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Jang YS, Seong HJ, Kwon SW, Lee YS, Im JA, Lee HL, Yoon YR, Lee SY. Clostridium acetobutylicum atpG-Knockdown Mutants Increase Extracellular pH in Batch Cultures. Front Bioeng Biotechnol 2021; 9:754250. [PMID: 34760879 PMCID: PMC8573202 DOI: 10.3389/fbioe.2021.754250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/11/2021] [Indexed: 11/24/2022] Open
Abstract
ATPase, a key enzyme involved in energy metabolism, has not yet been well studied in Clostridium acetobutylicum. Here, we knocked down the atpG gene encoding the ATPase gamma subunit in C. acetobutylicum ATCC 824 using a mobile group II intron system and analyzed the physiological characteristics of the atpG gene knockdown mutant, 824-2866KD. Properties investigated included cell growth, glucose consumption, production of major metabolites, and extracellular pH. Interestingly, in 2-L batch fermentations, 824-2866KD showed no significant difference in metabolite biosynthesis or cell growth compared with the parent ATCC 824. However, the pH value in 824-2866KD cultures at the late stage of the solventogenic phase was abnormally high (pH 6.12), compared with that obtained routinely in the culture of ATCC 824 (pH 5.74). This phenomenon was also observed in batch cultures of another C. acetobutylicum, BEKW-2866KD, an atpG-knockdown and pta-buk double-knockout mutant. The findings reported in this study suggested that ATPase is relatively minor than acid-forming pathway in ATP metabolism in C. acetobutylicum.
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Affiliation(s)
- Yu-Sin Jang
- Division of Applied Life Science (BK21), Department of Applied Life Chemistry, Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju, South Korea
| | - Hyeon Jeong Seong
- Division of Applied Life Science (BK21), Department of Applied Life Chemistry, Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju, South Korea
| | - Seong Woo Kwon
- Division of Applied Life Science (BK21), Department of Applied Life Chemistry, Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju, South Korea
| | - Yong-Suk Lee
- Division of Applied Life Science (BK21), Department of Applied Life Chemistry, Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju, South Korea
| | - Jung Ae Im
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Haeng Lim Lee
- Division of Applied Life Science (BK21), Department of Applied Life Chemistry, Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju, South Korea
| | - Ye Rin Yoon
- Division of Applied Life Science (BK21), Department of Applied Life Chemistry, Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju, South Korea
| | - Sang Yup Lee
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
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Li Y, Ma X, Weber J. Interaction between γC87 and γR242 residues participates in energy coupling between catalysis and proton translocation in Escherichia coli ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:679-687. [PMID: 31251901 DOI: 10.1016/j.bbabio.2019.06.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/19/2019] [Accepted: 06/22/2019] [Indexed: 11/25/2022]
Abstract
Functioning as a nanomotor, ATP synthase plays a vital role in the cellular energy metabolism. Interactions at the rotor and stator interface are critical to the energy transmission in ATP synthase. From mutational studies, we found that the γC87K mutation impairs energy coupling between proton translocation and nucleotide synthesis/hydrolysis. An additional glutamine mutation at γR242 (γR242Q) can restore efficient energy coupling to the γC87K mutant. Arrhenius plots and molecular dynamics simulations suggest that an extra hydrogen bond could form between the side chains of γC87K and βTPE381 in the γC87K mutant, thus impeding the free rotation of the rotor complex. In the enzyme with γC87K/γR242Q double mutations, the polar moiety of γR242Q side chain can form a hydrogen bond with γC87K, so that the amine group in the side chain of γC87K will not hydrogen-bond with βE381. As a conclusion, the intra-subunit interaction between positions γC87 and γR242 modulates the energy transmission in ATP synthase. This study should provide more information of residue interactions at the rotor and stator interface in order to further elucidate the energetic mechanism of ATP synthase.
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Affiliation(s)
- Yunxiang Li
- Department of Chemistry and Biochemistry, Texas Woman's University, Denton, TX 76204, USA; Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA.
| | - Xinyou Ma
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Joachim Weber
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; The Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
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3
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A γ-subunit point mutation in Chlamydomonas reinhardtii chloroplast F1Fo-ATP synthase confers tolerance to reactive oxygen species. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:966-974. [DOI: 10.1016/j.bbabio.2017.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/11/2017] [Accepted: 09/05/2017] [Indexed: 11/23/2022]
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Nakanishi-Matsui M, Sekiya M, Futai M. ATP synthase from Escherichia coli : Mechanism of rotational catalysis, and inhibition with the ε subunit and phytopolyphenols. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:129-140. [DOI: 10.1016/j.bbabio.2015.11.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/19/2015] [Accepted: 11/13/2015] [Indexed: 10/22/2022]
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Abstract
The F1F0-ATP synthase (EC 3.6.1.34) is a remarkable enzyme that functions as a rotary motor. It is found in the inner membranes of Escherichia coli and is responsible for the synthesis of ATP in response to an electrochemical proton gradient. Under some conditions, the enzyme functions reversibly and uses the energy of ATP hydrolysis to generate the gradient. The ATP synthase is composed of eight different polypeptide subunits in a stoichiometry of α3β3γδεab2c10. Traditionally they were divided into two physically separable units: an F1 that catalyzes ATP hydrolysis (α3β3γδε) and a membrane-bound F0 sector that transports protons (ab2c10). In terms of rotary function, the subunits can be divided into rotor subunits (γεc10) and stator subunits (α3β3δab2). The stator subunits include six nucleotide binding sites, three catalytic and three noncatalytic, formed primarily by the β and α subunits, respectively. The stator also includes a peripheral stalk composed of δ and b subunits, and part of the proton channel in subunit a. Among the rotor subunits, the c subunits form a ring in the membrane, and interact with subunit a to form the proton channel. Subunits γ and ε bind to the c-ring subunits, and also communicate with the catalytic sites through interactions with α and β subunits. The eight subunits are expressed from a single operon, and posttranscriptional processing and translational regulation ensure that the polypeptides are made at the proper stoichiometry. Recent studies, including those of other species, have elucidated many structural and rotary properties of this enzyme.
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Senan S, Prajapati JB, Joshi CG. Whole-genome based validation of the adaptive properties of Indian origin probiotic Lactobacillus helveticus MTCC 5463. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2015; 95:321-328. [PMID: 24798512 DOI: 10.1002/jsfa.6721] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 04/24/2014] [Accepted: 04/26/2014] [Indexed: 06/03/2023]
Abstract
BACKGROUND The aim of the study was to mine the Lactobacillus helveticus MTCC 5463 genome for genetic determinants to validate its ability to adapt to gut transit stresses and translate functionality to the host. RESULTS In silico analysis of the 1 911 350 bp single chromosome of the strain predicted that it had excellent adaptive features like the multisubunit F0F1 ATPase, conjugated bile salt hyrolase, chaperones like hsp33, HtrA, GroEL, GroES, dnaK, grpE, starvation-inducible proteins and heavy-metal transporting ATPases. The genome revealed genes for adhesion and aggregation including exopolysaccharides, capsular polysaccharides sortase, elongation factor Tu, aggregation promoting proteins, fibronectin-binding proteins, S-layer and mucus-binding proteins. We could identify genes conferring physiological benefits like immunostimulation, cholesterol reduction, antibacterial and folate production. Thus, through trait and gene matching, the study established that the strain possessed the genetic arsenal required to adapt to the gut milieu. The predictions of functional genes further validate the experimental evidences of adaptation and probiosis. CONCLUSION This study provides insight into the feasibility of applying probiogenomics to identify genes that could function as pre-selection criteria for identification of potential probiotic strains.
