1
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Chen Q, Li L, Samidurai A, Thompson J, Hu Y, Willard B, Lesnefsky EJ. Acute endoplasmic reticulum stress-induced mitochondria respiratory chain damage: The role of activated calpains. FASEB J 2024; 38:e23404. [PMID: 38197290 PMCID: PMC11032170 DOI: 10.1096/fj.202301158rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 11/19/2023] [Accepted: 12/19/2023] [Indexed: 01/11/2024]
Abstract
The induction of acute endoplasmic reticulum (ER) stress damages the electron transport chain (ETC) in cardiac mitochondria. Activation of mitochondria-localized calpain 1 (CPN1) and calpain 2 (CPN2) impairs the ETC in pathological conditions, including aging and ischemia-reperfusion in settings where ER stress is increased. We asked if the activation of calpains causes the damage to the ETC during ER stress. Control littermate and CPNS1 (calpain small regulatory subunit 1) deletion mice were used in the current study. CPNS1 is an essential subunit required to maintain CPN1 and CPN2 activities, and deletion of CPNS1 prevents their activation. Tunicamycin (TUNI, 0.4 mg/kg) was used to induce ER stress in C57BL/6 mice. Cardiac mitochondria were isolated after 72 h of TUNI treatment. ER stress was increased in both control littermate and CPNS1 deletion mice with TUNI treatment. The TUNI treatment activated both cytosolic and mitochondrial CPN1 and 2 (CPN1/2) in control but not in CPNS1 deletion mice. TUNI treatment led to decreased oxidative phosphorylation and complex I activity in control but not in CPNS1 deletion mice compared to vehicle. The contents of complex I subunits, including NDUFV2 and ND5, were decreased in control but not in CPNS1 deletion mice. TUNI treatment also led to decreased oxidation through cytochrome oxidase (COX) only in control mice. Proteomic study showed that subunit 2 of COX was decreased in control but not in CPNS1 deletion mice. Our results provide a direct link between activation of CPN1/2 and complex I and COX damage during acute ER stress.
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Affiliation(s)
- Qun Chen
- Department of Internal Medicine, Division of Cardiology, Pauley Heart Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Ling Li
- Proteomics Core, Cleveland Clinic, Cleveland, Ohio, USA
| | - Arun Samidurai
- Department of Internal Medicine, Division of Cardiology, Pauley Heart Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Jeremy Thompson
- Department of Internal Medicine, Division of Cardiology, Pauley Heart Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Ying Hu
- Department of Internal Medicine, Division of Cardiology, Pauley Heart Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | | | - Edward J. Lesnefsky
- Department of Internal Medicine, Division of Cardiology, Pauley Heart Center, Virginia Commonwealth University, Richmond, Virginia, USA
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia, USA
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia, USA
- Richmond Department of Veterans Affairs Medical Center, Richmond, Virginia, USA
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2
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F1·Fo ATP Synthase/ATPase: Contemporary View on Unidirectional Catalysis. Int J Mol Sci 2023; 24:ijms24065417. [PMID: 36982498 PMCID: PMC10049701 DOI: 10.3390/ijms24065417] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/05/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
F1·Fo-ATP synthases/ATPases (F1·Fo) are molecular machines that couple either ATP synthesis from ADP and phosphate or ATP hydrolysis to the consumption or production of a transmembrane electrochemical gradient of protons. Currently, in view of the spread of drug-resistant disease-causing strains, there is an increasing interest in F1·Fo as new targets for antimicrobial drugs, in particular, anti-tuberculosis drugs, and inhibitors of these membrane proteins are being considered in this capacity. However, the specific drug search is hampered by the complex mechanism of regulation of F1·Fo in bacteria, in particular, in mycobacteria: the enzyme efficiently synthesizes ATP, but is not capable of ATP hydrolysis. In this review, we consider the current state of the problem of “unidirectional” F1·Fo catalysis found in a wide range of bacterial F1·Fo and enzymes from other organisms, the understanding of which will be useful for developing a strategy for the search for new drugs that selectively disrupt the energy production of bacterial cells.
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3
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Changes within the central stalk of E. coli F 1F o ATP synthase observed after addition of ATP. Commun Biol 2023; 6:26. [PMID: 36631659 PMCID: PMC9834311 DOI: 10.1038/s42003-023-04414-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 01/03/2023] [Indexed: 01/13/2023] Open
Abstract
F1Fo ATP synthase functions as a biological generator and makes a major contribution to cellular energy production. Proton flow generates rotation in the Fo motor that is transferred to the F1 motor to catalyze ATP production, with flexible F1/Fo coupling required for efficient catalysis. F1Fo ATP synthase can also operate in reverse, hydrolyzing ATP and pumping protons, and in bacteria this function can be regulated by an inhibitory ε subunit. Here we present cryo-EM data showing E. coli F1Fo ATP synthase in different rotational and inhibited sub-states, observed following incubation with 10 mM MgATP. Our structures demonstrate how structural transitions within the inhibitory ε subunit induce torsional movement in the central stalk, thereby enabling its rotation within the Fο motor. This highlights the importance of the central rotor for flexible coupling of the F1 and Fo motors and provides further insight into the regulatory mechanism mediated by subunit ε.
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4
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Turina P. Modulation of the H +/ATP coupling ratio by ADP and ATP as a possible regulatory feature in the F-type ATP synthases. Front Mol Biosci 2022; 9:1023031. [PMID: 36275634 PMCID: PMC9583940 DOI: 10.3389/fmolb.2022.1023031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
F-type ATP synthases are transmembrane enzymes, which play a central role in the metabolism of all aerobic and photosynthetic cells and organisms, being the major source of their ATP synthesis. Catalysis occurs via a rotary mechanism, in which the free energy of a transmembrane electrochemical ion gradient is converted into the free energy of ATP phosphorylation from ADP and Pi, and vice versa. An ADP, tightly bound to one of the three catalytic sites on the stator head, is associated with catalysis inhibition, which is relieved by the transmembrane proton gradient and by ATP. By preventing wasteful ATP hydrolysis in times of low osmotic energy and low ATP/ADP ratio, such inhibition constitutes a classical regulatory feedback effect, likely to be an integral component of in vivo regulation. The present miniview focuses on an additional putative regulatory phenomenon, which has drawn so far little attention, consisting in a substrate-induced tuning of the H+/ATP coupling ratio during catalysis, which might represent an additional key to energy homeostasis in the cell. Experimental pieces of evidence in support of such a phenomenon are reviewed.
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Affiliation(s)
- Paola Turina
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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5
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Iwamoto-Kihara A. Regulatory Mechanisms and Environmental Adaptation of the F-ATPase Family. Biol Pharm Bull 2022; 45:1412-1418. [PMID: 36184497 DOI: 10.1248/bpb.b22-00419] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The F-type ATPase family of enzymes, including ATP synthases, are found ubiquitously in biological membranes. ATP synthesis from ADP and inorganic phosphate is driven by an electrochemical H+ gradient or H+ motive force, in which intramolecular rotation of F-type ATPase is generated with H+ transport across the membranes. Because this rotation is essential for energy coupling between catalysis and H+-transport, regulation of the rotation is important to adapt to environmental changes and maintain ATP concentration. Recently, a series of cryo-electron microscopy images provided detailed insights into the structure of the H+ pathway and the multiple subunit arrangement. However, the regulatory mechanism of the rotation has not been clarified. This review describes the inhibition mechanism of ATP hydrolysis in bacterial enzymes. In addition, properties of the F-type ATPase of Streptococcus mutans, which acts as a H+-pump in an acidic environment, are described. These findings may help in the development of novel antimicrobial agents.
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6
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Mendoza-Hoffmann F, Zarco-Zavala M, Ortega R, Celis-Sandoval H, Torres-Larios A, García-Trejo JJ. Evolution of the Inhibitory and Non-Inhibitory ε, ζ, and IF 1 Subunits of the F 1F O-ATPase as Related to the Endosymbiotic Origin of Mitochondria. Microorganisms 2022; 10:microorganisms10071372. [PMID: 35889091 PMCID: PMC9317440 DOI: 10.3390/microorganisms10071372] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/03/2022] [Accepted: 07/03/2022] [Indexed: 12/10/2022] Open
Abstract
The F1FO-ATP synthase nanomotor synthesizes >90% of the cellular ATP of almost all living beings by rotating in the “forward” direction, but it can also consume the same ATP pools by rotating in “reverse.” To prevent futile F1FO-ATPase activity, several different inhibitory proteins or domains in bacteria (ε and ζ subunits), mitochondria (IF1), and chloroplasts (ε and γ disulfide) emerged to block the F1FO-ATPase activity selectively. In this study, we analyze how these F1FO-ATPase inhibitory proteins have evolved. The phylogeny of the α-proteobacterial ε showed that it diverged in its C-terminal side, thus losing both the inhibitory function and the ATP-binding/sensor motif that controls this inhibition. The losses of inhibitory function and the ATP-binding site correlate with an evolutionary divergence of non-inhibitory α-proteobacterial ε and mitochondrial δ subunits from inhibitory bacterial and chloroplastidic ε subunits. Here, we confirm the lack of inhibitory function of wild-type and C-terminal truncated ε subunits of P. denitrificans. Taken together, the data show that ζ evolved to replace ε as the primary inhibitor of the F1FO-ATPase of free-living α-proteobacteria. However, the ζ inhibitory function was also partially lost in some symbiotic α-proteobacteria and totally lost in some strictly parasitic α-proteobacteria such as the Rickettsiales order. Finally, we found that ζ and IF1 likely evolved independently via convergent evolution before and after the endosymbiotic origin mitochondria, respectively. This led us to propose the ε and ζ subunits as tracer genes of the pre-endosymbiont that evolved into the actual mitochondria.
