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Chen Y, Cui M, Liu B, Gao L, Mitome N, Hirono-Hara Y, Hara KY, Méhes G, Miyake T. A Multienzyme Logic H + and Na + Biotransducer. ACS APPLIED MATERIALS & INTERFACES 2024; 16:37521-37529. [PMID: 38985575 DOI: 10.1021/acsami.4c05499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Sodium ions and protons regulate various fundamental processes at the cell and tissue levels across all biological kingdoms. It is therefore pivotal for bioelectronic devices, such as biosensors and biotransducers, to control the transport of these ions through biological membranes. Our study explores the regulation of proton and sodium concentrations by integrating an Na+-type ATP synthase, a glucose dehydrogenase (GDH), and a urease into a multienzyme logic system. This system is designed to operate using various chemical control input signals, while the output current corresponds to the local change in proton or sodium concentrations. Therein, a H+ and Na+ biotransducer was integrated to fulfill the roles of signal transducers for the monitoring and simultaneous control of Na+ and H+ levels, respectively. To increase the proton concentration at the output, we utilized GDH driven by the inputs of glucose and nicotinamide adenine dinucleotide (NAD+), while recorded the signal change from the biotransducer, together acting as an AND enzyme logic gate. On the contrary, we introduced urease enzyme which hydrolyzed urea to control the decrease in proton concentration, serving as a NOT gate and reset. By integrating these two enzyme logic gates we formed a simple multienzyme logic system for the control of proton concentrations. Furthermore, we also demonstrate a more complex, Na+-type ATP synthase-urease multienzyme logic system, controlled by the two different inputs of ADP and urea. By monitoring the voltage of the peak current as the output signal, this logic system acts as an AND enzyme logic gate. This study explores how multienzyme logic systems can modulate biologically important ion concentrations, opening the door toward advanced biological on-demand control of a variety of bioelectronic enzyme-based devices, such as biosensors and biotransducers.
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Affiliation(s)
- Yukun Chen
- Graduate School of Information, Production and Systems, Waseda University, 2-7 Hibikino, Wakamatsu, Kitakyushu, Fukuoka 808-0135, Japan
| | - Mingyin Cui
- Graduate School of Information, Production and Systems, Waseda University, 2-7 Hibikino, Wakamatsu, Kitakyushu, Fukuoka 808-0135, Japan
| | - Bingfu Liu
- Graduate School of Information, Production and Systems, Waseda University, 2-7 Hibikino, Wakamatsu, Kitakyushu, Fukuoka 808-0135, Japan
| | - Liyun Gao
- Graduate School of Information, Production and Systems, Waseda University, 2-7 Hibikino, Wakamatsu, Kitakyushu, Fukuoka 808-0135, Japan
| | - Noriyo Mitome
- Faculty of Education, Tokoha University, 6-1 Yayoicho, Suruga, Shizuoka, Shizuoka 422-8581, Japan
| | - Yoko Hirono-Hara
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Shizuoka, Suruga-ku 422-8526, Japan
| | - Kiyotaka Y Hara
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Shizuoka, Suruga-ku 422-8526, Japan
| | - Gábor Méhes
- Graduate School of Information, Production and Systems, Waseda University, 2-7 Hibikino, Wakamatsu, Kitakyushu, Fukuoka 808-0135, Japan
| | - Takeo Miyake
- Graduate School of Information, Production and Systems, Waseda University, 2-7 Hibikino, Wakamatsu, Kitakyushu, Fukuoka 808-0135, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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2
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Chang L, Cui H, Li F, Job Zhang YHP, Zhang L. ATP regeneration by ATPases for in vitro biotransformation. Biotechnol Adv 2024; 73:108377. [PMID: 38763231 DOI: 10.1016/j.biotechadv.2024.108377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/10/2024] [Accepted: 05/12/2024] [Indexed: 05/21/2024]
Abstract
Adenosine triphosphate (ATP) regeneration is a significant step in both living cells and in vitro biotransformation (ivBT). Rotary motor ATP synthases (ATPases), which regenerate ATP in living cells, have been widely assembled in biomimetic structures for in vitro ATP synthesis. In this review, we present a comprehensive overview of ATPases, including the working principle, orientation and distribution density properties of ATPases, as well as the assembly strategies and applications of ATPase-based ATP regeneration modules. The original sources of ATPases for in vitro ATP regeneration include chromatophores, chloroplasts, mitochondria, and inverted Escherichia coli (E. coli) vesicles, which are readily accessible but unstable. Although significant advances have been made in the assembly methods for ATPase-artificial membranes in recent decades, it remains challenging to replicate the high density and orientation of ATPases observed in vivo using in vitro assembly methods. The use of bioproton pumps or chemicals for constructing proton motive forces (PMF) enables the versatility and potential of ATPase-based ATP regeneration modules. Additionally, overall robustness can be achieved via membrane component selection, such as polymers offering great mechanical stability, or by constructing a solid supporting matrix through layer-by-layer assembly techniques. Finally, the prospects of ATPase-based ATP regeneration modules can be expected with the technological development of ATPases and artificial membranes.
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Affiliation(s)
- Lijing Chang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; In vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Huijuan Cui
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; In vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Fei Li
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; In vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Yi-Heng P Job Zhang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; In vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Lingling Zhang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; In vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
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3
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Beetham CM, Schuster CF, Kviatkovski I, Santiago M, Walker S, Gründling A. Histidine transport is essential for the growth of Staphylococcus aureus at low pH. PLoS Pathog 2024; 20:e1011927. [PMID: 38227607 PMCID: PMC10817146 DOI: 10.1371/journal.ppat.1011927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 01/26/2024] [Accepted: 12/28/2023] [Indexed: 01/18/2024] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen capable of causing many different human diseases. During colonization and infection, S. aureus will encounter a range of hostile environments, including acidic conditions such as those found on the skin and within macrophages. However, little is known about the mechanisms that S. aureus uses to detect and respond to low pH. Here, we employed a transposon sequencing approach to determine on a genome-wide level the genes required or detrimental for growth at low pH. We identified 31 genes that were essential for the growth of S. aureus at pH 4.5 and confirmed the importance of many of them through follow up experiments using mutant strains inactivated for individual genes. Most of the genes identified code for proteins with functions in cell wall assembly and maintenance. These data suggest that the cell wall has a more important role than previously appreciated in promoting bacterial survival when under acid stress. We also identified several novel processes previously not linked to the acid stress response in S. aureus. These include aerobic respiration and histidine transport, the latter by showing that one of the most important genes, SAUSA300_0846, codes for a previously uncharacterized histidine transporter. We further show that under acid stress, the expression of the histidine transporter gene is increased in WT S. aureus. In a S. aureus SAUSA300_0846 mutant strain expression of the histidine biosynthesis genes is induced under acid stress conditions allowing the bacteria to maintain cytosolic histidine levels. This strain is, however, unable to maintain its cytosolic pH to the same extent as a WT strain, revealing an important function specifically for histidine transport in the acid stress response of S. aureus.
