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Ahmad A, Akhtar J, Ahmad M, Khan MI, Wasim R, Islam A, Singh A. Bedaquiline: An Insight Into its Clinical Use in Multidrug-Resistant Pulmonary Tuberculosis. Drug Res (Stuttg) 2024; 74:269-279. [PMID: 38968950 DOI: 10.1055/a-2331-7061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2024]
Abstract
Every year, the World Health Organization reports 500,000 new cases of drug-resistant tuberculosis (TB), which poses a serious global danger. The increased number of XDR-TB and MDR-TB cases reported worldwide necessitates the use of new therapeutic approaches. The main issues with the antitubercular medications now in use for the treatment of multidrug-resistant tuberculosis are their poor side effect profile, reduced efficacy, and antimicrobial resistance. One possible remedy for these problems is bedaquiline. The need for better treatment strategies is highlighted by the strong minimum inhibitory concentrations that bedaquiline (BDQ), a novel anti-TB medicine, exhibits against both drug-resistant and drug-susceptible TB. Bedaquiline may be able to help with these problems. Bedaquiline is a medication that is first in its class and has a distinct and particular mode of action. Bedaquiline is an ATP synthase inhibitor that is specifically directed against Mycobacterium tuberculosis and some nontuberculous mycobacteria. It is metabolized by CYP3A4. Bedaquiline preclinical investigations revealed intralesional drug biodistribution. The precise intralesional and multi-compartment pharmacokinetics of bedaquiline were obtained using PET bioimaging and high-resolution autoradiography investigations. Reduced CFU counts were observed in another investigation after a 12-week course of therapy. Meta-analyses and systematic reviews of phase II trials on bedaquiline's efficacy in treating drug-resistant tuberculosis in patients reported higher rates of cure, better culture conversion, and lower death rates when taken in conjunction with a background regimen. Here is a thorough medication profile for bedaquiline to aid medical professionals in treating individuals with tuberculosis.
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Affiliation(s)
- Asad Ahmad
- Department of Pharmacy, Integral University, Lucknow, India
| | - Juber Akhtar
- Department of Pharmacy, Integral University, Lucknow, India
| | - Mohammad Ahmad
- Department of Pharmacy, Integral University, Lucknow, India
| | | | - Rufaida Wasim
- Department of Pharmacy, Integral University, Lucknow, India
| | - Anas Islam
- Department of Pharmacy, Integral University, Lucknow, India
| | - Aditya Singh
- Department of Pharmacy, Integral University, Lucknow, India
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2
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Shikanai T. Molecular Genetic Dissection of the Regulatory Network of Proton Motive Force in Chloroplasts. PLANT & CELL PHYSIOLOGY 2024; 65:537-550. [PMID: 38150384 DOI: 10.1093/pcp/pcad157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/27/2023] [Accepted: 12/08/2023] [Indexed: 12/29/2023]
Abstract
The proton motive force (pmf) generated across the thylakoid membrane rotates the Fo-ring of ATP synthase in chloroplasts. The pmf comprises two components: membrane potential (∆Ψ) and proton concentration gradient (∆pH). Acidification of the thylakoid lumen resulting from ∆pH downregulates electron transport in the cytochrome b6f complex. This process, known as photosynthetic control, is crucial for protecting photosystem I (PSI) from photodamage in response to fluctuating light. To optimize the balance between efficient photosynthesis and photoprotection, it is necessary to regulate pmf. Cyclic electron transport around PSI and pseudo-cyclic electron transport involving flavodiiron proteins contribute to the modulation of pmf magnitude. By manipulating the ratio between the two components of pmf, it is possible to modify the extent of photosynthetic control without affecting the pmf size. This adjustment can be achieved by regulating the movement of ions (such as K+ and Cl-) across the thylakoid membrane. Since ATP synthase is the primary consumer of pmf in chloroplasts, its activity must be precisely regulated to accommodate other mechanisms involved in pmf optimization. Although fragments of information about each regulatory process have been accumulated, a comprehensive understanding of their interactions is lacking. Here, I summarize current knowledge of the network for pmf regulation, mainly based on genetic studies.
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Affiliation(s)
- Toshiharu Shikanai
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, 606-8502 Japan
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3
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Kubo S, Okada Y. The ATPase asymmetry: Novel computational insight into coupling diverse F O motors with tripartite F 1. Biophys J 2024:S0006-3495(24)00178-4. [PMID: 38459696 DOI: 10.1016/j.bpj.2024.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/29/2024] [Accepted: 03/06/2024] [Indexed: 03/10/2024] Open
Abstract
ATP synthase, a crucial enzyme for cellular bioenergetics, operates via the coordinated coupling of an FO motor, which presents variable symmetry, and a tripartite F1 motor. Despite extensive research, the understanding of their coupling dynamics, especially with non-10-fold symmetrical FO motors, remains incomplete. This study investigates the coupling patterns between eightfold and ninefold FO motors and the constant threefold F1 motor using coarse-grained molecular dynamics simulations. We unveil that in the case of a ninefold FO motor, a 3-3-3 motion is most likely to occur, whereas a 3-3-2 motion predominates with an eightfold FO motor. Furthermore, our findings propose a revised model for the coupling method, elucidating that the pathways' energy usage is primarily influenced by F1 rotation and conformational changes hindered by the b-subunits. Our results present a crucial step toward comprehending the energy landscape and mechanisms governing ATP synthase operation.
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Affiliation(s)
- Shintaroh Kubo
- Department of Cell Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Yasushi Okada
- Department of Cell Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Physics, Graduate School of Science, The University of Tokyo, Tokyo, Japan; Universal Biology Institute and International Research Center for Neurointelligence, The University of Tokyo, Tokyo, Japan; Laboratory for Cell Polarity Regulation, Center for Biosystems Dynamics Research (BDR), RIKEN, Osaka, Japan
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4
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Singh R, Manna S, Nandanwar H, Purohit R. Bioactives from medicinal herb against bedaquiline resistant tuberculosis: removing the dark clouds from the horizon. Microbes Infect 2024; 26:105279. [PMID: 38128751 DOI: 10.1016/j.micinf.2023.105279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023]
Abstract
Tuberculosis is a contagious bacterial ailment that primarily affects the lungs and is brought on by the bacterium Mycobacterium tuberculosis (MTB). An antimycobacterial medication called bedaquiline (BQ) is specified to treat multidrug-resistant tuberculosis (MDR-TB). Despite its contemporary use in clinical practice, the mutations (D32 A/G/N/V/P) constrain the potential of BQ by causing transitions in the structural conformation of the atpE subunit-c after binding. In this study, we have taken the benzylisoquinoline alkaloids from thalictrum foliolosum due to its antimicrobial activity reported in prior literature. We used an efficient and optimized structure-based strategy to examine the wild type (WT) and mutated protein upon molecule binding. Our results emphasize the drastic decline in BQ binding affinity of mutant and WT atpE subunit-c complexes compared to thalirugidine (top hit) from thalictrum foliolosum. The decrease in BQ binding free energy is due to electrostatic energy because nearly every atom in a macromolecule harbors a partial charge, and molecules taking part in molecular recognition will interact electrostatically. Similarly, the high potential mean force of thalirugidine than BQ in WT and mutant complexes demonstrated the remarkable ability to eradicate mycobacteria efficiently. Furthermore, the Alamar blue cell viability and ATP determination assay were performed to validate the computational outcomes in search of novel antimycobacterial. Upon closer examination of the ATP determination assay, it became apparent that both BQ and thalirugidine showed similar reductions in ATP levels at their respective MICs, presenting a potential common mechanism of action.
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Affiliation(s)
- Rahul Singh
- Structural Bioinformatics Lab, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Souvik Manna
- CSIR-Institute of Microbial Technology, Sector-39, Chandigarh, 160036, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Hemraj Nandanwar
- CSIR-Institute of Microbial Technology, Sector-39, Chandigarh, 160036, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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5
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Fiebig A, Schnizlein MK, Pena-Rivera S, Trigodet F, Dubey AA, Hennessy MK, Basu A, Pott S, Dalal S, Rubin D, Sogin ML, Eren AM, Chang EB, Crosson S. Bile acid fitness determinants of a Bacteroides fragilis isolate from a human pouchitis patient. mBio 2024; 15:e0283023. [PMID: 38063424 PMCID: PMC10790697 DOI: 10.1128/mbio.02830-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 12/19/2023] Open
Abstract
IMPORTANCE The Gram-negative bacterium Bacteroides fragilis is a common member of the human gut microbiota that colonizes multiple host niches and can influence human physiology through a variety of mechanisms. Identification of genes that enable B. fragilis to grow across a range of host environments has been impeded in part by the relatively limited genetic tractability of this species. We have developed a high-throughput genetic resource for a B. fragilis strain isolated from a UC pouchitis patient. Bile acids limit microbial growth and are altered in abundance in UC pouches, where B. fragilis often blooms. Using this resource, we uncovered pathways and processes that impact B. fragilis fitness in bile and that may contribute to population expansions during bouts of gut inflammation.