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Affiliation(s)
- Francisco Mendoza-Hoffmann
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California (UABC)—Campus Tijuana, Tijuana C.P. 22390, Baja California, Mexico
- Correspondence: (F.M.-H.); (J.J.G.-T.)
| | - Mariel Zarco-Zavala
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de Mexico C.P. 04510, Coyoacan, Mexico
| | - Raquel Ortega
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de Mexico C.P. 04510, Coyoacan, Mexico
| | - Heliodoro Celis-Sandoval
- Instituto de Fisiología Celular (IFC), Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de Mexico C.P. 04510, Coyoacan, Mexico
| | - Alfredo Torres-Larios
- Instituto de Fisiología Celular (IFC), Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de Mexico C.P. 04510, Coyoacan, Mexico
| | - José J. García-Trejo
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de Mexico C.P. 04510, Coyoacan, Mexico
- Correspondence: (F.M.-H.); (J.J.G.-T.)
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7
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Nakano A, Kishikawa JI, Nakanishi A, Mitsuoka K, Yokoyama K. Structural basis of unisite catalysis of bacterial F 0F 1-ATPase. PNAS NEXUS 2022; 1:pgac116. [PMID: 36741449 PMCID: PMC9896953 DOI: 10.1093/pnasnexus/pgac116] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/07/2022] [Indexed: 06/17/2023]
Abstract
Adenosine triphosphate (ATP) synthases (F0F1-ATPases) are crucial for all aerobic organisms. F1, a water-soluble domain, can catalyze both the synthesis and hydrolysis of ATP with the rotation of the central γε rotor inside a cylinder made of α 3 β 3 in three different conformations (referred to as β E, β TP, and β DP). In this study, we determined multiple cryo-electron microscopy structures of bacterial F0F1 exposed to different reaction conditions. The structures of nucleotide-depleted F0F1 indicate that the ε subunit directly forces β TP to adopt a closed form independent of the nucleotide binding to β TP. The structure of F0F1 under conditions that permit only a single catalytic β subunit per enzyme to bind ATP is referred to as unisite catalysis and reveals that ATP hydrolysis unexpectedly occurs on β TP instead of β DP, where ATP hydrolysis proceeds in the steady-state catalysis of F0F1. This indicates that the unisite catalysis of bacterial F0F1 significantly differs from the kinetics of steady-state turnover with continuous rotation of the shaft.
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Affiliation(s)
- Atsuki Nakano
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto 603-8555, Japan
| | - Jun-ichi Kishikawa
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto 603-8555, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Atsuko Nakanishi
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto 603-8555, Japan
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, 7-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Kaoru Mitsuoka
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, 7-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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8
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Vu Huu K, Zangl R, Hoffmann J, Just A, Morgner N. Bacterial F-type ATP synthases follow a well-choreographed assembly pathway. Nat Commun 2022; 13:1218. [PMID: 35260553 PMCID: PMC8904574 DOI: 10.1038/s41467-022-28828-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 02/04/2022] [Indexed: 12/23/2022] Open
Abstract
F-type ATP synthases are multiprotein complexes composed of two separate coupled motors (F1 and FO) generating adenosine triphosphate (ATP) as the universal major energy source in a variety of relevant biological processes in mitochondria, bacteria and chloroplasts. While the structure of many ATPases is solved today, the precise assembly pathway of F1FO-ATP synthases is still largely unclear. Here, we probe the assembly of the F1 complex from Acetobacterium woodii. Using laser induced liquid bead ion desorption (LILBID) mass spectrometry, we study the self-assembly of purified F1 subunits in different environments under non-denaturing conditions. We report assembly requirements and identify important assembly intermediates in vitro and in cellula. Our data provide evidence that nucleotide binding is crucial for in vitro F1 assembly, whereas ATP hydrolysis appears to be less critical. We correlate our results with activity measurements and propose a model for the assembly pathway of a functional F1 complex. ATPases are the macromolecular machines for cellular energy production. Here the authors investigate factors that govern the assembly of the F1 complex from a bacterial F-type ATPase and relate differences in activity of complexes assembled in cells and in vitro to structural changes.
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Affiliation(s)
- Khanh Vu Huu
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | - Rene Zangl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | - Jan Hoffmann
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | - Alicia Just
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany.
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9
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Liu Y, Yu J, Wang M, Zeng Q, Fu X, Chang Z. A high-throughput genetically directed protein crosslinking analysis reveals the physiological relevance of the ATP synthase 'inserted' state. FEBS J 2021; 288:2989-3009. [PMID: 33128817 DOI: 10.1111/febs.15616] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 10/07/2020] [Accepted: 10/29/2020] [Indexed: 11/30/2022]
Abstract
ATP synthase, a highly conserved protein complex that has a subunit composition of α3 β3 γδεab2 c8-15 for the bacterial enzyme, is a key player in supplying energy to living organisms. This protein complex consists of a peripheral F1 sector (α3 β3 γδε) and a membrane-integrated Fo sector (ab2 c8-15 ). Structural analyses of the isolated protein components revealed that, remarkably, the C-terminal domain of its ε-subunit seems to adopt two dramatically different structures, but the physiological relevance of this conformational change remains largely unknown. In an attempt to decipher this, we developed a high-throughput in vivo protein photo-cross-linking analysis pipeline based on the introduction of the unnatural amino acid into the target protein via the scarless genome-targeted site-directed mutagenesis technique, and probing the cross-linked products via the high-throughput polyacrylamide gel electrophoresis technique. Employing this pipeline, we examined the interactions involving the C-terminal helix of the ε-subunit in cells living under a variety of experimental conditions. These studies enabled us to uncover that the bacterial ATP synthase exists as an equilibrium between the 'inserted' and 'noninserted' state in cells, maintaining a moderate but significant level of net ATP synthesis when shifting to the former upon exposing to unfavorable energetically stressful conditions. Such a mechanism allows the bacterial ATP synthases to proportionally and instantly switch between two reversible functional states in responding to changing environmental conditions. Importantly, this high-throughput approach could allow us to decipher the physiological relevance of protein-protein interactions identified under in vitro conditions or to unveil novel physiological context-dependent protein-protein interactions that are unknown before.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Protein Science, Peking University, Beijing, China
| | - Jiayu Yu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Protein Science, Peking University, Beijing, China
| | - Mengyuan Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Protein Science, Peking University, Beijing, China
| | - Qingfang Zeng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Protein Science, Peking University, Beijing, China
| | - Xinmiao Fu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Protein Science, Peking University, Beijing, China
| | - Zengyi Chang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Protein Science, Peking University, Beijing, China
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10
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Rotor subunits adaptations in ATP synthases from photosynthetic organisms. Biochem Soc Trans 2021; 49:541-550. [PMID: 33890627 PMCID: PMC8106487 DOI: 10.1042/bst20190936] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/17/2021] [Accepted: 03/22/2021] [Indexed: 11/17/2022]
Abstract
Driven by transmembrane electrochemical ion gradients, F-type ATP synthases are the primary source of the universal energy currency, adenosine triphosphate (ATP), throughout all domains of life. The ATP synthase found in the thylakoid membranes of photosynthetic organisms has some unique features not present in other bacterial or mitochondrial systems. Among these is a larger-than-average transmembrane rotor ring and a redox-regulated switch capable of inhibiting ATP hydrolysis activity in the dark by uniquely adapted rotor subunit modifications. Here, we review recent insights into the structure and mechanism of ATP synthases specifically involved in photosynthesis and explore the cellular physiological consequences of these adaptations at short and long time scales.
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11
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Miranda-Astudillo H, Zarco-Zavala M, García-Trejo JJ, González-Halphen D. Regulation of bacterial ATP synthase activity: A gear-shifting or a pawl-ratchet mechanism? FEBS J 2020; 288:3159-3163. [PMID: 33377595 DOI: 10.1111/febs.15671] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 12/14/2020] [Indexed: 11/30/2022]
Abstract
The F1 Fo -ATP synthase, a widely distributed nanomotor responsible of ATP synthesis, rotates its central rotor reversibly: In the clockwise direction when viewed from the Fo (with the observer facing the positive side of the energy transducing membrane and looking down into the negative side of the membrane), it functions as ATP synthase, while in counterclockwise sense, it operates as a proton-pumping ATP hydrolase. Regulation exerted by naturally occurring inhibitory proteins of the enzyme appears to function by avoiding ATP hydrolysis while preserving ATP synthesis. The work of Liu et al. describes an unbiased, elegant analytical pipeline that provides important insights into the inhibitory role of the ε-subunit of the bacterial F1 Fo -ATP synthase in vivo. We discuss if a gear-shifting versus a pawl-ratchet mechanism may explain the regulatory role of the ε-subunit.
