation(s)
- Qiang Huang
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (Q.H.)
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China (D.Z.); (Y.L.)
| | - Chunyan Chen
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (Q.H.)
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China (D.Z.); (Y.L.)
| | - Xiyang Wu
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China (D.Z.); (Y.L.)
| | - Yingfei Qin
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China (D.Z.); (Y.L.)
| | - Xinqiu Tan
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China (D.Z.); (Y.L.)
| | - Deyong Zhang
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China (D.Z.); (Y.L.)
| | - Yong Liu
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China (D.Z.); (Y.L.)
| | - Wei Li
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (Q.H.)
| | - Yue Chen
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (Q.H.)
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China (D.Z.); (Y.L.)
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Wang Z, Zhu S, Li C, Lyu L, Yu J, Wang D, Xu Z, Ni J, Gao B, Lu J, Yao YF. Gene essentiality profiling reveals a novel determinant of stresses preventing protein aggregation in Salmonella. Emerg Microbes Infect 2022; 11:1554-1571. [PMID: 35603550 PMCID: PMC9176671 DOI: 10.1080/22221751.2022.2081618] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Adaptation to various stresses during infection is important for Salmonella Typhimurium virulence, while the fitness determinants under infection-relevant stress conditions remain unknown. Here, we simulated conditions Salmonella encountered within the host or in the environment by 15 individual stresses as well as two model cell lines (epithelium and macrophage) to decipher the genes and pathways required for fitness. By high-resolution Tn-seq analysis, a total of 1242 genes were identified as essential for fitness under at least one stress condition. The comparative analysis of fitness determinants in 17 stress conditions indicated the essentiality of genes varied in different mimicking host niches. A total of 12 genes were identified as fitness determinants in all stress conditions, including recB, recC, and xseA (encode three exonuclease subunits necessary for DNA recombination repair) and a novel essential fitness gene yheM. YheM is a putative sulfurtransferase subunit that is responsible for tRNA modification, and our results showed that Salmonella lacking yheM accumulated more aggregates of endogenous protein than wild-type. Moreover, we established a scoring scheme for sRNA essentiality analysis and found STnc2080 of unknown function was essential for resistance to LL-37. In summary, we systematically dissected Salmonella gene essentiality profiling and demonstrated the general and specific adaptive requirements in infection-relevant niches. Our data not only provide valuable insights on how Salmonella responds to environmental stresses during infections but also highlight the potential clinical application of fitness determinants in vaccine development.
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Affiliation(s)
- Zuoqiang Wang
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Siqi Zhu
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, People's Republic of China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Congcong Li
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Lin Lyu
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Jingchen Yu
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Danni Wang
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Zhihong Xu
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Jinjing Ni
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Beile Gao
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, People's Republic of China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, People's Republic of China
| | - Jie Lu
- Department of Infectious Diseases, Shanghai Ruijin Hospital, Shanghai, People's Republic of China
| | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.,Department of Infectious Diseases, Shanghai Ruijin Hospital, Shanghai, People's Republic of China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, People's Republic of China
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3
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Insights into the origin of the high energy-conversion efficiency of F 1-ATPase. Proc Natl Acad Sci U S A 2019; 116:15924-15929. [PMID: 31341091 DOI: 10.1073/pnas.1906816116] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Our understanding of the rotary-coupling mechanism of F1-ATPase has been greatly enhanced in the last decade by advances in X-ray crystallography, single-molecular imaging, and theoretical models. Recently, Volkán-Kacsó and Marcus [S. Volkán-Kacsó, R. A. Marcus, Proc. Natl. Acad. Sci. U.S.A. 112, 14230 (2015)] presented an insightful thermodynamic model based on the Marcus reaction theory coupled with an elastic structural deformation term to explain the observed γ-rotation angle dependence of the adenosine triphosphate (ATP)/adenosine diphosphate (ADP) exchange rates of F1-ATPase. Although the model is successful in correlating single-molecule data, it is not in agreement with the available theoretical results. We describe a revision of the model, which leads to consistency with the simulation results and other experimental data on the F1-ATPase rotor compliance. Although the free energy liberated on ATP hydrolysis by F1-ATPase is rapidly dissipated as heat and so cannot contribute directly to the rotation, we show how, nevertheless, F1-ATPase functions near the maximum possible efficiency. This surprising result is a consequence of the differential binding of ATP and its hydrolysis products ADP and Pi along a well-defined pathway.