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Affiliation(s)
- Suja Senan
- Department of Dairy Microbiology, Sheth MC College of Dairy Science, Anand Agricultural University, Anand, 388110, India
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Chiwata R, Kohori A, Kawakami T, Shiroguchi K, Furuike S, Adachi K, Sutoh K, Yoshida M, Kinosita K. None of the rotor residues of F1-ATPase are essential for torque generation. Biophys J 2014; 106:2166-74. [PMID: 24853745 PMCID: PMC4052266 DOI: 10.1016/j.bpj.2014.04.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 04/04/2014] [Accepted: 04/07/2014] [Indexed: 11/28/2022] Open
Abstract
F1-ATPase is a powerful rotary molecular motor that can rotate an object several hundred times as large as the motor itself against the viscous friction of water. Forced reverse rotation has been shown to lead to ATP synthesis, implying that the mechanical work against the motor’s high torque can be converted into the chemical energy of ATP. The minimal composition of the motor protein is α3β3γ subunits, where the central rotor subunit γ turns inside a stator cylinder made of alternately arranged α3β3 subunits using the energy derived from ATP hydrolysis. The rotor consists of an axle, a coiled coil of the amino- and carboxyl-terminal α-helices of γ, which deeply penetrates the stator cylinder, and a globular protrusion that juts out from the stator. Previous work has shown that, for a thermophilic F1, significant portions of the axle can be truncated and the motor still rotates a submicron sized bead duplex, indicating generation of up to half the wild-type (WT) torque. Here, we inquire if any specific interactions between the stator and the rest of the rotor are needed for the generation of a sizable torque. We truncated the protruding portion of the rotor and replaced part of the remaining axle residues such that every residue of the rotor has been deleted or replaced in this or previous truncation mutants. This protrusionless construct showed an unloaded rotary speed about a quarter of the WT, and generated one-third to one-half of the WT torque. No residue-specific interactions are needed for this much performance. F1 is so designed that the basic rotor-stator interactions for torque generation and control of catalysis rely solely upon the shape and size of the rotor at very low resolution. Additional tailored interactions augment the torque to allow ATP synthesis under physiological conditions.
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Affiliation(s)
- Ryohei Chiwata
- Department of Physics, Faculty of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Ayako Kohori
- Department of Physics, Faculty of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Tomonari Kawakami
- Department of Physics, Faculty of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Katsuyuki Shiroguchi
- Department of Physics, Faculty of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Shou Furuike
- Department of Physics, Faculty of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Kengo Adachi
- Department of Physics, Faculty of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Kazuo Sutoh
- Department of Physics, Faculty of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Masasuke Yoshida
- ATP Synthesis Regulation Project, ICORP, Japan Science and Technology Agency (JST), Aomi 2-41, Koto-ku, Tokyo, Japan; Department of Molecular Bioscience, Kyoto Sangyo University, Motoyama, Kamigamo, Kyoto, Japan
| | - Kazuhiko Kinosita
- Department of Physics, Faculty of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan.
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8
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A unique mechanism of curcumin inhibition on F1 ATPase. Biochem Biophys Res Commun 2014; 452:940-4. [DOI: 10.1016/j.bbrc.2014.09.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 09/05/2014] [Indexed: 11/21/2022]
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9
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Sekiya M, Chiba E, Satoh M, Yamakoshi H, Iwabuchi Y, Futai M, Nakanishi-Matsui M. Strong inhibitory effects of curcumin and its demethoxy analog on Escherichia coli ATP synthase F1 sector. Int J Biol Macromol 2014; 70:241-5. [DOI: 10.1016/j.ijbiomac.2014.06.055] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 06/15/2014] [Accepted: 06/30/2014] [Indexed: 01/30/2023]
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10
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Senan S, Prajapati JB, Joshi CG. Comparative genome-scale analysis of niche-based stress-responsive genes in Lactobacillus helveticus strains. Genome 2014; 57:185-92. [DOI: 10.1139/gen-2014-0020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Next generation sequencing technologies with advanced bioinformatic tools present a unique opportunity to compare genomes from diverse niches. The identification of niche-specific stress-responsive genes can help in characterizing robust strains for multiple applications. In this study, we attempted to compare the stress-responsive genes of a potential probiotic strain, Lactobacillus helveticus MTCC 5463, and a cheese starter strain, Lactobacillus helveticus DPC 4571, from a gut and dairy niche, respectively. Sequencing of MTCC 5463 was done using 454 GS FLX, and contigs were assembled using GS Assembler software. Genome analysis was done using BLAST hits and the prokaryotic annotation server RAST. The MTCC 5463 genome carried multiple orthologs of genes governing stress responses, whereas the DPC 4571 genome lacked in the number of major stress-response proteins. The absence of the bile salt hydrolase gene in DPC 4571 and its presence in MTCC 5463 clearly indicated niche adaptation. Further, MTCC 5463 carried higher copy numbers of genes contributing towards heat, cold, osmotic, and oxidative stress resistance as compared with DPC 4571. Through comparative genomics, we could thus identify stress-responsive gene sets required to adapt to gut and dairy niches.
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Affiliation(s)
- Suja Senan
- Department of Dairy Microbiology, Sheth MC College of Dairy Science, Anand Agricultural University, Anand 388110, India
| | - Jashbhai B. Prajapati
- Department of Dairy Microbiology, Sheth MC College of Dairy Science, Anand Agricultural University, Anand 388110, India
| | - Chaitanya G. Joshi
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand 388110, India
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11
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Nakanishi-Matsui M, Sekiya M, Futai M. Rotating proton pumping ATPases: subunit/subunit interactions and thermodynamics. IUBMB Life 2013; 65:247-54. [PMID: 23441040 DOI: 10.1002/iub.1134] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 12/21/2012] [Indexed: 11/05/2022]
Abstract
In this article, we discuss single molecule observation of rotational catalysis by E. coli ATP synthase (F-ATPase) using small gold beads. Studies involving a low viscous drag probe showed the stochastic properties of the enzyme in alternating catalytically active and inhibited states. The importance of subunit interaction between the rotor and the stator, and thermodynamics of the catalysis are also discussed. "Single Molecule Enzymology" is a new trend for understanding enzyme mechanisms in biochemistry and physiology.
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Affiliation(s)
- Mayumi Nakanishi-Matsui
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Iwate Medical University, and Futai Special Laboratory, Yahaba, Iwate, Japan.
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12
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Plun-Favreau H, Burchell VS, Holmström KM, Yao Z, Deas E, Cain K, Fedele V, Moisoi N, Campanella M, Miguel Martins L, Wood NW, Gourine AV, Abramov AY. HtrA2 deficiency causes mitochondrial uncoupling through the F₁F₀-ATP synthase and consequent ATP depletion. Cell Death Dis 2012; 3:e335. [PMID: 22739987 PMCID: PMC3388244 DOI: 10.1038/cddis.2012.77] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Loss of the mitochondrial protease HtrA2 (Omi) in mice leads to mitochondrial dysfunction, neurodegeneration and premature death, but the mechanism underlying this pathology remains unclear. Using primary cultures from wild-type and HtrA2-knockout mice, we find that HtrA2 deficiency significantly reduces mitochondrial membrane potential in a range of cell types. This depolarisation was found to result from mitochondrial uncoupling, as mitochondrial respiration was increased in HtrA2-deficient cells and respiratory control ratio was dramatically reduced. HtrA2-knockout cells exhibit increased proton translocation through the ATP synthase, in combination with decreased ATP production and truncation of the F1 α-subunit, suggesting the ATP synthase as the source of the proton leak. Uncoupling in the HtrA2-deficient mice is accompanied by altered breathing pattern and, on a cellular level, ATP depletion and vulnerability to chemical ischaemia. We propose that this vulnerability may ultimately cause the neurodegeneration observed in these mice.
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Affiliation(s)
- H Plun-Favreau
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK.