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Affiliation(s)
- Héctor Miranda-Astudillo
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - José J García-Trejo
- Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Diego González-Halphen
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, Mexico
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12
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Jarman OD, Biner O, Hirst J. Regulation of ATP hydrolysis by the ε subunit, ζ subunit and Mg-ADP in the ATP synthase of Paracoccus denitrificans. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148355. [PMID: 33321110 PMCID: PMC8039183 DOI: 10.1016/j.bbabio.2020.148355] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 11/27/2020] [Accepted: 12/08/2020] [Indexed: 12/17/2022]
Abstract
F1FO-ATP synthase is a crucial metabolic enzyme that uses the proton motive force from respiration to regenerate ATP. For maximum thermodynamic efficiency ATP synthesis should be fully reversible, but the enzyme from Paracoccus denitrificans catalyzes ATP hydrolysis at far lower rates than it catalyzes ATP synthesis, an effect often attributed to its unique ζ subunit. Recently, we showed that deleting ζ increases hydrolysis only marginally, indicating that other common inhibitory mechanisms such as inhibition by the C-terminal domain of the ε subunit (ε-CTD) or Mg-ADP may be more important. Here, we created mutants lacking the ε-CTD, and double mutants lacking both the ε-CTD and ζ subunit. No substantial activation of ATP hydrolysis was observed in any of these strains. Instead, hydrolysis in even the double mutant strains could only be activated by oxyanions, the detergent lauryldimethylamine oxide, or a proton motive force, which are all considered to release Mg-ADP inhibition. Our results establish that P. denitrificans ATP synthase is regulated by a combination of the ε and ζ subunits and Mg-ADP inhibition.
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Affiliation(s)
- Owen D Jarman
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Olivier Biner
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Judy Hirst
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.
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13
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Krah A, Huber RG, McMillan DGG, Bond PJ. The Molecular Basis for Purine Binding Selectivity in the Bacterial ATP Synthase ϵ Subunit. Chembiochem 2020; 21:3249-3254. [PMID: 32608105 DOI: 10.1002/cbic.202000291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/30/2020] [Indexed: 12/21/2022]
Abstract
The ϵ subunit of ATP synthases has been proposed to regulate ATP hydrolysis in bacteria. Prevailing evidence supports the notion that when the ATP concentration falls below a certain threshold, the ϵ subunit changes its conformation from a non-inhibitory down-state to an extended up-state that then inhibits enzymatic ATP hydrolysis by binding to the catalytic domain. It has been demonstrated that the ϵ subunit from Bacillus PS3 is selective for ATP over other nucleotides, including GTP. In this study, the purine triphosphate selectivity is rationalized by using results from MD simulations and free energy calculations for the R103A/R115A mutant of the ϵ subunit from Bacillus PS3, which binds ATP more strongly than the wild-type protein. Our results are in good agreement with experimental data, and the elucidated molecular basis for selectivity could help to guide the design of novel GTP sensors.
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Affiliation(s)
- Alexander Krah
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Str. #07-01 Matrix, Singapore, 138671, Singapore.,Korea Institute for Advanced Study, School of Computational Sciences, 85 Hoegiro, Dongdaemun-gu, Seoul, 02455, Republic of Korea
| | - Roland G Huber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Str. #07-01 Matrix, Singapore, 138671, Singapore
| | - Duncan G G McMillan
- Delft University of Technology, Department of Biotechnology, Van der Maasweg 9, Delft, 2629HZ, The Netherlands
| | - Peter J Bond
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Str. #07-01 Matrix, Singapore, 138671, Singapore.,National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore, 117543, Singapore
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14
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Milgrom YM, Duncan TM. F-ATP-ase of Escherichia coli membranes: The ubiquitous MgADP-inhibited state and the inhibited state induced by the ε-subunit's C-terminal domain are mutually exclusive. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148189. [PMID: 32194063 DOI: 10.1016/j.bbabio.2020.148189] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/10/2020] [Accepted: 03/13/2020] [Indexed: 12/21/2022]
Abstract
ATP synthases are important energy-coupling, rotary motor enzymes in all kingdoms of life. In all F-type ATP synthases, the central rotor of the catalytic F1 complex is composed of the γ subunit and the N-terminal domain (NTD) of the ε subunit. In the enzymes of diverse bacteria, the C-terminal domain of ε (εCTD) can undergo a dramatic conformational change to trap the enzyme in a transiently inactive state. This inhibitory mechanism is absent in the mitochondrial enzyme, so the εCTD could provide a means to selectively target ATP synthases of pathogenic bacteria for antibiotic development. For Escherichia coli and other bacterial model systems, it has been difficult to dissect the relationship between ε inhibition and a MgADP-inhibited state that is ubiquitous for FOF1 from bacteria and eukaryotes. A prior study with the isolated catalytic complex from E. coli, EcF1, showed that these two modes of inhibition are mutually exclusive, but it has long been known that interactions of F1 with the membrane-embedded FO complex modulate inhibition by the εCTD. Here, we study membranes containing EcFOF1 with wild-type ε, ε lacking the full εCTD, or ε with a small deletion at the C-terminus. By using compounds with distinct activating effects on F-ATP-ase activity, we confirm that εCTD inhibition and ubiquitous MgADP inhibition are mutually exclusive for membrane-bound E. coli F-ATP-ase. We determine that most of the enzyme complexes in wild-type membranes are in the ε-inhibited state (>50%) or in the MgADP-inhibited state (30%).
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Affiliation(s)
- Yakov M Milgrom
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, 750 E Adams St, Syracuse, NY 13210, USA.
| | - Thomas M Duncan
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, 750 E Adams St, Syracuse, NY 13210, USA.
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15
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ATP-binding affinity of the ε subunit of thermophilic F 1-ATPase under label-free conditions. Biochem Biophys Rep 2020; 21:100725. [PMID: 31938734 PMCID: PMC6953521 DOI: 10.1016/j.bbrep.2020.100725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/29/2019] [Accepted: 01/03/2020] [Indexed: 12/31/2022] Open
Abstract
The ε subunits of several bacterial F1-ATPases bind ATP. ATP binding to the ε subunit has been shown to be involved in the regulation of F1-ATPase from thermophilic Bacillus sp. PS3 (TF1). We previously reported that the dissociation constant for ATP of wild-type ε subunit of TF1 at 25 °C is 4.3 μM by measuring changes in the fluorescence of the dye attached to the ε subunit (Kato, S. et al. (2007) J. Biol. Chem.282, 37618). However, we have recently noticed that this varies with the dye used. In this report, to determine the affinity for ATP under label-free conditions, we have measured the competitive displacement of 2′(3′)-O-N′-methylaniloyl-aminoadenosine-5′-triphosphate (Mant-ATP), a fluorescent analog of ATP, by ATP. The dissociation constant for ATP of wild-type ε subunit of TF1 at 25 °C was determined to be 0.29 μM, which is one order of magnitude higher affinity than previously reported values. The ε subunit of F1-ATPase from Bacillus PS3 specifically binds ATP. Fluorescent labeling of ε subunit for the measurement may affect binding affinity. ATP binding affinity under label-free conditions was determined. Affinity of ε subunit for ATP is revised.
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16
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Sikkema HR, Gaastra BF, Pols T, Poolman B. Cell Fuelling and Metabolic Energy Conservation in Synthetic Cells. Chembiochem 2019; 20:2581-2592. [PMID: 31381223 DOI: 10.1002/cbic.201900398] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Indexed: 12/14/2022]
Abstract
We are aiming for a blue print for synthesizing (moderately complex) subcellular systems from molecular components and ultimately for constructing life. However, without comprehensive instructions and design principles, we rely on simple reaction routes to operate the essential functions of life. The first forms of synthetic life will not make every building block for polymers de novo according to complex pathways, rather they will be fed with amino acids, fatty acids and nucleotides. Controlled energy supply is crucial for any synthetic cell, no matter how complex. Herein, we describe the simplest pathways for the efficient generation of ATP and electrochemical ion gradients. We have estimated the demand for ATP by polymer synthesis and maintenance processes in small cell-like systems, and we describe circuits to control the need for ATP. We also present fluorescence-based sensors for pH, ionic strength, excluded volume, ATP/ADP, and viscosity, which allow the major physicochemical conditions inside cells to be monitored and tuned.
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Affiliation(s)
- Hendrik R Sikkema
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Bauke F Gaastra
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Tjeerd Pols
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Bert Poolman
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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17
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Oliveras-González C, Linares M, Amabilino DB, Avarvari N. Large Synthetic Molecule that either Folds or Aggregates through Weak Supramolecular Interactions Determined by Solvent. ACS OMEGA 2019; 4:10108-10120. [PMID: 31460103 PMCID: PMC6648001 DOI: 10.1021/acsomega.9b01050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 05/29/2019] [Indexed: 05/12/2023]
Abstract
Weak noncovalent interactions between large disclike molecules in poorly solvating media generally lead to the formation of fibers where the molecules stack atop one another. Here, we show that a particular chiral spacing group between large aromatic moieties, which usually lead to columnar stacks, in this case gives rise to an intramolecularly folded structure in relatively polar solvents, but in very apolar solvents forms finite aggregates. The molecule that displays this behavior has a C 3 symmetric benzene-1,3,5-tris(3,3'-diamido-2,2'-bipyridine) (BTAB) core with three metalloporphyrin units appended to it through short chiral spacers. Quite well-defined chromophore arrangements are evident by circular dichroism (CD) spectroscopy of this compound in solution, where clear exciton coupled bands of porphyrins are observed. In more polar solvents where the molecules are dispersed, a relatively weak CD signal is observed as a result of intramolecular folding, a feature confirmed by molecular modeling. The intramolecular folding was confirmed by measuring the CD of a C 2 symmetric analogue. The C 3 symmetric BTAB cores that would normally be expected to stack in a chiral arrangement in apolar solvents show no indication of CD, suggesting that there is no transfer of chirality through it (although the expected planar conformation of the 2,2'-bipyridine unit is confirmed by NMR spectroscopy). The incorporation of the porphyrins on the 3,3'-diamino-2,2'-bipyridine moiety spaced by a chiral unit leaves the latter incapable of assembling through supramolecular π-π stacking. Rather, modeling indicates that the three metalloporphyrin units interact, thanks to van der Waals interactions, favoring their close interactions over that of the BTAB units. Atomic force microscopy shows that, in contrast to other examples of molecules with the same core, disclike aggregates (rather than fibrillar one dimensional aggregates) are favored by the C 3 symmetric molecule. The closed structures are formed through nondirectional interlocking of porphyrin rings. The chiral spacer between the rigid core and the porphyrin moieties is undoubtedly important in determining the outcome in polar or less polar solvents, as modeling shows that this joint in the molecule has two favored conformations that render the molecule relatively flat or convex.