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Chou YC, Hsiao YF, Hwang GJ, To K. Torque generation through the random movement of an asymmetric rotor: A potential rotational mechanism of the γ subunit of F(1)-ATPase. Phys Rev E 2016; 93:022408. [PMID: 26986363 DOI: 10.1103/physreve.93.022408] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Indexed: 11/07/2022]
Abstract
The rotation of the γ subunit of F(1)-ATPase is stochastic, processive, unidirectional, reversible through an external torque, and stepwise with a slow rotation. We propose a mechanism that can explain these properties of the rotary molecular motor, and that can determine the direction of rotation. The asymmetric structures of the γ subunit, both at the tip of the shaft (C and N termini) and at the part (ε subunit) protruding from the α(3)β(3) subunits, are critical. The torque required for stochastic rotation is generated from the impulsive reactive force due to the random collisions between the γ subunit and the quasihexagonal α(3)β(3) subunits. The rotation is the result of the random motion of the confined asymmetric γ subunit. The steps originate from the chemical reactions of the γ subunit and physical interaction between the γ subunit and the flexible protrusions of the α(3)β(3) subunits. An external torque as well as a configurational modification in the γ subunit (the central rotor) can reverse the rotational direction. We demonstrate the applicability of the mechanism to a macroscopic simulation system, which has the essential ingredients of the F(1)-ATPase structure, by reproducing the dynamic properties of the rotation.
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Affiliation(s)
- Y C Chou
- Department of Physics, National Tsing-Hua University, Hsinchu, Taiwan, Republic of China
| | - Yi-Feng Hsiao
- Department of Physics, National Tsing-Hua University, Hsinchu, Taiwan, Republic of China
| | - Gwo-Jen Hwang
- Department of Electronic Engineering, St. John's University, Tamsui District, New Taipei City, Taiwan, Republic of China
| | - Kiwing To
- Institute of Physics, Academia Sinca, Taipei, Taiwan, Republic of China
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Martín-García F, Mendieta-Moreno JI, Marcos-Alcalde I, Gómez-Puertas P, Mendieta J. Simulation of catalytic water activation in mitochondrial F1-ATPase using a hybrid quantum mechanics/molecular mechanics approach: an alternative role for β-Glu 188. Biochemistry 2013; 52:959-66. [PMID: 23320924 DOI: 10.1021/bi301109x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The use of quantum mechanics/molecular mechanics simulations to study the free energy landscape of the water activation at the catalytic site of mitochondrial F(1)-ATPase affords us insight into the generation of the nucleophile OH(-) prior to ATP hydrolysis. As a result, the ATP molecule was found to be the final proton acceptor. In the simulated pathway, the transfer of a proton to the nucleotide was not direct but occurred via a second water molecule in a manner similar to the Grotthuss mechanism proposed for proton diffusion. Residue β-Glu 188, previously described as the putative catalytic base, was found to be involved in the stabilization of a transient hydronium ion during water activation. Simulations in the absence of the carboxylate moiety of β-Glu 188 support this role.