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Buchert F, Schober Y, Römpp A, Richter ML, Forreiter C. Reactive oxygen species affect ATP hydrolysis by targeting a highly conserved amino acid cluster in the thylakoid ATP synthase γ subunit. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:2038-48. [PMID: 22727877 DOI: 10.1016/j.bbabio.2012.06.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 06/08/2012] [Accepted: 06/12/2012] [Indexed: 10/28/2022]
Abstract
The vast majority of organisms produce ATP by a membrane-bound rotating protein complex, termed F-ATP synthase. In chloroplasts, the corresponding enzyme generates ATP by using a transmembrane proton gradient generated during photosynthesis, a process releasing high amounts of molecular oxygen as a natural byproduct. Due to its chemical properties, oxygen can be reduced incompletely which generates several highly reactive oxygen species (ROS) that are able to oxidize a broad range of biomolecules. In extension to previous studies it could be shown that ROS dramatically decreased ATP synthesis in situ and affected the CF1 portion in vitro. A conserved cluster of three methionines and a cysteine on the chloroplast γ subunit could be identified by mass spectrometry to be oxidized by ROS. Analysis of amino acid substitutions in a hybrid F1 assembly system indicated that these residues were exclusive catalytic targets for hydrogen peroxide and singlet oxygen, although it could be deduced that additional unknown amino acid targets might be involved in the latter reaction. The cluster was tightly integrated in catalytic turnover since mutants varied in MgATPase rates, stimulation by sulfite and chloroplast-specific γ subunit redox-modulation. Some partial disruptions of the cluster by mutagenesis were dominant over others regarding their effects on catalysis and response to ROS.
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Affiliation(s)
- Felix Buchert
- Department of Plant Physiology, Justus-Liebig-University Giessen, Germany
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Sekiya M, Nakamoto RK, Nakanishi-Matsui M, Futai M. Binding of phytopolyphenol piceatannol disrupts β/γ subunit interactions and rate-limiting step of steady-state rotational catalysis in Escherichia coli F1-ATPase. J Biol Chem 2012; 287:22771-80. [PMID: 22582396 DOI: 10.1074/jbc.m112.374868] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In observations of single molecule behavior under V(max) conditions with minimal load, the F(1) sector of the ATP synthase (F-ATPase) rotates through continuous cycles of catalytic dwells (∼0.2 ms) and 120° rotation steps (∼0.6 ms). We previously established that the rate-limiting transition step occurs during the catalytic dwell at the initiation of the 120° rotation. Here, we use the phytopolyphenol, piceatannol, which binds to a pocket formed by contributions from α and β stator subunits and the carboxyl-terminal region of the rotor γ subunit. Piceatannol did not interfere with the movement through the 120° rotation step, but caused increased duration of the catalytic dwell. The duration time of the intrinsic inhibited state of F(1) also became significantly longer with piceatannol. All of the beads rotated at a lower rate in the presence of saturating piceatannol, indicating that the inhibitor stays bound throughout the rotational catalytic cycle. The Arrhenius plot of the temperature dependence of the reciprocal of the duration of the catalytic dwell (catalytic rate) indicated significantly increased activation energy of the rate-limiting step to trigger the 120° rotation. The activation energy was further increased by combination of piceatannol and substitution of γ subunit Met(23) with Lys, indicating that the inhibitor and the β/γ interface mutation affect the same transition step, even though they perturb physically separated rotor-stator interactions.
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Affiliation(s)
- Mizuki Sekiya
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, and Futai Special Laboratory, Iwate Medical University, Yahaba, Iwate 028-3694, Japan
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15
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Rotational catalysis in proton pumping ATPases: from E. coli F-ATPase to mammalian V-ATPase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1711-21. [PMID: 22459334 DOI: 10.1016/j.bbabio.2012.03.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2012] [Revised: 03/10/2012] [Accepted: 03/13/2012] [Indexed: 01/28/2023]
Abstract
We focus on the rotational catalysis of Escherichia coli F-ATPase (ATP synthase, F(O)F(1)). Using a probe with low viscous drag, we found stochastic fluctuation of the rotation rates, a flat energy pathway, and contribution of an inhibited state to the overall behavior of the enzyme. Mutational analyses revealed the importance of the interactions among β and γ subunits and the β subunit catalytic domain. We also discuss the V-ATPase, which has different physiological roles from the F-ATPase, but is structurally and mechanistically similar. We review the rotation, diversity of subunits, and the regulatory mechanism of reversible subunit dissociation/assembly of Saccharomyces cerevisiae and mammalian complexes. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).
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16
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Kohori A, Chiwata R, Hossain MD, Furuike S, Shiroguchi K, Adachi K, Yoshida M, Kinosita K. Torque generation in F1-ATPase devoid of the entire amino-terminal helix of the rotor that fills half of the stator orifice. Biophys J 2011; 101:188-95. [PMID: 21723829 DOI: 10.1016/j.bpj.2011.05.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Revised: 04/28/2011] [Accepted: 05/03/2011] [Indexed: 11/28/2022] Open
Abstract
F(1)-ATPase is an ATP-driven rotary molecular motor in which the central γ-subunit rotates inside a cylinder made of α(3)β(3) subunits. The amino and carboxyl termini of the γ rotor form a coiled coil of α-helices that penetrates the stator cylinder to serve as an axle. Crystal structures indicate that the axle is supported by the stator at two positions, at the orifice and by the hydrophobic sleeve surrounding the axle tip. The sleeve contacts are almost exclusively to the longer carboxyl-terminal helix, whereas nearly half the orifice contacts are to the amino-terminal helix. Here, we truncated the amino-terminal helix stepwise up to 50 residues, removing one half of the axle all the way up and far beyond the orifice. The half-sliced axle still rotated with an unloaded speed a quarter of the wild-type speed, with torque nearly half the wild-type torque. The truncations were made in a construct where the rotor tip was connected to a β-subunit via a short peptide linker. Linking alone did not change the rotational characteristics significantly. These and previous results show that nearly half the normal torque is generated if rotor-stator interactions either at the orifice or at the sleeve are preserved, suggesting that the make of the motor is quite robust.
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Affiliation(s)
- Ayako Kohori
- Department of Physics, Faculty of Science and Engineering, Waseda University, Shinjuku-ku,Tokyo, Japan
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17
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Arsenieva D, Symersky J, Wang Y, Pagadala V, Mueller DM. Crystal structures of mutant forms of the yeast F1 ATPase reveal two modes of uncoupling. J Biol Chem 2010; 285:36561-9. [PMID: 20843806 PMCID: PMC2978584 DOI: 10.1074/jbc.m110.174383] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 09/02/2010] [Indexed: 11/06/2022] Open
Abstract
The mitochondrial ATP synthase couples the flow of protons with the phosphorylation of ADP. A class of mutations, the mitochondrial genome integrity (mgi) mutations, has been shown to uncouple this process in the yeast mitochondrial ATP synthase. Four mutant forms of the yeast F(1) ATPase with mgi mutations were crystallized; the structures were solved and analyzed. The analysis identifies two mechanisms of structural uncoupling: one in which the empty catalytic site is altered and in doing so, apparently disrupts substrate (phosphate) binding, and a second where the steric hindrance predicted between γLeu83 and β(DP) residues, Leu-391 and Glu-395, located in Catch 2 region, is reduced allowing rotation of the γ-subunit with less impedance. Overall, the structures provide key insights into the critical interactions in the yeast ATP synthase involved in the coupling process.
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Affiliation(s)
- Diana Arsenieva
- From the Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, North Chicago, Illinois 60064
| | - Jindrich Symersky
- From the Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, North Chicago, Illinois 60064
| | - Yamin Wang
- From the Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, North Chicago, Illinois 60064
| | - Vijayakanth Pagadala
- From the Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, North Chicago, Illinois 60064
| | - David M. Mueller
- From the Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, North Chicago, Illinois 60064
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Nakanishi-Matsui M, Sekiya M, Nakamoto RK, Futai M. The mechanism of rotating proton pumping ATPases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1343-52. [PMID: 20170625 DOI: 10.1016/j.bbabio.2010.02.014] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Revised: 02/08/2010] [Accepted: 02/11/2010] [Indexed: 11/27/2022]
Abstract
Two proton pumps, the F-ATPase (ATP synthase, FoF1) and the V-ATPase (endomembrane proton pump), have different physiological functions, but are similar in subunit structure and mechanism. They are composed of a membrane extrinsic (F1 or V1) and a membrane intrinsic (Fo or Vo) sector, and couple catalysis of ATP synthesis or hydrolysis to proton transport by a rotational mechanism. The mechanism of rotation has been extensively studied by kinetic, thermodynamic and physiological approaches. Techniques for observing subunit rotation have been developed. Observations of micron-length actin filaments, or polystyrene or gold beads attached to rotor subunits have been highly informative of the rotational behavior of ATP hydrolysis-driven rotation. Single molecule FRET experiments between fluorescent probes attached to rotor and stator subunits have been used effectively in monitoring proton motive force-driven rotation in the ATP synthesis reaction. By using small gold beads with diameters of 40-60 nm, the E. coli F1 sector was found to rotate at surprisingly high speeds (>400 rps). This experimental system was used to assess the kinetics and thermodynamics of mutant enzymes. The results revealed that the enzymatic reaction steps and the timing of the domain interactions among the beta subunits, or between the beta and gamma subunits, are coordinated in a manner that lowers the activation energy for all steps and avoids deep energy wells through the rotationally-coupled steady-state reaction. In this review, we focus on the mechanism of steady-state F1-ATPase rotation, which maximizes the coupling efficiency between catalysis and rotation.
