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Sebők-Nagy K, Blastyák A, Juhász G, Páli T. Reversible binding of divalent cations to Ductin protein assemblies-A putative new regulatory mechanism of membrane traffic processes. Front Mol Biosci 2023; 10:1195010. [PMID: 37228584 PMCID: PMC10203432 DOI: 10.3389/fmolb.2023.1195010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023] Open
Abstract
Ductins are a family of homologous and structurally similar membrane proteins with 2 or 4 trans-membrane alpha-helices. The active forms of the Ductins are membranous ring- or star-shaped oligomeric assemblies and they provide various pore, channel, gap-junction functions, assist in membrane fusion processes and also serve as the rotor c-ring domain of V-and F-ATPases. All functions of the Ductins have been reported to be sensitive to the presence of certain divalent metal cations (Me2+), most frequently Cu2+ or Ca2+ ions, for most of the better known members of the family, and the mechanism of this effect is not yet known. Given that we have earlier found a prominent Me2+ binding site in a well-characterised Ductin protein, we hypothesise that certain divalent cations can structurally modulate the various functions of Ductin assemblies via affecting their stability by reversible non-covalent binding to them. A fine control of the stability of the assembly ranging from separated monomers through a loosely/weakly to tightly/strongly assembled ring might render precise regulation of Ductin functions possible. The putative role of direct binding of Me2+ to the c-ring subunit of active ATP hydrolase in autophagy and the mechanism of Ca2+-dependent formation of the mitochondrial permeability transition pore are also discussed.
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Affiliation(s)
- Krisztina Sebők-Nagy
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - András Blastyák
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Gábor Juhász
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Tibor Páli
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
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Sekiya M, Ikeda K, Yonai A, Ishikawa T, Shimoyama Y, Kodama Y, Sasaki M, Nakanishi-Matsui M. F-type proton-pumping atpase mediates acid tolerance in Streptococcus mutans. J Appl Microbiol 2023; 134:7117960. [PMID: 37055370 DOI: 10.1093/jambio/lxad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/01/2023] [Accepted: 04/12/2023] [Indexed: 04/15/2023]
Abstract
AIMS Streptococcus mutans is highly sensitive to inhibitors of proton-pumping F-type ATPase (F-ATPase) under acidic conditions. Herein, we investigated the role of S. mutans F-ATPase in acid tolerance using a bacterium expressing the F-ATPase β subunit at lower levels than the wild-type strain. METHODS AND RESULTS We generated a mutant S. mutans expressing the catalytic β subunit of F-ATPase at lower levels than the wild-type bacterium. The mutant cells exhibited a significantly slower growth rate at pH 5.30, whereas the rate was essentially the same as that of wild-type cells at pH 7.40. In addition, the colony-forming ability of the mutant was decreased at pH < 4.30, but not at pH 7.40. Thus, the growth rate and survival of S. mutans expressing low levels of the β subunit were reduced under acidic conditions. CONCLUSIONS Together with our previous observations, this study indicates that F-ATPase is involved in the acid tolerance mechanism of S. mutans by secreting protons from the cytoplasm.
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Affiliation(s)
- Mizuki Sekiya
- Division of Biochemistry, School of Pharmacy, Iwate Medical University, Yahaba, Iwate 028-3694, Japan
| | - Kazuya Ikeda
- Division of Biochemistry, School of Pharmacy, Iwate Medical University, Yahaba, Iwate 028-3694, Japan
| | - Ayaka Yonai
- Division of Biochemistry, School of Pharmacy, Iwate Medical University, Yahaba, Iwate 028-3694, Japan
| | - Taichi Ishikawa
- Division of Molecular Microbiology, School of Dentistry, Iwate Medical University, Yahaba, Iwate 028-3694, Japan
| | - Yu Shimoyama
- Division of Molecular Microbiology, School of Dentistry, Iwate Medical University, Yahaba, Iwate 028-3694, Japan
| | - Yoshitoyo Kodama
- Division of Molecular Microbiology, School of Dentistry, Iwate Medical University, Yahaba, Iwate 028-3694, Japan
| | - Minoru Sasaki
- Division of Molecular Microbiology, School of Dentistry, Iwate Medical University, Yahaba, Iwate 028-3694, Japan
| | - Mayumi Nakanishi-Matsui
- Division of Biochemistry, School of Pharmacy, Iwate Medical University, Yahaba, Iwate 028-3694, Japan
