1
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Nath S. Beyond binding change: the molecular mechanism of ATP hydrolysis by F 1-ATPase and its biochemical consequences. Front Chem 2023; 11:1058500. [PMID: 37324562 PMCID: PMC10266426 DOI: 10.3389/fchem.2023.1058500] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 05/10/2023] [Indexed: 06/17/2023] Open
Abstract
F1-ATPase is a universal multisubunit enzyme and the smallest-known motor that, fueled by the process of ATP hydrolysis, rotates in 120o steps. A central question is how the elementary chemical steps occurring in the three catalytic sites are coupled to the mechanical rotation. Here, we performed cold chase promotion experiments and measured the rates and extents of hydrolysis of preloaded bound ATP and promoter ATP bound in the catalytic sites. We found that rotation was caused by the electrostatic free energy change associated with the ATP cleavage reaction followed by Pi release. The combination of these two processes occurs sequentially in two different catalytic sites on the enzyme, thereby driving the two rotational sub-steps of the 120o rotation. The mechanistic implications of this finding are discussed based on the overall energy balance of the system. General principles of free energy transduction are formulated, and their important physical and biochemical consequences are analyzed. In particular, how exactly ATP performs useful external work in biomolecular systems is discussed. A molecular mechanism of steady-state, trisite ATP hydrolysis by F1-ATPase, consistent with physical laws and principles and the consolidated body of available biochemical information, is developed. Taken together with previous results, this mechanism essentially completes the coupling scheme. Discrete snapshots seen in high-resolution X-ray structures are assigned to specific intermediate stages in the 120o hydrolysis cycle, and reasons for the necessity of these conformations are readily understood. The major roles played by the "minor" subunits of ATP synthase in enabling physiological energy coupling and catalysis, first predicted by Nath's torsional mechanism of energy transduction and ATP synthesis 25 years ago, are now revealed with great clarity. The working of nine-stepped (bMF1, hMF1), six-stepped (TF1, EF1), and three-stepped (PdF1) F1 motors and of the α3β3γ subcomplex of F1 is explained by the same unified mechanism without invoking additional assumptions or postulating different mechanochemical coupling schemes. Some novel predictions of the unified theory on the mode of action of F1 inhibitors, such as sodium azide, of great pharmaceutical importance, and on more exotic artificial or hybrid/chimera F1 motors have been made and analyzed mathematically. The detailed ATP hydrolysis cycle for the enzyme as a whole is shown to provide a biochemical basis for a theory of "unisite" and steady-state multisite catalysis by F1-ATPase that had remained elusive for a very long time. The theory is supported by a probability-based calculation of enzyme species distributions and analysis of catalytic site occupancies by Mg-nucleotides and the activity of F1-ATPase. A new concept of energy coupling in ATP synthesis/hydrolysis based on fundamental ligand substitution chemistry has been advanced, which offers a deeper understanding, elucidates enzyme activation and catalysis in a better way, and provides a unified molecular explanation of elementary chemical events occurring at enzyme catalytic sites. As such, these developments take us beyond binding change mechanisms of ATP synthesis/hydrolysis proposed for oxidative phosphorylation and photophosphorylation in bioenergetics.
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Affiliation(s)
- Sunil Nath
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
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2
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Watanabe RR, Kiper BT, Zarco-Zavala M, Hara M, Kobayashi R, Ueno H, García-Trejo JJ, Li CB, Noji H. Rotary properties of hybrid F 1-ATPases consisting of subunits from different species. iScience 2023; 26:106626. [PMID: 37192978 PMCID: PMC10182284 DOI: 10.1016/j.isci.2023.106626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/14/2023] [Accepted: 04/03/2023] [Indexed: 05/18/2023] Open
Abstract
F1-ATPase (F1) is an ATP-driven rotary motor protein ubiquitously found in many species as the catalytic portion of FoF1-ATP synthase. Despite the highly conserved amino acid sequence of the catalytic core subunits: α and β, F1 shows diversity in the maximum catalytic turnover rate Vmax and the number of rotary steps per turn. To study the design principle of F1, we prepared eight hybrid F1s composed of subunits from two of three genuine F1s: thermophilic Bacillus PS3 (TF1), bovine mitochondria (bMF1), and Paracoccus denitrificans (PdF1), differing in the Vmax and the number of rotary steps. The Vmax of the hybrids can be well fitted by a quadratic model highlighting the dominant roles of β and the couplings between α-β. Although there exist no simple rules on which subunit dominantly determines the number of steps, our findings show that the stepping behavior is characterized by the combination of all subunits.
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Affiliation(s)
- Ryo R. Watanabe
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Busra Tas Kiper
- Department of Mathematics, Stockholm University, 106 91 Stockholm, Sweden
| | - Mariel Zarco-Zavala
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Mayu Hara
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Ryohei Kobayashi
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Hiroshi Ueno
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - José J. García-Trejo
- Department of Biology, Chemistry Faculty, National Autonomous University of Mexico, Mexico 04510, Mexico
| | - Chun-Biu Li
- Department of Mathematics, Stockholm University, 106 91 Stockholm, Sweden
- Corresponding author
| | - Hiroyuki Noji
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
- Corresponding author
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3
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Essential Role of the ε Subunit for Reversible Chemo-Mechanical Coupling in F 1-ATPase. Biophys J 2019; 114:178-187. [PMID: 29320685 DOI: 10.1016/j.bpj.2017.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/31/2017] [Accepted: 11/06/2017] [Indexed: 11/22/2022] Open
Abstract
F1-ATPase is a rotary motor protein driven by ATP hydrolysis. Among molecular motors, F1 exhibits unique high reversibility in chemo-mechanical coupling, synthesizing ATP from ADP and inorganic phosphate upon forcible rotor reversal. The ε subunit enhances ATP synthesis coupling efficiency to > 70% upon rotation reversal. However, the detailed mechanism has remained elusive. In this study, we performed stall-and-release experiments to elucidate how the ε subunit modulates ATP association/dissociation and hydrolysis/synthesis process kinetics and thermodynamics, key reaction steps for efficient ATP synthesis. The ε subunit significantly accelerated the rates of ATP dissociation and synthesis by two- to fivefold, whereas those of ATP binding and hydrolysis were not enhanced. Numerical analysis based on the determined kinetic parameters quantitatively reproduced previous findings of two- to fivefold coupling efficiency improvement by the ε subunit at the condition exhibiting the maximum ATP synthesis activity, a physiological role of F1-ATPase. Furthermore, fundamentally similar results were obtained upon ε subunit C-terminal domain truncation, suggesting that the N-terminal domain is responsible for the rate enhancement.
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4
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Akanuma G, Tagana T, Sawada M, Suzuki S, Shimada T, Tanaka K, Kawamura F, Kato-Yamada Y. C-terminal regulatory domain of the ε subunit of F o F 1 ATP synthase enhances the ATP-dependent H + pumping that is involved in the maintenance of cellular membrane potential in Bacillus subtilis. Microbiologyopen 2019; 8:e00815. [PMID: 30809948 PMCID: PMC6692558 DOI: 10.1002/mbo3.815] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 01/16/2019] [Accepted: 01/18/2019] [Indexed: 01/23/2023] Open
Abstract
The ε subunit of FoF1‐ATPase/synthase (FoF1) plays a crucial role in regulating FoF1 activity. To understand the physiological significance of the ε subunit‐mediated regulation of FoF1 in Bacillus subtilis, we constructed and characterized a mutant harboring a deletion in the C‐terminal regulatory domain of the ε subunit (ε∆C). Analyses using inverted membrane vesicles revealed that the ε∆C mutation decreased ATPase activity and the ATP‐dependent H+‐pumping activity of FoF1. To enhance the effects of ε∆C mutation, this mutation was introduced into a ∆rrn8 strain harboring only two of the 10 rrn (rRNA) operons (∆rrn8 ε∆C mutant strain). Interestingly, growth of the ∆rrn8 ε∆C mutant stalled at late‐exponential phase. During the stalled growth phase, the membrane potential of the ∆rrn8 ε∆C mutant cells was significantly reduced, which led to a decrease in the cellular level of 70S ribosomes. The growth stalling was suppressed by adding glucose into the culture medium. Our findings suggest that the C‐terminal region of the ε subunit is important for alleviating the temporal reduction in the membrane potential, by enhancing the ATP‐dependent H+‐pumping activity of FoF1.
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Affiliation(s)
- Genki Akanuma
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan.,Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan
| | - Tomoaki Tagana
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan
| | - Maho Sawada
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan
| | - Shota Suzuki
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan
| | - Tomohiro Shimada
- Laboratory for Chemistry and Life Science, Institute of Innovative Science, Tokyo Institute of Technology, Yokohama, Midori-ku, Japan
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute of Innovative Science, Tokyo Institute of Technology, Yokohama, Midori-ku, Japan
| | - Fujio Kawamura
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan
| | - Yasuyuki Kato-Yamada
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan.,Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan
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5
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Guo H, Suzuki T, Rubinstein JL. Structure of a bacterial ATP synthase. eLife 2019; 8:43128. [PMID: 30724163 PMCID: PMC6377231 DOI: 10.7554/elife.43128] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/02/2019] [Indexed: 01/20/2023] Open
Abstract
ATP synthases produce ATP from ADP and inorganic phosphate with energy from a transmembrane proton motive force. Bacterial ATP synthases have been studied extensively because they are the simplest form of the enzyme and because of the relative ease of genetic manipulation of these complexes. We expressed the Bacillus PS3 ATP synthase in Eschericia coli, purified it, and imaged it by cryo-EM, allowing us to build atomic models of the complex in three rotational states. The position of subunit ε shows how it is able to inhibit ATP hydrolysis while allowing ATP synthesis. The architecture of the membrane region shows how the simple bacterial ATP synthase is able to perform the same core functions as the equivalent, but more complicated, mitochondrial complex. The structures reveal the path of transmembrane proton translocation and provide a model for understanding decades of biochemical analysis interrogating the roles of specific residues in the enzyme.