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Affiliation(s)
- Mayumi Nakanishi-Matsui
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Iwate Medical University, Yahaba, Iwate 028-3694, Japan.
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19
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Sekiya M, Nakamoto RK, Al-Shawi MK, Nakanishi-Matsui M, Futai M. Temperature dependence of single molecule rotation of the Escherichia coli ATP synthase F1 sector reveals the importance of gamma-beta subunit interactions in the catalytic dwell. J Biol Chem 2009; 284:22401-22410. [PMID: 19502237 DOI: 10.1074/jbc.m109.009019] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The temperature-dependent rotation of F1-ATPase gamma subunit was observed in V(max) conditions at low viscous drag using a 60-nm gold bead (Nakanishi-Matsui, M., Kashiwagi, S., Hosokawa, H., Cipriano, D. J., Dunn, S. D., Wada, Y., and Futai, M. (2006) J. Biol. Chem. 281, 4126-4131). The Arrhenius slopes of the speed of the individual 120 degrees steps and reciprocal of the pause length between rotation steps were very similar, indicating a flat energy pathway followed by the rotationally coupled catalytic cycle. In contrast, the Arrhenius slope of the reciprocal pause length of the gammaM23K mutant F1 was significantly increased, whereas that of the rotation rate was similar to wild type. The effects of the rotor gammaM23K substitution and the counteracting effects of betaE381D mutation in the interacting stator subunits demonstrate that the rotor-stator interactions play critical roles in the utilization of stored elastic energy. The gammaM23K enzyme must overcome an abrupt activation energy barrier, forcing it onto a less favored pathway that results in uncoupling catalysis from rotation.
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Affiliation(s)
- Mizuki Sekiya
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, and Futai Special Laboratory, Iwate Medical University, Yahaba, Iwate 028-3694, Japan
| | - Robert K Nakamoto
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908
| | - Marwan K Al-Shawi
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908
| | - Mayumi Nakanishi-Matsui
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, and Futai Special Laboratory, Iwate Medical University, Yahaba, Iwate 028-3694, Japan
| | - Masamitsu Futai
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, and Futai Special Laboratory, Iwate Medical University, Yahaba, Iwate 028-3694, Japan
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Nakanishi-Matsui M, Futai M. Stochastic rotational catalysis of proton pumping F-ATPase. Philos Trans R Soc Lond B Biol Sci 2008; 363:2135-42. [PMID: 18339602 DOI: 10.1098/rstb.2008.2266] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
F-ATPases synthesize ATP from ADP and phosphate coupled with an electrochemical proton gradient in bacterial or mitochondrial membranes and can hydrolyse ATP to form the gradient. F-ATPases consist of a catalytic F1 and proton channel F0 formed from the alpha3beta3gammadelta and ab2c10 subunit complexes, respectively. The rotation of gammaepsilonc10 couples catalyses and proton transport. Consistent with the threefold symmetry of the alpha3beta3 catalytic hexamer, 120 degrees stepped revolution has been observed, each step being divided into two substeps. The ATP-dependent revolution exhibited stochastic fluctuation and was driven by conformation transmission of the beta subunit (phosphate-binding P-loop/alpha-helix B/loop/beta-sheet4). Recent results regarding mechanically driven ATP synthesis finally proved the role of rotation in energy coupling.
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21
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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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22
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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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24
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Futai M. Our research on proton pumping ATPases over three decades: their biochemistry, molecular biology and cell biology. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2007; 82:416-38. [PMID: 25792771 PMCID: PMC4338836 DOI: 10.2183/pjab.82.416] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2006] [Accepted: 12/11/2006] [Indexed: 05/24/2023]
Abstract
ATP is synthesized by F-type proton-translocating ATPases (F-ATPases) coupled with an electrochemical proton gradient established by an electron transfer chain. This mechanism is ubiquitously found in mitochondria, chloroplasts and bacteria. Vacuolar-type ATPases (V-ATPases) are found in endomembrane organelles, including lysosomes, endosomes, synaptic vesicles, etc., of animal and plant cells. These two physiologically different proton pumps exhibit similarities in subunit assembly, catalysis and the coupling mechanism from chemistry to proton transport through subunit rotation. We mostly discuss our own studies on the two proton pumps over the last three decades, including ones on purification, kinetic analysis, rotational catalysis and the diverse roles of acidic luminal organelles. The diversity of organellar proton pumps and their stochastic fluctuation are the important concepts derived recently from our studies.
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Affiliation(s)
- Masamitsu Futai
- Futai Special Laboratory, Microbial Chemistry Research Center, Microbial Chemistry Research Foundation, and Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Tokyo,
Japan
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25
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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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26
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Futai M, Sun-Wada GH, Wada Y. Proton pumping ATPases and diverse inside-acidic compartments. YAKUGAKU ZASSHI 2004; 124:243-60. [PMID: 15118237 DOI: 10.1248/yakushi.124.243] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Proton-translocating ATPases are essential cellular energy converters that transduce the chemical energy of ATP hydrolysis into transmembrane proton electrochemical potential differences. The structures, catalytic mechanism, and cellular functions of three major classes of ATPases including the F-type, V-type, and P-type ATPase are discussed in this review. Physiological roles of the acidic organelles and compartments contained are also discussed.
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Affiliation(s)
- Masamitsu Futai
- Division of Biological Sciences, Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki City, Osaka 567-0047, Japan.
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27
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Abstract
The vacuolar H(+)-ATPases (or V-ATPases) are a family of ATP-dependent proton pumps responsible for acidification of intracellular compartments and, in certain cases, proton transport across the plasma membrane of eukaryotic cells. They are multisubunit complexes composed of a peripheral domain (V(1)) responsible for ATP hydrolysis and an integral domain (V(0)) responsible for proton translocation. Based upon their structural similarity to the F(1)F(0) ATP synthases, the V-ATPases are thought to operate by a rotary mechanism in which ATP hydrolysis in V(1) drives rotation of a ring of proteolipid subunits in V(0). This review is focused on the current structural knowledge of the V-ATPases as it relates to the mechanism of ATP-driven proton translocation.
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Affiliation(s)
- Shoko Kawasaki-Nishi
- Department of Physiology, Tufts University School of Medicine, 136 Harrison Ave., Boston, MA 02111, USA
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28
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Nishio K, Iwamoto-Kihara A, Yamamoto A, Wada Y, Futai M. Subunit rotation of ATP synthase embedded in membranes: a or beta subunit rotation relative to the c subunit ring. Proc Natl Acad Sci U S A 2002; 99:13448-52. [PMID: 12357031 PMCID: PMC129693 DOI: 10.1073/pnas.202149599] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
ATP synthase F(o)F(1) (alpha(3)beta(3)gammadelta epsilon ab(2)c(10-14)) couples an electrochemical proton gradient and a chemical reaction through the rotation of its subunit assembly. In this study, we engineered F(o)F(1) to examine the rotation of the catalytic F(1) beta or membrane sector F(o) a subunit when the F(o) c subunit ring was immobilized; a biotin-tag was introduced onto the beta or a subunit, and a His-tag onto the c subunit ring. Membrane fragments were obtained from Escherichia coli cells carrying the recombinant plasmid for the engineered F(o)F(1) and were immobilized on a glass surface. An actin filament connected to the beta or a subunit rotated counterclockwise on the addition of ATP, and generated essentially the same torque as one connected to the c ring of F(o)F(1) immobilized through a His-tag linked to the alpha or beta subunit. These results established that the gamma epsilon c(10-14) and alpha(3)beta(3)deltaab(2) complexes are mechanical units of the membrane-embedded enzyme involved in rotational catalysis.