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Affiliation(s)
- Aretha Fiebig
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Matthew K. Schnizlein
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Selymar Pena-Rivera
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Florian Trigodet
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
- Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, Oldenburg, Germany
| | - Abhishek Anil Dubey
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Miette K. Hennessy
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Anindita Basu
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Sebastian Pott
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Sushila Dalal
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - David Rubin
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | | | - A. Murat Eren
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
- Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, Oldenburg, Germany
| | - Eugene B. Chang
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Sean Crosson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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6
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Fiebig A, Schnizlein MK, Pena-Rivera S, Trigodet F, Dubey AA, Hennessy M, Basu A, Pott S, Dalal S, Rubin D, Sogin ML, Murat Eren A, Chang EB, Crosson S. Bile acid fitness determinants of a Bacteroides fragilis isolate from a human pouchitis patient. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540287. [PMID: 37214927 PMCID: PMC10197588 DOI: 10.1101/2023.05.11.540287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Bacteroides fragilis comprises 1-5% of the gut microbiota in healthy humans but can expand to >50% of the population in ulcerative colitis (UC) patients experiencing inflammation. The mechanisms underlying such microbial blooms are poorly understood, but the gut of UC patients has physicochemical features that differ from healthy patients and likely impact microbial physiology. For example, levels of the secondary bile acid deoxycholate (DC) are highly reduced in the ileoanal J-pouch of UC colectomy patients. We isolated a B. fragilis strain from a UC patient with pouch inflammation (i.e. pouchitis) and developed it as a genetic model system to identify genes and pathways that are regulated by DC and that impact B. fragilis fitness in DC and crude bile. Treatment of B. fragilis with a physiologically relevant concentration of DC reduced cell growth and remodeled transcription of one-quarter of the genome. DC strongly induced expression of chaperones and select transcriptional regulators and efflux systems and downregulated protein synthesis genes. Using a barcoded collection of ≈50,000 unique insertional mutants, we further defined B. fragilis genes that contribute to fitness in media containing DC or crude bile. Genes impacting cell envelope functions including cardiolipin synthesis, cell surface glycosylation, and systems implicated in sodium-dependent bioenergetics were major bile acid fitness factors. As expected, there was limited overlap between transcriptionally regulated genes and genes that impacted fitness in bile when disrupted. Our study provides a genome-scale view of a B. fragilis bile response and genetic determinants of its fitness in DC and crude bile.
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Affiliation(s)
- Aretha Fiebig
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Matthew K. Schnizlein
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Selymar Pena-Rivera
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Florian Trigodet
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, Oldenburg, Germany
| | - Abhishek Anil Dubey
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Miette Hennessy
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Anindita Basu
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sebastian Pott
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sushila Dalal
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - David Rubin
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | | | - A. Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, Oldenburg, Germany
| | - Eugene B. Chang
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sean Crosson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
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7
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Ravin NV, Muntyan MS, Smolyakov DD, Rudenko TS, Beletsky AV, Mardanov AV, Grabovich MY. Metagenomics Revealed a New Genus ' Candidatus Thiocaldithrix dubininis' gen. nov., sp. nov. and a New Species ' Candidatus Thiothrix putei' sp. nov. in the Family Thiotrichaceae, Some Members of Which Have Traits of Both Na +- and H +-Motive Energetics. Int J Mol Sci 2023; 24:14199. [PMID: 37762502 PMCID: PMC10532065 DOI: 10.3390/ijms241814199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Two metagenome-assembled genomes (MAGs), GKL-01 and GKL-02, related to the family Thiotrichaceae have been assembled from the metagenome of bacterial mat obtained from a sulfide-rich thermal spring in the North Caucasus. Based on average amino acid identity (AAI) values and genome-based phylogeny, MAG GKL-01 represented a new genus within the Thiotrichaceae family. The GC content of the GKL-01 DNA (44%) differed significantly from that of other known members of the genus Thiothrix (50.1-55.6%). We proposed to assign GKL-01 to a new species and genus 'Candidatus Thiocaldithrix dubininis' gen. nov., sp. nov. GKL-01. The phylogenetic analysis and estimated distances between MAG GKL-02 and the genomes of the previously described species of the genus Thiothrix allowed assigning GKL-02 to a new species with the proposed name 'Candidatus Thiothrix putei' sp. nov. GKL-02 within the genus Thiothrix. Genome data first revealed the presence of both Na+-ATPases and H+-ATPases in several Thiothrix species. According to genomic analysis, bacteria GKL-01 and GKL-02 are metabolically versatile facultative aerobes capable of growing either chemolithoautotrophically or chemolithoheterotrophically in the presence of hydrogen sulfide and/or thiosulfate or chemoorganoheterotrophically.
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Affiliation(s)
- Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prospect, 33-2, 119071 Moscow, Russia; (N.V.R.); (A.V.B.); (A.V.M.)
| | - Maria S. Muntyan
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia
| | - Dmitry D. Smolyakov
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (D.D.S.); (T.S.R.)
| | - Tatyana S. Rudenko
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (D.D.S.); (T.S.R.)
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prospect, 33-2, 119071 Moscow, Russia; (N.V.R.); (A.V.B.); (A.V.M.)
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prospect, 33-2, 119071 Moscow, Russia; (N.V.R.); (A.V.B.); (A.V.M.)
| | - Margarita Yu. Grabovich
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (D.D.S.); (T.S.R.)
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8
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Kubo S, Niina T, Takada S. F O-F 1 coupling and symmetry mismatch in ATP synthase resolved in every F O rotation step. Biophys J 2023; 122:2898-2909. [PMID: 36171725 PMCID: PMC10397808 DOI: 10.1016/j.bpj.2022.09.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/18/2022] [Accepted: 09/26/2022] [Indexed: 11/19/2022] Open
Abstract
FOF1 ATP synthase, a ubiquitous enzyme that synthesizes most ATP in living cells, is composed of two rotary motors: a membrane-embedded proton-driven FO motor and a catalytic F1 motor. These motors share both central and peripheral stalks. Although both FO and F1 have pseudo-symmetric structures, their symmetries do not match. How symmetry mismatch is solved remains elusive because of the missing intermediate structures of the rotational steps. Here, for the case of Bacillus PS3 ATP synthases with three- and 10-fold symmetries in F1 and FO, respectively, we uncovered the mechanical couplings between FO and F1 at every 36° rotation step via molecular dynamics simulations and comparative studies of cryoelectron microscopy (cryo-EM) structures from three species. We found that the mismatch could be solved using several elements: 1) the F1 head partially rotates relative to the FO a subunit via elastic distortion of the b subunits, 2) the rotor is twisted, and 3) comparisons of cryo-EM structures further suggest that the c ring rotary angles can deviate from the symmetric ones. In addition, the F1 motor may have non-canonical structures, relieving stronger frustration. Thus, we provide new insights for solving the symmetry mismatch problem.
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Affiliation(s)
- Shintaroh Kubo
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan; Department of Anatomy and Cell Biology, McGill University, Montréal, Québec H3A 0C7, Canada.
| | - Toru Niina
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
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9
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Yamamoto H, Cheuk A, Shearman J, Nixon PJ, Meier T, Shikanai T. Impact of engineering the ATP synthase rotor ring on photosynthesis in tobacco chloroplasts. PLANT PHYSIOLOGY 2023; 192:1221-1233. [PMID: 36703219 PMCID: PMC10231360 DOI: 10.1093/plphys/kiad043] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 06/01/2023]
Abstract
The chloroplast ATP synthase produces the ATP needed for photosynthesis and plant growth. The trans-membrane flow of protons through the ATP synthase rotates an oligomeric assembly of c subunits, the c-ring. The ion-to-ATP ratio in rotary F1F0-ATP synthases is defined by the number of c-subunits in the rotor c-ring. Engineering the c-ring stoichiometry is, therefore, a possible route to manipulate ATP synthesis by the ATP synthase and hence photosynthetic efficiency in plants. Here, we describe the construction of a tobacco (Nicotiana tabacum) chloroplast atpH (chloroplastic ATP synthase subunit c gene) mutant in which the c-ring stoichiometry was increased from 14 to 15 c-subunits. Although the abundance of the ATP synthase was decreased to 25% of wild-type (WT) levels, the mutant lines grew as well as WT plants and photosynthetic electron transport remained unaffected. To synthesize the necessary ATP for growth, we found that the contribution of the membrane potential to the proton motive force was enhanced to ensure a higher proton flux via the c15-ring without unwanted low pH-induced feedback inhibition of electron transport. Our work opens avenues to manipulate plant ion-to-ATP ratios with potentially beneficial consequences for photosynthesis.