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Affiliation(s)
| | - Mathieu Linares
- Laboratory
of Organic Electronics, ITN, Campus Norrköping, Scientific Visualization
Group, ITN, Campus Norrköping, and Swedish e-Science Research Centre
(SeRC), Linköping University, SE-581 83 Linköping, Sweden
| | - David B. Amabilino
- School
of Chemistry, University of Nottingham, University Park, NG7 2RD Nottingham, U.K.
- GSK Carbon
Neutral Laboratories for Sustainable Chemistry, The University of Nottingham, Jubilee Campus, Triumph Road, NG7 2TU Nottingham, U.K.
| | - Narcis Avarvari
- MOLTECH-Anjou,
UMR 6200, CNRS, Univ. Angers, 2bd Lavoisier, 49045 Angers Cedex, France
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18
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The β-hairpin region of the cyanobacterial F 1-ATPase γ-subunit plays a regulatory role in the enzyme activity. Biochem J 2019; 476:1771-1780. [PMID: 31164401 DOI: 10.1042/bcj20190242] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/29/2019] [Accepted: 05/31/2019] [Indexed: 01/21/2023]
Abstract
The γ-subunit of cyanobacterial and chloroplast ATP synthase, the rotary shaft of F1-ATPase, equips a specific insertion region that is only observed in photosynthetic organisms. This region plays a physiologically pivotal role in enzyme regulation, such as in ADP inhibition and redox response. Recently solved crystal structures of the γ-subunit of F1-ATPase from photosynthetic organisms revealed that the insertion region forms a β-hairpin structure, which is positioned along the central stalk. The structure-function relationship of this specific region was studied by constraining the expected conformational change in this region caused by the formation of a disulfide bond between Cys residues introduced on the central stalk and this β-hairpin structure. This fixation of the β-hairpin region in the α3β3γ complex affects both ADP inhibition and the binding of the ε-subunit to the complex, indicating the critical role that the β-hairpin region plays as a regulator of the enzyme. This role must be important for the maintenance of the intracellular ATP levels in photosynthetic organisms.
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19
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Yamakita A, Liu Y, Futai M, Iwamoto-Kihara A. The carboxyl-terminal helical domain of the ATP synthase γ subunit is involved in ε subunit conformation and energy coupling. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:361-368. [PMID: 30876890 DOI: 10.1016/j.bbabio.2019.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 02/22/2019] [Accepted: 03/11/2019] [Indexed: 11/26/2022]
Abstract
The γ subunit located at the center of ATP synthase (FOF1) plays critical roles in catalysis. Escherichia coli mutant with Pro substitution of the γ subunit residue γLeu218, which are located the rotor shaft near the c subunit ring, decreased NADH-driven ATP synthesis activity and ATP hydrolysis-dependent H+ transport of membranes to ~60% and ~40% of the wild type, respectively, without affecting FOF1 assembly. Consistently, the mutant was defective in growth by oxidative phosphorylation, indicating that energy coupling is impaired by the mutation. The ε subunit conformations in the γLeu218Pro mutant enzyme were investigated by cross-linking between cysteine residues introduced into both the ε subunit (εCys118 and εCys134, in the second helix and the hook segment, respectively) and the γ subunit (γCys99 and γCys260, located in the globular domain and the carboxyl-terminal helix, respectively). In the presence of ADP, the two γ260 and ε134 cysteine residues formed a disulfide bond in both the γLeu218Pro mutant and the wild type, indicating that the hook segment of ε subunit penetrates into the α3β3-ring along with the γ subunits in both enzymes. However, γ260/ε134 cross-linking in the γLeu218Pro mutant decreased significantly in the presence of ATP, whereas this effect was small in the wild type. These results suggested that the γ subunit carboxyl-terminal helix containing γLeu218 is involved in the conformation of the ε subunit hook region during ATP hydrolysis and, therefore, is required for energy coupling in FOF1.
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Affiliation(s)
- Atsuyoshi Yamakita
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - YingTao Liu
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Masamitsu Futai
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Iwate Medical University, Yahaba, Iwate 028-3694, Japan
| | - Atsuko Iwamoto-Kihara
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan.
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20
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Sobti M, Ishmukhametov R, Bouwer JC, Ayer A, Suarna C, Smith NJ, Christie M, Stocker R, Duncan TM, Stewart AG. Cryo-EM reveals distinct conformations of E. coli ATP synthase on exposure to ATP. eLife 2019; 8:e43864. [PMID: 30912741 PMCID: PMC6449082 DOI: 10.7554/elife.43864] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 03/25/2019] [Indexed: 12/13/2022] Open
Abstract
ATP synthase produces the majority of cellular energy in most cells. We have previously reported cryo-EM maps of autoinhibited E. coli ATP synthase imaged without addition of nucleotide (Sobti et al. 2016), indicating that the subunit ε engages the α, β and γ subunits to lock the enzyme and prevent functional rotation. Here we present multiple cryo-EM reconstructions of the enzyme frozen after the addition of MgATP to identify the changes that occur when this ε inhibition is removed. The maps generated show that, after exposure to MgATP, E. coli ATP synthase adopts a different conformation with a catalytic subunit changing conformation substantially and the ε C-terminal domain transitioning via an intermediate 'half-up' state to a condensed 'down' state. This work provides direct evidence for unique conformational states that occur in E. coli ATP synthase when ATP binding prevents the ε C-terminal domain from entering the inhibitory 'up' state.
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Affiliation(s)
- Meghna Sobti
- Molecular, Structural and Computational Biology DivisionThe Victor Chang Cardiac Research InstituteDarlinghurstAustralia
- St Vincent’s Clinical School, Faculty of MedicineUNSW SydneySydneyAustralia
| | - Robert Ishmukhametov
- Department of Physics, Clarendon LaboratoryUniversity of OxfordOxfordUnited Kingdom
| | - James C Bouwer
- Molecular HorizonsThe University of WollongongWollongongAustralia
| | - Anita Ayer
- St Vincent’s Clinical School, Faculty of MedicineUNSW SydneySydneyAustralia
- Vascular Biology DivisionVictor Chang Cardiac Research InstituteDarlinghurstAustralia
| | - Cacang Suarna
- Vascular Biology DivisionVictor Chang Cardiac Research InstituteDarlinghurstAustralia
| | - Nicola J Smith
- St Vincent’s Clinical School, Faculty of MedicineUNSW SydneySydneyAustralia
- Molecular Cardiology and Biophysics DivisionVictor Chang Cardiac Research InstituteDarlinghurstAustralia
| | - Mary Christie
- Molecular, Structural and Computational Biology DivisionThe Victor Chang Cardiac Research InstituteDarlinghurstAustralia
- St Vincent’s Clinical School, Faculty of MedicineUNSW SydneySydneyAustralia
| | - Roland Stocker
- St Vincent’s Clinical School, Faculty of MedicineUNSW SydneySydneyAustralia
- Vascular Biology DivisionVictor Chang Cardiac Research InstituteDarlinghurstAustralia
| | - Thomas M Duncan
- Department of Biochemistry & Molecular BiologySUNY Upstate Medical UniversitySyracuse, NYUnited States
| | - Alastair G Stewart
- Molecular, Structural and Computational Biology DivisionThe Victor Chang Cardiac Research InstituteDarlinghurstAustralia
- St Vincent’s Clinical School, Faculty of MedicineUNSW SydneySydneyAustralia
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21
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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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22
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Lapashina AS, Feniouk BA. ADP-Inhibition of H+-F OF 1-ATP Synthase. BIOCHEMISTRY (MOSCOW) 2018; 83:1141-1160. [PMID: 30472953 DOI: 10.1134/s0006297918100012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
H+-FOF1-ATP synthase (F-ATPase, F-type ATPase, FOF1 complex) catalyzes ATP synthesis from ADP and inorganic phosphate in eubacteria, mitochondria, chloroplasts, and some archaea. ATP synthesis is powered by the transmembrane proton transport driven by the proton motive force (PMF) generated by the respiratory or photosynthetic electron transport chains. When the PMF is decreased or absent, ATP synthase catalyzes the reverse reaction, working as an ATP-dependent proton pump. The ATPase activity of the enzyme is regulated by several mechanisms, of which the most conserved is the non-competitive inhibition by the MgADP complex (ADP-inhibition). When ADP binds to the catalytic site without phosphate, the enzyme may undergo conformational changes that lock bound ADP, resulting in enzyme inactivation. PMF can induce release of inhibitory ADP and reactivate ATP synthase; the threshold PMF value required for enzyme reactivation might exceed the PMF for ATP synthesis. Moreover, membrane energization increases the catalytic site affinity to phosphate, thereby reducing the probability of ADP binding without phosphate and preventing enzyme transition to the ADP-inhibited state. Besides phosphate, oxyanions (e.g., sulfite and bicarbonate), alcohols, lauryldimethylamine oxide, and a number of other detergents can weaken ADP-inhibition and increase ATPase activity of the enzyme. In this paper, we review the data on ADP-inhibition of ATP synthases from different organisms and discuss the in vivo role of this phenomenon and its relationship with other regulatory mechanisms, such as ATPase activity inhibition by subunit ε and nucleotide binding in the noncatalytic sites of the enzyme. It should be noted that in Escherichia coli enzyme, ADP-inhibition is relatively weak and rather enhanced than prevented by phosphate.