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Affiliation(s)
- Kazuaki Nishio
- Division of Biological Sciences, Institute of Scientific and Industrial Research, Osaka University, Core Research for Evolutional Science and Technology (CREST) of the Japan Science and Technology Corporation, Osaka 567-0047, Japan
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29
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Müller M, Pänke O, Junge W, Engelbrecht S. F1-ATPase, the C-terminal end of subunit gamma is not required for ATP hydrolysis-driven rotation. J Biol Chem 2002; 277:23308-13. [PMID: 11964400 DOI: 10.1074/jbc.m201998200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ATP hydrolysis by the isolated F(1)-ATPase drives the rotation of the central shaft, subunit gamma, which is located within a hexagon formed by subunits (alphabeta)(3). The C-terminal end of gamma forms an alpha-helix which properly fits into the "hydrophobic bearing" provided by loops of subunits alpha and beta. This "bearing" is expected to be essential for the rotary function. We checked the importance of this contact region by successive C-terminal deletions of 3, 6, 9, 12, 15, and 18 amino acid residues (Escherichia coli F(1)-ATPase). The ATP hydrolysis activity of a load-free ensemble of F(1) with 12 residues deleted decreased to 24% of the control. EF(1) with deletions of 15 or 18 residues was inactive, probably because it failed to assemble. The average torque generated by a single molecule of EF(1) when loaded by a fluorescent actin filament was, however, unaffected by deletions of up to 12 residues, as was their rotational behavior (all samples rotated during 60 +/- 19% of the observation time). Activation energy analysis with the ensemble revealed a moderate decrease from 54 kJ/mol for EF(1) (full-length gamma) to 34 kJ/mol for EF(1)(gamma-12). These observations imply that the intactness of the C terminus of subunit gamma provides structural stability and/or routing during assembly of the enzyme, but that it is not required for the rotary action under load, proper.
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Affiliation(s)
- Martin Müller
- Universität Osnabrück, FB Biologie, Abt. Biophysik, Barbarastrasse 11, 49076 Osnabrück, Germany
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30
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Arata Y, Baleja JD, Forgac M. Cysteine-directed cross-linking to subunit B suggests that subunit E forms part of the peripheral stalk of the vacuolar H+-ATPase. J Biol Chem 2002; 277:3357-63. [PMID: 11724797 DOI: 10.1074/jbc.m109967200] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have employed a combination of site-directed mutagenesis and covalent cross-linking to identify subunits in close proximity to subunit B in the vacuolar H(+)-ATPase (V-ATPase) complex. Unique cysteine residues were introduced into a Cys-less form of subunit B, and the V-ATPase complex in isolated vacuolar membranes from each mutant strain was reacted with the bifunctional, photoactivable maleimide reagent 4-(N-maleimido)benzophenone. Photoactivation resulted in cross-linking of the unique sulfhydryl groups on subunit B with other subunits in the complex. Four of the eight mutants constructed containing a unique cysteine residue at Ala(15), Lys(45), Glu(494), or Thr(501) resulted in the formation of cross-linked products, which were recognized by Western blot analysis using antibodies against both subunits B and E. These products had a molecular mass of 84 kDa, consistent with a cross-linked product of subunits B and E. Molecular modeling of subunit B places Ala(15) and Lys(45) near the top of the V(1) structure (i.e. farthest from the membrane), whereas Glu(494) and Thr(501) are predicted to reside near the bottom of V(1), with all four residues predicted to be oriented toward the external surface of the complex. A model incorporating these and previous data is presented in which subunit E exists in an extended conformation on the outer surface of the A(3)B(3) hexamer that forms the core of the V(1) domain. This location for subunit E suggests that this subunit forms part of the peripheral stalk of the V-ATPase that links the V(1) and V(0) domains.
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Affiliation(s)
- Yoichiro Arata
- Departments of Physiology and Biochemistry, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
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31
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Iko Y, Sambongi Y, Tanabe M, Iwamoto-Kihara A, Saito K, Ueda I, Wada Y, Futai M. ATP synthase F(1) sector rotation. Defective torque generation in the beta subunit Ser-174 to Phe mutant and its suppression by second mutations. J Biol Chem 2001; 276:47508-11. [PMID: 11590180 DOI: 10.1074/jbc.m108803200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Subunit gamma of the ATP synthase F(1) sector is located at the center of the alpha(3)beta(3) hexamer and rotates unidirectionally during ATP hydrolysis, generating the rotational torque of approximately 45 pN.nm. A mutant F(1) with the betaSer-174 to Phe substitution (betaS174F) in the beta subunit generated lower torque ( approximately 17 pN.nm), indicating that betaS174F is mechanically defective, the first such mutant reported. The defective rotation of betaS174F was suppressed by a second-site mutation, betaGly-149 to Ala, betaIle-163 to Ala, or betaIle-166 to Ala in the same subunit, but not by betaLeu-238 to Ala. These results suggest that the region between betaGly-149 and betaSer-174 plays an important role in the coupling between ATP hydrolysis and mechanical work.
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Affiliation(s)
- Y Iko
- Division of Biological Sciences, Institute of Scientific and Industrial Research, Osaka University, CREST (Core Research for Evolutional Science and Technology) of Japan Science and Technology Corporation, Ibaraki, Osaka 567-0047, Japan
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32
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Wada Y, Sambongi Y, Futai M. Biological nano motor, ATP synthase F(o)F(1): from catalysis to gammaepsilonc(10-12) subunit assembly rotation. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1459:499-505. [PMID: 11004468 DOI: 10.1016/s0005-2728(00)00189-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Proton translocating ATPase (ATP synthase), a chemiosmotic enzyme, synthesizes ATP from ADP and phosphate coupling with the electrochemical ion gradient across the membrane. This enzyme has been studied extensively by combined genetic, biochemical and biophysical approaches. Such studies revealed a unique mechanism which transforms an electrochemical ion gradient into chemical energy through the rotation of a subunit assembly. Thus, this enzyme can be defined as a nano motor capable of coupling a chemical reaction and ion translocation, or more simply, as a protein complex carrying out rotational catalysis. In this article, we briefly discuss our recent work, emphasizing the rotation of subunit assembly (gammaepsilonc(10-12)) which is formed from peripheral and intrinsic membrane subunits.
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Affiliation(s)
- Y Wada
- Division of Biological Sciences, The Institute of Scientific and Industrial Research, Osaka University, CREST of Japan Science and Technology Corporation, Ibaraki, 567-0047, Japan
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33
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Xu T, Forgac M. Subunit D (Vma8p) of the yeast vacuolar H+-ATPase plays a role in coupling of proton transport and ATP hydrolysis. J Biol Chem 2000; 275:22075-81. [PMID: 10801866 DOI: 10.1074/jbc.m002983200] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To investigate the function of subunit D in the vacuolar H(+)-ATPase (V-ATPase) complex, random and site-directed mutagenesis was performed on the VMA8 gene encoding subunit D in yeast. Mutants were selected for the inability to grow at pH 7.5 but the ability to grow at pH 5.5. Mutations leading to reduced levels of subunit D in whole cell lysates were excluded from the analysis. Seven mutants were isolated that resulted in pH-dependent growth but that contained nearly wild-type levels of subunit D and nearly normal assembly of the V-ATPase as assayed by subunit A levels associated with isolated vacuoles. Each of these mutants contained 2-3 amino acid substitutions and resulted in loss of 60-100% of proton transport and 58-93% of concanamycin-sensitive ATPase activity. To identify the mutations responsible for the observed effects on activity, 14 single amino acid substitutions and 3 double amino acid substitutions were constructed by site-directed mutagenesis and analyzed as described above. Six of the single mutations and all three of the double mutations led to significant (>30%) loss of activity, with the mutations having the greatest effects on activity clustering in the regions Val(71)-Gly(80) and Lys(209)-Met(221). In addition, both M221V and the double mutant V71D/E220V led to significant uncoupling of proton transport and ATPase activity, whereas the double mutant G80D/K209E actually showed increased coupling efficiency. Both a mutant showing reduced coupling and a mutant with only 6% of wild-type proton transport activity showed normal dissociation of the V-ATPase complex in vivo in response to glucose deprivation. These results suggest that subunit D plays an important role in coupling of proton transport and ATP hydrolysis and that only low rates of turnover of the enzyme are required to support in vivo dissociation.