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Affiliation(s)
- Fernando Martín-García
- Molecular Modelling Group, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), C/Nicolás Cabrera 1, Cantoblanco, Madrid, Spain
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6
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Role of different Escherichia coli hydrogenases in H+ efflux and F₁F(o)-ATPase activity during glycerol fermentation at different pH values. Biosci Rep 2011; 31:179-84. [PMID: 20662772 DOI: 10.1042/bsr20100053] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Escherichia coli is able to ferment glycerol and produce H2 by different Hyds (hydrogenases). Wild-type whole cells were shown to extrude H+ through the F1Fo-ATPase and by other means with a lower rate compared with that under glucose fermentation. At pH 7.5, H+ efflux was stimulated in fhlA mutant (with defective transcriptional activator of Hyd-3 or Hyd-4) and was lowered in hyaB or hybC mutants (with defective Hyd-1 or Hyd-2) and hyaB hybC double mutant; DCCD (dicyclohexylcarbodi-imide)-sensitive H+ efflux was observed. At pH 5.5, H+ efflux in wild-type was lower compared with that at pH 7.5; it was increased in fhlA mutant and absent in hyaB hybC mutant. Membrane vesicle ATPase activity was lower in wild-type glycerol-fermented cells at pH 7.5 compared with that in glucose-fermented cells; 100 mM K+ did not stimulate ATPase activity. The latter at pH 7.5, compared with that in wild-type, was lower in hyaB and less in hybC mutants, stimulated in the hyaB hybC mutant and suppressed in the fhlA mutant; DCCD inhibited ATPase activity. At pH 5.5, the ATPase activities of hyaB and hybC mutants had similar values and were higher compared with that in wild-type; ATPase activity was suppressed in hyaB hybC and fhlA mutants. The results indicate that during glycerol fermentation, H+ was expelled also via F1Fo. At pH 7.5 Hyd-1 and Hyd-2 but not FhlA or Hyd-4 might be related to F1Fo or have their own H+-translocating ability. At pH 5.5, both Hyd-1 and Hyd-2 more than F1Fo might be involved in H+ efflux.
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How Biomolecular Motors Work: Synergy Between Single Molecule Experiments and Single Molecule Simulations. SINGLE MOLECULE SPECTROSCOPY IN CHEMISTRY, PHYSICS AND BIOLOGY 2010. [DOI: 10.1007/978-3-642-02597-6_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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8
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Abstract
It is proposed that the precellular stage of biological evolution unraveled within networks of inorganic compartments that harbored a diverse mix of virus‐like genetic elements. This stage of evolution might makes up the Last Universal Cellular Ancestor (LUCA) that more appropriately could be denoted Last Universal Cellular Ancestral State (LUCAS). Such a scenario recapitulates the ideas of J. B. S. Haldane sketched in his classic 1928 essay. However, unlike in Haldane's day, considerable support for this scenario exits today: lack of homology between core DNA replication system components in archaea and bacteria, distinct membrane chemistries and enzymes of lipid biosynthesis in archaea and bacteria, spread of several viral hallmark genes among diverse groups of viruses, and the extant archaeal and bacterial chromosomes appear to be shaped by accretion of diverse, smaller replicons. Under the viral model of precellular evolution, the key components of cells originated as components of virus‐like entities. The two surviving types of cellular life forms, archaea and bacteria, might have emerged from the LUCAS independently, along with, probably, numerous forms now extinct.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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9
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Abstract
The ATP synthase from Escherichia coli is a prototype of the ATP synthases that are found in many bacteria, in the mitochondria of eukaryotes, and in the chloroplasts of plants. It contains eight different types of subunits that have traditionally been divided into F(1), a water-soluble catalytic sector, and F(o), a membrane-bound ion transporting sector. In the current rotary model for ATP synthesis, the subunits can be divided into rotor and stator subunits. Several lines of evidence indicate that epsilon is one of the three rotor subunits, which rotate through 360 degrees. The three-dimensional structure of epsilon is known and its interactions with other subunits have been explored by several approaches. In light of recent work by our group and that of others, the role of epsilon in the ATP synthase from E. coli is discussed.
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Affiliation(s)
- S B Vik
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275, USA.
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10
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Xie P. On chemomechanical coupling of the F(1)-ATPase molecular motor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:955-62. [PMID: 19265667 DOI: 10.1016/j.bbabio.2009.02.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Revised: 02/19/2009] [Accepted: 02/19/2009] [Indexed: 10/21/2022]
Abstract
F(1)-ATPase catalyzes ATP hydrolysis to drive the central gamma-shaft rotating inside a hexameric cylinder composed of alternating alpha and beta subunits. Experiments showed that the rotation of gamma-shaft proceeds in steps of 120 degrees and each 120 degrees -rotation is composed of an 80 degrees substep and a 40 degrees substep. Here, based on the previously proposed models, an improved physical model for chemomechanical coupling of F(1)-ATPase is presented, with which the two-substep rotation is well explained. One substep is driven by the power stroke upon ATP binding, while the other one resulted from the passage of gamma-shaft from previous to next adjacent beta subunits via free diffusion. Using the model, the dynamics and kinetics of F(1)-ATPase, such as the rotating time of each substep, the dwell time at each pause and the rotation rate, are analytically studied. The theoretical results obtained with only three adjustable parameters reproduce the available experimental data well.