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Affiliation(s)
- A S Lapashina
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - B A Feniouk
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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23
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Mendoza-Hoffmann F, Zarco-Zavala M, Ortega R, García-Trejo JJ. Control of rotation of the F1FO-ATP synthase nanomotor by an inhibitory α-helix from unfolded ε or intrinsically disordered ζ and IF1 proteins. J Bioenerg Biomembr 2018; 50:403-424. [DOI: 10.1007/s10863-018-9773-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 09/13/2018] [Indexed: 12/14/2022]
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24
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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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25
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Hahn A, Vonck J, Mills DJ, Meier T, Kühlbrandt W. Structure, mechanism, and regulation of the chloroplast ATP synthase. Science 2018; 360:eaat4318. [PMID: 29748256 PMCID: PMC7116070 DOI: 10.1126/science.aat4318] [Citation(s) in RCA: 229] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 04/09/2018] [Indexed: 12/13/2022]
Abstract
The chloroplast adenosine triphosphate (ATP) synthase uses the electrochemical proton gradient generated by photosynthesis to produce ATP, the energy currency of all cells. Protons conducted through the membrane-embedded Fo motor drive ATP synthesis in the F1 head by rotary catalysis. We determined the high-resolution structure of the complete cF1Fo complex by cryo-electron microscopy, resolving side chains of all 26 protein subunits, the five nucleotides in the F1 head, and the proton pathway to and from the rotor ring. The flexible peripheral stalk redistributes differences in torsional energy across three unequal steps in the rotation cycle. Plant ATP synthase is autoinhibited by a β-hairpin redox switch in subunit γ that blocks rotation in the dark.
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Affiliation(s)
- Alexander Hahn
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
| | - Deryck J Mills
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
| | - Thomas Meier
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany.
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany.
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26
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Krah A, Zarco-Zavala M, McMillan DGG. Insights into the regulatory function of the ɛ subunit from bacterial F-type ATP synthases: a comparison of structural, biochemical and biophysical data. Open Biol 2018; 8:170275. [PMID: 29769322 PMCID: PMC5990651 DOI: 10.1098/rsob.170275] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 04/24/2018] [Indexed: 01/07/2023] Open
Abstract
ATP synthases catalyse the formation of ATP, the most common chemical energy storage unit found in living cells. These enzymes are driven by an electrochemical ion gradient, which allows the catalytic evolution of ATP by a binding change mechanism. Most ATP synthases are capable of catalysing ATP hydrolysis to varying degrees, and to prevent wasteful ATP hydrolysis, bacteria and mitochondria have regulatory mechanisms such as ADP inhibition. Additionally, ɛ subunit inhibition has also been described in three bacterial systems, Escherichia coli, Bacillus PS3 and Caldalkalibacillus thermarum TA2.A1. Previous studies suggest that the ɛ subunit is capable of undergoing an ATP-dependent conformational change from the ATP hydrolytic inhibitory 'extended' conformation to the ATP-induced non-inhibitory 'hairpin' conformation. A recently published crystal structure of the F1 domain of the C. thermarum TA2.A1 F1Fo ATP synthase revealed a mutant ɛ subunit lacking the ability to bind ATP in a hairpin conformation. This is a surprising observation considering it is an organism that performs no ATP hydrolysis in vivo, and appears to challenge the current dogma on the regulatory role of the ɛ subunit. This has prompted a re-examination of present knowledge of the ɛ subunits role in different organisms. Here, we compare published biochemical, biophysical and structural data involving ɛ subunit-mediated ATP hydrolysis regulation in a variety of organisms, concluding that the ɛ subunit from the bacterial F-type ATP synthases is indeed capable of regulating ATP hydrolysis activity in a wide variety of bacteria, making it a potentially valuable drug target, but its exact role is still under debate.
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Affiliation(s)
- Alexander Krah
- School of Computational Sciences, Korea Institute for Advanced Study, 85 Hoegiro Dongdaemun-gu, Seoul 02455, Republic of Korea
| | - Mariel Zarco-Zavala
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Duncan G G McMillan
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, Delft 2629 HZ, The Netherlands
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Joon S, Ragunathan P, Sundararaman L, Nartey W, Kundu S, Manimekalai MSS, Bogdanović N, Dick T, Grüber G. The NMR solution structure of Mycobacterium tuberculosis F-ATP synthase subunit ε provides new insight into energy coupling inside the rotary engine. FEBS J 2018; 285:1111-1128. [PMID: 29360236 DOI: 10.1111/febs.14392] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 11/30/2017] [Accepted: 01/18/2018] [Indexed: 11/27/2022]
Abstract
Mycobacterium tuberculosis (Mt) F1 F0 ATP synthase (α3 :β3 :γ:δ:ε:a:b:b':c9 ) is essential for the viability of growing and nongrowing persister cells of the pathogen. Here, we present the first NMR solution structure of Mtε, revealing an N-terminal β-barrel domain (NTD) and a C-terminal domain (CTD) composed of a helix-loop-helix with helix 1 and -2 being shorter compared to their counterparts in other bacteria. The C-terminal amino acids are oriented toward the NTD, forming a domain-domain interface between the NTD and CTD. The Mtε structure provides a novel mechanistic model of coupling c-ring- and ε rotation via a patch of hydrophobic residues in the NTD and residues of the CTD to the bottom of the catalytic α3 β3 -headpiece. To test our model, genome site-directed mutagenesis was employed to introduce amino acid changes in these two parts of the epsilon subunit. Inverted vesicle assays show that these mutations caused an increase in ATP hydrolysis activity and a reduction in ATP synthesis. The structural and enzymatic data are discussed in light of the transition mechanism of a compact and extended state of Mtε, which provides the inhibitory effects of this coupling subunit inside the rotary engine. Finally, the employment of these data with molecular docking shed light into the second binding site of the drug Bedaquiline. DATABASE Structural data are available in the PDB under the accession number 5YIO.
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Affiliation(s)
- Shin Joon
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Priya Ragunathan
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Lavanya Sundararaman
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Wilson Nartey
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Subhashri Kundu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Nebojša Bogdanović
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Thomas Dick
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA
| | - Gerhard Grüber
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
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28
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Mendoza-Hoffmann F, Pérez-Oseguera Á, Cevallos MÁ, Zarco-Zavala M, Ortega R, Peña-Segura C, Espinoza-Simón E, Uribe-Carvajal S, García-Trejo JJ. The Biological Role of the ζ Subunit as Unidirectional Inhibitor of the F 1F O-ATPase of Paracoccus denitrificans. Cell Rep 2018; 22:1067-1078. [PMID: 29386127 DOI: 10.1016/j.celrep.2017.12.106] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 09/09/2017] [Accepted: 12/28/2017] [Indexed: 11/16/2022] Open
Abstract
The biological roles of the three natural F1FO-ATPase inhibitors, ε, ζ, and IF1, on cell physiology remain controversial. The ζ subunit is a useful model for deletion studies since it mimics mitochondrial IF1, but in the F1FO-ATPase of Paracoccus denitrificans (PdF1FO), it is a monogenic and supernumerary subunit. Here, we constructed a P. denitrificans 1222 derivative (PdΔζ) with a deleted ζ gene to determine its role in cell growth and bioenergetics. The results show that the lack of ζ in vivo strongly restricts respiratory P. denitrificans growth, and this is restored by complementation in trans with an exogenous ζ gene. Removal of ζ increased the coupled PdF1FO-ATPase activity without affecting the PdF1FO-ATP synthase turnover, and the latter was not affected at all by ζ reconstitution in vitro. Therefore, ζ works as a unidirectional pawl-ratchet inhibitor of the PdF1FO-ATPase nanomotor favoring the ATP synthase turnover to improve respiratory cell growth and bioenergetics.
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Affiliation(s)
- Francisco Mendoza-Hoffmann
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Delegación Coyoacán, Ciudad de México (CDMX) 04510, México
| | - Ángeles Pérez-Oseguera
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, U.N.A.M., Cuernavaca, Morelos, México
| | - Miguel Ángel Cevallos
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, U.N.A.M., Cuernavaca, Morelos, México
| | | | - Raquel Ortega
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Delegación Coyoacán, Ciudad de México (CDMX) 04510, México
| | | | | | | | - José J García-Trejo
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Delegación Coyoacán, Ciudad de México (CDMX) 04510, México.
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29
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Varghese F, Blaza JN, Jones AJY, Jarman OD, Hirst J. Deleting the IF 1-like ζ subunit from Paracoccus denitrificans ATP synthase is not sufficient to activate ATP hydrolysis. Open Biol 2018; 8:170206. [PMID: 29367351 PMCID: PMC5795051 DOI: 10.1098/rsob.170206] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/26/2017] [Indexed: 11/12/2022] Open
Abstract
In oxidative phosphorylation, ATP synthases interconvert two forms of free energy: they are driven by the proton-motive force across an energy-transducing membrane to synthesize ATP and displace the ADP/ATP ratio from equilibrium. For thermodynamically efficient energy conversion they must be reversible catalysts. However, in many species ATP synthases are unidirectional catalysts (their rates of ATP hydrolysis are negligible), and in others mechanisms have evolved to regulate or minimize hydrolysis. Unidirectional catalysis by Paracoccus denitrificans ATP synthase has been attributed to its unique ζ subunit, which is structurally analogous to the mammalian inhibitor protein IF1 Here, we used homologous recombination to delete the ζ subunit from the P. denitrificans genome, and compared ATP synthesis and hydrolysis by the wild-type and knockout enzymes in inverted membrane vesicles and the F1-ATPase subcomplex. ATP synthesis was not affected by loss of the ζ subunit, and the rate of ATP hydrolysis increased by less than twofold, remaining negligible in comparison with the rates of the Escherichia coli and mammalian enzymes. Therefore, deleting the P. denitrificans ζ subunit is not sufficient to activate ATP hydrolysis. We close by considering our conclusions in the light of reversible catalysis and regulation in ATP synthase enzymes.