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Affiliation(s)
- T Xu
- Department of Physiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA.
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34
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Futai M, Omote H, Sambongi Y, Wada Y. Synthase (H(+) ATPase): coupling between catalysis, mechanical work, and proton translocation. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1458:276-88. [PMID: 10838044 DOI: 10.1016/s0005-2728(00)00080-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Coupling with electrochemical proton gradient, ATP synthase (F(0)F(1)) synthesizes ATP from ADP and phosphate. Mutational studies on high-resolution structure have been useful in understanding this complicated membrane enzyme. We discuss mainly the mechanism of catalysis in the beta subunit of F(1) sector and roles of the gamma subunit in energy coupling. The gamma-subunit rotation during catalysis is also discussed.
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Affiliation(s)
- M Futai
- Division of Biological Sciences, Institute of Scientific and Industrial Research, Osaka University, CREST, Japan Science and Technology Corporation, Ibaraki, 567-0047, Osaka, Japan.
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35
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Nakamoto RK, Ketchum CJ, Kuo PH, Peskova YB, Al-Shawi MK. Molecular mechanisms of rotational catalysis in the F(0)F(1) ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1458:289-99. [PMID: 10838045 DOI: 10.1016/s0005-2728(00)00081-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rotation of the F(0)F(1) ATP synthase gamma subunit drives each of the three catalytic sites through their reaction pathways. The enzyme completes three cycles and synthesizes or hydrolyzes three ATP for each 360 degrees rotation of the gamma subunit. Mutagenesis studies have yielded considerable information on the roles of interactions between the rotor gamma subunit and the catalytic beta subunits. Amino acid substitutions, such as replacement of the conserved gammaMet-23 by Lys, cause altered interactions between gamma and beta subunits that have dramatic effects on the transition state of the steady state ATP synthesis and hydrolysis reactions. The mutations also perturb transmission of specific conformational information between subunits which is important for efficient conversion of energy between rotation and catalysis, and render the coupling between catalysis and transport inefficient. Amino acid replacements in the transport domain also affect the steady state catalytic transition state indicating that rotation is involved in coupling to transport.
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Affiliation(s)
- R K Nakamoto
- Department of Molecular Physiology and Biological Physics, University of Virginia, P.O. Box 10011, Charlottesville, VA 22906-0011, USA.
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36
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Sambongi Y, Iko Y, Tanabe M, Omote H, Iwamoto-Kihara A, Ueda I, Yanagida T, Wada Y, Futai M. Mechanical rotation of the c subunit oligomer in ATP synthase (F0F1): direct observation. Science 1999; 286:1722-4. [PMID: 10576736 DOI: 10.1126/science.286.5445.1722] [Citation(s) in RCA: 388] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
F0F1, found in mitochondria or bacterial membranes, synthesizes adenosine 5'-triphosphate (ATP) coupling with an electrochemical proton gradient and also reversibly hydrolyzes ATP to form the gradient. An actin filament connected to a c subunit oligomer of F0 was able to rotate by using the energy of ATP hydrolysis. The rotary torque produced by the c subunit oligomer reached about 40 piconewton-nanometers, which is similar to that generated by the gamma subunit in the F1 motor. These results suggest that the gamma and c subunits rotate together during ATP hydrolysis and synthesis. Thus, coupled rotation may be essential for energy coupling between proton transport through F0 and ATP hydrolysis or synthesis in F1.
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Affiliation(s)
- Y Sambongi
- Division of Biological Sciences, Institute of Scientific and Industrial Research, Osaka University, CREST (Core Research for Evolutional Science and Technology) of Japan Science and Technology Corporation, Ibaraki, Osaka 567-0047, Japan
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37
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Nakamoto RK, Ketchum CJ, al-Shawi MK. Rotational coupling in the F0F1 ATP synthase. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 1999; 28:205-34. [PMID: 10410801 DOI: 10.1146/annurev.biophys.28.1.205] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The F0F1 ATP synthase is a large multisubunit complex that couples translocation of protons down an electrochemical gradient to the synthesis of ATP. Recent advances in structural analyses have led to the demonstration that the enzyme utilizes a rotational catalytic mechanism. Kinetic and biochemical evidence is consistent with the expected equal participation of the three catalytic sites in the alpha 3 beta 3 hexamer, which operate in sequential, cooperative reaction pathways. The rotation of the core gamma subunit plays critical roles in establishing the conformation of the sites and the cooperative interactions. Mutational analyses have shown that the rotor subunits are responsible for coupling and in doing so transmit specific conformational information between transport and catalysis.
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Affiliation(s)
- R K Nakamoto
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22906, USA.
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38
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Omote H, Sambonmatsu N, Saito K, Sambongi Y, Iwamoto-Kihara A, Yanagida T, Wada Y, Futai M. The gamma-subunit rotation and torque generation in F1-ATPase from wild-type or uncoupled mutant Escherichia coli. Proc Natl Acad Sci U S A 1999; 96:7780-4. [PMID: 10393898 PMCID: PMC22138 DOI: 10.1073/pnas.96.14.7780] [Citation(s) in RCA: 121] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The rotation of the gamma-subunit has been included in the binding-change mechanism of ATP synthesis/hydrolysis by the proton ATP synthase (FOF1). The Escherichia coli ATP synthase was engineered for rotation studies such that its ATP hydrolysis and synthesis activity is similar to that of wild type. A fluorescently labeled actin filament connected to the gamma-subunit of the F1 sector rotated on addition of ATP. This progress enabled us to analyze the gammaM23K (the gamma-subunit Met-23 replaced by Lys) mutant, which is defective in energy coupling between catalysis and proton translocation. We found that the F1 sector produced essentially the same frictional torque, regardless of the mutation. These results suggest that the gammaM23K mutant is defective in the transformation of the mechanical work into proton translocation or vice versa.
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Affiliation(s)
- H Omote
- Division of Biological Sciences, Institute of Scientific and Industrial Research, Osaka University, CREST of Japan Science and Technology Corporation, Ibaraki, Osaka 567-0047, Japan
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39
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Omote H, Tainaka K, Fujie K, Iwamoto-Kihara A, Wada Y, Futai M. Stability of the Escherichia coli ATP synthase F0F1 complex is dependent on interactions between gamma Gln-269 and the beta subunit loop beta Asp-301-beta Asp-305. Arch Biochem Biophys 1998; 358:277-82. [PMID: 9784240 DOI: 10.1006/abbi.1998.0856] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The role of the conserved sequence motif 301DDLTDP306 in the F0F1 ATP synthase beta subunit was assessed by mutagenic analysis in the Escherichia coli enzyme. Mutations gave variable effects on F1 sector activity, stability, and membrane binding to the F0 sector. Upon solubilization, F1 sectors of the betaD302E and betaD305E mutants (betaAsp-302 and betaAsp-305 replaced by glutamate) dissociated into subunits, while mutants with other beta305 substitutions failed to assemble. Membrane ATPase activities of beta301 and 302 mutants were 20-70% of wild type. Replacements of the gamma subunit Gln-269 had similar effects. The membrane ATPase activities of the gammaQ269E or gammaQ269D mutants were significantly lower and their F1 sectors dissociated into subunits upon solubilization. These results suggest that the beta301-305 loop and the gamma subunit region around Gln-269 form a key region for the assembly of alpha3 beta3 gamma complex. These results are consistent with the X-ray crystallographic structure of bovine F1 (J. P. Abrahams, A. G. W. Leslie, R. Lutter, and J. E. Walker (1994) Nature 370, 621-628) where the beta301DDLTD305 loop directly interacts with gammaGln-269.