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Affiliation(s)
- Ping Xie
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
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11
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Extremely High Frequency Electromagnetic Radiation Enforces Bacterial Effects of Inhibitors and Antibiotics. Cell Biochem Biophys 2008; 51:97-103. [DOI: 10.1007/s12013-008-9020-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2008] [Indexed: 11/25/2022]
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Scanlon JAB, Al-Shawi MK, Nakamoto RK. A rotor-stator cross-link in the F1-ATPase blocks the rate-limiting step of rotational catalysis. J Biol Chem 2008; 283:26228-40. [PMID: 18628203 DOI: 10.1074/jbc.m804858200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The F(0)F(1)-ATP synthase couples the functions of H(+) transport and ATP synthesis/hydrolysis through the efficient transmission of energy mediated by rotation of the centrally located gamma, epsilon, and c subunits. To understand the gamma subunit role in the catalytic mechanism, we previously determined the partial rate constants and devised a minimal kinetic model for the rotational hydrolytic mode of the F(1)-ATPase enzyme that uniquely fits the pre-steady state and steady state data ( Baylis Scanlon, J. A., Al-Shawi, M. K., Le, N. P., and Nakamoto, R. K. (2007) Biochemistry 46, 8785-8797 ). Here we directly test the model using two single cysteine mutants, betaD380C and betaE381C, which can be used to reversibly inhibit rotation upon formation of a cross-link with the conserved gammaCys-87. In the pre-steady state, the gamma-beta cross-linked enzyme at high Mg.ATP conditions retained the burst of hydrolysis but was not able to release P(i). These data show that the rate-limiting rotation step, k(gamma), occurs after hydrolysis and before P(i) release. This analysis provides additional insights into how the enzyme achieves efficient coupling and implicates the betaGlu-381 residue for proper formation of the rate-limiting transition state involving gamma subunit rotation.
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Affiliation(s)
- Joanne A Baylis Scanlon
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
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13
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Nakamoto RK, Baylis Scanlon JA, Al-Shawi MK. The rotary mechanism of the ATP synthase. Arch Biochem Biophys 2008; 476:43-50. [PMID: 18515057 DOI: 10.1016/j.abb.2008.05.004] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 05/06/2008] [Accepted: 05/13/2008] [Indexed: 11/29/2022]
Abstract
The F0F1 ATP synthase is a large complex of at least 22 subunits, more than half of which are in the membranous F0 sector. This nearly ubiquitous transporter is responsible for the majority of ATP synthesis in oxidative and photo-phosphorylation, and its overall structure and mechanism have remained conserved throughout evolution. Most examples utilize the proton motive force to drive ATP synthesis except for a few bacteria, which use a sodium motive force. A remarkable feature of the complex is the rotary movement of an assembly of subunits that plays essential roles in both transport and catalytic mechanisms. This review addresses the role of rotation in catalysis of ATP synthesis/hydrolysis and the transport of protons or sodium.
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Affiliation(s)
- Robert K Nakamoto
- Department of Molecular Physiology and Biological Physics, University of Virginia, P.O. Box 800736, Charlottesville, VA 22908-0736, USA.