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Volkán-Kacsó S, Le LQ, Zhu K, Su H, Marcus RA. Method to extract multiple states in F 1-ATPase rotation experiments from jump distributions. Proc Natl Acad Sci U S A 2019; 116:25456-61. [PMID: 31776250 DOI: 10.1073/pnas.1915314116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A method is proposed for analyzing fast (10 μs) single-molecule rotation trajectories in F1 adenosinetriphosphatase ([Formula: see text]-ATPase). This method is based on the distribution of jumps in the rotation angle that occur in the transitions during the steps between subsequent catalytic dwells. The method is complementary to the "stalling" technique devised by H. Noji et al. [Biophys. Rev. 9, 103-118, 2017], and can reveal multiple states not directly detectable as steps. A bimodal distribution of jumps is observed at certain angles, due to the system being in either of 2 states at the same rotation angle. In this method, a multistate theory is used that takes into account a viscoelastic fluctuation of the imaging probe. Using an established sequence of 3 specific states, a theoretical profile of angular jumps is predicted, without adjustable parameters, that agrees with experiment for most of the angular range. Agreement can be achieved at all angles by assuming a fourth state with an ∼10 μs lifetime and a dwell angle about 40° after the adenosine 5'-triphosphate (ATP) binding dwell. The latter result suggests that the ATP binding in one β subunit and the adenosine 5'-diphosphate (ADP) release from another β subunit occur via a transient whose lifetime is ∼10 μs and is about 6 orders of magnitude smaller than the lifetime for ADP release from a singly occupied [Formula: see text]-ATPase. An internal consistency test is given by comparing 2 independent ways of obtaining the relaxation time of the probe. They agree and are ∼15 μs.
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Gahura O, Panicucci B, Váchová H, Walker JE, Zíková A. Inhibition of F 1 -ATPase from Trypanosoma brucei by its regulatory protein inhibitor TbIF 1. FEBS J 2018; 285:4413-4423. [PMID: 30288927 DOI: 10.1111/febs.14672] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/19/2018] [Accepted: 10/01/2018] [Indexed: 12/30/2022]
Abstract
Hydrolysis of ATP by the mitochondrial F-ATPase is inhibited by a protein called IF1 . In the parasitic flagellate, Trypanosoma brucei, this protein, known as TbIF1 , is expressed exclusively in the procyclic stage, where the F-ATPase is synthesizing ATP. In the bloodstream stage, where TbIF1 is absent, the F-ATPase hydrolyzes ATP made by glycolysis and compensates for the absence of a proton pumping respiratory chain by translocating protons into the intermembrane space, thereby maintaining the essential mitochondrial membrane potential. We have defined regions and amino acid residues of TbIF1 that are required for its inhibitory activity by analyzing the binding of several modified recombinant inhibitors to F1 -ATPase isolated from the procyclic stage of T. brucei. Kinetic measurements revealed that the C-terminal portion of TbIF1 facilitates homodimerization, but it is not required for the inhibitory activity, similar to the bovine and yeast orthologs. However, in contrast to bovine IF1 , the inhibitory capacity of the C-terminally truncated TbIF1 diminishes with decreasing pH, similar to full length TbIF1 . This effect does not involve the dimerization of active dimers to form inactive tetramers. Over a wide pH range, the full length and C-terminally truncated TbIF1 form dimers and monomers, respectively. TbIF1 has no effect on bovine F1 -ATPase, and this difference in the mechanism of regulation of the F-ATPase between the host and the parasite could be exploited in the design of drugs to combat human and animal African trypanosomiases.
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Affiliation(s)
- Ondřej Gahura
- Institute of Parasitology, Biology Centre Czech Academy of Science, České Budějovice, Czech Republic
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, UK
| | - Brian Panicucci
- Institute of Parasitology, Biology Centre Czech Academy of Science, České Budějovice, Czech Republic
| | - Hana Váchová
- Institute of Parasitology, Biology Centre Czech Academy of Science, České Budějovice, Czech Republic
| | - John E Walker
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, UK
| | - Alena Zíková
- Institute of Parasitology, Biology Centre Czech Academy of Science, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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Volkán-Kacsó S, Marcus RA. Theory of long binding events in single-molecule-controlled rotation experiments on F 1-ATPase. Proc Natl Acad Sci U S A 2017; 114:7272-7. [PMID: 28652332 DOI: 10.1073/pnas.1705960114] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The theory of elastic group transfer for the binding and release rate constants for nucleotides in F1-ATPase as a function of the rotor angle is further extended in several respects. (i) A method is described for predicting the experimentally observed lifetime distribution of long binding events in the controlled rotation experiments by taking into account the hydrolysis and synthesis reactions occurring during these events. (ii) A method is also given for treating the long binding events in the experiments and obtaining the rate constants for the hydrolysis and synthesis reactions occurring during these events. (iii) The theory in the previous paper is given in a symmetric form, an extension that simplifies the application of the theory to experiments. It also includes a theory-based correction of the reported "on" and "off" rates by calculating the missed events. A near symmetry of the data about the angle of -40° and a "turnover" in the binding rate data vs. rotor angle for angles greater than [Formula: see text]40° is also discussed.