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Affiliation(s)
- Hui Guo
- The Hospital for Sick Children Research Institute, Toronto, Canada.,Department of Medical Biophysics, The University of Toronto, Toronto, Canada
| | - Toshiharu Suzuki
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.,Department of Molecular Bioscience, Kyoto-Sangyo University, Kyoto, Japan
| | - John L Rubinstein
- The Hospital for Sick Children Research Institute, Toronto, Canada.,Department of Medical Biophysics, The University of Toronto, Toronto, Canada.,Department of Biochemistry, The University of Toronto, Toronto, Canada
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6
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Jin Z, Sun L, Yang G, Pei Y. Hydrogen Sulfide Regulates Energy Production to Delay Leaf Senescence Induced by Drought Stress in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:1722. [PMID: 30532763 PMCID: PMC6265512 DOI: 10.3389/fpls.2018.01722] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 11/06/2018] [Indexed: 05/09/2023]
Abstract
Hydrogen sulfide (H2S) is a novel gasotransmitter in both mammals and plants. H2S plays important roles in various plant developmental processes and stress responses. Leaf senescence is the last developmental stage and is a sequential degradation process that eventually leads to leaf death. A mutation of the H2S-producing enzyme-encoding gene L-cysteine desulfhydrase1 (DES1) leads to premature leaf senescence but the underlying mechanisms are not clear. In this present study, wild-type, DES1 defective mutant (des1) and over-expression (OE-DES1) Arabidopsis plants were used to investigate the underlying mechanism of H2S signaling in energy production and leaf senescence under drought stress. The des1 mutant was more sensitive to drought stress and displayed accelerated leaf senescence, while the leaves of OE-DES1 contained adequate chlorophyll levels, accompanied by significantly increased drought resistance. Under drought stress, the expression levels of ATPβ-1, -2, and -3 were significantly downregulated in des1 and significantly upregulated in OE-DES1, and ATPε showed the opposite trend. Senescence-associated gene (SAG) 12 correlated with age-dependent senescence and participated in the drought resistance of OE-DES1. SAG13, which was induced by environmental factors, responded positively to drought stress in des1 plants, while there was no significant difference in the SAG29 expression between des1 and OE-DES1. Using transmission electron microscopy, the mitochondria of des1 were severely damaged and bubbled in older leaves, while OE-DES1 had complete mitochondrial structures and a homogeneous matrix. Additionally, mitochondria isolated from OE-DES1 increased the H2S production rate, H2S content and ATPase activity level, as well as reduced swelling and lowered the ATP content in contrast with wild-type and des1 significantly. Therefore, at subcellular levels, H2S appeared to determine the ability of mitochondria to regulate energy production and protect against cellular aging, which subsequently delayed leaf senescence under drought-stress conditions in plants.
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Affiliation(s)
- Zhuping Jin
- School of Life Science, Shanxi University, Taiyuan, China
| | - Limin Sun
- School of Life Science, Shanxi University, Taiyuan, China
| | - Guangdong Yang
- School of Life Science, Shanxi University, Taiyuan, China
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, Canada
| | - Yanxi Pei
- School of Life Science, Shanxi University, Taiyuan, China
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7
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Bogdanović N, Sundararaman L, Kamariah N, Tyagi A, Bhushan S, Ragunathan P, Shin J, Dick T, Grüber G. Structure and function of Mycobacterium-specific components of F-ATP synthase subunits α and ε. J Struct Biol 2018; 204:420-434. [PMID: 30342092 DOI: 10.1016/j.jsb.2018.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/08/2018] [Accepted: 10/16/2018] [Indexed: 01/21/2023]
Abstract
The Mycobacterium tuberculosis (Mtb) F1FO-ATP synthase (α3:β3:γ:δ:ε:a:b:b':c9) is an essential enzyme that supplies energy for both the aerobic growing and the hypoxic dormant stage of the mycobacterial life cycle. Employing the heterologous F-ATP synthase model system αchi3:β3:γ we showed previously, that transfer of the C-terminal domain (CTD) of Mtb subunit α (Mtα514-549) to a standard F-ATP synthase α subunit suppresses ATPase activity. Here we determined the 3D reconstruction from electron micrographs of the αchi3:β3:γ complex reconstituted with the Mtb subunit ε (Mtε), which has been shown to crosstalk with the CTD of Mtα. Together with the first solution shape of Mtb subunit α (Mtα), derived from solution X-ray scattering, the structural data visualize the extended C-terminal stretch of the mycobacterial subunit α. In addition, Mtε mutants MtεR62L, MtεE87A, Mtε6-121, and Mtε1-120, reconstituted with αchi3:β3:γ provided insight into their role in coupling and in trapping inhibiting MgADP. NMR solution studies of MtεE87A gave insights into how this residue contributes to stability and crosstalk between the N-terminal domain (NTD) and the CTD of Mtε. Analyses of the N-terminal mutant Mtε6-121 highlight the differences of the NTD of mycobacterial subunit ε to the well described Geobacillus stearothermophilus or Escherichia coli counterparts. These data are discussed in context of a crosstalk between the very N-terminal amino acids of Mtε and the loop region of one c subunit of the c-ring turbine for coupling of proton-translocation and ATP synthesis activity.
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Affiliation(s)
- Nebojša Bogdanović
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Lavanya Sundararaman
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Neelagandan Kamariah
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Anu Tyagi
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Shashi Bhushan
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore; NTU Institute of Structural Biology, Nanyang Technological University, Republic of Singapore
| | - Priya Ragunathan
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Joon Shin
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Thomas Dick
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Republic of Singapore; Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, 225 Warren Street, Newark, NJ 07103, USA
| | - Gerhard Grüber
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore.
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8
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Zarco-Zavala M, Mendoza-Hoffmann F, García-Trejo JJ. Unidirectional regulation of the F 1F O-ATP synthase nanomotor by the ζ pawl-ratchet inhibitor protein of Paracoccus denitrificans and related α-proteobacteria. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2018; 1859:762-774. [PMID: 29886048 DOI: 10.1016/j.bbabio.2018.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 05/28/2018] [Accepted: 06/05/2018] [Indexed: 12/20/2022]
Abstract
The ATP synthase is a reversible nanomotor that gyrates its central rotor clockwise (CW) to synthesize ATP and in counter clockwise (CCW) direction to hydrolyse it. In bacteria and mitochondria, two natural inhibitor proteins, namely the ε and IF1 subunits, prevent the wasteful CCW F1FO-ATPase activity by blocking γ rotation at the αDP/βDP/γ interface of the F1 portion. In Paracoccus denitrificans and related α-proteobacteria, we discovered a different natural F1-ATPase inhibitor named ζ. Here we revise the functional and structural data showing that this novel ζ subunit, although being different to ε and IF1, it also binds to the αDP/βDP/γ interface of the F1 of P. denitrificans. ζ shifts its N-terminal inhibitory domain from an intrinsically disordered protein region (IDPr) to an α-helix when inserted in the αDP/βDP/γ interface. We showed for the first time the key role of a natural ATP synthase inhibitor by the distinctive phenotype of a Δζ knockout mutant in P. denitrificans. ζ blocks exclusively the CCW F1FO-ATPase rotation without affecting the CW-F1FO-ATP synthase turnover, confirming that ζ is important for respiratory bacterial growth by working as a unidirectional pawl-ratchet PdF1FO-ATPase inhibitor, thus preventing the wasteful consumption of cellular ATP. In summary, ζ is a useful model that mimics mitochondrial IF1 but in α-proteobacteria. The structural, functional, and endosymbiotic evolutionary implications of this ζ inhibitor are discussed to shed light on the natural control mechanisms of the three natural inhibitor proteins (ε, ζ, and IF1) of this unique ATP synthase nanomotor, essential for life.
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Affiliation(s)
- Mariel Zarco-Zavala
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Delegación Coyoacán, Ciudad de México (CDMX), CP 04510, Mexico; Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Francisco Mendoza-Hoffmann
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Delegación Coyoacán, Ciudad de México (CDMX), CP 04510, Mexico
| | - José J García-Trejo
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Delegación Coyoacán, Ciudad de México (CDMX), CP 04510, Mexico.
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9
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Sielaff H, Duncan TM, Börsch M. The regulatory subunit ε in Escherichia coli F OF 1-ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:775-788. [PMID: 29932911 DOI: 10.1016/j.bbabio.2018.06.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 06/13/2018] [Accepted: 06/14/2018] [Indexed: 11/16/2022]
Abstract
F-type ATP synthases are extraordinary multisubunit proteins that operate as nanomotors. The Escherichia coli (E. coli) enzyme uses the proton motive force (pmf) across the bacterial plasma membrane to drive rotation of the central rotor subunits within a stator subunit complex. Through this mechanical rotation, the rotor coordinates three nucleotide binding sites that sequentially catalyze the synthesis of ATP. Moreover, the enzyme can hydrolyze ATP to turn the rotor in the opposite direction and generate pmf. The direction of net catalysis, i.e. synthesis or hydrolysis of ATP, depends on the cell's bioenergetic conditions. Different control mechanisms have been found for ATP synthases in mitochondria, chloroplasts and bacteria. This review discusses the auto-inhibitory behavior of subunit ε found in FOF1-ATP synthases of many bacteria. We focus on E. coli FOF1-ATP synthase, with insights into the regulatory mechanism of subunit ε arising from structural and biochemical studies complemented by single-molecule microscopy experiments.
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Affiliation(s)
- Hendrik Sielaff
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Thomas M Duncan
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany.
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10
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Kondo K, Takeyama Y, Sunamura EI, Madoka Y, Fukaya Y, Isu A, Hisabori T. Amputation of a C-terminal helix of the γ subunit increases ATP-hydrolysis activity of cyanobacterial F 1 ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:319-325. [PMID: 29470949 DOI: 10.1016/j.bbabio.2018.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 02/09/2018] [Accepted: 02/14/2018] [Indexed: 12/01/2022]
Abstract
F1 is a soluble part of FoF1-ATP synthase and performs a catalytic process of ATP hydrolysis and synthesis. The γ subunit, which is the rotary shaft of F1 motor, is composed of N-terminal and C-terminal helices domains, and a protruding Rossman-fold domain located between the two major helices parts. The N-terminal and C-terminal helices domains of γ assemble into an antiparallel coiled-coil structure, and are almost embedded into the stator ring composed of α3β3 hexamer of the F1 molecule. Cyanobacterial and chloroplast γ subunits harbor an inserted sequence of 30 or 39 amino acids length within the Rossman-fold domain in comparison with bacterial or mitochondrial γ. To understand the structure-function relationship of the γ subunit, we prepared a mutant F1-ATP synthase of a thermophilic cyanobacterium, Thermosynechococcus elongatus BP-1, in which the γ subunit is split into N-terminal α-helix along with the inserted sequence and the remaining C-terminal part. The obtained mutant showed higher ATP-hydrolysis activities than those containing the wild-type γ. Contrary to our expectation, the complexes containing the split γ subunits were mostly devoid of the C-terminal helix. We further investigated the effect of post-assembly cleavage of the γ subunit. We demonstrate that insertion of the nick between two helices of the γ subunit imparts resistance to ADP inhibition, and the C-terminal α-helix is dispensable for ATP-hydrolysis activity and plays a crucial role in the assembly of F1-ATP synthase.