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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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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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16
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Wu Y, Ilan B, Voth GA. Charge delocalization in proton channels, II: the synthetic LS2 channel and proton selectivity. Biophys J 2006; 92:61-9. [PMID: 17056732 PMCID: PMC1697870 DOI: 10.1529/biophysj.106.091942] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this study, the minimalist synthetic LS2 channel is used as a prototype to examine the selectivity of protons over other cations. The free-energy profiles along the transport pathway of LS2 are calculated for three cation species: a realistic delocalized proton (including Grotthuss shuttling)--H(+), a classical (nonshuttling) hydronium--H(3)O(+), and a potassium cation--K(+). The overall barrier for K(+) is approximately twice as large as that for H(+), explaining the >100 times larger maximal ion conductance for the latter, in qualitative agreement with the experimental result. The profile for the classical hydronium is quantitatively intermediate between those of H(+) and K(+) and qualitatively more similar to that of H(+), for which the locations of the peaks are well correlated with the troughs of the pore radius profile. There is a strong correlation between the free-energy profiles and the very different characteristic hydration structures of the three cation species. This work suggests that the passage of various cations through ion channels cannot always be explained by simple electrostatic desolvation considerations.
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Affiliation(s)
- Yujie Wu
- Center for Biophysical Modeling and Simulation, Department of Chemistry, University of Utah, Salt Lake City, Utah, 84112-0850, USA
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17
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Abstract
It is proposed that the pre-cellular stage of biological evolution, including the Last Universal Common Ancestor (LUCA) of modern cellular life forms, occurred within networks of inorganic compartments that hosted a diverse mix of virus-like genetic elements. This viral model of cellular origin recapitulates the early ideas of J.B.S. Haldane, sketched in his 1928 essay on the origin of life. However, unlike in Haldane's day, there is substantial empirical support for this scenario from three major lines of evidence provided by comparative genomics: (i) the lack of homology among the core components of the DNA replication systems between the two primary lines of descent of cellular life forms, archaea and bacteria, (ii) the similar lack of homology between the enzymes of lipid biosynthesis in conjunction with distinct membrane chemistries in archaea and bacteria, and (iii) the spread of several viral hallmark genes, which encode proteins with key functions in viral replication and morphogenesis, among numerous and extremely diverse groups of viruses, in contrast to their absence in cellular life forms. Under the viral model of pre-cellular evolution, the key elements of cells including the replication apparatus, membranes, molecular complexes involved in membrane transport and translocation, and others originated as components of virus-like entities. This model alleviates, at least in part, the challenge of the emergence of the immensely complex organization of modern cells.
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Affiliation(s)
- Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda
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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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19
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Abstract
Many essential functions of living cells are performed by nanoscale protein motors. The best characterized of these is F(o)F1-ATP synthase, the smallest rotary motor. This rotary motor catalyzes the synthesis of ATP with high efficiency under conditions where the reactants (ADP, H2PO4(-)) and the product (ATP) are present in the cell at similar concentrations. We present a detailed structure-based kinetic model for the mechanism of action of F1-ATPase and demonstrate the role of different protein conformations for substrate binding during ATP synthesis and ATP hydrolysis. The model shows that the pathway for ATP hydrolysis is not simply the pathway for ATP synthesis in reverse. The findings of the model also explain why the cellular concentration of ATP does not inhibit ATP synthesis.
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Affiliation(s)
- Yi Qin Gao
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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20
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Abstract
We present a mesoscopic model for ATP synthesis by F(1)F(o) ATPase. The model combines the existing experimental knowledge of the F(1) enzyme into a consistent mathematical model that illuminates how the stages in synthesis are related to the protein structure. For example, the model illuminates how specific interactions between the gamma, epsilon, and alpha(3)beta(3) subunits couple the F(o) motor to events at the catalytic sites. The model also elucidates the origin of ADP inhibition of F(1) in its hydrolysis mode. The methodology we develop for constructing the structure-based model should prove useful in modeling other protein motors.
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Affiliation(s)
- Jianhua Xing
- Departments of Molecular Cell Biology, University of California, Berkeley, CA 94720-1132, USA
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21
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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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22
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Abstract
ATP synthase uses a rotary mechanism to carry out its cellular function of manufacturing ATP. The central gamma-shaft rotates inside a hexameric cylinder composed of alternating alpha- and beta-subunits. When operating in the hydrolysis direction under high frictional loads and low ATP concentrations, a coordinated mechanochemical cycle in the three catalytic sites of the beta-subunits rotates the gamma-shaft in three 120 degrees steps. At low frictional loads, the 120 degrees steps alternate with three ATP-independent substeps separated by approximately 30 degrees. We present a quantitative model that accounts for these substeps and show that the observed pauses are due to 1), the asymmetry of the F(1) hexamer that produces a propeller-like motion of the power-stroke and 2), the relatively tight binding of ADP to the catalytic sites.