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Gerle C. On the structural possibility of pore-forming mitochondrial FoF1 ATP synthase. Biochim Biophys Acta 2016; 1857:1191-1196. [PMID: 26968896 DOI: 10.1016/j.bbabio.2016.03.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 02/23/2016] [Accepted: 03/01/2016] [Indexed: 12/31/2022]
Abstract
The mitochondrial permeability transition is an inner mitochondrial membrane event involving the opening of the permeability transition pore concomitant with a sudden efflux of matrix solutes and breakdown of membrane potential. The mitochondrial F(o)F(1) ATP synthase has been proposed as the molecular identity of the permeability transition pore. The likeliness of potential pore-forming sites in the mitochondrial F(o)F(1) ATP synthase is discussed and a new model, the death finger model, is described. In this model, movement of a p-side density that connects the lipid-plug of the c-ring with the distal membrane bending Fo domain allows reversible opening of the c-ring and structural cross-talk with OSCP and the catalytic (αβ)(3) hexamer. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.
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Affiliation(s)
- Christoph Gerle
- Picobiology Institute, Department of Life Science, Graduate School of Life Science, University of Hyogo, Kamigori, Japan; Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kawaguchi, Japan.
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Yamato I, Kakinuma Y, Murata T. Operating principles of rotary molecular motors: differences between F 1 and V 1 motors. Biophys Physicobiol 2016; 13:37-44. [PMID: 27924256 PMCID: PMC5042177 DOI: 10.2142/biophysico.13.0_37] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/11/2016] [Indexed: 12/01/2022] Open
Abstract
Among the many types of bioenergy-transducing machineries, F- and V-ATPases are unique bio- and nano-molecular rotary motors. The rotational catalysis of F1-ATPase has been investigated in detail, and molecular mechanisms have been proposed based on the crystal structures of the complex and on extensive single-molecule rotational observations. Recently, we obtained crystal structures of bacterial V1-ATPase (A3B3 and A3B3DF complexes) in the presence and absence of nucleotides. Based on these new structures, we present a novel model for the rotational catalysis mechanism of V1-ATPase, which is different from that of F1-ATPases.
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Affiliation(s)
- Ichiro Yamato
- Department of Biological Science and Technology, Tokyo University of Science, Tokyo 125-8585, Japan
| | - Yoshimi Kakinuma
- Laboratory of Molecular Physiology and Genetics, Faculty of Agriculture, Ehime University, Matsuyama, Ehime 790-8566, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba 263-8522, Japan; Molecular Chirality Research Center, Chiba University, Chiba 263-8522, Japan; JST, PRESTO, Chiba 263-8522, Japan
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Morales-Ríos E, Montgomery MG, Leslie AGW, García-Trejo JJ, Walker JE. Structure of a catalytic dimer of the α- and β-subunits of the F-ATPase from Paracoccus denitrificans at 2.3 Å resolution. Acta Crystallogr F Struct Biol Commun 2015; 71:1309-17. [PMID: 26457523 PMCID: PMC4601596 DOI: 10.1107/s2053230x15016076] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 08/27/2015] [Indexed: 02/02/2023] Open
Abstract
The structures of F-ATPases have predominantly been determined from mitochondrial enzymes, and those of the enzymes in eubacteria have been less studied. Paracoccus denitrificans is a member of the α-proteobacteria and is related to the extinct protomitochondrion that became engulfed by the ancestor of eukaryotic cells. The P. denitrificans F-ATPase is an example of a eubacterial F-ATPase that can carry out ATP synthesis only, whereas many others can catalyse both the synthesis and the hydrolysis of ATP. Inhibition of the ATP hydrolytic activity of the P. denitrificans F-ATPase involves the ζ inhibitor protein, an α-helical protein that binds to the catalytic F1 domain of the enzyme. This domain is a complex of three α-subunits and three β-subunits, and one copy of each of the γ-, δ- and ℇ-subunits. Attempts to crystallize the F1-ζ inhibitor complex yielded crystals of a subcomplex of the catalytic domain containing the α- and β-subunits only. Its structure was determined to 2.3 Å resolution and consists of a heterodimer of one α-subunit and one β-subunit. It has no bound nucleotides, and it corresponds to the `open' or `empty' catalytic interface found in other F-ATPases. The main significance of this structure is that it aids in the determination of the structure of the intact membrane-bound F-ATPase, which has been crystallized.