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Affiliation(s)
- Kumiko Kondo
- Laboratory for Chemistry and Life Science, Tokyo Institute of Technology, Nagatsuta 4259-R1-8, Midori-Ku, Yokohama 226-8503, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo 102-0075, Japan
| | - Yu Takeyama
- Laboratory for Chemistry and Life Science, Tokyo Institute of Technology, Nagatsuta 4259-R1-8, Midori-Ku, Yokohama 226-8503, Japan
| | - Ei-Ichiro Sunamura
- Laboratory for Chemistry and Life Science, Tokyo Institute of Technology, Nagatsuta 4259-R1-8, Midori-Ku, Yokohama 226-8503, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo 102-0075, Japan
| | - Yuka Madoka
- Laboratory for Chemistry and Life Science, Tokyo Institute of Technology, Nagatsuta 4259-R1-8, Midori-Ku, Yokohama 226-8503, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo 102-0075, Japan
| | - Yuki Fukaya
- Laboratory for Chemistry and Life Science, Tokyo Institute of Technology, Nagatsuta 4259-R1-8, Midori-Ku, Yokohama 226-8503, Japan
| | - Atsuko Isu
- Laboratory for Chemistry and Life Science, Tokyo Institute of Technology, Nagatsuta 4259-R1-8, Midori-Ku, Yokohama 226-8503, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo 102-0075, Japan
| | - Toru Hisabori
- Laboratory for Chemistry and Life Science, Tokyo Institute of Technology, Nagatsuta 4259-R1-8, Midori-Ku, Yokohama 226-8503, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo 102-0075, Japan.
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11
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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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12
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Shirakihara Y, Shiratori A, Tanikawa H, Nakasako M, Yoshida M, Suzuki T. Structure of a thermophilic F1-ATPase inhibited by an ε-subunit: deeper insight into the ε-inhibition mechanism. FEBS J 2015; 282:2895-913. [PMID: 26032434 DOI: 10.1111/febs.13329] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 05/19/2015] [Accepted: 05/26/2015] [Indexed: 11/28/2022]
Abstract
F1-ATPase (F1) is the catalytic sector in F(o)F1-ATP synthase that is responsible for ATP production in living cells. In catalysis, its three catalytic β-subunits undergo nucleotide occupancy-dependent and concerted open-close conformational changes that are accompanied by rotation of the γ-subunit. Bacterial and chloroplast F1 are inhibited by their own ε-subunit. In the ε-inhibited Escherichia coli F1 structure, the ε-subunit stabilizes the overall conformation (half-closed, closed, open) of the β-subunits by inserting its C-terminal helix into the α3β3 cavity. The structure of ε-inhibited thermophilic F1 is similar to that of E. coli F1, showing a similar conformation of the ε-subunit, but the thermophilic ε-subunit stabilizes another unique overall conformation (open, closed, open) of the β-subunits. The ε-C-terminal helix 2 and hook are conserved between the two structures in interactions with target residues and in their positions. Rest of the ε-C-terminal domains are in quite different conformations and positions, and have different modes of interaction with targets. This region is thought to serve ε-inhibition differently. For inhibition, the ε-subunit contacts the second catches of some of the β- and α-subunits, the N- and C-terminal helices, and some of the Rossmann fold segments. Those contacts, as a whole, lead to positioning of those β- and α- second catches in ε-inhibition-specific positions, and prevent rotation of the γ-subunit. Some of the structural features are observed even in IF1 inhibition in mitochondrial F1.
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Affiliation(s)
| | | | | | - Masayoshi Nakasako
- The Institute of Molecular and Cellular Biosciences, The University of Tokyo, Japan
| | - Masasuke Yoshida
- The Chemical Resources Laboratory, Tokyo Institute of Technology, Yokohama, Japan.,ERATO, Japan Science and Technology Corporation (JST), Yokohama, Japan
| | - Toshiharu Suzuki
- The Chemical Resources Laboratory, Tokyo Institute of Technology, Yokohama, Japan.,ERATO, Japan Science and Technology Corporation (JST), Yokohama, Japan
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13
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Rühle T, Leister D. Assembly of F1F0-ATP synthases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:849-60. [PMID: 25667968 DOI: 10.1016/j.bbabio.2015.02.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 01/28/2015] [Accepted: 02/02/2015] [Indexed: 12/31/2022]
Abstract
F1F0-ATP synthases are multimeric protein complexes and common prerequisites for their correct assembly are (i) provision of subunits in appropriate relative amounts, (ii) coordination of membrane insertion and (iii) avoidance of assembly intermediates that uncouple the proton gradient or wastefully hydrolyse ATP. Accessory factors facilitate these goals and assembly occurs in a modular fashion. Subcomplexes common to bacteria and mitochondria, but in part still elusive in chloroplasts, include a soluble F1 intermediate, a membrane-intrinsic, oligomeric c-ring, and a membrane-embedded subcomplex composed of stator subunits and subunit a. The final assembly step is thought to involve association of the preformed F1-c10-14 with the ab2 module (or the ab8-stator module in mitochondria)--mediated by binding of subunit δ in bacteria or OSCP in mitochondria, respectively. Despite the common evolutionary origin of F1F0-ATP synthases, the set of auxiliary factors required for their assembly in bacteria, mitochondria and chloroplasts shows clear signs of evolutionary divergence. This article is part of a Special Issue entitled: Chloroplast Biogenesis.
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Affiliation(s)
- Thilo Rühle
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität München (LMU), Großhaderner Straße 2, 82152 Planegg-Martinsried, Germany.
| | - Dario Leister
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität München (LMU), Großhaderner Straße 2, 82152 Planegg-Martinsried, Germany.
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14
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Lu P, Lill H, Bald D. ATP synthase in mycobacteria: special features and implications for a function as drug target. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1208-18. [PMID: 24513197 DOI: 10.1016/j.bbabio.2014.01.022] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 01/28/2014] [Accepted: 01/29/2014] [Indexed: 10/25/2022]
Abstract
ATP synthase is a ubiquitous enzyme that is largely conserved across the kingdoms of life. This conservation is in accordance with its central role in chemiosmotic energy conversion, a pathway utilized by far by most living cells. On the other hand, in particular pathogenic bacteria whilst employing ATP synthase have to deal with energetically unfavorable conditions such as low oxygen tensions in the human host, e.g. Mycobacterium tuberculosis can survive in human macrophages for an extended time. It is well conceivable that such ATP synthases may carry idiosyncratic features that contribute to efficient ATP production. In this review genetic and biochemical data on mycobacterial ATP synthase are discussed in terms of rotary catalysis, stator composition, and regulation of activity. ATP synthase in mycobacteria is of particular interest as this enzyme has been validated as a target for promising new antibacterial drugs. A deeper understanding of the working of mycobacterial ATP synthase and its atypical features can provide insight in adaptations of bacterial energy metabolism. Moreover, pinpointing and understanding critical differences as compared with human ATP synthase may provide input for the design and development of selective ATP synthase inhibitors as antibacterials. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
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Affiliation(s)
- Ping Lu
- Department of Molecular Cell Biology, AIMMS, Faculty of Earth- and Life Sciences, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Holger Lill
- Department of Molecular Cell Biology, AIMMS, Faculty of Earth- and Life Sciences, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Dirk Bald
- Department of Molecular Cell Biology, AIMMS, Faculty of Earth- and Life Sciences, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
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15
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ε subunit of Bacillus subtilis F1-ATPase relieves MgADP inhibition. PLoS One 2013; 8:e73888. [PMID: 23967352 PMCID: PMC3742539 DOI: 10.1371/journal.pone.0073888] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 07/23/2013] [Indexed: 11/19/2022] Open
Abstract
MgADP inhibition, which is considered as a part of the regulatory system of ATP synthase, is a well-known process common to all F1-ATPases, a soluble component of ATP synthase. The entrapment of inhibitory MgADP at catalytic sites terminates catalysis. Regulation by the ε subunit is a common mechanism among F1-ATPases from bacteria and plants. The relationship between these two forms of regulatory mechanisms is obscure because it is difficult to distinguish which is active at a particular moment. Here, using F1-ATPase from Bacillus subtilis (BF1), which is strongly affected by MgADP inhibition, we can distinguish MgADP inhibition from regulation by the ε subunit. The ε subunit did not inhibit but activated BF1. We conclude that the ε subunit relieves BF1 from MgADP inhibition.
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16
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ATP binding to the ϵ subunit of thermophilic ATP synthase is crucial for efficient coupling of ATPase and H+ pump activities. Biochem J 2011; 437:135-40. [PMID: 21510843 DOI: 10.1042/bj20110443] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
ATP binding to the ϵ subunit of F1-ATPase, a soluble subcomplex of TFoF1 (FoF1-ATPase synthase from the thermophilic Bacillus strain PS3), affects the regulation of F1-ATPase activity by stabilizing the compact, ATPase-active, form of the ϵ subunit [Kato, S., Yoshida, M. and Kato-Yamada, Y. (2007) J. Biol. Chem. 282, 37618-37623]. In the present study, we report how ATP binding to the ϵ subunit affects ATPase and H+ pumping activities in the holoenzyme TFoF1. Wild-type TFoF1 showed significant H+ pumping activity when ATP was used as the substrate. However, GTP, which bound poorly to the ϵ subunit, did not support efficient H+ pumping. Addition of small amounts of ATP to the GTP substrate restored coupling between GTPase and H+ pumping activities. Similar uncoupling was observed when TFoF1 contained an ATP-binding-deficient ϵ subunit, even with ATP as a substrate. Further analysis suggested that the compact conformation of the ϵ subunit induced by ATP binding was required to couple ATPase and H+ pumping activities in TFoF1 unless the ϵ subunit was in its extended-state conformation. The present study reveals a novel role of the ϵ subunit as an ATP-sensitive regulator of the coupling of ATPase and H+ pumping activities of TFoF1.
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17
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Suzuki T, Wakabayashi C, Tanaka K, Feniouk BA, Yoshida M. Modulation of nucleotide specificity of thermophilic F(o)F(1)-ATP Synthase by epsilon-subunit. J Biol Chem 2011; 286:16807-13. [PMID: 21454506 PMCID: PMC3089524 DOI: 10.1074/jbc.m110.209965] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 03/18/2011] [Indexed: 11/06/2022] Open
Abstract
The C-terminal two α-helices of the ε-subunit of thermophilic Bacillus F(o)F(1)-ATP synthase (TF(o)F(1)) adopt two conformations: an extended long arm ("up-state") and a retracted hairpin ("down-state"). As ATP becomes poor, ε changes the conformation from the down-state to the up-state and suppresses further ATP hydrolysis. Using TF(o)F(1) expressed in Escherichia coli, we compared TF(o)F(1) with up- and down-state ε in the NTP (ATP, GTP, UTP, and CTP) synthesis reactions. TF(o)F(1) with the up-state ε was achieved by inclusion of hexokinase in the assay and TF(o)F(1) with the down-state ε was represented by εΔc-TF(o)F(1), in which ε lacks C-terminal helices and hence cannot adopt the up-state under any conditions. The results indicate that TF(o)F(1) with the down-state ε synthesizes GTP at the same rate of ATP, whereas TF(o)F(1) with the up-state ε synthesizes GTP at a half-rate. Though rates are slow, TF(o)F(1) with the down-state ε even catalyzes UTP and CTP synthesis. Authentic TF(o)F(1) from Bacillus cells also synthesizes ATP and GTP at the same rate in the presence of adenosine 5'-(β,γ-imino)triphosphate (AMP-PNP), an ATP analogue that has been known to stabilize the down-state. NTP hydrolysis and NTP-driven proton pumping activity of εΔc-TF(o)F(1) suggests similar modulation of nucleotide specificity in NTP hydrolysis. Thus, depending on its conformation, ε-subunit modulates substrate specificity of TF(o)F(1).