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Affiliation(s)
- Sean X Sun
- Department of Mechanical Engineering and Whitaker Institute of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
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23
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Dittrich M, Hayashi S, Schulten K. ATP hydrolysis in the betaTP and betaDP catalytic sites of F1-ATPase. Biophys J 2004; 87:2954-67. [PMID: 15315950 PMCID: PMC1304769 DOI: 10.1529/biophysj.104.046128] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The enzyme F1-adenosine triphosphatase (ATPase) is a molecular motor that converts the chemical energy stored in the molecule adenosine triphosphate (ATP) into mechanical rotation of its gamma-subunit. During steady-state catalysis, the three catalytic sites of F1 operate in a cooperative fashion such that at every instant each site is in a different conformation corresponding to a different stage along the catalytic cycle. Notwithstanding a large amount of biochemical and, recently, structural data, we still lack an understanding of how ATP hydrolysis in F1 is coupled to mechanical motion and how the catalytic sites achieve cooperativity during rotatory catalysis. In this publication, we report combined quantum mechanical/molecular mechanical simulations of ATP hydrolysis in the betaTP and betaDP catalytic sites of F1-ATPase. Our simulations reveal a dramatic change in the reaction energetics from strongly endothermic in betaTP to approximately equienergetic in betaDP. The simulations identify the responsible protein residues, the arginine finger alphaR373 being the most important one. Similar to our earlier study of betaTP, we find a multicenter proton relay mechanism to be the energetically most favorable hydrolysis pathway. The results elucidate how cooperativity between catalytic sites might be achieved by this remarkable molecular motor.
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Affiliation(s)
- Markus Dittrich
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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24
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Trchounian A. Escherichia coli proton-translocating F0F1-ATP synthase and its association with solute secondary transporters and/or enzymes of anaerobic oxidation–reduction under fermentation. Biochem Biophys Res Commun 2004; 315:1051-7. [PMID: 14985119 DOI: 10.1016/j.bbrc.2004.02.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2004] [Indexed: 11/26/2022]
Abstract
The Escherichia coli proton-translocating F0F1-ATP synthase has a priority in H+ circulation through the membrane in maintaining proton-motive force in the context of ATP synthesis and hydrolysis. Recent advances in the study of this complex under fermentative growth have led to hypothesis that, in the absence of oxidative phosphorylation, F0F1 is implicated as an essential part of H+ movement and ATP hydrolysis, associated with solute secondary transporters and/or enzymes of anaerobic oxidation-reduction. These associations can result from a protein-protein interaction by dithiol-disulfide interchange. In such associations F0F1 has novel functions in bacterial cell physiology.
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Affiliation(s)
- Armen Trchounian
- Department of Biophysics of the Biological Faculty, Yerevan State University, 1 A. Manoukian Street, 375049 Yerevan, Armenia.
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25
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Gao YQ, Yang W, Marcus RA, Karplus M. A model for the cooperative free energy transduction and kinetics of ATP hydrolysis by F1-ATPase. Proc Natl Acad Sci U S A 2003; 100:11339-44. [PMID: 14500780 PMCID: PMC208758 DOI: 10.1073/pnas.1334188100] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although the binding change mechanism of rotary catalysis by which F1-ATPase hydrolyzes ATP has been supported by equilibrium, kinetic, and structural observations, many questions concerning the function remain unanswered. Because of the importance of this enzyme, the search for a full understanding of its mechanism is a key problem in structural biology. Making use of the results of free energy simulations and experimental binding constant measurements, a model is developed for the free energy change during the hydrolysis cycle. This model makes possible the development of a kinetic scheme for ATP hydrolysis by F1-ATPase, in which the rate constants are associated with specific configurations of the beta subunits. An essential new element is that the strong binding site for ADP,Pi is shown to be the betaDP site, in contrast to the strong binding site for ATP, which is betaTP. This result provides a rationale for the rotation of the gamma subunit, which induces the cooperativity required for a tri-site binding change mechanism. The model explains a series of experimental data, including the ATP concentration dependence of the rate of hydrolysis and catalytic site occupation for both the Escherichia coli F1-ATPase (EcF1) and Thermophilic Bacillus PS3 F1-ATPase (TF1), which have different behavior.