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Affiliation(s)
- Catrin M. Beetham
- Section of Molecular Microbiology and Centre for Bacterial Resistance Biology, Imperial College London, London, United Kingdom
| | - Christopher F. Schuster
- Section of Molecular Microbiology and Centre for Bacterial Resistance Biology, Imperial College London, London, United Kingdom
| | - Igor Kviatkovski
- Section of Molecular Microbiology and Centre for Bacterial Resistance Biology, Imperial College London, London, United Kingdom
| | - Marina Santiago
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Suzanne Walker
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Angelika Gründling
- Section of Molecular Microbiology and Centre for Bacterial Resistance Biology, Imperial College London, London, United Kingdom
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4
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Semenov AY, Tikhonov AN. Electrometric and Electron Paramagnetic Resonance Measurements of a Difference in the Transmembrane Electrochemical Potential: Photosynthetic Subcellular Structures and Isolated Pigment-Protein Complexes. MEMBRANES 2023; 13:866. [PMID: 37999352 PMCID: PMC10673362 DOI: 10.3390/membranes13110866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023]
Abstract
A transmembrane difference in the electrochemical potentials of protons (ΔμH+) serves as a free energy intermediate in energy-transducing organelles of the living cell. The contributions of two components of the ΔμH+ (electrical, Δψ, and concentrational, ΔpH) to the overall ΔμH+ value depend on the nature and lipid composition of the energy-coupling membrane. In this review, we briefly consider several of the most common instrumental (electrometric and EPR) methods for numerical estimations of Δψ and ΔpH. In particular, the kinetics of the flash-induced electrometrical measurements of Δψ in bacterial chromatophores, isolated bacterial reaction centers, and Photosystems I and II of the oxygenic photosynthesis, as well as the use of pH-sensitive molecular indicators and kinetic data regarding pH-dependent electron transport in chloroplasts, have been reviewed. Further perspectives on the application of these methods to solve some fundamental and practical problems of membrane bioenergetics are discussed.
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Affiliation(s)
- Alexey Yu. Semenov
- A.N. Belozersky Institute of Physical-Chemical Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia;
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Kubo S, Takada S. Rotational Mechanism of F O Motor in the F-Type ATP Synthase Driven by the Proton Motive Force. Front Microbiol 2022; 13:872565. [PMID: 35783438 PMCID: PMC9243769 DOI: 10.3389/fmicb.2022.872565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
In FOF1 ATP synthase, driven by the proton motive force across the membrane, the FO motor rotates the central rotor and induces conformational changes in the F1 motor, resulting in ATP synthesis. Recently, many near-atomic resolution structural models have been obtained using cryo-electron microscopy. Despite high resolution, however, static information alone cannot elucidate how and where the protons pass through the FO and how proton passage is coupled to FO rotation. Here, we review theoretical and computational studies based on FO structure models. All-atom molecular dynamics (MD) simulations elucidated changes in the protonation/deprotonation of glutamate-the protein-carrier residue-during rotation and revealed the protonation states that form the "water wire" required for long-range proton hopping. Coarse-grained MD simulations unveiled a free energy surface based on the protonation state and rotational angle of the rotor. Hybrid Monte Carlo and MD simulations showed how proton transfer is coupled to rotation.
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Affiliation(s)
- Shintaroh Kubo
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
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6
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ATP synthesis in an ancient ATP synthase at low driving forces. Proc Natl Acad Sci U S A 2022; 119:e2201921119. [PMID: 35512103 DOI: 10.1073/pnas.2201921119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceThe ATP synthases of many anaerobic archaea have an unusual motor subunit c that otherwise is only found in eukaryotic V1VO ATPases. The evolutionary switch from synthase to hydrolase is thought to be caused by a doubling of the rotor subunit c, followed by a loss of the ion binding site. By purification and reconstitution of an ATP synthase with a V-type c subunit, we have unequivocally demonstrated, against expectations, the capability of such an enzyme to synthesize ATP at physiological relevant driving forces of 90 to 150 mV. This is the long-awaited answer to an eminent question in microbial energetics and physiology, especially for life near the thermodynamic limit of ATP synthesis.
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7
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Juhaszova M, Kobrinsky E, Zorov DB, Nuss HB, Yaniv Y, Fishbein KW, de Cabo R, Montoliu L, Gabelli SB, Aon MA, Cortassa S, Sollott SJ. ATP Synthase K +- and H +-Fluxes Drive ATP Synthesis and Enable Mitochondrial K +-"Uniporter" Function: I. Characterization of Ion Fluxes. FUNCTION (OXFORD, ENGLAND) 2021; 3:zqab065. [PMID: 35229078 PMCID: PMC8867323 DOI: 10.1093/function/zqab065] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 01/07/2023]
Abstract
ATP synthase (F1Fo) synthesizes daily our body's weight in ATP, whose production-rate can be transiently increased several-fold to meet changes in energy utilization. Using purified mammalian F1Fo-reconstituted proteoliposomes and isolated mitochondria, we show F1Fo can utilize both ΔΨm-driven H+- and K+-transport to synthesize ATP under physiological pH = 7.2 and K+ = 140 mEq/L conditions. Purely K+-driven ATP synthesis from single F1Fo molecules measured by bioluminescence photon detection could be directly demonstrated along with simultaneous measurements of unitary K+ currents by voltage clamp, both blocked by specific Fo inhibitors. In the presence of K+, compared to osmotically-matched conditions in which this cation is absent, isolated mitochondria display 3.5-fold higher rates of ATP synthesis, at the expense of 2.6-fold higher rates of oxygen consumption, these fluxes being driven by a 2.7:1 K+: H+ stoichiometry. The excellent agreement between the functional data obtained from purified F1Fo single molecule experiments and ATP synthase studied in the intact mitochondrion under unaltered OxPhos coupling by K+ presence, is entirely consistent with K+ transport through the ATP synthase driving the observed increase in ATP synthesis. Thus, both K+ (harnessing ΔΨm) and H+ (harnessing its chemical potential energy, ΔμH) drive ATP generation during normal physiology.