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Affiliation(s)
- Toshiharu Suzuki
- From the ATP Synthesis Regulation Project, International Research Project (ICORP), Japan Science and Technology Corporation, Aomi 2-41, Tokyo 135-0064 and
| | - Chiaki Wakabayashi
- From the ATP Synthesis Regulation Project, International Research Project (ICORP), Japan Science and Technology Corporation, Aomi 2-41, Tokyo 135-0064 and
| | - Kazumi Tanaka
- From the ATP Synthesis Regulation Project, International Research Project (ICORP), Japan Science and Technology Corporation, Aomi 2-41, Tokyo 135-0064 and
| | - Boris A. Feniouk
- From the ATP Synthesis Regulation Project, International Research Project (ICORP), Japan Science and Technology Corporation, Aomi 2-41, Tokyo 135-0064 and
| | - Masasuke Yoshida
- From the ATP Synthesis Regulation Project, International Research Project (ICORP), Japan Science and Technology Corporation, Aomi 2-41, Tokyo 135-0064 and
- the Department of Molecular Bioscience, Kyoto Sangyo University, Kamigamo, Kyoto 603-8555, Japan
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18
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Abstract
F(o)F(1)-ATP synthase is one of the most ubiquitous enzymes; it is found widely in the biological world, including the plasma membrane of bacteria, inner membrane of mitochondria and thylakoid membrane of chloroplasts. However, this enzyme has a unique mechanism of action: it is composed of two mechanical rotary motors, each driven by ATP hydrolysis or proton flux down the membrane potential of protons. The two molecular motors interconvert the chemical energy of ATP hydrolysis and proton electrochemical potential via the mechanical rotation of the rotary shaft. This unique energy transmission mechanism is not found in other biological systems. Although there are other similar man-made systems like hydroelectric generators, F(o)F(1)-ATP synthase operates on the nanometre scale and works with extremely high efficiency. Therefore, this enzyme has attracted significant attention in a wide variety of fields from bioenergetics and biophysics to chemistry, physics and nanoscience. This review summarizes the latest findings about the two motors of F(o)F(1)-ATP synthase as well as a brief historical background.
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Affiliation(s)
- Daichi Okuno
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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19
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The regulatory C-terminal domain of subunit ε of F₀F₁ ATP synthase is dispensable for growth and survival of Escherichia coli. J Bacteriol 2011; 193:2046-52. [PMID: 21335453 DOI: 10.1128/jb.01422-10] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The C-terminal domain of subunit ε of the bacterial F₀F₁ ATP synthase is reported to be an intrinsic inhibitor of ATP synthesis/hydrolysis activity in vitro, preventing wasteful hydrolysis of ATP under low-energy conditions. Mutants defective in this regulatory domain exhibited no significant difference in growth rate, molar growth yield, membrane potential, or intracellular ATP concentration under a wide range of growth conditions and stressors compared to wild-type cells, suggesting this inhibitory domain is dispensable for growth and survival of Escherichia coli.
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20
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Haruyama T, Hirono-Hara Y, Kato-Yamada Y. Inhibition of thermophilic F 1-ATPase by the ε subunit takes different path from the ADP-Mg inhibition. Biophysics (Nagoya-shi) 2010; 6:59-65. [PMID: 27857586 PMCID: PMC5036666 DOI: 10.2142/biophysics.6.59] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Accepted: 11/28/2010] [Indexed: 12/01/2022] Open
Abstract
The F1-ATPase, the soluble part of FoF1-ATP synthase, is a rotary molecular motor consisting of α3β3γδε. The γ and ε subunits rotate relative to the α3β3δ sub-complex on ATP hydrolysis by the β subunit. The ε subunit is known as an endogenous inhibitor of the ATPase activity of the F1-ATPase and is believed to function as a regulator of the ATP synthase. This inhibition by the ε subunit (ε inhibition) of F1-ATPase from thermophilic Bacillus PS3 was analyzed by single molecule measurements. By using a mutant ε subunit deficient in ATP binding, reversible transitions between active and inactive states were observed. Analysis of pause and rotation durations showed that the ε inhibition takes a different path from the ADP-Mg inhibition. Furthermore, the addition of the mutant ε subunit to the α3β3γ sub-complex was found to facilitate recovery of the ATPase activity from the ADP-Mg inhibition. Thus, it was concluded that these two inhibitions are essentially exclusive of each other.
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Affiliation(s)
- Takamitsu Haruyama
- Department of Life Science, Rikkyo University, 3-34-1, Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan; Frontier Project "Adaptation and Evolution of Extremophile", College of Science, Rikkyo University, 3-34-1, Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Yoko Hirono-Hara
- Institute of Industrial Science, the University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Yasuyuki Kato-Yamada
- Department of Life Science, Rikkyo University, 3-34-1, Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan; Frontier Project "Adaptation and Evolution of Extremophile", College of Science, Rikkyo University, 3-34-1, Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
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21
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Sunamura EI, Konno H, Imashimizu-Kobayashi M, Sugano Y, Hisabori T. Physiological impact of intrinsic ADP inhibition of cyanobacterial FoF1 conferred by the inherent sequence inserted into the gammasubunit. PLANT & CELL PHYSIOLOGY 2010; 51:855-65. [PMID: 20421199 DOI: 10.1093/pcp/pcq061] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The F(o)F(1)-ATPase, which synthesizes ATP with a rotary motion, is highly regulated in vivo in order to function efficiently, although there remains a limited understanding of the physiological significance of this regulation. Compared with its bacterial and mitochondrial counterparts, the gamma subunit of cyanobacterial F(1), which makes up the central shaft of the motor enzyme, contains an additional inserted region. Although deletion of this region results in the acceleration of the rate of ATP hydrolysis, the functional significance of the region has not yet been determined. By analysis of rotation, we successfully determined that this region confers the ability to shift frequently into an ADP inhibition state; this is a highly conserved regulatory mechanism which prevents ATP synthase from carrying out the reverse reaction. We believe that the physiological significance of this increased likelihood of shifting into the ADP inhibition state allows the intracellular ATP levels to be maintained, which is especially critical for photosynthetic organisms.
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Affiliation(s)
- Ei-Ichiro Sunamura
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259-R1-8, Midori-Ku, Yokohama 226-8503, Japan
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22
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Saita EI, Iino R, Suzuki T, Feniouk BA, Kinosita K, Yoshida M. Activation and stiffness of the inhibited states of F1-ATPase probed by single-molecule manipulation. J Biol Chem 2010; 285:11411-7. [PMID: 20154086 DOI: 10.1074/jbc.m109.099143] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
F(1)-ATPase (F(1)), a soluble portion of F(o)F(1)-ATP synthase (F(o)F(1)), is an ATP-driven motor in which gammaepsilon subunits rotate in the alpha(3)beta(3) cylinder. Activity of F(1) and F(o)F(1) from Bacillus PS3 is attenuated by the epsilon subunit in an inhibitory extended form. In this study we observed ATP-dependent transition of epsilon in single F(1) molecules from extended form to hairpin form by fluorescence resonance energy transfer. The results justify the previous bulk experiments and ensure that fraction of F(1) with hairpin epsilon directly determines the fraction of active F(1) at any ATP concentration. Next, mechanical activation and stiffness of epsilon-inhibited F(1) were examined by the forced rotation of magnetic beads attached to gamma. Compared with ADP inhibition, which is another manner of inhibition, rotation by a larger angle was required for the activation from epsilon inhibition when the beads were forced to rotate to ATP hydrolysis direction, and more torque was required to reach the same rotation angle when beads were forced to rotate to ATP synthesis direction. The results imply that if F(o)F(1) is resting in the epsilon-inhibited state, F(o) motor must transmit to gamma a torque larger than expected from thermodynamic equilibrium to initiate ATP synthesis.
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Affiliation(s)
- Ei-ichiro Saita
- ICORP ATP Synthesis Regulation Project, Japan Science and Technology Corporation, Aomi 2-3-6, Tokyo 135-0064, Japan
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23
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Structural and functional analysis of the intrinsic inhibitor subunit epsilon of F1-ATPase from photosynthetic organisms. Biochem J 2009; 425:85-94. [PMID: 19785575 DOI: 10.1042/bj20091247] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The epsilon subunit, a small subunit located in the F1 domain of ATP synthase and comprising two distinct domains, an N-terminal beta-sandwich structure and a C-terminal alpha-helical region, serves as an intrinsic inhibitor of ATP hydrolysis activity. This inhibitory function is especially important in photosynthetic organisms as the enzyme cannot synthesize ATP in the dark, but may catalyse futile ATP hydrolysis reactions. To understand the structure-function relationship of this subunit in F1 from photosynthetic organisms, we solved the NMR structure of the epsilon subunit of ATP synthase obtained from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1, and examined the flexibility of the C-terminal domains using molecular dynamics simulations. In addition, we revealed the significance of the C-terminal alpha-helical region of the epsilon subunit in determining the binding affinity to the complex based on the assessment of the inhibition of ATPase activity by the cyanobacterial epsilon subunit and the chimaeric subunits composed of the N-terminal domain from the cyanobacterium and the C-terminal domain from spinach. The differences observed in the structural and biochemical properties of chloroplast and bacterial epsilon subunits explains the distinctive characteristics of the epsilon subunits in the ATPase complex of the photosynthetic organism.