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Affiliation(s)
- Yi Qin Gao
- Noyes Laboratory of Chemical Physics, 127-72, California Institute of Technology, Pasadena, CA 91125, USA
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26
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Mnatsakanyan N, Poladian A, Bagramyan K, Trchounian A. The number of accessible SH-groups in Escherichia coli membrane vesicles is increased by ATP or by formate. Biochem Biophys Res Commun 2003; 308:655-9. [PMID: 12914800 DOI: 10.1016/s0006-291x(03)01460-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The number of accessible SH-groups was determined in membrane vesicles prepared from Escherichia coli growing in fermentation conditions at slightly alkaline pH on glucose with or without added formate. Addition of ATP or formate to the vesicles caused a approximately 1.4-fold increase in the number of accessible SH-groups. The increase was inhibited by treatment with N-ethylmaleimide or the presence of the F(0)F(1)-ATPase inhibitors N,N(')-dicyclohexylcarbodiimide or sodium azide. The increase in accessible SH-groups was also absent in strains with the ATP synthase operon deleted or with the single F(0) domain cysteine Cysb21 changed to Ala. Using hyc and hyf mutants, it was shown that the increase was also largely dependent on hydrogenase 4 or hydrogenase 3, main components of formate hydrogen lyase, when bacteria were grown in the absence or presence of added formate. These results suggest a relationship between the F(0)F(1)-ATP synthase and hydrogenase 4 or hydrogenase 3 under fermentation conditions.
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Affiliation(s)
- Nelli Mnatsakanyan
- Department of Biophysics of the Biological Faculty, Yerevan State University, Armenia
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27
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Bagramyan K, Mnatsakanyan N, Trchounian A. Formate increases the F0F1-ATPase activity in Escherichia coli growing on glucose under anaerobic conditions at slightly alkaline pH. Biochem Biophys Res Commun 2003; 306:361-5. [PMID: 12804571 DOI: 10.1016/s0006-291x(03)00967-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Escherichia coli growing on glucose under anaerobic conditions at slightly alkaline pH carries out a mixed-acid fermentation resulting in the production of formate among the other products that can be excreted or further oxidized to H(2) and CO(2). H(2) production is largely dependent on formate dehydrogenase H and hydrogenases 3 and 4 constituting two formate hydrogen lyases, and on the F(0)F(1)-ATPase. In this study, it has been shown that formate markedly increased ATPase activity in membrane vesicles. This activity was significantly (1.8-fold) stimulated by 100mM K(+) and inhibited by N,N(')-dicyclohexylcarbodiimide and sodium azide. The increase in ATPase activity was absent in atp, trkA, and hyf but not in hyc mutants. ATPase activity was also markedly increased by formate when bacteria were fermenting glucose with external formate (30mM) in the growth medium. However this activity was not stimulated by K(+) and absent in atp and hyc but not in hyf mutants. The effects of formate on ATPase activity disappeared when cells were performing anaerobic (nitrate/nitrite) or aerobic respiration. These results suggest that the F(0)F(1)-ATPase activity is dependent on K(+) uptake TrkA system and hydrogenase 4, and on hydrogenase 3 when cells are fermenting glucose in the absence and presence of external formate, respectively.
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Affiliation(s)
- Karine Bagramyan
- Department of Biophysics of the Biological Faculty, Yerevan State University, 1 Alex Manougian Str., 375049, Yerevan, Armenia
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28
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Abstract
Topical questions in ATP synthase research are: (1) how do protons cause subunit rotation and how does rotation generate ATP synthesis from ADP+Pi? (2) How does hydrolysis of ATP generate subunit rotation and how does rotation bring about uphill transport of protons? The finding that ATP synthase is not just an enzyme but rather a unique nanomotor is attracting a diverse group of researchers keen to find answers. Here we review the most recent work on rapidly developing areas within the field and present proposals for enzymatic and mechanoenzymatic mechanisms.