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Affiliation(s)
- Hiroshi Yamamoto
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Anthony Cheuk
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK
| | - Julia Shearman
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK
| | - Peter J Nixon
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK
| | - Thomas Meier
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK
| | - Toshiharu Shikanai
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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10
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Mackieh R, Al-Bakkar N, Kfoury M, Roufayel R, Sabatier JM, Fajloun Z. Inhibitors of ATP Synthase as New Antibacterial Candidates. Antibiotics (Basel) 2023; 12:antibiotics12040650. [PMID: 37107012 PMCID: PMC10135114 DOI: 10.3390/antibiotics12040650] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
ATP, the power of all cellular functions, is constantly used and produced by cells. The enzyme called ATP synthase is the energy factory in all cells, which produces ATP by adding inorganic phosphate (Pi) to ADP. It is found in the inner, thylakoid and plasma membranes of mitochondria, chloroplasts and bacteria, respectively. Bacterial ATP synthases have been the subject of multiple studies for decades, since they can be genetically manipulated. With the emergence of antibiotic resistance, many combinations of antibiotics with other compounds that enhance the effect of these antibiotics have been proposed as approaches to limit the spread of antibiotic-resistant bacteria. ATP synthase inhibitors, such as resveratrol, venturicidin A, bedaquiline, tomatidine, piceatannol, oligomycin A and N,N-dicyclohexylcarbodiimide were the starting point of these combinations. However, each of these inhibitors target ATP synthase differently, and their co-administration with antibiotics increases the susceptibility of pathogenic bacteria. After a brief description of the structure and function of ATP synthase, we aim in this review to highlight therapeutic applications of the major bacterial ATP synthase inhibitors, including animal’s venoms, and to emphasize their importance in decreasing the activity of this enzyme and subsequently eradicating resistant bacteria as ATP synthase is their source of energy.
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11
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Akutsu H. Strategies for elucidation of the structure and function of the large membrane protein complex, F oF 1-ATP synthase, by nuclear magnetic resonance. Biophys Chem 2023; 296:106988. [PMID: 36898347 DOI: 10.1016/j.bpc.2023.106988] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/26/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023]
Abstract
Nuclear magnetic resonance (NMR) investigation of large membrane proteins requires well-focused questions and critical techniques. Here, research strategies for FoF1-ATP synthase, a membrane-embedded molecular motor, are reviewed, focusing on the β-subunit of F1-ATPase and c-subunit ring of the enzyme. Segmental isotope-labeling provided 89% assignment of the main chain NMR signals of thermophilic Bacillus (T)F1β-monomer. Upon nucleotide binding to Lys164, Asp252 was shown to switch its hydrogen-bonding partner from Lys164 to Thr165, inducing an open-to-closed bend motion of TF1β-subunit. This drives the rotational catalysis. The c-ring structure determined by solid-state NMR showed that cGlu56 and cAsn23 of the active site took a hydrogen-bonded closed conformation in membranes. In 505 kDa TFoF1, the specifically isotope-labeled cGlu56 and cAsn23 provided well-resolved NMR signals, which revealed that 87% of the residue pairs took a deprotonated open conformation at the Foa-c subunit interface, whereas they were in the closed conformation in the lipid-enclosed region.
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Affiliation(s)
- Hideo Akutsu
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan.
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12
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Nesci S. Bacterial and mammalian F1FO-ATPase: Structural similarities and divergences to exploit in the battle against Mycobacterium tuberculosis. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023. [DOI: 10.1016/bs.ircmb.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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13
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Nath S. The Need for Consistency with Physical Laws and Logic in Choosing Between Competing Molecular Mechanisms in Biological Processes: A Case Study in Modeling ATP Synthesis. FUNCTION (OXFORD, ENGLAND) 2022; 3:zqac054. [PMID: 36340246 PMCID: PMC9629475 DOI: 10.1093/function/zqac054] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 11/05/2022]
Abstract
Traditionally, proposed molecular mechanisms of fundamental biological processes have been tested against experiment. However, owing to a plethora of reasons-difficulty in designing, carrying out, and interpreting key experiments, use of different experimental models and systems, conduct of studies under widely varying experimental conditions, fineness in distinctions between competing mechanisms, complexity of the scientific issues, and the resistance of some scientists to discoveries that are contrary to popularly held beliefs-this has not solved the problem despite decades of work in the field/s. The author would like to prescribe an alternative way: that of testing competing models/mechanisms for their adherence to scientific laws and principles, and checking for errors in logic. Such tests are fairly commonly carried out in the mathematics, physics, and engineering literature. Further, reported experimental measurements should not be smaller than minimum detectable values for the measurement technique employed and should truly reflect function of the actual system without inapplicable extrapolation. Progress in the biological fields would be greatly accelerated, and considerable scientific acrimony avoided by adopting this approach. Some examples from the fundamental field of ATP synthesis in oxidative phosphorylation (OXPHOS) have been reviewed that also serve to illustrate the approach. The approach has never let the author down in his 35-yr-long experience on biological mechanisms. This change in thinking should lead to a considerable saving of both time and resources, help channel research efforts toward solution of the right problems, and hopefully provide new vistas to a younger generation of open-minded biological scientists.
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Affiliation(s)
- Sunil Nath
- Address correspondence to S.N. (e-mail: ; )
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14
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Marshansky V. Discovery and Study of Transmembrane Rotary Ion-Translocating Nano-Motors: F-ATPase/Synthase of Mitochondria/Bacteria and V-ATPase of Eukaryotic Cells. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:702-719. [PMID: 36171652 DOI: 10.1134/s000629792208003x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 06/16/2023]
Abstract
This review discusses the history of discovery and study of the operation of the two rotary ion-translocating ATPase nano-motors: (i) F-ATPase/synthase (holocomplex F1FO) of mitochondria/bacteria and (ii) eukaryotic V-ATPase (holocomplex V1VO). Vacuolar adenosine triphosphatase (V-ATPase) is a transmembrane multisubunit complex found in all eukaryotes from yeast to humans. It is structurally and functionally similar to the F-ATPase/synthase of mitochondria/bacteria and the A-ATPase/synthase of archaebacteria, which indicates a common evolutionary origin of the rotary ion-translocating nano-motors built into cell membranes and invented by Nature billions of years ago. Previously we have published several reviews on this topic with appropriate citations of our original research. This review is focused on the historical analysis of the discovery and study of transmembrane rotary ion-translocating ATPase nano-motors functioning in bacteria, eukaryotic cells and mitochondria of animals.
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15
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Todokoro Y, Kang SJ, Suzuki T, Ikegami T, Kainosho M, Yoshida M, Fujiwara T, Akutsu H. Chemical Conformation of the Essential Glutamate Site of the c-Ring within Thermophilic Bacillus F oF 1-ATP Synthase Determined by Solid-State NMR Based on its Isolated c-Ring Structure. J Am Chem Soc 2022; 144:14132-14139. [PMID: 35905443 DOI: 10.1021/jacs.2c03580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proton translocation through the membrane-embedded Fo component of F-type ATP synthase (FoF1) is facilitated by the rotation of the Fo c-subunit ring (c-ring), carrying protons at essential acidic amino acid residues. Cryo-electron microscopy (Cryo-EM) structures of FoF1 suggest a unique proton translocation mechanism. To elucidate it based on the chemical conformation of the essential acidic residues of the c-ring in FoF1, we determined the structure of the isolated thermophilic Bacillus Fo (tFo) c-ring, consisting of 10 subunits, in membranes by solid-state NMR. This structure contains a distinct proton-locking conformation, wherein Asn23 (cN23) CγO and Glu56 (cE56) CδOH form a hydrogen bond in a closed form. We introduced stereo-array-isotope-labeled (SAIL) Glu and Asn into the tFoc-ring to clarify the chemical conformation of these residues in tFoF1-ATP synthase (tFoF1). Two well-separated 13C signals could be detected for cN23 and cE56 in a 505 kDa membrane protein complex, respectively, thereby suggesting the presence of two distinct chemical conformations. Based on the signal intensity and structure of the tFoc-ring and tFoF1, six pairs of cN23 and cE56 surrounded by membrane lipids take the closed form, whereas the other four in the a-c interface employ the deprotonated open form at a proportion of 87%. This indicates that the a-c interface is highly hydrophilic. The pKa values of the four cE56 residues in the a-c interface were estimated from the cN23 signal intensity in the open and closed forms and distribution of polar residues around each cE56. The results favor a rotation of the c-ring for ATP synthesis.