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24
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Modulation of nucleotide binding to the catalytic sites of thermophilic F(1)-ATPase by the epsilon subunit: implication for the role of the epsilon subunit in ATP synthesis. Biochem Biophys Res Commun 2009; 390:230-4. [PMID: 19785990 DOI: 10.1016/j.bbrc.2009.09.092] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Accepted: 09/23/2009] [Indexed: 11/22/2022]
Abstract
Effect of epsilon subunit on the nucleotide binding to the catalytic sites of F(1)-ATPase from the thermophilic Bacillus PS3 (TF(1)) has been tested by using alpha(3)beta(3)gamma and alpha(3)beta(3)gammaepsilon complexes of TF(1) containing betaTyr341 to Trp substitution. The nucleotide binding was assessed with fluorescence quenching of the introduced Trp. The presence of the epsilon subunit weakened ADP binding to each catalytic site, especially to the highest affinity site. This effect was also observed when GDP or IDP was used. The ratio of the affinity of the lowest to the highest nucleotide binding sites had changed two orders of magnitude by the epsilon subunit. The differences may relate to the energy required for the binding change in the ATP synthesis reaction and contribute to the efficient ATP synthesis.
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25
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Iino R, Hasegawa R, Tabata KV, Noji H. Mechanism of inhibition by C-terminal alpha-helices of the epsilon subunit of Escherichia coli FoF1-ATP synthase. J Biol Chem 2009; 284:17457-64. [PMID: 19411254 DOI: 10.1074/jbc.m109.003798] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The epsilon subunit of bacterial FoF1-ATP synthase (FoF1), a rotary motor protein, is known to inhibit the ATP hydrolysis reaction of this enzyme. The inhibitory effect is modulated by the conformation of the C-terminal alpha-helices of epsilon, and the "extended" but not "hairpin-folded" state is responsible for inhibition. Although the inhibition of ATP hydrolysis by the C-terminal domain of epsilon has been extensively studied, the effect on ATP synthesis is not fully understood. In this study, we generated an Escherichia coli FoF1 (EFoF1) mutant in which the epsilon subunit lacked the C-terminal domain (FoF1epsilonDeltaC), and ATP synthesis driven by acid-base transition (DeltapH) and the K+-valinomycin diffusion potential (DeltaPsi) was compared in detail with that of the wild-type enzyme (FoF1epsilonWT). The turnover numbers (kcat) of FoF1epsilonWT were severalfold lower than those of FoF1epsilonDeltaC. FoF1epsilonWT showed higher Michaelis constants (Km). The dependence of the activities of FoF1epsilonWT and FoF1epsilonDeltaC on various combinations of DeltapH and DeltaPsi was similar, suggesting that the rate-limiting step in ATP synthesis was unaltered by the C-terminal domain of epsilon. Solubilized FoF1epsilonWT also showed lower kcat and higher Km values for ATP hydrolysis than the corresponding values of FoF1epsilonDeltaC. These results suggest that the C-terminal domain of the epsilon subunit of EFoF1 slows multiple elementary steps in both the ATP synthesis/hydrolysis reactions by restricting the rotation of the gamma subunit.
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Affiliation(s)
- Ryota Iino
- Institute of Scientific and Industrial Research, Osaka University, 567-0047 Osaka, Japan.
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26
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Effect of epsilon subunit on the rotation of thermophilic Bacillus F1-ATPase. FEBS Lett 2009; 583:1121-6. [PMID: 19265694 DOI: 10.1016/j.febslet.2009.02.038] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2009] [Revised: 02/24/2009] [Accepted: 02/26/2009] [Indexed: 11/22/2022]
Abstract
F(1)-ATPase is an ATP-driven motor in which gammaepsilon rotates in the alpha(3)beta(3)-cylinder. It is attenuated by MgADP inhibition and by the epsilon subunit in an inhibitory form. The non-inhibitory form of epsilon subunit of thermophilic Bacillus PS3 F(1)-ATPase is stabilized by ATP-binding with micromolar K(d) at 25 degrees C. Here, we show that at [ATP]>2 microM, epsilon does not affect rotation of PS3 F(1)-ATPase but, at 200 nM ATP, epsilon prolongs the pause of rotation caused by MgADP inhibition while the frequency of the pause is unchanged. It appears that epsilon undergoes reversible transition to the inhibitory form at [ATP] below K(d).
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27
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Genome-wide screen in Francisella novicida for genes required for pulmonary and systemic infection in mice. Infect Immun 2008; 77:232-44. [PMID: 18955478 DOI: 10.1128/iai.00978-08] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Francisella tularensis is a gram-negative, highly infectious, aerosolizable facultative intracellular pathogen that causes the potentially life-threatening disease tularemia. To date there is no approved vaccine available, and little is known about the molecular mechanisms important for infection, survival, and dissemination at different times of infection. We report the first whole-genome screen using an inhalation mouse model to monitor infection in the lung and dissemination to the liver and spleen. We queried a comprehensive library of 2,998 sequence-defined transposon insertion mutants in Francisella novicida strain U112 using a microarray-based negative-selection screen. We were able to track the behavior of 1,029 annotated genes, equivalent to a detection rate of 75% and corresponding to approximately 57% of the entire F. novicida genome. As expected, most transposon mutants retained the ability to colonize, but 125 candidate virulence genes (12%) could not be detected in at least one of the three organs. They fell into a variety of functional categories, with one-third having no annotated function and a statistically significant enrichment of genes involved in transcription. Based on the observation that behavior during complex pool infections correlated with the degree of attenuation during single-strain infection we identified nine genes expected to strongly contribute to infection. These included two genes, those for ATP synthase C (FTN_1645) and thioredoxin (FTN_1415), that when mutated allowed increased host survival and conferred protection in vaccination experiments.
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28
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Abstract
F1F0 ATP synthases convert energy stored in an electrochemical gradient of H+ or Na+ across the membrane into mechanical rotation, which is subsequently converted into the chemical bond energy of ATP. The majority of cellular ATP is produced by the ATP synthase in organisms throughout the biological kingdom and therefore under diverse environmental conditions. The ATP synthase of each particular cell is confronted with specific challenges, imposed by the specific environment, and thus by necessity must adapt to these conditions for optimal operation. Examples of these adaptations include diverse mechanisms for regulating the ATP hydrolysis activity of the enzyme, the utilization of different coupling ions with distinct ion binding characteristics, different ion-to-ATP ratios reflected by variations in the size of the rotor c ring, the mode of ion delivery to the binding sites, and the different contributions of the electrical and chemical gradients to the driving force.
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Affiliation(s)
- Christoph von Ballmoos
- Institut für Mikrobiologie, ETH Zürich, Wolfgang-Pauli Strasse 10, CH-8093 Zürich, Switzerland
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29
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Regulatory mechanisms of proton-translocating F(O)F (1)-ATP synthase. Results Probl Cell Differ 2007; 45:279-308. [PMID: 18026702 DOI: 10.1007/400_2007_043] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
H(+)-F(O)F(1)-ATP synthase catalyzes synthesis of ATP from ADP and inorganic phosphate using the energy of transmembrane electrochemical potential difference of proton (deltamu(H)(+). The enzyme can also generate this potential difference by working as an ATP-driven proton pump. Several regulatory mechanisms are known to suppress the ATPase activity of F(O)F(1): 1. Non-competitive inhibition by MgADP, a feature shared by F(O)F(1) from bacteria, chloroplasts and mitochondria 2. Inhibition by subunit epsilon in chloroplast and bacterial enzyme 3. Inhibition upon oxidation of two cysteines in subunit gamma in chloroplast F(O)F(1) 4. Inhibition by an additional regulatory protein (IF(1)) in mitochondrial enzyme In this review we summarize the information available on these regulatory mechanisms and discuss possible interplay between them.
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30
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Kato S, Yoshida M, Kato-Yamada Y. Role of the epsilon subunit of thermophilic F1-ATPase as a sensor for ATP. J Biol Chem 2007; 282:37618-23. [PMID: 17933866 DOI: 10.1074/jbc.m707509200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The epsilon subunit of F(1)-ATPase from the thermophilic Bacillus PS3 (TF(1)) has been shown to bind ATP. The precise nature of the regulatory role of ATP binding to the epsilon subunit remains to be determined. To address this question, 11 mutants of the epsilon subunit were prepared, in which one of the basic or acidic residues was substituted with alanine. ATP binding to these mutants was tested by gel-filtration chromatography. Among them, four mutants that showed no ATP binding were selected and reconstituted with the alpha(3)beta(3)gamma complex of TF(1). The ATPase activity of the resulting alpha(3)beta(3)gammaepsilon complexes was measured, and the extent of inhibition by the mutant epsilon subunits was compared in each case. With one exception, weaker binding of ATP correlated with greater inhibition of ATPase activity. These results clearly indicate that ATP binding to the epsilon subunit plays a regulatory role and that ATP binding may stabilize the ATPase-active form of TF(1) by fixing the epsilon subunit into the folded conformation.
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Affiliation(s)
- Shigeyuki Kato
- Department of Life Science, College of Science, Rikkyo (St Paul's) University, Tokyo, Japan
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31
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Konno H, Murakami-Fuse T, Fujii F, Koyama F, Ueoka-Nakanishi H, Pack CG, Kinjo M, Hisabori T. The regulator of the F1 motor: inhibition of rotation of cyanobacterial F1-ATPase by the epsilon subunit. EMBO J 2006; 25:4596-604. [PMID: 16977308 PMCID: PMC1589999 DOI: 10.1038/sj.emboj.7601348] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2006] [Accepted: 08/22/2006] [Indexed: 11/09/2022] Open
Abstract
The chloroplast-type F(1) ATPase is the key enzyme of energy conversion in chloroplasts, and is regulated by the endogenous inhibitor epsilon, tightly bound ADP, the membrane potential and the redox state of the gamma subunit. In order to understand the molecular mechanism of epsilon inhibition, we constructed an expression system for the alpha(3)beta(3)gamma subcomplex in thermophilic cyanobacteria allowing thorough investigation of epsilon inhibition. epsilon Inhibition was found to be ATP-independent, and different to that observed for bacterial F(1)-ATPase. The role of the additional region on the gamma subunit of chloroplast-type F(1)-ATPase in epsilon inhibition was also determined. By single molecule rotation analysis, we succeeded in assigning the pausing angular position of gamma in epsilon inhibition, which was found to be identical to that observed for ATP hydrolysis, product release and ADP inhibition, but distinctly different from the waiting position for ATP binding. These results suggest that the epsilon subunit of chloroplast-type ATP synthase plays an important regulator for the rotary motor enzyme, thus preventing wasteful ATP hydrolysis.