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Affiliation(s)
| | | | | | | | | | - Kenneth W Fishbein
- Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Rafael de Cabo
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Lluis Montoliu
- National Centre for Biotechnology (CNB-CSIC), Biomedical Research Networking Center on Rare Diseases (CIBERER-ISCIII), 28049, Madrid, Spain
| | - Sandra B Gabelli
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Miguel A Aon
- Laboratory of Cardiovascular Science, National Institute on Aging, NIH, Baltimore, MD 21224, USA,Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Sonia Cortassa
- Laboratory of Cardiovascular Science, National Institute on Aging, NIH, Baltimore, MD 21224, USA
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8
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Hou R, Wang Z. Thermodynamic marking of F OF 1 ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148369. [PMID: 33454313 DOI: 10.1016/j.bbabio.2021.148369] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 12/02/2020] [Accepted: 01/05/2021] [Indexed: 11/29/2022]
Abstract
FOF1 ATP synthase is a ~100% efficient molecular machine for energy conversion in biology, and holds great lessons for man-made energy technology and nanotechnology. In light of formidable biocomplexity of the FOF1 machinery, its modeling from pure physical principles remains difficult and rare. Here we construct a thermodynamic model of FOF1 from experimentally accessible quantities plus a single entropy production that generally has vanishingly small values (<1kB). Based on the physical inputs, this model captures FOF1 performance observed over an exhaustively wide range of proton-motive force and nucleotide concentrations. The model predicts a distinct 1/8kBT slope for ATP synthesis rate versus proton-motive force, which is verified by experimental data and represents a profound thermodynamic marking of this amazingly efficient machine operating near a universal limit of the 2nd law of thermodynamics. The model further predicts two symmetries of heat productions, which are testable by available experimental techniques and offer quantitative constraints on FOF1's possible mechanisms behind its ~100% efficiency.
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Affiliation(s)
- Ruizheng Hou
- Department of Applied Physics, School of Science, Xi'an University of Technology, Xi'an, Shaan Xi 710048, China.
| | - Zhisong Wang
- Department of Physics and NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117542, Singapore
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9
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Soga N, Ota A, Nakajima K, Watanabe R, Ueno H, Noji H. Monodisperse Liposomes with Femtoliter Volume Enable Quantitative Digital Bioassays of Membrane Transporters and Cell-Free Gene Expression. ACS NANO 2020; 14:11700-11711. [PMID: 32864949 DOI: 10.1021/acsnano.0c04354] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Digital bioassays have emerged as a new category of bioanalysis. However, digital bioassays for membrane transporter proteins have not been well established yet despite high demands in molecular physiology and molecular pharmacology due to the lack of biologically functional monodisperse liposomes with femtoliter volumes. Here, we established a simple and robust method to produce femtoliter-sized liposomes (femto-liposomes). We prepared 106 monodispersed water-in-oil droplets stabilized by a lipid monolayer using a polyethylene glycol-coated femtoliter reactor array device. Droplets were subjected to the optimized emulsion transfer process for femto-liposome production. Liposomes were monodispersed (coefficient of variation = 5-15%) and had suitable diameter (0.6-5.3 μm) and uniform volumes of subfemtoliter or a few femtoliters; thus, they were termed uniform femto-liposomes. The unilamellarity of uniform femto-liposomes allowed quantitative single-molecule analysis of passive and active transporter proteins: α-hemolysin and FoF1-ATPase. Digital gene expression in uniform femto-liposomes (cell-free transcription and translation from single DNA molecules) was also demonstrated, showing the versatility of digital assays for membrane transporter proteins and cell-free synthetic biology.
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Affiliation(s)
- Naoki Soga
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Akira Ota
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kota Nakajima
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Rikiya Watanabe
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- PRIME, Japan Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
| | - Hiroshi Ueno
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiroyuki Noji
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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10
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Kishikawa JI, Nakanishi A, Furuta A, Kato T, Namba K, Tamakoshi M, Mitsuoka K, Yokoyama K. Mechanical inhibition of isolated V o from V/A-ATPase for proton conductance. eLife 2020; 9:56862. [PMID: 32639230 PMCID: PMC7367684 DOI: 10.7554/elife.56862] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/07/2020] [Indexed: 12/18/2022] Open
Abstract
V-ATPase is an energy converting enzyme, coupling ATP hydrolysis/synthesis in the hydrophilic V1 domain, with proton flow through the Vo membrane domain, via rotation of the central rotor complex relative to the surrounding stator apparatus. Upon dissociation from the V1 domain, the Vo domain of the eukaryotic V-ATPase can adopt a physiologically relevant auto-inhibited form in which proton conductance through the Vo domain is prevented, however the molecular mechanism of this inhibition is not fully understood. Using cryo-electron microscopy, we determined the structure of both the holo V/A-ATPase and isolated Vo at near-atomic resolution, respectively. These structures clarify how the isolated Vo domain adopts the auto-inhibited form and how the holo complex prevents formation of the inhibited Vo form.