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Affiliation(s)
- Yasuto Todokoro
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan.,Technical Support Division, School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka 560-0043, Japan
| | - Su-Jin Kang
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan.,Department of Biophysics and Chemical Biology, Seoul National University, Gwanak-Gu, Seoul 151-742, Republic of Korea.,College of Pharmacy, Dongduk Women's University, Seoul 02748, Republic of Korea
| | - Toshiharu Suzuki
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama 226-0026, Japan
| | - Takahisa Ikegami
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Masatsune Kainosho
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Masasuke Yoshida
- Department of Molecular Bioscience, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto 603-8555, Japan
| | - Toshimichi Fujiwara
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan
| | - Hideo Akutsu
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan.,Department of Biophysics and Chemical Biology, Seoul National University, Gwanak-Gu, Seoul 151-742, Republic of Korea.,Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
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16
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Meier-Credo J, Preiss L, Wüllenweber I, Resemann A, Nordmann C, Zabret J, Suckau D, Michel H, Nowaczyk MM, Meier T, Langer JD. Top-Down Identification and Sequence Analysis of Small Membrane Proteins Using MALDI-MS/MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1293-1302. [PMID: 35758524 PMCID: PMC9264385 DOI: 10.1021/jasms.2c00102] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Identification and sequence determination by mass spectrometry have become routine analyses for soluble proteins. Membrane proteins, however, remain challenging targets due to their hydrophobicity and poor annotation. In particular small membrane proteins often remain unnoticed as they are largely inaccessible to Bottom-Up proteomics. Recent advances in structural biology, though, have led to multiple membrane protein complex structures being determined at sufficiently high resolution to detect uncharacterized, small subunits. In this work we offer a guide for the mass spectrometric characterization of solvent extraction-based purifications of small membrane proteins isolated from protein complexes and cellular membranes. We first demonstrate our Top-Down MALDI-MS/MS approach on a Photosystem II preparation, analyzing target protein masses between 2.5 and 9 kDa with high accuracy and sensitivity. Then we apply our technique to purify and sequence the mycobacterial ATP synthase c subunit, the molecular target of the antibiotic drug bedaquiline. We show that our approach can be used to directly track and pinpoint single amino acid mutations that lead to antibiotic resistance in only 4 h. While not applicable as a high-throughput pipeline, our MALDI-MS/MS and ISD-based approach can identify and provide valuable sequence information on small membrane proteins, which are inaccessible to conventional Bottom-Up techniques. We show that our approach can be used to unambiguously identify single-point mutations leading to antibiotic resistance in mycobacteria.
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Affiliation(s)
- Jakob Meier-Credo
- Proteomics, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
- Proteomics, Max
Planck Institute for Brain Research, Max-von-Laue-Strasse 4, 60438 Frankfurt am Main, Germany
| | - Laura Preiss
- Structural
Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
| | - Imke Wüllenweber
- Proteomics, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
- Proteomics, Max
Planck Institute for Brain Research, Max-von-Laue-Strasse 4, 60438 Frankfurt am Main, Germany
| | - Anja Resemann
- Bruker
Daltonics GmbH & Co. KG, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | - Christoph Nordmann
- Bruker
Daltonics GmbH & Co. KG, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | - Jure Zabret
- Department
of Plant Biochemistry, Ruhr University Bochum, 44780 Bochum, Germany
| | - Detlev Suckau
- Bruker
Daltonics GmbH & Co. KG, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | - Hartmut Michel
- Molecular
Membrane Biology, Max Planck Institute of
Biophysics, Max-von-Laue-Strasse
3, 60438 Frankfurt
am Main, Germany
| | - Marc M. Nowaczyk
- Department
of Plant Biochemistry, Ruhr University Bochum, 44780 Bochum, Germany
| | - Thomas Meier
- Department
of Life Sciences, Imperial College London, Exhibition Road, SW7 2AZ London, United Kingdom
| | - Julian D. Langer
- Proteomics, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
- Proteomics, Max
Planck Institute for Brain Research, Max-von-Laue-Strasse 4, 60438 Frankfurt am Main, Germany
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17
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Kühlbrandt W. Forty years in cryoEM of membrane proteins. Microscopy (Oxf) 2022; 71:i30-i50. [PMID: 35275191 PMCID: PMC8855526 DOI: 10.1093/jmicro/dfab041] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 10/05/2021] [Accepted: 11/10/2021] [Indexed: 12/13/2022] Open
Abstract
In a surprisingly short time, electron cryo-microscopy (cryoEM) has developed from a niche technique in structural biology to a mainstream method practiced in a rapidly growing number of laboratories around the world. From its beginnings about 40 years ago, cryoEM has had a major impact on the study of membrane proteins, in particular the energy-converting systems from bacterial, mitochondrial and chloroplast membranes. Early work on two-dimensional crystals attained resolutions ∼3.5 Å, but at present, single-particle cryoEM delivers much more detailed structures without crystals. Electron cryo-tomography of membranes and membrane-associated proteins adds valuable context, usually at lower resolution. The review ends with a brief outlook on future prospects.
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Affiliation(s)
- Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, Frankfurt am Main 60438, Germany
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18
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Mitome N, Kubo S, Ohta S, Takashima H, Shigefuji Y, Niina T, Takada S. Cooperation among c-subunits of F oF 1-ATP synthase in rotation-coupled proton translocation. eLife 2022; 11:69096. [PMID: 35107420 PMCID: PMC8809890 DOI: 10.7554/elife.69096] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 12/21/2021] [Indexed: 01/23/2023] Open
Abstract
In FoF1-ATP synthase, proton translocation through Fo drives rotation of the c-subunit oligomeric ring relative to the a-subunit. Recent studies suggest that in each step of the rotation, key glutamic acid residues in different c-subunits contribute to proton release to and proton uptake from the a-subunit. However, no studies have demonstrated cooperativity among c-subunits toward FoF1-ATP synthase activity. Here, we addressed this using Bacillus PS3 ATP synthase harboring a c-ring with various combinations of wild-type and cE56D, enabled by genetically fused single-chain c-ring. ATP synthesis and proton pump activities were decreased by a single cE56D mutation and further decreased by double cE56D mutations. Moreover, activity further decreased as the two mutation sites were separated, indicating cooperation among c-subunits. Similar results were obtained for proton transfer-coupled molecular simulations. The simulations revealed that prolonged proton uptake in mutated c-subunits is shared between two c-subunits, explaining the cooperation observed in biochemical assays. Cells need to be able to store and transfer energy to fuel their various activities. To do this, they produce a small molecule called ATP to carry the energy, which is then released when the ATP is broken down. An enzyme found in plants, animals and bacteria, called FoF1 ATP synthase, can both create and use ATP. When it does this, protons, or positive hydrogen ions, are transported across cellular boundaries called membranes. The region of the enzyme that is responsible for pumping the protons contains different parts known as the c-ring and the a-subunit. The movement of protons drives the c-ring to rotate relative to the a-subunit, which leads to producing ATP. Previous research using simulations and the protein structures found there are two or three neighbouring amino acids in the c-ring that face the a-subunit, suggesting that these amino acids act together to drive the rotation. To test this hypothesis, Mitome et al. mutated these amino acids to examine the effect on the enzyme’s ability to produce ATP. A single mutation reduced the production of ATP, which decreased even further with mutations in two of the amino acids. The extent of this decrease depended on the distance between the two mutations in the c-ring. Simulations of these changes also found similar results. This indicates there is coordination between different parts of the c-ring to increase the rate of ATP production. This study offers new insights into the molecular processes controlling ATP synthesis and confirms previous theoretical research. This will interest specialists in bioenergetics because it addresses a fundamental biological question with broad impact.
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Affiliation(s)
- Noriyo Mitome
- Faculty of Education, Tokoha University, Shizuoka, Japan.,Department of Chemistry and Biochemistry, National Institute of Technology, Numazu College, Numazu, Japan.,Department of Chemical and Biological Engineering, National Institute of Technology, Ube College, Ube, Japan
| | - Shintaroh Kubo
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Sumie Ohta
- Department of Chemistry and Biochemistry, National Institute of Technology, Numazu College, Numazu, Japan
| | - Hikaru Takashima
- Department of Chemical and Biological Engineering, National Institute of Technology, Ube College, Ube, Japan
| | - Yuto Shigefuji
- Department of Chemical and Biological Engineering, National Institute of Technology, Ube College, Ube, Japan
| | - Toru Niina
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
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19
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Central Carbon Metabolism, Sodium-Motive Electron Transfer, and Ammonium Formation by the Vaginal Pathogen Prevotella bivia. Int J Mol Sci 2021; 22:ijms222111925. [PMID: 34769356 PMCID: PMC8585091 DOI: 10.3390/ijms222111925] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 11/17/2022] Open
Abstract
Replacement of the Lactobacillus dominated vaginal microbiome by a mixed bacterial population including Prevotella bivia is associated with bacterial vaginosis (BV). To understand the impact of P. bivia on this microbiome, its growth requirements and mode of energy production were studied. Anoxic growth with glucose depended on CO2 and resulted in succinate formation, indicating phosphoenolpyruvate carboxylation and fumarate reduction as critical steps. The reductive branch of fermentation relied on two highly active, membrane-bound enzymes, namely the quinol:fumarate reductase (QFR) and Na+-translocating NADH:quinone oxidoreductase (NQR). Both enzymes were characterized by activity measurements, in-gel fluorography, and VIS difference spectroscopy, and the Na+-dependent build-up of a transmembrane voltage was demonstrated. NQR is a potential drug target for BV treatment since it is neither found in humans nor in Lactobacillus. In P. bivia, the highly active enzymes L-asparaginase and aspartate ammonia lyase catalyze the conversion of asparagine to the electron acceptor fumarate. However, the by-product ammonium is highly toxic. It has been proposed that P. bivia depends on ammonium-utilizing Gardnerella vaginalis, another typical pathogen associated with BV, and provides key nutrients to it. The product pattern of P. bivia growing on glucose in the presence of mixed amino acids substantiates this notion.