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Affiliation(s)
- Febin Varghese
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - James N Blaza
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Andrew J Y Jones
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Owen D Jarman
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Judy Hirst
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
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30
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Zharova TV, Vinogradov AD. Functional heterogeneity of F o·F 1H +-ATPase/synthase in coupled Paracoccus denitrificans plasma membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:939-944. [PMID: 28803911 DOI: 10.1016/j.bbabio.2017.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/10/2017] [Accepted: 08/09/2017] [Indexed: 11/16/2022]
Abstract
Fo·F1H+-ATPase/synthase in coupled plasma membrane vesicles of Paracoccus denitrificans catalyzes ATP hydrolysis and/or ATP synthesis with comparable enzyme turnover. Significant difference in pH-profile of these alternative activities is seen: decreasing pH from 8.0 to 7.0 results in reversible inhibition of hydrolytic activity, whereas ATP synthesis activity is not changed. The inhibition of ATPase activity upon acidification results from neither change in ADP(Mg2+)-induced deactivation nor the energy-dependent enzyme activation. Vmax, not apparent KmATP is affected by lowering the pH. Venturicidin noncompetitively inhibits ATP synthesis and coupled ATP hydrolysis, showing significant difference in the affinity to its inhibitory site depending on the direction of the catalysis. This difference cannot be attributed to variations of the substrate-enzyme intermediates for steady-state forward and back reactions or to possible equilibrium between ATP hydrolase and ATP synthase Fo·F1 modes of the opposite directions of catalysis. The data are interpreted as to suggest that distinct non-equilibrated molecular isoforms of Fo·F1 ATP synthase and ATP hydrolase exist in coupled energy-transducing membranes.
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Affiliation(s)
- Tatyana V Zharova
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119234, Russian Federation
| | - Andrei D Vinogradov
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119234, Russian Federation.
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31
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Krah A, Kato-Yamada Y, Takada S. The structural basis of a high affinity ATP binding ε subunit from a bacterial ATP synthase. PLoS One 2017; 12:e0177907. [PMID: 28542497 PMCID: PMC5436830 DOI: 10.1371/journal.pone.0177907] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 05/04/2017] [Indexed: 01/09/2023] Open
Abstract
The ε subunit from bacterial ATP synthases functions as an ATP sensor, preventing ATPase activity when the ATP concentration in bacterial cells crosses a certain threshold. The R103A/R115A double mutant of the ε subunit from thermophilic Bacillus PS3 has been shown to bind ATP two orders of magnitude stronger than the wild type protein. We use molecular dynamics simulations and free energy calculations to derive the structural basis of the high affinity ATP binding to the R103A/R115A double mutant. Our results suggest that the double mutant is stabilized by an enhanced hydrogen-bond network and fewer repulsive contacts in the ligand binding site. The inferred structural basis of the high affinity mutant may help to design novel nucleotide sensors based on the ε subunit from bacterial ATP synthases.
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Affiliation(s)
- Alexander Krah
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, Japan
- School of Computational Sciences, Korea Institute for Advanced Study, Dongdaemun-gu, Seoul, Republic of Korea
- * E-mail:
| | - Yasuyuki Kato-Yamada
- Department of Life Science, College of Science, Rikkyo University, Nishi-Ikebukuro, Toshima-ku, Tokyo, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, Japan
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32
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Trypanosoma brucei TbIF1 inhibits the essential F1-ATPase in the infectious form of the parasite. PLoS Negl Trop Dis 2017; 11:e0005552. [PMID: 28414727 PMCID: PMC5407850 DOI: 10.1371/journal.pntd.0005552] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 04/27/2017] [Accepted: 04/04/2017] [Indexed: 12/01/2022] Open
Abstract
The mitochondrial (mt) FoF1-ATP synthase of the digenetic parasite, Trypanosoma brucei, generates ATP during the insect procyclic form (PF), but becomes a perpetual consumer of ATP in the mammalian bloodstream form (BF), which lacks a canonical respiratory chain. This unconventional dependence on FoF1-ATPase is required to maintain the essential mt membrane potential (Δψm). Normally, ATP hydrolysis by this rotary molecular motor is restricted to when eukaryotic cells experience sporadic hypoxic conditions, during which this compulsory function quickly depletes the cellular ATP pool. To protect against this cellular treason, the highly conserved inhibitory factor 1 (IF1) binds the enzyme in a manner that solely inhibits the hydrolytic activity. Intriguingly, we were able to identify the IF1 homolog in T. brucei (TbIF1), but determined that its expression in the mitochondrion is tightly regulated throughout the life cycle as it is only detected in PF cells. TbIF1 appears to primarily function as an emergency brake in PF cells, where it prevented the restoration of the Δψm by FoF1-ATPase when respiration was chemically inhibited. In vitro, TbIF1 overexpression specifically inhibits the hydrolytic activity but not the synthetic capability of the FoF1-ATP synthase in PF mitochondria. Furthermore, low μM amounts of recombinant TbIF1 achieve the same inhibition of total mt ATPase activity as the FoF1-ATPase specific inhibitors, azide and oligomycin. Therefore, even minimal ectopic expression of TbIF1 in BF cells proved lethal as the indispensable Δψm collapsed due to inhibited FoF1-ATPase. In summary, we provide evidence that T. brucei harbors a natural and potent unidirectional inhibitor of the vital FoF1-ATPase activity that can be exploited for future structure-based drug design. Enzymes are catalysts that drive both a forward and reverse chemical reaction depending on the thermodynamic properties. FoF1-ATP synthase is a multiprotein enzyme that under normal physiological conditions generates ATP. However, when respiration is impeded, this rotary molecular machine reverses and hydrolyzes ATP to pump protons and maintain the essential mitochondrial membrane potential. While this activity is exceptional in most eukaryotic cells, the unique composition of the Trypanosoma brucei mitochondrion dictates that the infectious stage of this human parasite is utterly dependent on the hydrolytic activity of FoF1-ATPase. While searching for better chemotherapeutics against Human African Trypanosomiasis, several trypanocidal compounds were determined to interact with this enzyme, but they indiscriminately inhibit both the ATP hydrolytic and synthetic activities. A more promising approach involves the conserved eukaryotic protein IF1, a unidirectional inhibitor that prevents just ATP hydrolysis. Auspiciously, we identified this protein homolog in T. brucei (TbIF1) and its expression is tightly regulated between life stages of the parasite. Importantly, the introduction of exogenous TbIF1 protein specifically inhibits FoF1-ATPase and is lethal for the infectious stage of T. brucei. Therefore, we have identified a natural inhibitor of an essential and druggable enzyme that can be exploited for future structure-based drug design.
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33
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Noji H, Ueno H, McMillan DGG. Catalytic robustness and torque generation of the F 1-ATPase. Biophys Rev 2017; 9:103-118. [PMID: 28424741 PMCID: PMC5380711 DOI: 10.1007/s12551-017-0262-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 03/13/2017] [Indexed: 12/28/2022] Open
Abstract
The F1-ATPase is the catalytic portion of the FoF1 ATP synthase and acts as a rotary molecular motor when it hydrolyzes ATP. Two decades have passed since the single-molecule rotation assay of F1-ATPase was established. Although several fundamental issues remain elusive, basic properties of F-type ATPases as motor proteins have been well characterized, and a large part of the reaction scheme has been revealed by the combination of extensive structural, biochemical, biophysical, and theoretical studies. This review is intended to provide a concise summary of the fundamental features of F1-ATPases, by use of the well-described model F1 from the thermophilic Bacillus PS3 (TF1). In the last part of this review, we focus on the robustness of the rotary catalysis of F1-ATPase to provide a perspective on the re-designing of novel molecular machines.
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Affiliation(s)
- Hiroyuki Noji
- 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
| | - Duncan G. G. McMillan
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo, 113-8656 Japan
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34
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AKUTSU H. Dynamic mechanisms driving conformational conversions of the β and ε subunits involved in rotational catalysis of F 1-ATPase. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2017; 93:630-647. [PMID: 29021512 PMCID: PMC5743862 DOI: 10.2183/pjab.93.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/16/2017] [Indexed: 05/26/2023]
Abstract
F-type ATPase is a ubiquitous molecular motor. Investigations on thermophilic F1-ATPase and its subunits, β and ε, by NMR were reviewed. Using specific isotope labeling, pKa of the putative catalytic carboxylate in β was estimated. Segmental isotope-labeling enabled us to monitor most residues of β, revealing that the conformational conversion from open to closed form of β on nucleotide binding found in ATPase was an intrinsic property of β and could work as a driving force of the rotational catalysis. A stepwise conformational change was driven by switching of the hydrogen bond networks involving Walker A and B motifs. Segmentally labeled ATPase provided a well resolved NMR spectra, revealing while the open form of β was identical for β monomer and ATPase, its closed form could be different. ATP-binding was also a critical factor in the conformational conversion of ε, an ATP hydrolysis inhibitor. Its structural elucidation was described.