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Affiliation(s)
- Jun-Ichi Kishikawa
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan.,Institute for Protein Research, Osaka University, Suita, Japan
| | - Atsuko Nakanishi
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan.,Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Research Center for Ultra-High Voltage Electron Microscopy, Mihogaoka, Osaka, Japan
| | - Aya Furuta
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan
| | - Takayuki Kato
- Institute for Protein Research, Osaka University, Suita, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,RIKEN Center for Biosystems Dynamics Research and SPring-8 Center, Suita, Japan.,JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Japan
| | - Masatada Tamakoshi
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Sciences, Horinouchi, Hachioji, Tokyo, Japan
| | - Kaoru Mitsuoka
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Research Center for Ultra-High Voltage Electron Microscopy, Mihogaoka, Osaka, Japan
| | - Ken Yokoyama
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan
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11
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Molecular dynamics simulation of proton-transfer coupled rotations in ATP synthase F O motor. Sci Rep 2020; 10:8225. [PMID: 32427921 PMCID: PMC7237500 DOI: 10.1038/s41598-020-65004-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 03/12/2020] [Indexed: 11/10/2022] Open
Abstract
The FO motor in FOF1 ATP synthase rotates its rotor driven by the proton motive force. While earlier studies elucidated basic mechanisms therein, recent advances in high-resolution cryo-electron microscopy enabled to investigate proton-transfer coupled FO rotary dynamics at structural details. Here, taking a hybrid Monte Carlo/molecular dynamics simulation method, we studied reversible dynamics of a yeast mitochondrial FO. We obtained the 36°-stepwise rotations of FO per one proton transfer in the ATP synthesis mode and the proton pumping in the ATP hydrolysis mode. In both modes, the most prominent path alternatively sampled states with two and three deprotonated glutamates in c-ring, by which the c-ring rotates one step. The free energy transduction efficiency in the model FO motor reached ~ 90% in optimal conditions. Moreover, mutations in key glutamate and a highly conserved arginine increased proton leakage and markedly decreased the coupling, in harmony with previous experiments. This study provides a simple framework of simulations for chemical-reaction coupled molecular dynamics calling for further studies in ATP synthase and others.
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12
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Kinetic coupling of the respiratory chain with ATP synthase, but not proton gradients, drives ATP production in cristae membranes. Proc Natl Acad Sci U S A 2020; 117:2412-2421. [PMID: 31964824 DOI: 10.1073/pnas.1917968117] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Mitochondria have a characteristic ultrastructure with invaginations of the inner membrane called cristae that contain the protein complexes of the oxidative phosphorylation system. How this particular morphology of the respiratory membrane impacts energy conversion is currently unknown. One proposed role of cristae formation is to facilitate the establishment of local proton gradients to fuel ATP synthesis. Here, we determined the local pH values at defined sublocations within mitochondria of respiring yeast cells by fusing a pH-sensitive GFP to proteins residing in different mitochondrial subcompartments. Only a small proton gradient was detected over the inner membrane in wild type or cristae-lacking cells. Conversely, the obtained pH values did barely permit ATP synthesis in a reconstituted system containing purified yeast F1F0 ATP synthase, although, thermodynamically, a sufficiently high driving force was applied. At higher driving forces, where robust ATP synthesis was observed, a P-side pH value of 6 increased the ATP synthesis rate 3-fold compared to pH 7. In contrast, when ATP synthase was coreconstituted with an active proton-translocating cytochrome oxidase, ATP synthesis readily occurred at the measured, physiological pH values. Our study thus reveals that the morphology of the inner membrane does not influence the subcompartmental pH values and is not necessary for robust oxidative phosphorylation in mitochondria. Instead, it is likely that the dense packing of the oxidative phosphorylation complexes in the cristae membranes assists kinetic coupling between proton pumping and ATP synthesis.
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13
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Hamsanathan S, Musser SM. The Tat protein transport system: intriguing questions and conundrums. FEMS Microbiol Lett 2019; 365:5000164. [PMID: 29897510 DOI: 10.1093/femsle/fny123] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/11/2018] [Indexed: 12/21/2022] Open
Abstract
The Tat machinery catalyzes the transport of folded proteins across the cytoplasmic membrane in bacteria and the thylakoid membrane in plants. Transport occurs only in the presence of an electric field (Δψ) and/or a pH (ΔpH) gradient, and thus, Tat transport is considered to be dependent on the proton motive force (pmf). This presents a fundamental and major challenge, namely, that the Tat system catalyzes the movement of large folded protein cargos across a membrane without collapse of ion gradients. Current models argue that the active translocon assembles de novo for each cargo transported, thus providing an effective gating mechanism to minimize ion leakage. A limited structural understanding of the intermediates occurring during transport and the role of the pmf in stabilizing and/or driving this process have hindered the development of more detailed models. A fundamental question that remains unanswered is whether the pmf is actually 'consumed', providing an energetic driving force for transport, or alternatively, whether its presence is instead necessary to provide the appropriate environment for the translocon components to become active. Including addressing this issue in greater detail, we explore a series of additional questions that challenge current models, and, hopefully, motivate future work.
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Affiliation(s)
- Shruthi Hamsanathan
- Department of Molecular and Cellular Medicine, College of Medicine, The Texas A&M Health Science Center, Texas A&M University, 1114 TAMU, College Station, TX 77843, USA
| | - Siegfried M Musser
- Department of Molecular and Cellular Medicine, College of Medicine, The Texas A&M Health Science Center, Texas A&M University, 1114 TAMU, College Station, TX 77843, USA
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14
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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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15
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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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16
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Abstract
Emerging microtechnologies are aimed at developing a microsystem with densely packed array structure, i.e., an array with a femtoliter reaction chamber, for highly sensitive and quantitative biological assays. Here, we describe a novel femtoliter chamber array system (arrayed lipid bilayer chambers, ALBiC) that contains approximately a million femtoliter chambers, each sealed with a phospholipid bilayer membrane with extremely high efficiency (>90%). This novel platform enables detection of membrane transporter activity at the single-molecule level and thus expands the applicability of femtoliter chamber arrays to highly sensitive assays of transporters.