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Affiliation(s)
- H Omote
- Institute of Scientific and Industrial Research, Osaka University, Osaka, Ibaraki, 567-0047, Japan
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40
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Abstract
The structure of the core catalytic unit of ATP synthase, alpha 3 beta 3 gamma, has been determined by X-ray crystallography, revealing a roughly symmetrical arrangement of alternating alpha and beta subunits around a central cavity in which helical portions of gamma are found. A low-resolution structural model of F0, based on electron spectroscopic imaging, locates subunit a and the two copies of subunit b outside of a subunit c oligomer. The structures of individual subunits epsilon and c (largely) have been solved by NMR spectroscopy, but the oligomeric structure of c is still unknown. The structures of subunits a and delta remain undefined, that of b has not yet been defined but biochemical evidence indicates a credible model. Subunits gamma, epsilon, b, and delta are at the interface between F1 and F0; gamma epsilon complex forms one element of the stalk, interacting with c at the base and alpha and beta at the top. The locations of b and delta are less clear. Elucidation of the structure F0, of the stalk, and of the entire F1F0 remains a challenging goal.
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Affiliation(s)
- J Weber
- Department of Biochemistry, University of Rochester Medical Center, NY 14642, USA
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41
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Al-Shawi MK, Ketchum CJ, Nakamoto RK. Energy coupling, turnover, and stability of the F0F1 ATP synthase are dependent on the energy of interaction between gamma and beta subunits. J Biol Chem 1997; 272:2300-6. [PMID: 8999937 DOI: 10.1074/jbc.272.4.2300] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Replacement of the F0F1 ATP synthase gamma subunit Met-23 with Lys (gammaM23K) perturbs coupling efficiency between transport and catalysis (Shin, K., Nakamoto, R. K., Maeda, M., and Futai, M. (1992) J. Biol. Chem. 267, 20835-20839). We demonstrate here that the gammaM23K mutation causes altered interactions between subunits. Binding of delta or epsilon subunits stabilizes the alpha3beta3gamma complex, which becomes destabilized by the mutation. Significantly, the inhibition of F1 ATP hydrolysis by the epsilon subunit is no longer relieved when the gammaM23K mutant F1 is bound to F0. Steady state Arrhenius analysis reveals that the gammaM23K enzyme has increased activation energies for the catalytic transition state. These results suggest that the mutation causes the formation of additional bonds within the enzyme that must be broken in order to achieve the transition state. Based on the x-ray crystallographic structure of Abrahams et al. (Abrahams, J. P., Leslie, A. G. W., Lutter, R., and Walker, J. E. (1994) Nature 370, 621-628), the additional bond is likely due to gammaM23K forming an ionized hydrogen bond with one of the betaGlu-381 residues. Two second site mutations, gammaQ269R and gammaR242C, suppress the effects of gammaM23K and decrease activation energies for the gammaM23K enzyme. We conclude that gammaM23K is an added function mutation that increases the energy of interaction between gamma and beta subunits. The additional interaction perturbs transmission of conformational information such that epsilon inhibition of ATPase activity is not relieved and coupling efficiency is lowered.
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Affiliation(s)
- M K Al-Shawi
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
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42
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Abstract
An X-ray structure of the F1 portion of the mitochondrial ATP synthase shows asymmetry and differences in nucleotide binding of the catalytic beta subunits that support the binding change mechanism with an internal rotation of the gamma subunit. Other structural and mutational probes of the F1 and F0 portions of the ATP synthase are reviewed, together with kinetic and other evaluations of catalytic site occupancy and behavior during hydrolysis or synthesis of ATP. Subunit function as related to proton translocation and rotational catalysis is considered. Physical demonstrations of the gamma subunit rotation have been achieved. The findings have implications for other enzymatic catalyses.
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Affiliation(s)
- P D Boyer
- Molecular Biology Institute, University of California, Los Angeles 90095-1570, USA
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43
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Futai M, Omote H. Conformational transmission in ATP synthase during catalysis: search for large structural changes. J Bioenerg Biomembr 1996; 28:409-14. [PMID: 8951087 DOI: 10.1007/bf02113982] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Escherichia coli ATP synthase has eight subunits and functions through transmission of conformational changes between subunits. Defective mutation at beta Gly-149 was suppressed by the second mutations at the outer surface of the beta subunit, indicating that the defect by the first mutation was suppressed by the second mutation through long range conformation transmission. Extensive mutant/pseudorevertant studies revealed that beta/alpha and beta/gamma subunits interactions are important for the energy coupling between catalysis and H+ translocation. In addition, long range interaction between amino and carboxyl terminal regions of the gamma subunit has a critical role(s) for energy coupling. These results suggest that the dynamic conformation change and its transmission are essential for ATP synthase.
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Affiliation(s)
- M Futai
- Division of Biological Sciences, Osaka University, Japan
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44
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Haughton MA, Capaldi RA. The Escherichia coli F1-ATPase mutant beta Tyr-297-->Cys: functional studies and asymmetry of the enzyme under various nucleotide conditions based on reaction of the introduced Cys with N-ethylmaleimide and 7-chloro-4-nitrobenzofurazan. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1276:154-60. [PMID: 8816947 DOI: 10.1016/0005-2728(96)00073-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Conversion of residue beta Tyr-297 of the Escherichia coli F1-ATPase (ECF1) to a Cys in the mutant beta Y297C led to impaired oxidative phosphorylation based on growth curves. The ATPase activity of ECF1 isolated from the mutant beta Y297C was only 1% of wild-type activity, but the residual activity involves cooperative multi-site enzyme turnover based on inhibition by DCCD and azide. ATPase activity could be increased to 8%, and 13% of wild-type by reaction of the introduced Cys with N-ethyl maleimide (NEM), and 7-chloro-4-nitrobenzofurazan (NbfCl), respectively, suggesting that enzymatic function is improved by an increased hydrophobicity of residue beta Cys-297. The mutation beta Tyr-297-->Cys had no effect on nucleotide binding in studies with the fluorescent analog lin-benzo-ADP. The asymmetry of ECF1 was investigated in the mutants beta Y297C and beta Y297C:E381C/epsilon S108C by examining the relative reactivity of Cys-297 in the three copies of the beta subunit under different nucleotide binding conditions. In agreement with a previous study (Haughton, M.A. and Capaldi, R.A. (1995) J. Biol. Chem., 270, 20568-20574), the asymmetry was maintained under all nucleotide conditions. The NbfCl reaction site was found to be beta free, which is also the site most reactive to NEM, beta epsilon is the second site which reacts with NbfCl or NEM, while the third site, beta gamma, is poorly reactive to either reagent.
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Affiliation(s)
- M A Haughton
- Institute of Molecular Biology, University of Oregon, Eugene 97403-1229, USA
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45
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Komatsu-Takaki M. Energizing effects of illumination on the reactivities of lysine residues of the gamma subunit of chloroplast ATP synthase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 236:470-5. [PMID: 8612618 DOI: 10.1111/j.1432-1033.1996.00470.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Incubation of chloroplast thylakoids with pyridoxal 5'-phosphate for a short time (5 s) modified the lysine residues of the gamma subunit of ATP synthase. Energization of thylakoids by illumination increased the reactivity of Lys24 by a factor of three and decreased the reactivity of Lys30 to 60%. The reactivities of these residues reached their maximum and minimum values, respectively, within 1 s after the onset of illumination. Illumination of thylakoids increased the reactivities of Lys222 and Lys231 in two steps by a factor of three. The first step was completed within 1 s and the second step was completed 20-30 s after the onset of illumination. In the presence of 10 mM NH4Cl, illumination of thylakoids did not change the reactivities of these lysine residues. These results suggest that the Lys24- and Lys30-containing region of the gamma subunit changes its conformation rapidly in response to delta mu H+ and that the Lys222- and Lys231-containing region of the gamma subunit changes its conformation in two steps in response to delta mu H+ formation.