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Affiliation(s)
- Hiroki Konno
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama, Japan
- ATP System Project, Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Corporation (JST), Nagatsuta-cho, Midori-ku, Yokohama, Japan
| | - Tomoe Murakami-Fuse
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama, Japan
- ATP System Project, Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Corporation (JST), Nagatsuta-cho, Midori-ku, Yokohama, Japan
| | - Fumihiko Fujii
- Laboratory of Supramolecular Biophysics, Research Institute for Electronic Science, Hokkaido University, Kita-ku, Sapporo, Hokkaido, Japan
| | - Fumie Koyama
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama, Japan
- ATP System Project, Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Corporation (JST), Nagatsuta-cho, Midori-ku, Yokohama, Japan
| | - Hanayo Ueoka-Nakanishi
- ATP System Project, Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Corporation (JST), Nagatsuta-cho, Midori-ku, Yokohama, Japan
| | - Chan-Gi Pack
- Laboratory of Supramolecular Biophysics, Research Institute for Electronic Science, Hokkaido University, Kita-ku, Sapporo, Hokkaido, Japan
| | - Masataka Kinjo
- Laboratory of Supramolecular Biophysics, Research Institute for Electronic Science, Hokkaido University, Kita-ku, Sapporo, Hokkaido, Japan
| | - Toru Hisabori
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama, Japan
- ATP System Project, Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Corporation (JST), Nagatsuta-cho, Midori-ku, Yokohama, Japan
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259-R1-8, Midori-Ku, Yokohama, Kanagawa 226-8503, Japan. Tel.: +81 45 924 5234; Fax: +81 45 924 5277; E-mail:
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32
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Iizuka S, Kato S, Yoshida M, Kato-Yamada Y. gammaepsilon Sub-complex of thermophilic ATP synthase has the ability to bind ATP. Biochem Biophys Res Commun 2006; 349:1368-71. [PMID: 16982032 DOI: 10.1016/j.bbrc.2006.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2006] [Accepted: 09/01/2006] [Indexed: 11/29/2022]
Abstract
The isolated epsilon subunit of F(1)-ATPase from thermophilic Bacillus PS3 (TF(1)) binds ATP [Y. Kato-Yamada, M. Yoshida, J. Biol. Chem. 278 (2003) 36013]. The obvious question is whether the ATP binding concern with the regulation of ATP synthase activity or not. If so, the epsilon subunit even in the ATP synthase complex should have the ability to bind ATP. To check if the ATP binding to the epsilon subunit within the ATP synthase complex may occur, the gammaepsilon sub-complex of TF(1) was prepared and ATP binding was examined. The results clearly showed that the gammaepsilon sub-complex can bind ATP.
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Affiliation(s)
- Satoshi Iizuka
- Department of Life Science, College of Science, Rikkyo University, 3-34-1, Nishi-Ikebukuro, Tokyo 171-8501, Japan
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33
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Abstract
The prokaryotic V-type ATPase/synthases (prokaryotic V-ATPases) have simpler subunit compositions than eukaryotic V-ATPases, and thus are useful subjects for studying chemical, physical and structural properties of V-ATPase. In this review, we focus on the results of recent studies on the structure/function relationships in the V-ATPase from the eubacterium Thermus thermophilus. First, we describe single-molecule analyses of T. thermophilus V-ATPase. Using the single-molecule technique, it was established that the V-ATPase is a rotary motor. Second, we discuss arrangement of subunits in V-ATPase. Third, the crystal structure of the C-subunit (homolog of eukaryotic d-subunit) is described. This funnel-shape subunit appears to cap the proteolipid ring in the V(0) domain in order to accommodate the V(1) central stalk. This structure seems essential for the regulatory reversible association/dissociation of the V(1) and the V(0) domains. Last, we discuss classification of the V-ATPase family. We propose that the term prokaryotic V-ATPases should be used rather than the term archaeal-type ATPase (A-ATPase).
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Affiliation(s)
- Ken Yokoyama
- ATP System Project, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Nagatsuta, Midori-ku, Yokohama, Japan.
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34
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Keis S, Stocker A, Dimroth P, Cook GM. Inhibition of ATP hydrolysis by thermoalkaliphilic F1Fo-ATP synthase is controlled by the C terminus of the epsilon subunit. J Bacteriol 2006; 188:3796-804. [PMID: 16707672 PMCID: PMC1482892 DOI: 10.1128/jb.00040-06] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The F(1)F(o)-ATP synthases of alkaliphilic bacteria exhibit latent ATPase activity, and for the thermoalkaliphile Bacillus sp. strain TA2.A1, this activity is intrinsic to the F(1) moiety. To study the mechanism of ATPase inhibition, we developed a heterologous expression system in Escherichia coli to produce TA2F(1) complexes from this thermoalkaliphile. Like the native F(1)F(o)-ATP synthase, the recombinant TA2F(1) was blocked in ATP hydrolysis activity, and this activity was stimulated by the detergent lauryldimethylamine oxide. To determine if the C-terminal domain of the epsilon subunit acts as an inhibitor of ATPase activity and if an electrostatic interaction plays a role, a TA2F(1) mutant with either a truncated epsilon subunit [i.e., TA2F(1)(epsilon(DeltaC))] or substitution of basic residues in the second alpha-helix of epsilon with nonpolar alanines [i.e., TA2F(1)(epsilon(6A))] was constructed. Both mutants showed ATP hydrolysis activity at low and high concentrations of ATP. Treatment of the purified F(1)F(o)-ATP synthase and TA2F(1)(epsilon(WT)) complex with proteases revealed that the epsilon subunit was resistant to proteolytic digestion. In contrast, the epsilon subunit of TA2F(1)(epsilon(6A)) was completely degraded by trypsin, indicating that the C-terminal arm was in a conformation where it was no longer protected from proteolytic digestion. In addition, ATPase activity was not further activated by protease treatment when compared to the untreated control, supporting the observation that epsilon was responsible for inhibition of ATPase activity. To study the effect of the alanine substitutions in the epsilon subunit in the entire holoenzyme, we reconstituted recombinant TA2F(1) complexes with F(1)-stripped native membranes of strain TA2.A1. The reconstituted TA2F(o)F(1)(epsilon(WT)) was blocked in ATP hydrolysis and exhibited low levels of ATP-driven proton pumping consistent with the F(1)F(o)-ATP synthase in native membranes. Reconstituted TA2F(o)F(1)(epsilon(6A)) exhibited ATPase activity that correlated with increased ATP-driven proton pumping, confirming that the epsilon subunit also inhibits ATPase activity of TA2F(o)F(1).
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Affiliation(s)
- Stefanie Keis
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, P.O. Box 56, Dunedin, New Zealand
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35
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Iino R, Murakami T, Iizuka S, Kato-Yamada Y, Suzuki T, Yoshida M. Real-time monitoring of conformational dynamics of the epsilon subunit in F1-ATPase. J Biol Chem 2005; 280:40130-4. [PMID: 16203732 DOI: 10.1074/jbc.m506160200] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
It has been proposed that C-terminal two alpha-helices of the epsilon subunit of F1-ATPase can undergo conformational transition between retracted folded-hairpin form and extended form. Here, using F(1) from thermophilic Bacillus PS3, we monitored this transition in real time by fluorescence resonance energy transfer (FRET) between a donor dye and an acceptor dye attached to N terminus of the gamma subunit and C terminus of the epsilon subunit, respectively. High FRET (extended form) of F1 turned to low FRET (retracted form) by ATP, which then reverted as ATP was hydrolyzed to ADP. 5'-Adenyl-beta,gamma-imidodiphosphate, ADP + AlF4-, ADP + NaN3, and GTP also caused the retracted form, indicating that ATP binding to the catalytic beta subunits induces the transition. The ATP-induced transition from high FRET to low FRET occurred in a similar time scale to the ATP-induced activation of ATPase from inhibition by the epsilon subunit, although detailed kinetics were not the same. The transition became faster as temperature increased, but the extrapolated rate at 65 degrees C (physiological temperature of Bacillus PS3) was still too slow to assign the transition as an obligate step in the catalytic turnover. Furthermore, binding affinity of ATP to the isolated epsilon subunit was weakened as temperature increased, and the dissociation constant extrapolated to 65 degrees C reached to 0.67 mm, a consistent value to assume that the epsilon subunit acts as a sensor of ATP concentration in the cell.
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Affiliation(s)
- Ryota Iino
- ATP System Project, ERATO, Japan Science and Technology Agency, Nagatsuta 5800-3, Yokohama 226-0026, Japan
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36
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Kato-Yamada Y. Isolated epsilon subunit of Bacillus subtilis F1-ATPase binds ATP. FEBS Lett 2005; 579:6875-8. [PMID: 16337201 DOI: 10.1016/j.febslet.2005.11.036] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2005] [Accepted: 11/14/2005] [Indexed: 11/22/2022]
Abstract
Previously, we demonstrated ATP binding to the isolated epsilon subunit of F1-ATPase from thermophilic Bacillus PS3 [Kato-Yamada Y., Yoshida M. (2003) J. Biol. Chem. 278, 36013]. However, whether it is a general feature of the epsilon subunit from other sources is yet unclear. Here, using a sensitive method to detect weak interactions between fluorescently labeled epsilon subunit and nucleotide, it was shown that the epsilon subunit of F1-ATPase from Bacillus subtilis also bound ATP. The dissociation constant for ATP binding at room temperature was calculated to be 2 mM, which may be suitable for sensing cellular ATP concentration in vivo.
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Affiliation(s)
- Yasuyuki Kato-Yamada
- Department of Life Sciences and Frontier Project Life's Adaptation Strategies to Environmental Changes, College of Science, Rikkyo (St. Paul's) University, 3-34-1, Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan.
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37
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Rondelez Y, Tresset G, Nakashima T, Kato-Yamada Y, Fujita H, Takeuchi S, Noji H. Highly coupled ATP synthesis by F1-ATPase single molecules. Nature 2005; 433:773-7. [PMID: 15716957 DOI: 10.1038/nature03277] [Citation(s) in RCA: 238] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2004] [Accepted: 12/08/2004] [Indexed: 11/09/2022]
Abstract
F1-ATPase is the smallest known rotary motor, and it rotates in an anticlockwise direction as it hydrolyses ATP. Single-molecule experiments point towards three catalytic events per turn, in agreement with the molecular structure of the complex. The physiological function of F1 is ATP synthesis. In the ubiquitous F0F1 complex, this energetically uphill reaction is driven by F0, the partner motor of F1, which forces the backward (clockwise) rotation of F1, leading to ATP synthesis. Here, we have devised an experiment combining single-molecule manipulation and microfabrication techniques to measure the yield of this mechanochemical transformation. Single F1 molecules were enclosed in femtolitre-sized hermetic chambers and rotated in a clockwise direction using magnetic tweezers. When the magnetic field was switched off, the F1 molecule underwent anticlockwise rotation at a speed proportional to the amount of synthesized ATP. At 10 Hz, the mechanochemical coupling efficiency was low for the alpha3beta3gamma subcomplex (F1-epsilon)), but reached up to 77% after reconstitution with the epsilon-subunit (F1+epsilon)). We provide here direct evidence that F1 is designed to tightly couple its catalytic reactions with the mechanical rotation. Our results suggest that the epsilon-subunit has an essential function during ATP synthesis.