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17
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Abstract
Bedaquiline (BDQ), an inhibitor of the mycobacterial F1Fo-ATP synthase, has revolutionized the antitubercular drug discovery program by defining energy metabolism as a potent new target space. Several studies have recently suggested that BDQ ultimately causes mycobacterial cell death through a phenomenon known as uncoupling. The biochemical basis underlying this, in BDQ, is unresolved and may represent a new pathway to the development of effective therapeutics. In this communication, we demonstrate that BDQ can inhibit ATP synthesis in Escherichia coli by functioning as a H+/K+ ionophore, causing transmembrane pH and potassium gradients to be equilibrated. Despite the apparent lack of a BDQ-binding site, incorporating the E. coli Fo subunit into liposomes enhanced the ionophoric activity of BDQ. We discuss the possibility that localization of BDQ at F1Fo-ATP synthases enables BDQ to create an uncoupled microenvironment, by antiporting H+/K+ Ionophoric properties may be desirable in high-affinity antimicrobials targeting integral membrane proteins.
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18
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Tikhonov AN. Photosynthetic Electron and Proton Transport in Chloroplasts: EPR Study of ΔpH Generation, an Overview. Cell Biochem Biophys 2017; 75:421-432. [PMID: 28488221 DOI: 10.1007/s12013-017-0797-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/12/2017] [Indexed: 11/30/2022]
Abstract
This is a brief overview focused on the electron paramagnetic resonance applications to the study of the proton transport processes in chloroplasts. After brief description of structural and functional organization of the chloroplast electron transport chain, our attention is focused on the measurements of trans-thylakoid pH difference (ΔpH) with pH-sensitive spin-probes. The use of spin-probes is based either (i) on measuring the ΔpH-partitioning of spin-probes between the thylakoid lumen and external volume, or (ii) on monitoring changes in the electron paramagnetic resonance spectra of pH-sensitive nitroxide radicals located in the lumen. Along with the use of spin-probes, the intra-thylakoid pH (pHin) can be determined by the "kinetic" method, which relies on the fact that the rate-limiting step in the chain of photosynthetic electron transfer (plastoquinol oxidation by the cytochrome b 6 f complex) is controlled by pHin. The results of ΔpH determinations in chloroplasts based on the use of pH-sensitive spin-probes and measurements of post-illumination reduction of photoreaction centers of Photosystem I are discussed in the context of the problem of energy coupling in laterally heterogeneous lamellar system of chloroplasts.
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Affiliation(s)
- Alexander N Tikhonov
- Department of Biophysics, Faculty of Physics, M.V. Lomonosov, Moscow State University, Moscow, Russia.
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19
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Abstract
FoF1-ATP synthase (FoF1) couples H+ flow in Fo domain and ATP synthesis/hydrolysis in F1 domain through rotation of the central rotor shaft, and the H+/ATP ratio is crucial to understand the coupling mechanism and energy yield in cells. Although H+/ATP ratio of the perfectly coupling enzyme can be predicted from the copy number of catalytic β subunits and that of H+ binding c subunits as c/β, the actual H+/ATP ratio can vary depending on coupling efficiency. Here, we report actual H+/ATP ratio of thermophilic Bacillus FoF1, whose c/β is 10/3. Proteoliposomes reconstituted with the FoF1 were energized with ΔpH and Δψ by the acid-base transition and by valinomycin-mediated diffusion potential of K+ under various [ATP]/([ADP]⋅[Pi]) conditions, and the initial rate of ATP synthesis/hydrolysis was measured. Analyses of thermodynamically equilibrated states, where net ATP synthesis/hydrolysis is zero, show linear correlation between the chemical potential of ATP synthesis/hydrolysis and the proton motive force, giving the slope of the linear function, that is, H+/ATP ratio, 3.3 ± 0.1. This value agrees well with the c/β ratio. Thus, chemomechanical coupling between Fo and F1 is perfect.
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20
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Vershubskii AV, Trubitsin BV, Priklonskii VI, Tikhonov AN. Lateral heterogeneity of the proton potential along the thylakoid membranes of chloroplasts. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:388-401. [DOI: 10.1016/j.bbamem.2016.11.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 11/20/2016] [Accepted: 11/29/2016] [Indexed: 02/06/2023]
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21
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Biophysical comparison of ATP synthesis mechanisms shows a kinetic advantage for the rotary process. Proc Natl Acad Sci U S A 2016; 113:11220-11225. [PMID: 27647911 DOI: 10.1073/pnas.1608533113] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The ATP synthase (F-ATPase) is a highly complex rotary machine that synthesizes ATP, powered by a proton electrochemical gradient. Why did evolution select such an elaborate mechanism over arguably simpler alternating-access processes that can be reversed to perform ATP synthesis? We studied a systematic enumeration of alternative mechanisms, using numerical and theoretical means. When the alternative models are optimized subject to fundamental thermodynamic constraints, they fail to match the kinetic ability of the rotary mechanism over a wide range of conditions, particularly under low-energy conditions. We used a physically interpretable, closed-form solution for the steady-state rate for an arbitrary chemical cycle, which clarifies kinetic effects of complex free-energy landscapes. Our analysis also yields insights into the debated "kinetic equivalence" of ATP synthesis driven by transmembrane pH and potential difference. Overall, our study suggests that the complexity of the F-ATPase may have resulted from positive selection for its kinetic advantage.
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Turina P, Petersen J, Gräber P. Thermodynamics of proton transport coupled ATP synthesis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:653-64. [PMID: 26940516 DOI: 10.1016/j.bbabio.2016.02.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 01/16/2016] [Accepted: 02/28/2016] [Indexed: 10/22/2022]
Abstract
The thermodynamic H(+)/ATP ratio of the H(+)-ATP synthase from chloroplasts was measured in proteoliposomes after energization of the membrane by an acid base transition (Turina et al. 2003 [13], 418-422). The method is discussed, and all published data obtained with this system are combined and analyzed as a single dataset. This meta-analysis led to the following results. 1) At equilibrium, the transmembrane ΔpH is energetically equivalent to the transmembrane electric potential difference. 2) The standard free energy for ATP synthesis (reference reaction) is ΔG°(ref)=33.8±1.3kJ/mol. 3) The thermodynamic H(+)/ATP ratio, as obtained from the shift of the ATP synthesis equilibrium induced by changing the transmembrane ΔpH (varying either pH(in) or pH(out)) is 4.0±0.1. The structural H(+)/ATP ratio, calculated from the ratio of proton binding sites on the c-subunit-ring in F(0) to the catalytic nucleotide binding sites on the β-subunits in F(1), is c/β=14/3=4.7. We infer that the energy of 0.7 protons per ATP that flow through the enzyme, but do not contribute to shifting the ATP/(ADP·Pi) ratio, is used for additional processes within the enzyme, such as activation, and/or energy dissipation, due e.g. to internal uncoupling. The ratio between the thermodynamic and the structural H(+)/ATP values is 0.85, and we conclude that this value represents the efficiency of the chemiosmotic energy conversion within the chloroplast H(+)-ATP synthase.