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20
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A Sodium-Translocating Module Linking Succinate Production to Formation of Membrane Potential in Prevotella bryantii. Appl Environ Microbiol 2021; 87:e0121121. [PMID: 34469197 PMCID: PMC8516057 DOI: 10.1128/aem.01211-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Ruminants such as cattle and sheep depend on the breakdown of carbohydrates from plant-based feedstuff, which is accomplished by the microbial community in the rumen. Roughly 40% of the members of the rumen microbiota belong to the family Prevotellaceae, which ferments sugars to organic acids such as acetate, propionate, and succinate. These substrates are important nutrients for the ruminant. In a metaproteome analysis of the rumen of cattle, proteins that are homologous to the Na+-translocating NADH:quinone oxidoreductase (NQR) and the quinone:fumarate reductase (QFR) were identified in different Prevotella species. Here, we show that fumarate reduction to succinate in anaerobically growing Prevotella bryantii is coupled to chemiosmotic energy conservation by a supercomplex composed of NQR and QFR. This sodium-translocating NADH:fumarate oxidoreductase (SNFR) supercomplex was enriched by blue native PAGE (BN-PAGE) and characterized by in-gel enzyme activity staining and mass spectrometry. High NADH oxidation (850 nmol min-1 mg-1), quinone reduction (490 nmol min-1 mg-1), and fumarate reduction (1,200 nmol min-1 mg-1) activities, together with high expression levels, demonstrate that SNFR represents a charge-separating unit in P. bryantii. Absorption spectroscopy of SNFR exposed to different substrates revealed intramolecular electron transfer from the flavin adenine dinucleotide (FAD) cofactor in NQR to heme b cofactors in QFR. SNFR catalyzed the stoichiometric conversion of NADH and fumarate to NAD+ and succinate. We propose that the regeneration of NAD+ in P. bryantii is intimately linked to the buildup of an electrochemical gradient which powers ATP synthesis by electron transport phosphorylation. IMPORTANCE Feeding strategies for ruminants are designed to optimize nutrient efficiency for animals and to prevent energy losses like enhanced methane production. Key to this are the fermentative reactions of the rumen microbiota, dominated by Prevotella spp. We show that succinate formation by P. bryantii is coupled to NADH oxidation and sodium gradient formation by a newly described supercomplex consisting of Na+-translocating NADH:quinone oxidoreductase (NQR) and fumarate reductase (QFR), representing the sodium-translocating NADH:fumarate oxidoreductase (SNFR) supercomplex. SNFR is the major charge-separating module, generating an electrochemical sodium gradient in P. bryantii. Our findings offer clues to the observation that use of fumarate as feed additive does not significantly increase succinate production, or decrease methanogenesis, by the microbial community in the rumen.
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21
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Xue Q, Zhao D, Zhang S, Zhou H, Zuo Z, Zhou J, Li M, Xiang H. Highly integrated adaptive mechanisms in Spiribacter halalkaliphilus, a bacterium abundant in Chinese soda-saline lakes. Environ Microbiol 2021; 23:6463-6482. [PMID: 34587356 PMCID: PMC9292931 DOI: 10.1111/1462-2920.15794] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 11/29/2022]
Abstract
Soda-saline lakes are polyextreme environments inhabited by many haloalkaliphiles, including one of the most abundant Spiribacter species. However, its mechanisms of adaptation are not ecophysiologically characterized. Based on a large-scale cultivation strategy, we obtained a representative isolate of this Spiribacter species whose relative abundance was the highest (up to 15.63%) in a wide range of salinities in the soda-saline lakes in Inner Mongolia, China. This species is a chemoorganoheterotrophic haloalkaliphile. It has a small and streamlined genome and utilizes a wide variety of compatible solutes to resist osmotic pressure and multiple monovalent cation/proton antiporters for pH homeostasis. In addition to growth enhancement by light under microaerobic conditions, cell growth, organic substrate consumption and polyhydroxybutyrate biosynthesis were also improved by inorganic sulfide. Both quantitative RT-PCR and enzymatic assays verified that sulfide:quinone oxidoreductase was upregulated during this process. Metatranscriptomic analysis indicated that all genes related to environmental adaptation were transcribed in natural environments. Overall, this study has identified a novel abundant haloalkaliphile with multiple and highly integrated adaptive strategies and found that inorganic sulfide was able to improve the adaptation of a heterotroph to polyextreme environments.
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Affiliation(s)
- Qiong Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dahe Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shengjie Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Heng Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhenqiang Zuo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ming Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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22
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Nirody JA, Budin I, Rangamani P. ATP synthase: Evolution, energetics, and membrane interactions. J Gen Physiol 2021; 152:152111. [PMID: 32966553 PMCID: PMC7594442 DOI: 10.1085/jgp.201912475] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/24/2020] [Indexed: 12/24/2022] Open
Abstract
The synthesis of ATP, life’s “universal energy currency,” is the most prevalent chemical reaction in biological systems and is responsible for fueling nearly all cellular processes, from nerve impulse propagation to DNA synthesis. ATP synthases, the family of enzymes that carry out this endless task, are nearly as ubiquitous as the energy-laden molecule they are responsible for making. The F-type ATP synthase (F-ATPase) is found in every domain of life and has facilitated the survival of organisms in a wide range of habitats, ranging from the deep-sea thermal vents to the human intestine. Accordingly, there has been a large amount of work dedicated toward understanding the structural and functional details of ATP synthases in a wide range of species. Less attention, however, has been paid toward integrating these advances in ATP synthase molecular biology within the context of its evolutionary history. In this review, we present an overview of several structural and functional features of the F-type ATPases that vary across taxa and are purported to be adaptive or otherwise evolutionarily significant: ion channel selectivity, rotor ring size and stoichiometry, ATPase dimeric structure and localization in the mitochondrial inner membrane, and interactions with membrane lipids. We emphasize the importance of studying these features within the context of the enzyme’s particular lipid environment. Just as the interactions between an organism and its physical environment shape its evolutionary trajectory, ATPases are impacted by the membranes within which they reside. We argue that a comprehensive understanding of the structure, function, and evolution of membrane proteins—including ATP synthase—requires such an integrative approach.
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Affiliation(s)
- Jasmine A Nirody
- Center for Studies in Physics and Biology, The Rockefeller University, New York, NY.,All Souls College, University of Oxford, Oxford, UK
| | - Itay Budin
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA
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23
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Schenkel M, Treff A, Deber CM, Krainer G, Schlierf M. Heat treatment of thioredoxin fusions increases the purity of α-helical transmembrane protein constructs. Protein Sci 2021; 30:1974-1982. [PMID: 34191368 PMCID: PMC8376418 DOI: 10.1002/pro.4150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/22/2021] [Indexed: 01/05/2023]
Abstract
Membrane proteins play key roles in cellular signaling and transport, represent the majority of drug targets, and are implicated in many diseases. Their relevance renders them important subjects for structural, biophysical, and functional investigations. However, obtaining membrane proteins in high purities is often challenging with conventional purification steps alone. To address this issue, we present here an approach to increase the purity of α-helical transmembrane proteins. Our approach exploits the Thioredoxin (Trx) tag system, which is able to confer some of its favorable properties, such as high solubility and thermostability, to its fusion partners. Using Trx fusions of transmembrane helical hairpin constructs derived from the human cystic fibrosis transmembrane conductance regulator (CFTR) and a bacterial ATP synthase, we establish conditions for the successful implementation of the selective heat treatment procedure to increase sample purity. We further examine systematically its efficacy with respect to different incubation times and temperatures using quantitative gel electrophoresis. We find that minute-timescale heat treatment of Trx-tagged fusion constructs with temperatures ranging from 50 to 90°C increases the purity of the membrane protein samples from ~60 to 98% even after affinity purification. We show that this single-step approach is even applicable in cases where regular selective heat purification from crude extracts, as reported for Trx fusions to soluble proteins, fails. Overall, our approach is easy to integrate into existing purification strategies and provides a facile route for increasing the purity of membrane protein constructs after purification by standard chromatography approaches.
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Affiliation(s)
- Mathias Schenkel
- B CUBE – Center for Molecular BioengineeringTU DresdenDresdenGermany
| | - Antoine Treff
- B CUBE – Center for Molecular BioengineeringTU DresdenDresdenGermany
| | - Charles M. Deber
- Division of Molecular Medicine, Research InstituteHospital for Sick ChildrenTorontoOntarioCanada
| | - Georg Krainer
- B CUBE – Center for Molecular BioengineeringTU DresdenDresdenGermany
- Centre for Misfolding Diseases, Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
| | - Michael Schlierf
- B CUBE – Center for Molecular BioengineeringTU DresdenDresdenGermany
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24
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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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25
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Furusawa G, Diyana T, Lau NS. Metabolic strategies of dormancy of a marine bacterium Microbulbifer aggregans CCB-MM1: Its alternative electron transfer chain and sulfate-reducing pathway. Genomics 2021; 114:443-455. [PMID: 33689784 DOI: 10.1016/j.ygeno.2021.02.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 01/26/2021] [Accepted: 02/28/2021] [Indexed: 12/26/2022]
Abstract
Bacterial dormancy plays a crucial role in maintaining the functioning and diversity of microbial communities in natural environments. However, the metabolic regulations of the dormancy of bacteria in natural habitats, especially marine habitats, have remained largely unknown. A marine bacterium, Microbulbifer aggregans CCB-MM1 exhibits rod-to-coccus cell shape change during the dormant state. Therefore, to clarify the metabolic regulation of the dormancy, differential gene expression analysis based on RNA-Seq was performed between rod- (vegetative), intermediate, and coccus-shaped cells (dormancy). The RNA-Seq data revealed that one of two distinct electron transfer chains was upregulated in the dormancy. Dissimilatory sulfite reductase and soluble hydrogenase were also highly upregulated in the dormancy. In addition, induction of the dormancy of MM1 in the absence of MgSO4 was slower than that in the presence of MgSO4. These results indicate that the sulfate-reducing pathway plays an important role in entering the dormancy of MM1.