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Affiliation(s)
- M Komatsu-Takaki
- Department of Chemistry, Faculty of Pharmaceutical Sciences, Teikyo University, Japan
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46
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Jeanteur-De Beukelaer C, Omote H, Iwamoto-Kihara A, Maeda M, Futai M. Beta-gamma subunit interaction is required for catalysis by H(+)-ATPase (ATP synthase). Beta subunit amino acid replacements suppress a gamma subunit mutation having a long unrelated carboxyl terminus. J Biol Chem 1995; 270:22850-4. [PMID: 7559418 DOI: 10.1074/jbc.270.39.22850] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The mechanisms of energy coupling and catalytic co-operativity are not yet understood for H(+)-ATPase (ATP synthase). An Escherichia coli gamma subunit frameshift mutant (downstream of Thr-gamma 277) could not grow by oxidative phosphorylation because both mechanisms were defective (Iwamoto, A., Miki, J., Maeda, M., and Futai, M. (1990) J. Biol. Chem. 265, 5043-5048). The defect(s) of the gamma frameshift was obvious, because the mutant subunit had a carboxyl terminus comprising 16 residues different from those in the wild type. However, in this study, we surprisingly found that an Arg-beta 52-->Cys or Gly-beta 150-->Asp replacement could suppress the deleterious effects of the gamma frameshift. The membranes of the two mutants (gamma frameshift/Cys-beta 52 with or without a third mutation, Val-beta 77-->Ala) exhibited increased oxidative phosphorylation, together with 70-100% of the wild type ATPase activity. Similarly, the gamma frameshift/Asp-beta 150 mutant could grow by oxidative phosphorylation, although this mutant had low membrane ATPase activity. These results suggest that the beta subunit mutation suppressed the defects of catalytic cooperativity and/or energy coupling in the gamma mutant, consistent with the notion that conformational transmission between the two subunits is pertinent for this enzyme.
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47
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Matsui T, Yoshida M. Expression of the wild-type and the Cys-/Trp-less alpha 3 beta 3 gamma complex of thermophilic F1-ATPase in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA 1995; 1231:139-46. [PMID: 7662694 DOI: 10.1016/0005-2728(95)00070-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The alpha, beta and gamma subunits of F1-ATPase from thermophilic Bacillus PS3 were expressed in Escherichia coli cells simultaneously in large amounts. Most of the expressed subunits assembled into a form of alpha 3 beta 3 gamma complex in E. coli cells and this complex was easily purified to homogeneity. The recombinant alpha 3 beta 3 gamma complex thus obtained showed similar enzymatic properties to the alpha 3 beta 3 gamma complex obtained by in vitro reconstitution from individual subunits (Yokoyama, K. et al. (1989) J. Biol. Chem. 264, 21837-21841) except that the former had several-fold higher ATPase activity than the latter. Using this expression system, a mutant alpha 3 beta 3 gamma complex with no Trp and Cys was generated by replacing alpha Cys193 and alpha Trp463 with Ser and Phe, respectively. This mutant complex was functionally intact, indicating both residues are not essential for catalysis. The Cys-/Trp-less complex is a convenient 'second wild type' enzyme from which one can generate mutants with Trp (as a fluorescent probe) or Cys (as an acceptor of a variety of probes) at desired positions without concern for 'background' Trp and Cys residues.
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Affiliation(s)
- T Matsui
- Research Laboratory of Resources Utilization, Tokyo Institute of Technology, Yokohama, Japan
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48
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Nakamoto RK, al-Shawi MK, Futai M. The ATP synthase gamma subunit. Suppressor mutagenesis reveals three helical regions involved in energy coupling. J Biol Chem 1995; 270:14042-6. [PMID: 7775464 DOI: 10.1074/jbc.270.23.14042] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
A role in coupling proton transport to catalysis of ATP synthesis has been demonstrated for the Escherichia coli F0F1 ATP synthase gamma subunit. Previously, functional interactions between the terminal regions that were important for coupling were shown by finding several mutations in the carboxyl-terminal region of the gamma subunit (involving residues at positions 242 and 269-280) that restored efficient coupling to the mutation, gamma Met-23-->Lys (Nakamoto, R. K., Maeda, M., and Futai, M. (1993) J. Biol. Chem. 268, 867-872). In this study, we used suppressor mutagenesis to establish that the terminal regions can be separated into three interacting segments. Second-site mutations that cause pseudo reversion of the primary mutations, gamma Gln-269-->Glu or gamma Thr-273-->Val, map to an amino-terminal segment with changes at residues 18, 34, and 35, and to a segment near the carboxyl terminus with changes at residues 236, 238, 242, and 246. Each second-site mutation suppressed the effects of both gamma Gln-269-->Glu and gamma Thr-273-->Val, and restored efficient coupling to enzyme complexes containing either of the primary mutations. Mapping of these residues in the recently reported x-ray crystallographic structure of the F1 complex (Abrahams, J. P., Leslie, A. G., Lutter, R., and Walker, J. E. (1994) Nature 370, 621-628), reveals that the second-site mutations do not directly interact with gamma Gln-269 and gamma Thr-273 and that the effect of suppression occurs at a distance. We propose that the three gamma subunit segments defined by suppressor mutagenesis, residues gamma 18-35, gamma 236-246, and gamma 269-280, constitute a domain that is critical for both catalytic function and energy coupling.
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Affiliation(s)
- R K Nakamoto
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908, USA
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49
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50
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Futai M, Park M, Iwamoto A, Omote H, Maeda M. Catalysis and energy coupling of H(+)-ATPase (ATP synthase): molecular biological approaches. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1187:165-70. [PMID: 8075111 DOI: 10.1016/0005-2728(94)90104-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The molecular biological approach has provided important information for understanding the F0F1 H(+)-ATPase. This article focuses on our recent results on the catalytic site in the beta subunit, and the roles of alpha/beta subunit interaction and amino/carboxyl terminal interaction of the gamma subunit in energy coupling. Extensive mutagenesis of the beta subunit revealed that beta Lys-155, beta Thr-156, beta Glu-181 and beta Arg-182 are essential catalytic residues. beta Glu-185 is not absolutely essential, but a carboxyl residue may be necessary at this position. A pseudo-revertant analysis positioned beta Gly-172, beta Ser-174, beta Glu-192 and beta Val-198 in the proximity of beta Gly-149. The finding of the roles of beta Gly-149, beta Lys-155, and beta Thr-156 emphasized the importance of the glycine-rich sequence (Gly-X-X-X-X-Gly-Lys-Thr/Ser, E. coli beta residues between beta Gly-149 and beta Thr-156) conserved in many nucleotide binding proteins. The A subunits of vacuolar type ATPases may have a similar catalytic mechanism because they have conserved glycine-rich and Gly-Glu-Arg (corresponding to beta Gly-180-beta Arg-182) sequences. The results of these mutational studies are consistent with the labeling of beta Lys-155 and beta Lys-201 with AP3-PL, and of beta Glu-192 with DCCD [15]. The DCCD-binding residue of a thermophilic Bacillus corresponds to beta Glu-181, an essential catalytic residue discussed above. The defective coupling of the beta Ser-174-->Phe mutant was suppressed by the second mutation alpha Arg-296-->Cys, indicating the importance of alpha/beta interaction in energy coupling. The gamma subunit, especially its amino/carboxyl interaction, seems to be essential for energy coupling between catalysis and transport judging from studies on gamma Met-23-->Lys or Arg mutation and second-site mutations which suppressed the gamma Lys-23 mutation. Thus the conserved gamma Met-23 is not absolutely essential but is located in the important region for amino/carboxyl interaction for energy coupling.
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Affiliation(s)
- M Futai
- Department of Organic Chemistry and Biochemistry, Osaka University, Japan
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