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Affiliation(s)
- Paola Turina
- Department of Biology, BiGeA, University of Bologna, Via Irnerio 42, I-40126 Bologna, Italy
| | - Jan Petersen
- Biomedicine Discovery Institute, Monash University, 1 Wellington Rd., Clayton, Vic 3800, Australia
| | - Peter Gräber
- Institut für Physikalische Chemie, University of Freiburg, Albertstr, 23a, D-79104 Freiburg, Germany.
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23
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von Ballmoos C, Biner O, Nilsson T, Brzezinski P. Mimicking respiratory phosphorylation using purified enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:321-31. [PMID: 26707617 DOI: 10.1016/j.bbabio.2015.12.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 11/17/2015] [Accepted: 12/16/2015] [Indexed: 11/26/2022]
Abstract
The enzymes of oxidative phosphorylation is a striking example of the functional association of multiple enzyme complexes, working together to form ATP from cellular reducing equivalents. These complexes, such as cytochrome c oxidase or the ATP synthase, are typically investigated individually and therefore, their functional interplay is not well understood. Here, we present methodology that allows the co-reconstitution of purified terminal oxidases and ATP synthases in synthetic liposomes. The enzymes are functionally coupled via proton translocation where upon addition of reducing equivalents the oxidase creates and maintains a transmembrane electrochemical proton gradient that energizes the synthesis of ATP by the F1F0 ATP synthase. The method has been tested with the ATP synthases from Escherichia coli and spinach chloroplasts, and with the quinol and cytochrome c oxidases from E. coli and Rhodobacter sphaeroides, respectively. Unlike in experiments with the ATP synthase reconstituted alone, the setup allows in vitro ATP synthesis under steady state conditions, with rates up to 90 ATP×s(-1)×enzyme(-1). We have also used the novel system to study the phenomenon of "mild uncoupling" as observed in mitochondria upon addition of low concentrations of ionophores (e.g. FCCP, SF6847) and the recoupling effect of 6-ketocholestanol. While we could reproduce the described effects, our data with the in vitro system does not support the idea of a direct interaction between a mitochondrial protein and the uncoupling agents as proposed earlier.
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Affiliation(s)
- Christoph von Ballmoos
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
| | - Olivier Biner
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Tobias Nilsson
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
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24
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Abstract
Mitochondrial dynamics, fission and fusion, were first identified in yeast with investigation in heart cells beginning only in the last 5 to 7 years. In the ensuing time, it has become evident that these processes are not only required for healthy mitochondria, but also, that derangement of these processes contributes to disease. The fission and fusion proteins have a number of functions beyond the mitochondrial dynamics. Many of these functions are related to their membrane activities, such as apoptosis. However, other functions involve other areas of the mitochondria, such as OPA1's role in maintaining cristae structure and preventing cytochrome c leak, and its essential (at least a 10 kDa fragment of OPA1) role in mtDNA replication. In heart disease, changes in expression of these important proteins can have detrimental effects on mitochondrial and cellular function.
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Affiliation(s)
- A A Knowlton
- Molecular & Cellular Cardiology, Division of Cardiovascular Medicine and Pharmacology Department, University of California, Davis, and The Department of Veteran's Affairs, Northern California VA, Sacramento, California, USA
| | - T T Liu
- Molecular & Cellular Cardiology, Division of Cardiovascular Medicine and Pharmacology Department, University of California, Davis, and The Department of Veteran's Affairs, Northern California VA, Sacramento, California, USA
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25
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Hoitzing H, Johnston IG, Jones NS. What is the function of mitochondrial networks? A theoretical assessment of hypotheses and proposal for future research. Bioessays 2015; 37:687-700. [PMID: 25847815 PMCID: PMC4672710 DOI: 10.1002/bies.201400188] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mitochondria can change their shape from discrete isolated organelles to a large continuous reticulum. The cellular advantages underlying these fused networks are still incompletely understood. In this paper, we describe and compare hypotheses regarding the function of mitochondrial networks. We use mathematical and physical tools both to investigate existing hypotheses and to generate new ones, and we suggest experimental and modelling strategies. Among the novel insights we underline from this work are the possibilities that (i) selective mitophagy is not required for quality control because selective fusion is sufficient; (ii) increased connectivity may have non-linear effects on the diffusion rate of proteins; and (iii) fused networks can act to dampen biochemical fluctuations. We hope to convey to the reader that quantitative approaches can drive advances in the understanding of the physiological advantage of these morphological changes.
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Affiliation(s)
- Hanne Hoitzing
- Department of Mathematics, Imperial College London, London, UK
| | - Iain G Johnston
- Department of Mathematics, Imperial College London, London, UK
| | - Nick S Jones
- Department of Mathematics, Imperial College London, London, UK
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26
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Nakanishi A, Kishikawa JI, Tamakoshi M, Yokoyama K. The ingenious structure of central rotor apparatus in VoV1; key for both complex disassembly and energy coupling between V1 and Vo. PLoS One 2015; 10:e0119602. [PMID: 25756791 PMCID: PMC4355294 DOI: 10.1371/journal.pone.0119602] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 01/14/2015] [Indexed: 11/25/2022] Open
Abstract
Vacuolar type rotary H+-ATPases (VoV1) couple ATP synthesis/hydrolysis by V1 with proton translocation by Vo via rotation of a central rotor apparatus composed of the V1-DF rotor shaft, a socket-like Vo-C (eukaryotic Vo-d) and the hydrophobic rotor ring. Reconstitution experiments using subcomplexes revealed a weak binding affinity of V1-DF to Vo-C despite the fact that torque needs to be transmitted between V1-DF and Vo-C for the tight energy coupling between V1 and Vo. Mutation of a short helix at the tip of V1-DF caused intramolecular uncoupling of VoV1, suggesting that proper fitting of the short helix of V1-D into the socket of Vo-C is required for tight energy coupling between V1 and Vo. To account for the apparently contradictory properties of the interaction between V1-DF and Vo-C (weak binding affinity but strict requirement for torque transmission), we propose a model in which the relationship between V1-DF and Vo-C corresponds to that between a slotted screwdriver and a head of slotted screw. This model is consistent with our previous result in which the central rotor apparatus is not the major factor for the association of V1 with Vo (Kishikawa and Yokoyama, J Biol Chem. 2012 24597-24603).