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Affiliation(s)
- Go Furusawa
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia.
| | - Tarmizi Diyana
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia
| | - Nyok-Sean Lau
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia
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26
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Bedaquiline: Current status and future perspectives. J Glob Antimicrob Resist 2021; 25:48-59. [PMID: 33684606 DOI: 10.1016/j.jgar.2021.02.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 01/28/2021] [Accepted: 02/17/2021] [Indexed: 12/21/2022] Open
Abstract
The development of drug-resistant tuberculosis (TB) is a major threat worldwide. Based on World Health Organization (WHO) reports, it is estimated that more than 500 000 new cases of drug-resistant TB occur annually. In addition, there are alarming reports of increasing multidrug-resistant TB (MDR-TB) and the emergence of extensively drug-resistant TB (XDR-TB) from different countries of the world. Therefore, new options for TB therapy are required. Bedaquiline (BDQ), a novel anti-TB drug, has significant minimum inhibitory concentrations (MICs) both against drug-susceptible and drug-resistant TB. Moreover, BDQ was recently approved for therapy of MDR-TB. The current narrative review summarises the available data on BDQ resistance, describes its antimicrobial properties, and provides new perspectives on clinical use of this novel anti-TB agent.
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27
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Calisto F, Sousa FM, Sena FV, Refojo PN, Pereira MM. Mechanisms of Energy Transduction by Charge Translocating Membrane Proteins. Chem Rev 2021; 121:1804-1844. [PMID: 33398986 DOI: 10.1021/acs.chemrev.0c00830] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Life relies on the constant exchange of different forms of energy, i.e., on energy transduction. Therefore, organisms have evolved in a way to be able to harvest the energy made available by external sources (such as light or chemical compounds) and convert these into biological useable energy forms, such as the transmembrane difference of electrochemical potential (Δμ̃). Membrane proteins contribute to the establishment of Δμ̃ by coupling exergonic catalytic reactions to the translocation of charges (electrons/ions) across the membrane. Irrespectively of the energy source and consequent type of reaction, all charge-translocating proteins follow two molecular coupling mechanisms: direct- or indirect-coupling, depending on whether the translocated charge is involved in the driving reaction. In this review, we explore these two coupling mechanisms by thoroughly examining the different types of charge-translocating membrane proteins. For each protein, we analyze the respective reaction thermodynamics, electron transfer/catalytic processes, charge-translocating pathways, and ion/substrate stoichiometries.
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Affiliation(s)
- Filipa Calisto
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Patricia N Refojo
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
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28
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Westphal L, Litty D, Müller V. Functional production of an archaeal ATP synthase with a V-type c subunit in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148378. [PMID: 33460587 DOI: 10.1016/j.bbabio.2021.148378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/18/2020] [Accepted: 01/09/2021] [Indexed: 11/18/2022]
Abstract
ATP synthases are the key elements of cellular bioenergetics and present in any life form and the overall structure and function of this rotary energy converter is conserved in all domains of life. However, ancestral microbes, the archaea, have a unique and huge diversity in the size and number of ion-binding sites in their membrane-embedded rotor subunit c. Due to the harsh conditions for ATP synthesis in these life forms it has never been possible to address the consequences of these unusual c subunits for ATP synthesis. Recently, we have found a Na+-dependent archaeal ATP synthase with a V-type c subunit in a mesophilic bacterium and here, we have cloned and expressed the genes in the ATP synthase-negative strain Escherichia coli DK8. The enzyme was present in membranes of E. coli DK8 and catalyzed ATP hydrolysis with a rate of 35 nmol·min-1·mg protein-1. Inverted membrane vesicles of this strain were then checked for their ability to synthesize ATP. Indeed, ATP was synthesized driven by NADH oxidation despite the V-type c subunit. ATP synthesis was dependent on Na+ and inhibited by ionophores. Most importantly, ATPase activity was inhibited by DCCD and this inhibition was relieved by addition of Na+, indicating a functional coupling of the F1 and FO domains, a prerequisite for studies on structure-function relationship. A first step in this direction was the exchange of a conserved arginine (Arg530) in the FO motor subunit a which led to loss of ATP synthesis whereas ATP hydrolysis was retained.
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Affiliation(s)
- Lars Westphal
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Dennis Litty
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Volker Müller
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany.
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29
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Katsyv A, Müller V. Overcoming Energetic Barriers in Acetogenic C1 Conversion. Front Bioeng Biotechnol 2020; 8:621166. [PMID: 33425882 PMCID: PMC7793690 DOI: 10.3389/fbioe.2020.621166] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 11/19/2020] [Indexed: 11/13/2022] Open
Abstract
Currently one of the biggest challenges for society is to combat global warming. A solution to this global threat is the implementation of a CO2-based bioeconomy and a H2-based bioenergy economy. Anaerobic lithotrophic bacteria such as the acetogenic bacteria are key players in the global carbon and H2 cycle and thus prime candidates as driving forces in a H2- and CO2-bioeconomy. Naturally, they convert two molecules of CO2via the Wood-Ljungdahl pathway (WLP) to one molecule of acetyl-CoA which can be converted to different C2-products (acetate or ethanol) or elongated to C4 (butyrate) or C5-products (caproate). Since there is no net ATP generation from acetate formation, an electron-transport phosphorylation (ETP) module is hooked up to the WLP. ETP provides the cell with additional ATP, but the ATP gain is very low, only a fraction of an ATP per mol of acetate. Since acetogens live at the thermodynamic edge of life, metabolic engineering to obtain high-value products is currently limited by the low energy status of the cells that allows for the production of only a few compounds with rather low specificity. To set the stage for acetogens as production platforms for a wide range of bioproducts from CO2, the energetic barriers have to be overcome. This review summarizes the pathway, the energetics of the pathway and describes ways to overcome energetic barriers in acetogenic C1 conversion.
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Affiliation(s)
- Alexander Katsyv
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
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30
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Kozlova MI, Bushmakin IM, Belyaeva JD, Shalaeva DN, Dibrova DV, Cherepanov DA, Mulkidjanian AY. Expansion of the "Sodium World" through Evolutionary Time and Taxonomic Space. BIOCHEMISTRY. BIOKHIMIIA 2020; 85:1518-1542. [PMID: 33705291 DOI: 10.1134/s0006297920120056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In 1986, Vladimir Skulachev and his colleagues coined the term "Sodium World" for the group of diverse organisms with sodium (Na)-based bioenergetics. Albeit only few such organisms had been discovered by that time, the authors insightfully noted that "the great taxonomic variety of organisms employing the Na-cycle points to the ubiquitous distribution of this novel type of membrane-linked energy transductions". Here we used tools of bioinformatics to follow expansion of the Sodium World through the evolutionary time and taxonomic space. We searched for those membrane protein families in prokaryotic genomes that correlate with the use of the Na-potential for ATP synthesis by different organisms. In addition to the known Na-translocators, we found a plethora of uncharacterized protein families; most of them show no homology with studied proteins. In addition, we traced the presence of Na-based energetics in many novel archaeal and bacterial clades, which were recently identified by metagenomic techniques. The data obtained support the view that the Na-based energetics preceded the proton-dependent energetics in evolution and prevailed during the first two billion years of the Earth history before the oxygenation of atmosphere. Hence, the full capacity of Na-based energetics in prokaryotes remains largely unexplored. The Sodium World expanded owing to the acquisition of new functions by Na-translocating systems. Specifically, most classes of G-protein-coupled receptors (GPCRs), which are targeted by almost half of the known drugs, appear to evolve from the Na-translocating microbial rhodopsins. Thereby the GPCRs of class A, with 700 representatives in human genome, retained the Na-binding site in the center of the transmembrane heptahelical bundle together with the capacity of Na-translocation. Mathematical modeling showed that the class A GPCRs could use the energy of transmembrane Na-potential for increasing both their sensitivity and selectivity. Thus, GPCRs, the largest protein family coded by human genome, stem from the Sodium World, which encourages exploration of other Na-dependent enzymes of eukaryotes.