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38
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Konno H, Suzuki T, Bald D, Yoshida M, Hisabori T. Significance of the epsilon subunit in the thiol modulation of chloroplast ATP synthase. Biochem Biophys Res Commun 2004; 318:17-24. [PMID: 15110747 DOI: 10.1016/j.bbrc.2004.03.179] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2004] [Indexed: 11/24/2022]
Abstract
To understand the regulatory function of the gamma and epsilon subunits of chloroplast ATP synthase in the membrane integrated complex, we constructed a chimeric FoF1 complex of thermophilic bacteria. When a part of the chloroplast F1 gamma subunit was introduced into the bacterial FoF1 complex, the inverted membrane vesicles with this chimeric FoF1 did not exhibit the redox sensitive ATP hydrolysis activity, which is a common property of the chloroplast ATP synthase. However, when the whole part or the C-terminal alpha-helices region of the epsilon subunit was substituted with the corresponding region from CF1-epsilon together with the mutation of gamma, the redox regulation property emerged. In contrast, ATP synthesis activity did not become redox sensitive even if both the regulatory region of CF1-gamma and the entire epsilon subunit from CF1 were introduced. These results provide important features for the regulation of FoF1 by these subunits: (1) the interaction between gamma and epsilon is important for the redox regulation of FoF1 complex by the gamma subunit, and (2) a certain structural matching between these regulatory subunits and the catalytic core of the enzyme must be required to confer the complete redox regulation mechanism to the bacterial FoF1. In addition, a structural requirement for the redox regulation of ATP hydrolysis activity might be different from that for the ATP synthesis activity.
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Affiliation(s)
- Hiroki Konno
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259-R1-8, Midori-ku, Yokohama 226-8503, Japan
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39
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Keis S, Kaim G, Dimroth P, Cook GM. Cloning and molecular characterization of the atp operon encoding for the F1F0-ATP synthase from a thermoalkaliphilic Bacillus sp. strain TA2.A1. ACTA ACUST UNITED AC 2004; 1676:112-7. [PMID: 14732496 DOI: 10.1016/j.bbaexp.2003.11.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The genes encoding the subunits for the F(1)F(0)-ATP synthase from Bacillus sp. strain TA2.A1 were cloned as three overlapping fragments and sequenced. The nine genes were organized in an operon with the gene order atpIBEFHAGDC encoding the i, a, c, b, delta, alpha, gamma, beta, and epsilon subunits, respectively. Northern blot analysis showed a maximum transcript of approximately 7.2 kb, which corresponds to the size of the atp operon and demonstrated that the nine genes are transcribed as a single polycistronic message. The alkaliphilic-specific residues Lys(218) and Gly(245) were conserved in subunit a of strain TA2.A1. Analysis of the C-terminal domain of the epsilon subunit showed several clusters of basic residues which are predicted to form a strong electrostatic interaction with the DELSDED motif in the beta subunit from strain TA2.A1, and may explain the blockage of this enzyme in the ATP hydrolysis direction.
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Affiliation(s)
- Stefanie Keis
- Department of Microbiology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
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40
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Imamura H, Ikeda C, Yoshida M, Yokoyama K. The F subunit of Thermus thermophilus V1-ATPase promotes ATPase activity but is not necessary for rotation. J Biol Chem 2004; 279:18085-90. [PMID: 14963028 DOI: 10.1074/jbc.m314204200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
V(1)-ATPase from the thermophilic bacterium Thermus thermophilus is a molecular rotary motor with a subunit composition of A(3)B(3)DF, and its central rotor is composed of the D and F subunits. To determine the role of the F subunit, we generated an A(3)B(3)D subcomplex and compared it with A(3)B(3)DF. The ATP hydrolyzing activity of A(3)B(3)D (V(max) = 20 s(-1)) was lower than that of A(3)B(3)DF (V(max) = 31 s(-1)) and was more susceptible to MgADP inhibition during ATP hydrolysis. A(3)B(3)D was able to bind the F subunit to form A(3)B(3)DF. The C-terminally truncated F((Delta85-106)) subunit was also bound to A(3)B(3)D, but the F((Delta69-106)) subunit was not, indicating the importance of residues 69-84 of the F subunit for association with A(3)B(3)D. The ATPase activity of A(3)B(3)DF((Delta85-106)) (V(max) = 24 s(-1)) was intermediate between that of A(3)B(3)D and A(3)B(3)DF. A single molecule experiment showed the rotation of the D subunit in A(3)B(3)D, implying that the F subunit is a dispensable component for rotation itself. Thus, the F subunit binds peripherally to the D subunit, but promotes V(1)-ATPase catalysis.
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Affiliation(s)
- Hiromi Imamura
- ATP System Project, Exploration Research for Advanced Technology, Japan Science and Technology Agency, 5800-3 Nagatsuta, Midori-ku, Yokohama 226-0026, Japan
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41
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Zharova TV, Vinogradov AD. Energy-dependent transformation of F0.F1-ATPase in Paracoccus denitrificans plasma membranes. J Biol Chem 2004; 279:12319-24. [PMID: 14722115 DOI: 10.1074/jbc.m311397200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
F(0).F(1)-ATP synthase in tightly coupled inside-out vesicles derived from Paracoccus denitrificans catalyzes rapid respiration-supported ATP synthesis, whereas their ATPase activity is very low. In the present study, the conditions required to reveal the Deltamu(H+)-generating ATP hydrolase activity of the bacterial enzyme have been elucidated. Energization of the membranes by respiration results in strong activation of the venturicidin-sensitive ATP hydrolysis, which is coupled with generation of Deltamũ(H+). Partial uncoupling stimulates the proton-translocating ATP hydrolysis, whereas complete uncoupling results in inhibition of the ATPase activity. The presence of inorganic phosphate is indispensable for the steady-state turnover of the Deltamũ(H+)-activated ATPase. The collapse of Deltamũ(H+) brings about rapid deactivation of the enzyme, which has been subjected to pre-energization. The rate and extent of the deactivation depend on protein concentration, i.e. the more vesicles are present in the assay mixture, the higher the rate and extent of the deactivation is seen. Sulfite and the ADP-trapping system protect ATPase against the Deltamũ(H+) collapse-induced deactivation, whereas phosphate delays the rate of deactivation. A low concentration of ADP (<1 microm) increases the rate of deactivation. Taken together, the results suggest that latent proton-translocating ATPase in P. denitrificans is kinetically equivalent to the previously characterized ADP(Mg2+)-inhibited, azide-trapped bovine heart mitochondrial F(0).F(1)-ATPase (Galkin, M. A., and Vinogradov, A. D. (1999) FEBS Lett. 448, 123-126). A Deltamũ(H+)-sensitive mechanism operates in P. denitrificans that prevents physiologically wasteful consumption of ATP by F(0).F(1)-ATPase (synthase) complex when the latter is unable to maintain certain value of Deltamũ(H+).
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Affiliation(s)
- Tatyana V Zharova
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119992, Russian Federation
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42
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Suzuki T, Murakami T, Iino R, Suzuki J, Ono S, Shirakihara Y, Yoshida M. F0F1-ATPase/synthase is geared to the synthesis mode by conformational rearrangement of epsilon subunit in response to proton motive force and ADP/ATP balance. J Biol Chem 2003; 278:46840-6. [PMID: 12881515 DOI: 10.1074/jbc.m307165200] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The epsilon subunit in F0F1-ATPase/synthase undergoes drastic conformational rearrangement, which involves the transition of two C-terminal helices between a hairpin "down"-state and an extended "up"-state, and the enzyme with the up-fixed epsilon cannot catalyze ATP hydrolysis but can catalyze ATP synthesis (Tsunoda, S. P., Rodgers, A. J. W., Aggeler, R., Wilce, M. C. J., Yoshida, M., and Capaldi, R. A. (2001) Proc. Natl. Acad. Sci. U. S. A. 98, 6560-6564). Here, using cross-linking between introduced cysteine residues as a probe, we have investigated the causes of the transition. Our findings are as follows. (i) In the up-state, the two helices of epsilon are fully extended to insert the C terminus into a deeper position in the central cavity of F1 than was thought previously. (ii) Without a nucleotide, epsilon is in the up-state. ATP induces the transition to the down-state, and ADP counteracts the action of ATP. (iii) Conversely, the enzyme with the down-state epsilon can bind an ATP analogue, 2',3'-O-(2,4,6-trinitrophenyl)-ATP, much faster than the enzyme with the up-state epsilon. (iv) Proton motive force stabilizes the up-state. Thus, responding to the increase of proton motive force and ADP, F0F1-ATPase/synthase would transform the epsilon subunit into the up-state conformation and change gear to the mode for ATP synthesis.
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Affiliation(s)
- Toshiharu Suzuki
- ATP System Project, Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Corporation (JST), Nagatsuta 5800-2, Yokohama 226-0026, Japan
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43
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Abstract
F1-ATPase, a soluble part of the F0F1-ATP synthase, has subunit structure alpha3beta3gammadeltaepsilon in which nucleotide-binding sites are located in the alpha and beta subunits and, as believed, in none of the other subunits. However, we report here that the isolated epsilon subunit of F1-ATPase from thermophilic Bacillus strain PS3 can bind ATP. The binding was directly demonstrated by isolating the epsilon subunit-ATP complex with gel filtration chromatography. The binding was not dependent on Mg2+ but was highly specific for ATP; however, ADP, GTP, UTP, and CTP failed to bind. The epsilon subunit lacking the C-terminal helical hairpin was unable to bind ATP. Although ATP binding to the isolated epsilon subunits from other organisms has not been detected under the same conditions, a possibility emerges that the epsilon subunit acts as a built in cellular ATP level sensor of F0F1-ATP synthase.