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Affiliation(s)
- Hideo AKUTSU
- Institute for Protein Research, Osaka University, Osaka, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
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35
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D'Alessandro M, Turina P, Melandri BA, Dunn SD. Modulation of coupling in the Escherichia coli ATP synthase by ADP and P i: Role of the ε subunit C-terminal domain. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1858:34-44. [PMID: 27751906 DOI: 10.1016/j.bbabio.2016.10.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 08/06/2016] [Accepted: 10/13/2016] [Indexed: 01/28/2023]
Abstract
The ε-subunit of ATP-synthase is an endogenous inhibitor of the hydrolysis activity of the complex and its α-helical C-terminal domain (εCTD) undergoes drastic changes among at least two different conformations. Even though this domain is not essential for ATP synthesis activity, there is evidence for its involvement in the coupling mechanism of the pump. Recently, it was proposed that coupling of the ATP synthase can vary as a function of ADP and Pi concentration. In the present work, we have explored the possible role of the εCTD in this ADP- and Pi-dependent coupling, by examining an εCTD-lacking mutant of Escherichia coli. We show that the loss of Pi-dependent coupling can be observed also in the εCTD-less mutant, but the effects of Pi on both proton pumping and ATP hydrolysis were much weaker in the mutant than in the wild-type. We also show that the εCTD strongly influences the binding of ADP to a very tight binding site (half-maximal effect≈1nM); binding at this site induces higher coupling in EFOF1 and increases responses to Pi. It is proposed that one physiological role of the εCTD is to regulate the kinetics and affinity of ADP/Pi binding, promoting ADP/Pi-dependent coupling.
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Affiliation(s)
- M D'Alessandro
- Department of Biology, Laboratory of Biochemistry and Biophysics, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy
| | - P Turina
- Department of Biology, Laboratory of Biochemistry and Biophysics, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy.
| | - B A Melandri
- Department of Biology, Laboratory of Biochemistry and Biophysics, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy
| | - S D Dunn
- Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
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36
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Nakanishi-Matsui M, Sekiya M, Futai M. ATP synthase from Escherichia coli : Mechanism of rotational catalysis, and inhibition with the ε subunit and phytopolyphenols. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:129-140. [DOI: 10.1016/j.bbabio.2015.11.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/19/2015] [Accepted: 11/13/2015] [Indexed: 10/22/2022]
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37
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On the ATP binding site of the ε subunit from bacterial F-type ATP synthases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:332-40. [PMID: 26780667 DOI: 10.1016/j.bbabio.2016.01.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 12/11/2015] [Accepted: 01/14/2016] [Indexed: 11/20/2022]
Abstract
F-type ATP synthases are reversible machinery that not only synthesize adenosine triphosphate (ATP) using an electrochemical gradient across the membrane, but also can hydrolyze ATP to pump ions under certain conditions. To prevent wasteful ATP hydrolysis, subunit ε in bacterial ATP synthases changes its conformation from the non-inhibitory down- to the inhibitory up-state at a low cellular ATP concentration. Recently, a crystal structure of the ε subunit in complex with ATP was solved in a non-biologically relevant dimeric form. Here, to derive the functional ATP binding site motif, we carried out molecular dynamics simulations and free energy calculations. Our results suggest that the ATP binding site markedly differs from the experimental resolved one; we observe a reorientation of several residues, which bind to ATP in the crystal structure. In addition we find that an Mg(2+) ion is coordinated by ATP, replacing interactions of the second chain in the crystal structure. Thus we demonstrate more generally the influence of crystallization effects on ligand binding sites and their respective binding modes. Furthermore, we propose a role for two highly conserved residues to control the ATP binding/unbinding event, which have not been considered before. Additionally our results provide the basis for the rational development of new biosensors based on subunit ε, as shown previously for novel sensors measuring the ATP concentration in cells.
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38
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García-Trejo JJ, Zarco-Zavala M, Mendoza-Hoffmann F, Hernández-Luna E, Ortega R, Mendoza-Hernández G. The Inhibitory Mechanism of the ζ Subunit of the F1FO-ATPase Nanomotor of Paracoccus denitrificans and Related α-Proteobacteria. J Biol Chem 2016; 291:538-46. [PMID: 26546676 PMCID: PMC4705375 DOI: 10.1074/jbc.m115.688143] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 11/02/2015] [Indexed: 01/08/2023] Open
Abstract
The ζ subunit is a novel inhibitor of the F1FO-ATPase of Paracoccus denitrificans and related α-proteobacteria. It is different from the bacterial (ϵ) and mitochondrial (IF1) inhibitors. The N terminus of ζ blocks rotation of the γ subunit of the F1-ATPase of P. denitrificans (Zarco-Zavala, M., Morales-Ríos, E., Mendoza-Hernández, G., Ramírez-Silva, L., Pérez-Hernández, G., and García-Trejo, J. J. (2014) FASEB J. 24, 599-608) by a hitherto unknown quaternary structure that was first modeled here by structural homology and protein docking. The F1-ATPase and F1-ζ models of P. denitrificans were supported by cross-linking, limited proteolysis, mass spectrometry, and functional data. The final models show that ζ enters into F1-ATPase at the open catalytic αE/βE interface, and two partial γ rotations lock the N terminus of ζ in an "inhibition-general core region," blocking further γ rotation, while the ζ globular domain anchors it to the closed αDP/βDP interface. Heterologous inhibition of the F1-ATPase of P. denitrificans by the mitochondrial IF1 supported both the modeled ζ binding site at the αDP/βDP/γ interface and the endosymbiotic α-proteobacterial origin of mitochondria. In summary, the ζ subunit blocks the intrinsic rotation of the nanomotor by inserting its N-terminal inhibitory domain at the same rotor/stator interface where the mitochondrial IF1 or the bacterial ϵ binds. The proposed pawl mechanism is coupled to the rotation of the central γ subunit working as a ratchet but with structural differences that make it a unique control mechanism of the nanomotor to favor the ATP synthase activity over the ATPase turnover in the α-proteobacteria.
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Affiliation(s)
| | | | | | | | - Raquel Ortega
- From the Departamento de Biología, Facultad de Química, and
| | - Guillermo Mendoza-Hernández
- the Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, Delegación Coyoacán, D.F., CP 04510, México
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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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Linking structural features from mitochondrial and bacterial F-type ATP synthases to their distinct mechanisms of ATPase inhibition. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:94-102. [DOI: 10.1016/j.pbiomolbio.2015.06.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 06/25/2015] [Accepted: 06/26/2015] [Indexed: 01/11/2023]
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41
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On the Mg2+ binding site of the ε subunit from bacterial F-type ATP synthases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1101-12. [DOI: 10.1016/j.bbabio.2015.05.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 05/20/2015] [Accepted: 05/22/2015] [Indexed: 11/19/2022]
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Shah NB, Duncan TM. Aerobic Growth of Escherichia coli Is Reduced, and ATP Synthesis Is Selectively Inhibited when Five C-terminal Residues Are Deleted from the ϵ Subunit of ATP Synthase. J Biol Chem 2015; 290:21032-21041. [PMID: 26160173 PMCID: PMC4543661 DOI: 10.1074/jbc.m115.665059] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 06/19/2015] [Indexed: 11/06/2022] Open
Abstract
F-type ATP synthases are rotary nanomotor enzymes involved in cellular energy metabolism in eukaryotes and eubacteria. The ATP synthase from Gram-positive and -negative model bacteria can be autoinhibited by the C-terminal domain of its ϵ subunit (ϵCTD), but the importance of ϵ inhibition in vivo is unclear. Functional rotation is thought to be blocked by insertion of the latter half of the ϵCTD into the central cavity of the catalytic complex (F1). In the inhibited state of the Escherichia coli enzyme, the final segment of ϵCTD is deeply buried but has few specific interactions with other subunits. This region of the ϵCTD is variable or absent in other bacteria that exhibit strong ϵ-inhibition in vitro. Here, genetically deleting the last five residues of the ϵCTD (ϵΔ5) caused a greater defect in respiratory growth than did the complete absence of the ϵCTD. Isolated membranes with ϵΔ5 generated proton-motive force by respiration as effectively as with wild-type ϵ but showed a nearly 3-fold decrease in ATP synthesis rate. In contrast, the ϵΔ5 truncation did not change the intrinsic rate of ATP hydrolysis with membranes. Further, the ϵΔ5 subunit retained high affinity for isolated F1 but reduced the maximal inhibition of F1-ATPase by ϵ from >90% to ∼20%. The results suggest that the ϵCTD has distinct regulatory interactions with F1 when rotary catalysis operates in opposite directions for the hydrolysis or synthesis of ATP.
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Affiliation(s)
- Naman B Shah
- Department of Biochemistry and Molecular Biology, State University of New York, Upstate Medical University, Syracuse, New York 13210
| | - Thomas M Duncan
- Department of Biochemistry and Molecular Biology, State University of New York, Upstate Medical University, Syracuse, New York 13210.