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Affiliation(s)
- Atsuko Nakanishi
- Department of Molecular Biosciences, Kyoto Sangyo University, Motoyama Kamigamo, Kita-ku, Kyoto, Japan
| | - Jun-ichi Kishikawa
- Department of Molecular Biosciences, Kyoto Sangyo University, Motoyama Kamigamo, Kita-ku, Kyoto, Japan
| | - Masatada Tamakoshi
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Horinouchi, Hachioji, Tokyo, Japan
| | - Ken Yokoyama
- Department of Molecular Biosciences, Kyoto Sangyo University, Motoyama Kamigamo, Kita-ku, Kyoto, Japan
- * E-mail:
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27
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Medvedev ES, Stuchebrukhov AA. Mechanisms of generation of local ΔpH in mitochondria and bacteria. BIOCHEMISTRY (MOSCOW) 2015; 79:425-34. [PMID: 24954593 DOI: 10.1134/s000629791405006x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The concepts of global and local coupling between proton generators, the enzymes of the respiratory chain, and the consumer, the ATP synthase, coexist in the theory of oxidative phosphorylation. Global coupling is trivial proton transport via the aqueous medium, whereas local coupling implies that the protons pumped are consumed before they escape to the bulk phase. In this work, the conditions for the occurrence of local coupling are explored. It is supposed that the membrane retains protons near its surface and that the proton current generated by the proton pumps rapidly decreases with increasing proton motive force (pmf). It is shown that the competition between the processes of proton translocation across the membrane and their dissipation from the surface to the bulk can result in transient generation of a local ΔpH in reply to a sharp change in pmf; the appearance of local ΔpH, in turn, leads to rapid recovery of the pmf, and hence, it provides for stabilization of the potential at the membrane. Two mechanisms of such kind are discussed: 1) pH changes in the surface area due to proton pumping develop faster than those due to proton escape to the bulk; 2) the former does not take place, but the protons leaving the surface do not equilibrate with the bulk immediately; rather, they give rise to a non-equilibrium concentration near the surface and, as a result, to a back proton flow to the surface. The first mechanism is more efficient, but it does not occur in mitochondria and neutrophilic bacteria, whereas the second can produce ΔpH on the order of unity. In the absence of proton retardation at the surface, local ΔpH does not arise, whereas the formation of global ΔpH is possible only at buffer concentration of less than 10 mM. The role of the mechanisms proposed in transitions between States 3 and 4 of the respiratory chain is discussed. The main conclusion is that surface protons, under conditions where they play a role, support stabilization of the membrane pmf and rapid communication between proton generators and consumers, while their contribution to the energetics is not significant.
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Affiliation(s)
- E S Medvedev
- Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka, Moscow Region, 142432, Russia.
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28
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Ueno H, Minagawa Y, Hara M, Rahman S, Yamato I, Muneyuki E, Noji H, Murata T, Iino R. Torque generation of Enterococcus hirae V-ATPase. J Biol Chem 2014; 289:31212-23. [PMID: 25258315 DOI: 10.1074/jbc.m114.598177] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
V-ATPase (V(o)V1) converts the chemical free energy of ATP into an ion-motive force across the cell membrane via mechanical rotation. This energy conversion requires proper interactions between the rotor and stator in V(o)V1 for tight coupling among chemical reaction, torque generation, and ion transport. We developed an Escherichia coli expression system for Enterococcus hirae V(o)V1 (EhV(o)V1) and established a single-molecule rotation assay to measure the torque generated. Recombinant and native EhV(o)V1 exhibited almost identical dependence of ATP hydrolysis activity on sodium ion and ATP concentrations, indicating their functional equivalence. In a single-molecule rotation assay with a low load probe at high ATP concentration, EhV(o)V1 only showed the "clear" state without apparent backward steps, whereas EhV1 showed two states, "clear" and "unclear." Furthermore, EhV(o)V1 showed slower rotation than EhV1 without the three distinct pauses separated by 120° that were observed in EhV1. When using a large probe, EhV(o)V1 showed faster rotation than EhV1, and the torque of EhV(o)V1 estimated from the continuous rotation was nearly double that of EhV1. On the other hand, stepping torque of EhV1 in the clear state was comparable with that of EhV(o)V1. These results indicate that rotor-stator interactions of the V(o) moiety and/or sodium ion transport limit the rotation driven by the V1 moiety, and the rotor-stator interactions in EhV(o)V1 are stabilized by two peripheral stalks to generate a larger torque than that of isolated EhV1. However, the torque value was substantially lower than that of other rotary ATPases, implying the low energy conversion efficiency of EhV(o)V1.