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Affiliation(s)
- Edgar Morales-Ríos
- The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, England
| | - Martin G. Montgomery
- The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, England
| | - Andrew G. W. Leslie
- The Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, England
| | - José J. García-Trejo
- Departmento de Biología, Facultad Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - John E. Walker
- The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, England
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Morales-Rios E, Watt IN, Zhang Q, Ding S, Fearnley IM, Montgomery MG, Wakelam MJO, Walker JE. Purification, characterization and crystallization of the F-ATPase from Paracoccus denitrificans. Open Biol 2015; 5:150119. [PMID: 26423580 PMCID: PMC4593670 DOI: 10.1098/rsob.150119] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The structures of F-ATPases have been determined predominantly with mitochondrial enzymes, but hitherto no F-ATPase has been crystallized intact. A high-resolution model of the bovine enzyme built up from separate sub-structures determined by X-ray crystallography contains about 85% of the entire complex, but it lacks a crucial region that provides a transmembrane proton pathway involved in the generation of the rotary mechanism that drives the synthesis of ATP. Here the isolation, characterization and crystallization of an integral F-ATPase complex from the α-proteobacterium Paracoccus denitrificans are described. Unlike many eubacterial F-ATPases, which can both synthesize and hydrolyse ATP, the P. denitrificans enzyme can only carry out the synthetic reaction. The mechanism of inhibition of its ATP hydrolytic activity involves a ζ inhibitor protein, which binds to the catalytic F₁-domain of the enzyme. The complex that has been crystallized, and the crystals themselves, contain the nine core proteins of the complete F-ATPase complex plus the ζ inhibitor protein. The formation of crystals depends upon the presence of bound bacterial cardiolipin and phospholipid molecules; when they were removed, the complex failed to crystallize. The experiments open the way to an atomic structure of an F-ATPase complex.
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Affiliation(s)
- Edgar Morales-Rios
- The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Ian N. Watt
- The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | | | - Shujing Ding
- The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Ian M. Fearnley
- The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Martin G. Montgomery
- The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | | | - John E. Walker
- The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK,e-mail:
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Brandt K, Maiwald S, Herkenhoff-Hesselmann B, Gnirß K, Greie JC, Dunn SD, Deckers-Hebestreit G. Individual interactions of the b subunits within the stator of the Escherichia coli ATP synthase. J Biol Chem 2013; 288:24465-79. [PMID: 23846684 DOI: 10.1074/jbc.m113.465633] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
FOF1 ATP synthases are rotary nanomotors that couple proton translocation across biological membranes to the synthesis/hydrolysis of ATP. During catalysis, the peripheral stalk, composed of two b subunits and subunit δ in Escherichia coli, counteracts the torque generated by the rotation of the central stalk. Here we characterize individual interactions of the b subunits within the stator by use of monoclonal antibodies and nearest neighbor analyses via intersubunit disulfide bond formation. Antibody binding studies revealed that the C-terminal region of one of the two b subunits is principally involved in the binding of subunit δ, whereas the other one is accessible to antibody binding without impact on the function of FOF1. Individually substituted cysteine pairs suitable for disulfide cross-linking between the b subunits and the other stator subunits (b-α, b-β, b-δ, and b-a) were screened and combined with each other to discriminate between the two b subunits (i.e. bI and bII). The results show the b dimer to be located at a non-catalytic α/β cleft, with bI close to subunit α, whereas bII is proximal to subunit β. Furthermore, bI can be linked to subunit δ as well as to subunit a. Among the subcomplexes formed were a-bI-α, bII-β, α-bI-bII-β, and a-bI-δ. Taken together, the data obtained define the different positions of the two b subunits at a non-catalytic interface and imply that each b subunit has a different role in generating stability within the stator. We suggest that bI is functionally related to the single b subunit present in mitochondrial ATP synthase.
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Affiliation(s)
- Karsten Brandt
- Department of Microbiology, University of Osnabrück, 49069 Osnabrück, Germany
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