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Affiliation(s)
- M I Kozlova
- School of Physics, Osnabrueck University, Osnabrueck, 49069, Germany. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - I M Bushmakin
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - J D Belyaeva
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - D N Shalaeva
- School of Physics, Osnabrueck University, Osnabrueck, 49069, Germany.
| | - D V Dibrova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - D A Cherepanov
- Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia.
| | - A Y Mulkidjanian
- School of Physics, Osnabrueck University, Osnabrueck, 49069, Germany. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.,School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia
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31
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The 3 × 120° rotary mechanism of Paracoccus denitrificans F 1-ATPase is different from that of the bacterial and mitochondrial F 1-ATPases. Proc Natl Acad Sci U S A 2020; 117:29647-29657. [PMID: 33168750 PMCID: PMC7703542 DOI: 10.1073/pnas.2003163117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The rotation of Paracoccus denitrificans F1-ATPase (PdF1) was studied using single-molecule microscopy. At all concentrations of adenosine triphosphate (ATP) or a slowly hydrolyzable ATP analog (ATPγS), above or below K m, PdF1 showed three dwells per turn, each separated by 120°. Analysis of dwell time between steps showed that PdF1 executes binding, hydrolysis, and probably product release at the same dwell. The comparison of ATP binding and catalytic pauses in single PdF1 molecules suggested that PdF1 executes both elementary events at the same rotary position. This point was confirmed in an inhibition experiment with a nonhydrolyzable ATP analog (AMP-PNP). Rotation assays in the presence of adenosine diphosphate (ADP) or inorganic phosphate at physiological concentrations did not reveal any obvious substeps. Although the possibility of the existence of substeps remains, all of the datasets show that PdF1 is principally a three-stepping motor similar to bacterial vacuolar (V1)-ATPase from Thermus thermophilus This contrasts with all other known F1-ATPases that show six or nine dwells per turn, conducting ATP binding and hydrolysis at different dwells. Pauses by persistent Mg-ADP inhibition or the inhibitory ζ-subunit were also found at the same angular position of the rotation dwell, supporting the simplified chemomechanical scheme of PdF1 Comprehensive analysis of rotary catalysis of F1 from different species, including PdF1, suggests a clear trend in the correlation between the numbers of rotary steps of F1 and Fo domains of F-ATP synthase. F1 motors with more distinctive steps are coupled with proton-conducting Fo rings with fewer proteolipid subunits, giving insight into the design principle the F1Fo of ATP synthase.
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32
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Berger S, Cabrera-Orefice A, Jetten MSM, Brandt U, Welte CU. Investigation of central energy metabolism-related protein complexes of ANME-2d methanotrophic archaea by complexome profiling. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148308. [PMID: 33002447 DOI: 10.1016/j.bbabio.2020.148308] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/07/2020] [Accepted: 09/09/2020] [Indexed: 02/02/2023]
Abstract
The anaerobic oxidation of methane is important for mitigating emissions of this potent greenhouse gas to the atmosphere and is mediated by anaerobic methanotrophic archaea. In a 'Candidatus Methanoperedens BLZ2' enrichment culture used in this study, methane is oxidized to CO2 with nitrate being the terminal electron acceptor of an anaerobic respiratory chain. Energy conservation mechanisms of anaerobic methanotrophs have mostly been studied at metagenomic level and hardly any protein data is available at this point. To close this gap, we used complexome profiling to investigate the presence and subunit composition of protein complexes involved in energy conservation processes. All enzyme complexes and their subunit composition involved in reverse methanogenesis were identified. The membrane-bound enzymes of the respiratory chain, such as F420H2:quinone oxidoreductase, membrane-bound heterodisulfide reductase, nitrate reductases and Rieske cytochrome bc1 complex were all detected. Additional or putative subunits such as an octaheme subunit as part of the Rieske cytochrome bc1 complex were discovered that will be interesting targets for future studies. Furthermore, several soluble proteins were identified, which are potentially involved in oxidation of reduced ferredoxin produced during reverse methanogenesis leading to formation of small organic molecules. Taken together these findings provide an updated, refined picture of the energy metabolism of the environmentally important group of anaerobic methanotrophic archaea.
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Affiliation(s)
- Stefanie Berger
- Institute for Wetland and Water Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands.
| | - Alfredo Cabrera-Orefice
- Molecular Bioenergetics Group, Radboud Institute for Molecular Life Sciences, Department of Pediatrics, Radboud University Medical Center, Geert-Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Mike S M Jetten
- Institute for Wetland and Water Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands.
| | - Ulrich Brandt
- Molecular Bioenergetics Group, Radboud Institute for Molecular Life Sciences, Department of Pediatrics, Radboud University Medical Center, Geert-Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands.
| | - Cornelia U Welte
- Institute for Wetland and Water Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands.
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33
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Nath S. A Novel Conceptual Model for the Dual Role of FOF1-ATP Synthase in Cell Life and Cell Death. Biomol Concepts 2020; 11:143-152. [PMID: 32827389 DOI: 10.1515/bmc-2020-0014] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 07/22/2020] [Indexed: 12/31/2022] Open
Abstract
The mitochondrial permeability transition (MPT) has been one of the longstanding enigmas in biology. Its cause is currently at the center of an extensive scientific debate, and several hypotheses on its molecular nature have been put forward. The present view holds that the transition arises from the opening of a high-conductance channel in the energy-transducing membrane, the permeability transition pore (PTP), also called the mitochondrial megachannel or the multiconductance channel (MMC). Here, the novel hypothesis is proposed that the aqueous access channels at the interface of the c-ring and the a-subunit of FO in the FOF1-ATP synthase are repurposed during induction of apoptosis and constitute the elusive PTP/ MMC. A unifying principle based on regulation by local potentials is advanced to rationalize the action of the myriad structurally and chemically diverse inducers and inhibitors of PTP/MMC. Experimental evidence in favor of the hypothesis and its differences from current models of PTP/MMC are summarized. The hypothesis explains in considerable detail how the binding of Ca2+ to a β-catalytic site (site 3) in the F1 portion of ATP synthase triggers the opening of the PTP/MMC. It is also shown to connect to longstanding proposals within Nath's torsional mechanism of energy transduction and ATP synthesis as to how the binding of MgADP to site 3 does not induce PTP/MMC, but instead catalyzes physiological ATP synthesis in cell life. In the author's knowledge, this is the first model that explains how Ca2+ transforms the FOF1-ATP synthase from an exquisite energy-conserving enzyme in cell life into an energy-dissipating structure that promotes cell death. This has major implications for basic as well as for clinical research, such as for the development of drugs that target the MPT, given the established role of PTP/MMC dysregulation in cancer, ischemia, cardiac hypertrophy, and various neurodegenerative diseases.
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Affiliation(s)
- Sunil Nath
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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34
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Krah A, Marzinek JK, Bond PJ. Characterizing the Hydration Properties of Proton Binding Sites in the ATP Synthase c-Rings of Bacillus Species. J Phys Chem B 2020; 124:7176-7183. [PMID: 32687713 DOI: 10.1021/acs.jpcb.0c03896] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The membrane-embedded domain of ATP synthases contains the c-ring, which translocates ions across the membrane, and its resultant rotation is coupled to ATP synthesis in the extramembranous domain. During rotation, the c-ring becomes accessible on both sides of the lipid bilayer to solvent via channels connected to the other membrane-embedded component, the a subunit, and thereby allows the ion to be released into the solvent environment. In recent times, many experimental structures of c-rings from different species have been solved. In some of these, a water molecule with a proposed "structural role" has been identified within the c-ring ion binding site, but in general, the requirement for high resolution to resolve specific water densities complicates their interpretation. In the present study, we use molecular dynamics (MD) simulations and rigorous free energy calculations to characterize the dynamics and energetics of a water molecule within the ion binding site of the c-ring from Bacillus pseudofirmus OF4, in its wild type (WT) and P51A mutant forms, along with the c-ring from thermophilic Bacillus PS3. Our data suggest that a water molecule stably binds to the P51A mutant, as well as helping to identify a bound water molecule in Bacillus PS3 whose presence was previously overlooked due to the limited resolution of the structural data. Sequence analysis further identifies a novel conserved sequence motif that is likely required to harbor a water molecule for stable ion coordination in the binding site of such proteins.
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Affiliation(s)
- Alexander Krah
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Jan K Marzinek
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Peter J Bond
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
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35
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Mitochondrial F-ATP synthase as the permeability transition pore. Pharmacol Res 2020; 160:105081. [PMID: 32679179 DOI: 10.1016/j.phrs.2020.105081] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 07/06/2020] [Accepted: 07/10/2020] [Indexed: 12/27/2022]
Abstract
The current state of research on the mitochondrial permeability transition pore (PTP) can be described in terms of three major problems: molecular identity, atomic structure and gating mechanism. In this review these three problems are discussed in the light of recent findings with special emphasis on the discovery that the PTP is mitochondrial F-ATP synthase (mtFoF1). Novel features of the mitochondrial F-ATP synthase emerging from the success of single particle cryo electron microscopy (cryo-EM) to determine F-ATP synthase structures are surveyed along with their possible involvement in pore formation. Also, current findings from the gap junction field concerning the involvement of lipids in channel closure are examined. Finally, an earlier proposal denoted as the 'Death Finger' is discussed as a working model for PTP gating.