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Affiliation(s)
- Yasuyuki Kato-Yamada
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8503, Japan
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44
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Cook GM, Keis S, Morgan HW, von Ballmoos C, Matthey U, Kaim G, Dimroth P. Purification and biochemical characterization of the F1Fo-ATP synthase from thermoalkaliphilic Bacillus sp. strain TA2.A1. J Bacteriol 2003; 185:4442-9. [PMID: 12867453 PMCID: PMC165752 DOI: 10.1128/jb.185.15.4442-4449.2003] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2003] [Accepted: 05/01/2003] [Indexed: 11/20/2022] Open
Abstract
We describe here purification and biochemical characterization of the F(1)F(o)-ATP synthase from the thermoalkaliphilic organism Bacillus sp. strain TA2.A1. The purified enzyme produced the typical subunit pattern of an F(1)F(o)-ATP synthase on a sodium dodecyl sulfate-polyacrylamide gel, with F(1) subunits alpha, beta, gamma, delta, and epsilon and F(o) subunits a, b, and c. The subunits were identified by N-terminal protein sequencing and mass spectroscopy. A notable feature of the ATP synthase from strain TA2.A1 was its specific blockage in ATP hydrolysis activity. ATPase activity was unmasked by using the detergent lauryldimethylamine oxide (LDAO), which activated ATP hydrolysis >15-fold. This activation was the same for either the F(1)F(o) holoenzyme or the isolated F(1) moiety, and therefore latent ATP hydrolysis activity is an intrinsic property of F(1). After reconstitution into proteoliposomes, the enzyme catalyzed ATP synthesis driven by an artificially induced transmembrane electrical potential (Deltapsi). A transmembrane proton gradient or sodium ion gradient in the absence of Deltapsi was not sufficient to drive ATP synthesis. ATP synthesis was eliminated by the electrogenic protonophore carbonyl cyanide m-chlorophenylhydrazone, while the electroneutral Na(+)/H(+) antiporter monensin had no effect. Neither ATP synthesis nor ATP hydrolysis was stimulated by Na(+) ions, suggesting that protons are the coupling ions of the ATP synthase from strain TA2.A1, as documented previously for mesophilic alkaliphilic Bacillus species. The ATP synthase was specifically modified at its c subunits by N,N'-dicyclohexylcarbodiimide, and this modification inhibited ATP synthesis.
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Affiliation(s)
- Gregory M Cook
- Department of Microbiology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand.
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Hisabori T, Konno H, Ichimura H, Strotmann H, Bald D. Molecular devices of chloroplast F(1)-ATP synthase for the regulation. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1555:140-6. [PMID: 12206906 DOI: 10.1016/s0005-2728(02)00269-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In chloroplasts, synthesis of ATP is energetically coupled with the utilization of a proton gradient formed by photosynthetic electron transport. The involved enzyme, the chloroplast ATP synthase, can potentially hydrolyze ATP when the magnitude of the transmembrane electrochemical potential difference of protons (Delta(micro)H(+)) is small, e.g. at low light intensity or in the dark. To prevent this wasteful consumption of ATP, the activity of chloroplast ATP synthase is regulated as the occasion may demand. As regulation systems Delta(micro)H(+) activation, thiol modulation, tight binding of ADP and the role of the intrinsic inhibitory subunit epsilon is well documented. In this article, we discuss recent progress in understanding of the regulation system of the chloroplast ATP synthase at the molecular level.
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Affiliation(s)
- Toru Hisabori
- Chemical Resources Laboratory, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan.
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46
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Hara KY, Kato-Yamada Y, Kikuchi Y, Hisabori T, Yoshida M. The role of the betaDELSEED motif of F1-ATPase: propagation of the inhibitory effect of the epsilon subunit. J Biol Chem 2001; 276:23969-73. [PMID: 11279233 DOI: 10.1074/jbc.m009303200] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In F(1)-ATPase, a rotary motor enzyme, the region of the conserved DELSEED motif in the beta subunit moves and contacts the rotor gamma subunit when the nucleotide fills the catalytic site, and the acidic nature of the motif was previously assumed to play a critical role in rotation. Our previous work, however, disproved the assumption (Hara, K. Y., Noji, H., Bald, D., Yasuda, R., Kinosita, K., Jr., and Yoshida, M. (2000) J. Biol. Chem. 275, 14260-14263), and the role of this motif remained unknown. Here, we found that the epsilon subunit, an intrinsic inhibitor, was unable to inhibit the ATPase activity of a mutant thermophilic F(1)-ATPase in which all of the five acidic residues in the DELSEED motif were replaced with alanines, although the epsilon subunit in the mutant F(1)-ATPase assumed the inhibitory form. In addition, the replacement of basic residues in the C-terminal region of the epsilon subunit by alanines caused a decrease of the inhibitory effect. Partial replacement of the acidic residues in the DELSEED motif of the beta subunit or of the basic residues in the C-terminal alpha-helix of the epsilon subunit induced a partial effect. We here conclude that the epsilon subunit exerts its inhibitory effect through the electrostatic interaction with the DELSEED motif of the beta subunit.
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Affiliation(s)
- K Y Hara
- Chemical Resources Laboratory, R-1, Tokyo Institute of Technology, Nagatsuta 4259, Yokohama, 226-8503, Japan
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47
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Tsunoda SP, Rodgers AJ, Aggeler R, Wilce MC, Yoshida M, Capaldi RA. Large conformational changes of the epsilon subunit in the bacterial F1F0 ATP synthase provide a ratchet action to regulate this rotary motor enzyme. Proc Natl Acad Sci U S A 2001; 98:6560-4. [PMID: 11381110 PMCID: PMC34392 DOI: 10.1073/pnas.111128098] [Citation(s) in RCA: 149] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The F(1)F(0) ATP synthase is the smallest motor enzyme known. Previous studies had established that the central stalk, made of the gamma and epsilon subunits in the F(1) part and c subunit ring in the F(0) part, rotates relative to a stator composed of alpha(3)beta(3)deltaab(2) during ATP hydrolysis and synthesis. How this rotation is regulated has been less clear. Here, we show that the epsilon subunit plays a key role by acting as a switch of this motor. Two different arrangements of the epsilon subunit have been visualized recently. The first has been observed in beef heart mitochondrial F(1)-ATPase where the C-terminal portion is arranged as a two-alpha-helix hairpin structure that extends away from the alpha(3)beta(3) region, and toward the position of the c subunit ring in the intact F(1)F(0). The second arrangement was observed in a structure determination of a complex of the gamma and epsilon subunits of the Escherichia coli F(1)-ATPase. In this, the two C-terminal helices are apart and extend along the gamma to interact with the alpha and beta subunits in the intact complex. We have been able to trap these two arrangements by cross-linking after introducing appropriate Cys residues in E. coli F(1)F(0), confirming that both conformations of the epsilon subunit exist in the enzyme complex. With the C-terminal domain of epsilon toward the F(0), ATP hydrolysis is activated, but the enzyme is fully coupled in both ATP hydrolysis and synthesis. With the C-terminal domain toward the F(1) part, ATP hydrolysis is inhibited and yet the enzyme is fully functional in ATP synthesis; i.e., it works in one direction only. These results help explain the inhibitory action of the epsilon subunit in the F(1)F(0) complex and argue for a ratchet function of this subunit.
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Affiliation(s)
- S P Tsunoda
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403-1229, USA
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Tsunoda SP, Aggeler R, Yoshida M, Capaldi RA. Rotation of the c subunit oligomer in fully functional F1Fo ATP synthase. Proc Natl Acad Sci U S A 2001; 98:898-902. [PMID: 11158567 PMCID: PMC14681 DOI: 10.1073/pnas.98.3.898] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The F(1)F(o)-type ATP synthase is the smallest motor enzyme known. Previous studies had established that the central gamma and epsilon subunits of the F(1) part rotate relative to a stator of alpha(3)beta(3) and delta subunits during catalysis. We now show that the ring of c subunits in the F(o) part moves along with the gamma and epsilon subunits. This was demonstrated by linking the three rotor subunits with disulfide bridges between cysteine residues introduced genetically at the interfaces between the gamma, epsilon, and c subunits. Essentially complete cross-linking of the gamma, epsilon, and c subunits was achieved by using CuCl(2) to induce oxidation. This fixing of the three subunits together had no significant effect on ATP hydrolysis, proton translocation, or ATP synthesis, and each of these functions retained inhibitor sensitivity. These results unequivocally place the c subunit oligomer in the rotor part of this molecular machine.
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Affiliation(s)
- S P Tsunoda
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403-1229, USA
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Rotation of the c subunit oligomer in fully functional F1Fo ATP synthase. Proc Natl Acad Sci U S A 2001. [PMID: 11158567 PMCID: PMC14681 DOI: 10.1073/pnas.031564198] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The F(1)F(o)-type ATP synthase is the smallest motor enzyme known. Previous studies had established that the central gamma and epsilon subunits of the F(1) part rotate relative to a stator of alpha(3)beta(3) and delta subunits during catalysis. We now show that the ring of c subunits in the F(o) part moves along with the gamma and epsilon subunits. This was demonstrated by linking the three rotor subunits with disulfide bridges between cysteine residues introduced genetically at the interfaces between the gamma, epsilon, and c subunits. Essentially complete cross-linking of the gamma, epsilon, and c subunits was achieved by using CuCl(2) to induce oxidation. This fixing of the three subunits together had no significant effect on ATP hydrolysis, proton translocation, or ATP synthesis, and each of these functions retained inhibitor sensitivity. These results unequivocally place the c subunit oligomer in the rotor part of this molecular machine.
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50
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Kato-Yamada Y, Yoshida M, Hisabori T. Movement of the helical domain of the epsilon subunit is required for the activation of thermophilic F1-ATPase. J Biol Chem 2000; 275:35746-50. [PMID: 10958801 DOI: 10.1074/jbc.m006575200] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The inhibitory effect of epsilon subunit in F(1)-ATPase from thermophilic Bacillus PS3 was examined focusing on the structure-function relationship. For this purpose, we designed a mutant for epsilon subunit similar to the one constructed by Schulenberg and Capaldi (Schulenberg, B., and Capaldi, R. A. (1999) J. Biol. Chem. 274, 28351-28355). We introduced two cysteine residues at the interface of N-terminal beta-sandwich domain (S48C) and C-terminal alpha-helical domain (N125C) of epsilon subunit. The alpha(3)beta(3)gammaepsilon complex containing the reduced form of this mutant epsilon subunit showed suppressed ATPase activity and gradual activation during the measurement. This activation pattern was similar to the complex with the wild type epsilon subunit. The conformation of the mutant epsilon subunit must be fixed and similar to the reported three-dimensional structure of the isolated epsilon subunit, when the intramolecular disulfide bridge was formed on this subunit by oxidation. This oxidized mutant epsilon subunit could form the alpha(3)beta(3)gammaepsilon complex but did not show any inhibitory effect. The complex was converted to the activated state, and the cross-link in the mutant epsilon subunit in the complex was efficiently formed in the presence of ATP-Mg, whereas no cross-link was observed without ATP-Mg, suggesting the conformation of the oxidized mutant epsilon subunit must be similar to that in the activated state complex. A non-hydrolyzable analog of ATP, 5'-adenylyl-beta,gamma-imidodiphosphate, could stimulate the formation of the cross-link on the epsilon subunit. Furthermore, the cross-link formation was stimulated by nucleotides even when this mutant epsilon subunit was assembled with a mutant alpha(3)beta(3)gamma complex lacking non-catalytic sites. These results indicate that binding of ATP to the catalytic sites induces a conformational change in the epsilon subunit and triggers transition of the complex from the suppressed state to the activated state.
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Affiliation(s)
- Y Kato-Yamada
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8503, Japan
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