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Affiliation(s)
- Hiroshi Ueno
- From the Department of Physics, Faculty of Science and Engineering, Chuo University, Tokyo 112-8551, Japan
| | - Yoshihiro Minagawa
- the Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Mayu Hara
- the Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Suhaila Rahman
- the Department of Biological Science and Technology, Tokyo University of Science, Tokyo 125-8585, Japan
| | - Ichiro Yamato
- the Department of Biological Science and Technology, Tokyo University of Science, Tokyo 125-8585, Japan
| | - Eiro Muneyuki
- From the Department of Physics, Faculty of Science and Engineering, Chuo University, Tokyo 112-8551, Japan
| | - Hiroyuki Noji
- the Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Takeshi Murata
- the Department of Chemistry, Graduate School of Science, Chiba University, Chiba 263-8522, Japan, JST, PRESTO, Chiba 263-8522, Japan,
| | - Ryota Iino
- the Okazaki Institute for Integrative Bioscience, Institute for Molecular Science, National Institutes of Natural Sciences, Aichi 444-8787, Japan, and the Department of Functional Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Kanagawa 240-0193, Japan
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29
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Arrayed lipid bilayer chambers allow single-molecule analysis of membrane transporter activity. Nat Commun 2014; 5:4519. [PMID: 25058452 PMCID: PMC4124872 DOI: 10.1038/ncomms5519] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 06/25/2014] [Indexed: 11/09/2022] Open
Abstract
Nano- to micron-size reaction chamber arrays (femtolitre chamber arrays) have facilitated the development of sensitive and quantitative biological assays, such as single-molecule enzymatic assays, digital PCR and digital ELISA. However, the versatility of femtolitre chamber arrays is limited to reactions that occur in aqueous solutions. Here we report an arrayed lipid bilayer chamber system (ALBiC) that contains sub-million femtolitre chambers, each sealed with a stable 4-μm-diameter lipid bilayer membrane. When reconstituted with a limiting amount of the membrane transporter proteins α-hemolysin or F0F1-ATP synthase, the chambers within the ALBiC exhibit stochastic and quantized transporting activities. This demonstrates that the single-molecule analysis of passive and active membrane transport is achievable with the ALBiC system. This new platform broadens the versatility of femtolitre chamber arrays and paves the way for novel applications aimed at furthering our mechanistic understanding of membrane proteins' function.
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30
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Zarecki R, Oberhardt MA, Yizhak K, Wagner A, Shtifman Segal E, Freilich S, Henry CS, Gophna U, Ruppin E. Maximal sum of metabolic exchange fluxes outperforms biomass yield as a predictor of growth rate of microorganisms. PLoS One 2014; 9:e98372. [PMID: 24866123 PMCID: PMC4035307 DOI: 10.1371/journal.pone.0098372] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 05/01/2014] [Indexed: 11/18/2022] Open
Abstract
Growth rate has long been considered one of the most valuable phenotypes that can be measured in cells. Aside from being highly accessible and informative in laboratory cultures, maximal growth rate is often a prime determinant of cellular fitness, and predicting phenotypes that underlie fitness is key to both understanding and manipulating life. Despite this, current methods for predicting microbial fitness typically focus on yields [e.g., predictions of biomass yield using GEnome-scale metabolic Models (GEMs)] or notably require many empirical kinetic constants or substrate uptake rates, which render these methods ineffective in cases where fitness derives most directly from growth rate. Here we present a new method for predicting cellular growth rate, termed SUMEX, which does not require any empirical variables apart from a metabolic network (i.e., a GEM) and the growth medium. SUMEX is calculated by maximizing the SUM of molar EXchange fluxes (hence SUMEX) in a genome-scale metabolic model. SUMEX successfully predicts relative microbial growth rates across species, environments, and genetic conditions, outperforming traditional cellular objectives (most notably, the convention assuming biomass maximization). The success of SUMEX suggests that the ability of a cell to catabolize substrates and produce a strong proton gradient enables fast cell growth. Easily applicable heuristics for predicting growth rate, such as what we demonstrate with SUMEX, may contribute to numerous medical and biotechnological goals, ranging from the engineering of faster-growing industrial strains, modeling of mixed ecological communities, and the inhibition of cancer growth.
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Affiliation(s)
- Raphy Zarecki
- School of Computer Sciences, and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Matthew A. Oberhardt
- School of Computer Sciences, and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Molecular Microbiology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (MAO); (ER)
| | - Keren Yizhak
- School of Computer Sciences, and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Allon Wagner
- School of Computer Sciences, and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ella Shtifman Segal
- Department of Molecular Microbiology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Shiri Freilich
- Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Christopher S. Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Uri Gophna
- Department of Molecular Microbiology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Eytan Ruppin
- School of Computer Sciences, and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (MAO); (ER)
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Watanabe R. Rotary catalysis of FoF1-ATP synthase. Biophysics (Nagoya-shi) 2013; 9:51-6. [PMID: 27493540 PMCID: PMC4629669 DOI: 10.2142/biophysics.9.51] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 04/22/2013] [Indexed: 12/01/2022] Open
Abstract
The synthesis of ATP, the key reaction of biological energy metabolism, is accomplished by the rotary motor protein; FoF1-ATP synthase (FoF1). In vivo, FoF1, located on the cell membrane, carries out ATP synthesis by using the proton motive force. This heterologous energy conversion is supposed to be mediated by the mechanical rotation of FoF1; however, it still remained unclear. Recently, we developed the novel experimental setup to reproduce the proton motive force in vitro and succeeded in directly observing the proton-driven rotation of FoF1. In this review, we describe the interesting working principles determined so far for FoF1 and then introduce results from our recent study.
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Affiliation(s)
- Rikiya Watanabe
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
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Mashkovtseva E, Boronovsky S, Nartsissov Y. Combined mathematical methods in the description of the F(o)F(1)-ATP synthase catalytic cycle. Math Biosci 2013; 243:117-25. [PMID: 23499574 DOI: 10.1016/j.mbs.2013.02.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 02/15/2013] [Accepted: 02/21/2013] [Indexed: 11/26/2022]
Abstract
The FoF1-ATP synthase is one of the key enzymes in supplying energy production in almost all living systems. In this paper, we provide a theoretical description of its catalytic cycle using combined mathematical methods. These methods include Langevin dynamics for the rotation of the central protein core and the Monte-Carlo method to model nucleotide and proton binding. This model is the first in which ATP synthesis and hydrolysis can occur depending on the nucleotide concentration and system conditions. The main advantage of the presented model is the possibility of obtaining results for both single-molecular protein-machines and large ensembles of proteins. The calculated rates are close to the experimentally measured rates for a single enzyme. The model has been formalised as a computer simulation that allows researchers to evaluate ATP production in different types of living cells.
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