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Affiliation(s)
- Joachim Weber
- Department of Biochemistry and Biophysics, Box 712, University of Rochester Medical Center, Rochester, NY 14642, USA
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29
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Pacheco-Moisés F, Minauro-Sanmiguel F, Bravo C, García JJ. Sulfite inhibits the F1F0-ATP synthase and activates the F1F0-ATPase of Paracoccus denitrificans. J Bioenerg Biomembr 2002; 34:269-78. [PMID: 12392190 DOI: 10.1023/a:1020252401675] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The F1F0 complex of Paracoccus denitrificans (PdF1F0) is the fastest ATP synthase but the slowest ATPase. Sulfite exerts maximal activation of the PdF1F0-ATPase (Pacheco-Moisés, F., García, J. J., Rodríguez-Zavala, J. S., and Moreno-Sánchez, R. (2000). Eur J. Biochem. 267, 993-1000) but its effect on the PdF1F0-ATP synthase activity remains unknown. Therefore, we studied the effect of sulfite on ATP synthesis and 32Pi <--> ATP exchange reactions of inside-out membrane vesicles of P. denitrificans. Sulfite inhibited both reactions under conditions of maximal delta pH and normal sensitivity to dicyclohexylcarbodiimide. Sulfite increased by 10- and 5-fold the K0.5 for Mg2+-ADP and Pi during ATP synthesis, respectively, and by 4-fold the IC50 of Mg2+-ADP for inhibition of the PdF1F0-ATPase activity. Thus, sulfite exerts opposite effects on the forward and reverse functioning of the PdF1F0 complex. These effects are not due to membrane or PdF1F0 uncoupling. Kinetic and structural modifications that could account for these results are discussed.
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Affiliation(s)
- Fermín Pacheco-Moisés
- Departamento de Bioquímica, Instituto Nacional de Cardiología, Ignacio Chavez, México, DF, México
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Senior AE, Nadanaciva S, Weber J. The molecular mechanism of ATP synthesis by F1F0-ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1553:188-211. [PMID: 11997128 DOI: 10.1016/s0005-2728(02)00185-8] [Citation(s) in RCA: 292] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
ATP synthesis by oxidative phosphorylation and photophosphorylation, catalyzed by F1F0-ATP synthase, is the fundamental means of cell energy production. Earlier mutagenesis studies had gone some way to describing the mechanism. More recently, several X-ray structures at atomic resolution have pictured the catalytic sites, and real-time video recordings of subunit rotation have left no doubt of the nature of energy coupling between the transmembrane proton gradient and the catalytic sites in this extraordinary molecular motor. Nonetheless, the molecular events that are required to accomplish the chemical synthesis of ATP remain undefined. In this review we summarize current state of knowledge and present a hypothesis for the molecular mechanism of ATP synthesis.
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Affiliation(s)
- Alan E Senior
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Box 712, 601 Elmwood Avenue, Rochester, NY 14642, USA.
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31
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Abstract
We present a mechanism for F(1)-ATPase in which hydrolysis of MgATP in the high-affinity catalytic site at the alpha/beta interface drives rotation of the gamma subunit via conformational changes in the alpha subunit. During hydrolysis, transition state formation and separation of P(i) from MgADP causes movement of portions of alpha, transmitted via two Arg residues which are hydrogen-bonded to the gamma-phosphate of MgATP, alphaArg376 and betaArg182; the latter is also hydrogen-bonded to interfacial alpha residues between alpha346 and alpha349. Changes in alpha conformation then push on gamma, resulting in rotation. Supporting evidence from the literature and from new data is discussed.
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Affiliation(s)
- J Weber
- Department of Biochemistry and Biophysics, Box 712, University of Rochester Medical Center, 14642, Rochester, NY, USA
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