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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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Xu T, Pagadala V, Mueller DM. Understanding structure, function, and mutations in the mitochondrial ATP synthase. MICROBIAL CELL 2015; 2:105-125. [PMID: 25938092 PMCID: PMC4415626 DOI: 10.15698/mic2015.04.197] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The mitochondrial ATP synthase is a multimeric enzyme complex with an overall molecular weight of about 600,000 Da. The ATP synthase is a molecular motor composed of two separable parts: F1 and Fo. The F1 portion contains the catalytic sites for ATP synthesis and protrudes into the mitochondrial matrix. Fo forms a proton turbine that is embedded in the inner membrane and connected to the rotor of F1. The flux of protons flowing down a potential gradient powers the rotation of the rotor driving the synthesis of ATP. Thus, the flow of protons though Fo is coupled to the synthesis of ATP. This review will discuss the structure/function relationship in the ATP synthase as determined by biochemical, crystallographic, and genetic studies. An emphasis will be placed on linking the structure/function relationship with understanding how disease causing mutations or putative single nucleotide polymorphisms (SNPs) in genes encoding the subunits of the ATP synthase, will affect the function of the enzyme and the health of the individual. The review will start by summarizing the current understanding of the subunit composition of the enzyme and the role of the subunits followed by a discussion on known mutations and their effect on the activity of the ATP synthase. The review will conclude with a summary of mutations in genes encoding subunits of the ATP synthase that are known to be responsible for human disease, and a brief discussion on SNPs.
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Affiliation(s)
- Ting Xu
- Department of Biochemistry and Molecular Biology, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago, IL 60064
| | - Vijayakanth Pagadala
- Department of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC
| | - David M Mueller
- Department of Biochemistry and Molecular Biology, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago, IL 60064
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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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Rodriguez AD, Dunn SD, Konermann L. ATP-induced dimerization of the F0F1 ε subunit from Bacillus PS3: a hydrogen exchange-mass spectrometry study. Biochemistry 2014; 53:4072-80. [PMID: 24870150 DOI: 10.1021/bi5004684] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
F0F1 ATP synthase harnesses a transmembrane electrochemical gradient for the production of ATP. When operated in reverse, this multiprotein complex catalyzes ATP hydrolysis. In bacteria, the ε subunit is involved in regulating this ATPase activity. Also, ε is essential for coupling ATP hydrolysis (or synthesis) to proton translocation. The ε subunit consists of a β sandwich and two C-terminal helices, α1 and α2. The protein can switch from a compact fold to an alternate conformation where α1 and α2 are separated, resulting in an extended structure. ε from the thermophile Bacillus PS3 (Tε) binds ATP with high affinity such that this protein may function as an intracellular ATP level sensor. ATP binding to isolated Tε triggers a major conformational transition. Earlier data were interpreted in terms of an ATP + Tεextended → ATP·Tεcompact transition that may mimic aspects of the regulatory switching within F0F1 (Yagi et al. (2007) Proc. Natl. Acad. Sci. U.S.A., 104, 11233–11238). In this work, we employ complementary biophysical techniques for examining the ATP-induced conformational switching of isolated Tε. CD spectroscopy confirmed the occurrence of a large-scale conformational transition upon ATP binding, consistent with the formation of stable helical structure. Hydrogen/deuterium exchange (HDX) mass spectrometry revealed that this transition is accompanied by a pronounced stabilization in the vicinity of the ATP-binding pocket. Surprisingly, dramatic stabilization is also seen in the β8−β9 region, which is remote from the site of ATP interaction. Analytical ultracentrifugation uncovered a previously unrecognized feature of Tε: a high propensity to undergo dimerization in the presence of ATP. Comparison with existing crystallography data strongly suggests that the unexpected β8−β9 HDX protection is due to newly formed protein–protein contacts. Hence, ATP binding to isolated Tε proceeds according to 2ATP + 2Tεextended → (ATP·Tεcompact)2. Implications of this dimerization propensity for the possible role of Tε as an antibiotic target are discussed.
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Nakanishi-Matsui M, Sekiya M, Yano S, Futai M. Inhibition of F1-ATPase rotational catalysis by the carboxyl-terminal domain of the ϵ subunit. J Biol Chem 2014; 289:30822-30831. [PMID: 25228697 DOI: 10.1074/jbc.m114.578872] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Escherichia coli ATP synthase (F0F1) couples catalysis and proton transport through subunit rotation. The ϵ subunit, an endogenous inhibitor, lowers F1-ATPase activity by decreasing the rotation speed and extending the duration of the inhibited state (Sekiya, M., Hosokawa, H., Nakanishi-Matsui, M., Al-Shawi, M. K., Nakamoto, R. K., and Futai, M. (2010) Single molecule behavior of inhibited and active states of Escherichia coli ATP synthase F1 rotation. J. Biol. Chem. 285, 42058-42067). In this study, we constructed a series of ϵ subunits truncated successively from the carboxyl-terminal domain (helix 1/loop 2/helix 2) and examined their effects on rotational catalysis (ATPase activity, average rotation rate, and duration of inhibited state). As expected, the ϵ subunit lacking helix 2 caused about ½-fold reduced inhibition, and that without loop 2/helix 2 or helix 1/loop 2/helix 2 showed a further reduced effect. Substitution of ϵSer(108) in loop 2 and ϵTyr(114) in helix 2, which possibly interact with the β and γ subunits, respectively, decreased the inhibitory effect. These results suggest that the carboxyl-terminal domain of the ϵ subunit plays a pivotal role in the inhibition of F1 rotation through interaction with other subunits.
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Affiliation(s)
- Mayumi Nakanishi-Matsui
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Iwate Medical University, Nishitokuta 2-1-1, Yahaba, Iwate 028-3694, Japan.
| | - Mizuki Sekiya
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Iwate Medical University, Nishitokuta 2-1-1, Yahaba, Iwate 028-3694, Japan
| | - Shio Yano
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Iwate Medical University, Nishitokuta 2-1-1, Yahaba, Iwate 028-3694, Japan
| | - Masamitsu Futai
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Iwate Medical University, Nishitokuta 2-1-1, Yahaba, Iwate 028-3694, Japan
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ATPase/synthase activity of Paracoccus denitrificans Fo·F1 as related to the respiratory control phenomenon. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1322-9. [PMID: 24732246 DOI: 10.1016/j.bbabio.2014.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 03/21/2014] [Accepted: 04/01/2014] [Indexed: 02/04/2023]
Abstract
The time course of ATP synthesis, oxygen consumption, and change in the membrane potential in Paracoccus denitrificans inside-out plasma membrane vesicles was traced. ATP synthesis initiated by the addition of a limited amount of either ADP or inorganic phosphate proceeded up to very low residual concentrations of the limiting substrate. Accumulated ATP did not decrease the rate of its synthesis initiated by the addition of ADP. The amount of residual ADP determined at State 4 respiration was independent of ten-fold variation of Pi or the presence of ATP. The pH-dependence of Km for Pi could not be fitted to a simple phosphoric acid dissociation curve. Partial inhibition of respiration resulted in a decrease in the rate of ATP synthesis without affecting the ATP/ADP reached at State 4. At pH8.0, hydrolysis of ATP accumulated at State 4 was induced by a low concentration of an uncoupler, whereas complete uncoupling results in rapid inactivation of ATPase. At pH7.0, no reversal of the ATP synthase reaction by the uncoupler was seen. The data show that ATP/ADP×Pi ratio maintained at State 4 is not in equilibrium with respiratory-generated driving force. Possible mechanisms of kinetic control and unidirectional operation of the Fo·F1-ATP synthase are discussed.
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Oka H, Hosokawa H, Nakanishi-Matsui M, Dunn SD, Futai M, Iwamoto-Kihara A. Elastic rotation of Escherichia coli FOF1 having ε subunit fused with cytochrome b562 or flavodoxin reductase. Biochem Biophys Res Commun 2014; 446:889-93. [DOI: 10.1016/j.bbrc.2014.03.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 03/05/2014] [Indexed: 10/25/2022]
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50
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Zarco-Zavala M, Morales-Ríos E, Mendoza-Hernández G, Ramírez-Silva L, Pérez-Hernández G, García-Trejo JJ. The ζ subunit of the F1FO-ATP synthase of α-proteobacteria controls rotation of the nanomotor with a different structure. FASEB J 2014; 28:2146-57. [PMID: 24522203 DOI: 10.1096/fj.13-241430] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The ζ subunit is a novel natural inhibitor of the α-proteobacterial F1FO-ATPase described originally in Paracoccus denitrificans. To characterize the mechanism by which this subunit inhibits the F1FO nanomotor, the ζ subunit of Paracoccus denitrificans (Pd-ζ) was analyzed by the combination of kinetic, biochemical, bioinformatic, proteomic, and structural approaches. The ζ subunit causes full inhibition of the sulfite-activated PdF1-ATPase with an apparent IC50 of 270 nM by a mechanism independent of the ε subunit. The inhibitory region of the ζ subunit resides in the first 14 N-terminal residues of the protein, which protrude from the 4-α-helix bundle structure of the isolated ζ subunit, as resolved by NMR. Cross-linking experiments show that the ζ subunit interacts with rotor (γ) and stator (α, β) subunits of the F1-ATPase, indicating that the ζ subunit hinders rotation of the central stalk. In addition, a putatively regulatory nucleotide-binding site was found in the ζ subunit by isothermal titration calorimetry. Together, the data show that the ζ subunit controls the rotation of F1FO-ATPase by a mechanism reminiscent of, but different from, those described for mitochondrial IF1 and bacterial ε subunits where the 4-α-helix bundle of ζ seems to work as an anchoring domain that orients the N-terminal inhibitory domain to hinder rotation of the central stalk.
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Affiliation(s)
- Mariel Zarco-Zavala
- 1Universidad Nacional Autónoma de México (UNAM), Facultad de Química, Departamento de Biología, Circuito Escolar, s/n, Laboratorio 206, Edificio F, Ciudad Universitaria, Coyoacán, CP 04510, México, DF.
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