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36
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Peng W, Casey AK, Fernandez J, Carpinone EM, Servage KA, Chen Z, Li Y, Tomchick DR, Starai VJ, Orth K. A distinct inhibitory mechanism of the V-ATPase by Vibrio VopQ revealed by cryo-EM. Nat Struct Mol Biol 2020; 27:589-597. [PMID: 32424347 DOI: 10.1038/s41594-020-0429-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 04/01/2020] [Indexed: 12/18/2022]
Abstract
The Vibrio parahaemolyticus T3SS effector VopQ targets host-cell V-ATPase, resulting in blockage of autophagic flux and neutralization of acidic compartments. Here, we report the cryo-EM structure of VopQ bound to the Vo subcomplex of the V-ATPase. VopQ inserts into membranes and forms an unconventional pore while binding directly to subunit c of the V-ATPase membrane-embedded subcomplex Vo. We show that VopQ arrests yeast growth in vivo by targeting the immature Vo subcomplex in the endoplasmic reticulum (ER), thus providing insight into the observation that VopQ kills cells in the absence of a functional V-ATPase. VopQ is a bacterial effector that has been discovered to inhibit a host-membrane megadalton complex by coincidentally binding its target, inserting into a membrane and disrupting membrane potential. Collectively, our results reveal a mechanism by which bacterial effectors modulate host cell biology and provide an invaluable tool for future studies on V-ATPase-mediated membrane fusion and autophagy.
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Affiliation(s)
- Wei Peng
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Amanda K Casey
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jessie Fernandez
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Kelly A Servage
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Zhe Chen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yang Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Diana R Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vincent J Starai
- Department of Microbiology, University of Georgia, Athens, GA, USA
- Department of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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37
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Molecular dynamics simulation of proton-transfer coupled rotations in ATP synthase F O motor. Sci Rep 2020; 10:8225. [PMID: 32427921 PMCID: PMC7237500 DOI: 10.1038/s41598-020-65004-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 03/12/2020] [Indexed: 11/10/2022] Open
Abstract
The FO motor in FOF1 ATP synthase rotates its rotor driven by the proton motive force. While earlier studies elucidated basic mechanisms therein, recent advances in high-resolution cryo-electron microscopy enabled to investigate proton-transfer coupled FO rotary dynamics at structural details. Here, taking a hybrid Monte Carlo/molecular dynamics simulation method, we studied reversible dynamics of a yeast mitochondrial FO. We obtained the 36°-stepwise rotations of FO per one proton transfer in the ATP synthesis mode and the proton pumping in the ATP hydrolysis mode. In both modes, the most prominent path alternatively sampled states with two and three deprotonated glutamates in c-ring, by which the c-ring rotates one step. The free energy transduction efficiency in the model FO motor reached ~ 90% in optimal conditions. Moreover, mutations in key glutamate and a highly conserved arginine increased proton leakage and markedly decreased the coupling, in harmony with previous experiments. This study provides a simple framework of simulations for chemical-reaction coupled molecular dynamics calling for further studies in ATP synthase and others.
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Correlation between the numbers of rotation steps in the ATPase and proton-conducting domains of F- and V-ATPases. Biophys Rev 2020; 12:303-307. [PMID: 32270445 PMCID: PMC7242557 DOI: 10.1007/s12551-020-00668-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 02/25/2020] [Indexed: 12/16/2022] Open
Abstract
This letter reports the correlation in the number of distinct rotation steps between the F1/V1 and Fo/Vo domains that constitute common rotary F- and V-ATP synthases/ATPases. Recent single-molecule studies on the F1-ATPase revealed differences in the number of discrete steps in rotary catalysis between different organisms—6 steps per turn in bacterial types and mitochondrial F1 from yeast, and 9 steps in the mammalian mitochondrial F1 domains. The number of rotational steps that Fo domain makes is thought to correspond to that of proteolipid subunits within the rotating c-ring present in Fo. Structural studies on Fo and in the whole ATP synthase complex have shown a large diversity in the number of proteolipid subunits. Interestingly, 6 steps in F1 are always paired with 10 steps in Fo, whereas 9 steps in F1 are paired with 8 steps in Fo. The correlation in the number of steps has also been revealed for two types of V-ATPases: one having 6 steps in V1 paired with 10 steps in Vo, and the other one having 3 steps in V1 paired with 12 steps in Vo. Although the abovementioned correlations await further confirmation, the results suggest a clear trend; ATPase motors with more steps have proton-conducting motors with less steps. In addition, ATPases with 6 steps are always paired with proton-conducting domains with 10 steps.
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Triple Mycobacterial ATP-synthase mutations impedes Bedaquiline binding: Atomistic and structural perspectives. Comput Biol Chem 2020; 85:107204. [DOI: 10.1016/j.compbiolchem.2020.107204] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 01/06/2020] [Accepted: 01/13/2020] [Indexed: 01/07/2023]
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Unusual features of the c-ring of F 1F O ATP synthases. Sci Rep 2019; 9:18547. [PMID: 31811229 PMCID: PMC6897951 DOI: 10.1038/s41598-019-55092-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 11/19/2019] [Indexed: 11/23/2022] Open
Abstract
Membrane integral ATP synthases produce adenosine triphosphate, the universal “energy currency” of most organisms. However, important details of proton driven energy conversion are still unknown. We present the first high-resolution structure (2.3 Å) of the in meso crystallized c-ring of 14 subunits from spinach chloroplasts. The structure reveals molecular mechanisms of intersubunit contacts in the c14-ring, and it shows additional electron densities inside the c-ring which form circles parallel to the membrane plane. Similar densities were found in all known high-resolution structures of c-rings of F1FO ATP synthases from archaea and bacteria to eukaryotes. The densities might originate from isoprenoid quinones (such as coenzyme Q in mitochondria and plastoquinone in chloroplasts) that is consistent with differential UV-Vis spectroscopy of the c-ring samples, unusually large distance between polar/apolar interfaces inside the c-ring and universality among different species. Although additional experiments are required to verify this hypothesis, coenzyme Q and its analogues known as electron carriers of bioenergetic chains may be universal cofactors of ATP synthases, stabilizing c-ring and prevent ion leakage through it.
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Revisiting the protomotive vectorial motion of F 0-ATPase. Proc Natl Acad Sci U S A 2019; 116:19484-19489. [PMID: 31511421 DOI: 10.1073/pnas.1909032116] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The elucidation of the detailed mechanism used by F0 to convert proton gradient to torque and rotational motion presents a major puzzle despite significant biophysical and structural progress. Although the conceptual model has advanced our understanding of the working principles of such systems, it is crucial to explore the actual mechanism using structure-based models that actually reproduce a unidirectional proton-driven rotation. Our previous work used a coarse-grained (CG) model to simulate the action of F0 However, the simulations were based on a very tentative structural model of the interaction between subunit a and subunit c. Here, we again use a CG model but with a recent cryo-EM structure of cF1F0 and also explore the proton path using our water flooding and protein dipole Langevin dipole semimacroscopic formalism with its linear response approximation version (PDLD/S-LRA) approaches. The simulations are done in the combined space defined by the rotational coordinate and the proton transport coordinate. The study reproduced the effect of the protomotive force on the rotation of the F0 while establishing the electrostatic origin of this effect. Our landscape reproduces the correct unidirectionality of the synthetic direction of the F0 rotation and shows that it reflects the combined electrostatic coupling between the proton transport path and the c-ring conformational change. This work provides guidance for further studies in other proton-driven mechanochemical systems and should lead (when combined with studies of F1) to a complete energy transduction picture of the F0F1-ATPase system.
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Lai LTF, Yu C, Wong JSK, Lo HS, Benlekbir S, Jiang L, Lau WCY. Subnanometer resolution cryo-EM structure of Arabidopsis thaliana ATG9. Autophagy 2019; 16:575-583. [PMID: 31276439 DOI: 10.1080/15548627.2019.1639300] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Macroautophagy/autophagy is an essential process for the maintenance of cellular homeostasis by recycling macromolecules under normal and stress conditions. ATG9 (autophagy related 9) is the only integral membrane protein in the autophagy core machinery and has a central role in mediating autophagosome formation. In cells, ATG9 exists on mobile vesicles that traffic to the growing phagophore, providing an essential membrane source for the formation of autophagosomes. Here we report the three-dimensional structure of ATG9 from Arabidopsis thaliana at 7.8 Å resolution, determined by single particle cryo-electron microscopy. ATG9 organizes into a homotrimer, with each protomer contributing at least six transmembrane α-helices. At the center of the trimer, the protomers interact via their membrane-embedded and C-terminal cytoplasmic regions. Combined with prediction of protein contacts using sequence co-evolutionary information, the structure provides molecular insights into the ATG9 architecture and testable hypotheses for the molecular mechanism of autophagy progression regulated by ATG9.Abbreviations: 2D: 2-dimensional; 3D: 3-dimensional; AtATG9: Arabidopsis ATG9; Atg: autophagy-related; ATG9: autophagy-related protein 9; cryo-EM: cryo-electron microscopy; DDM: dodecyl maltoside; GraDeR: gradient-based detergent removal; LMNG: lauryl maltose-neopentyl glycol; PAS: phagophore assembly site; PtdIns3K: phosphatidylinositol 3-kinase.
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Affiliation(s)
- Louis Tung Faat Lai
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
| | - Chuanyang Yu
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
| | - Jan Siu Kei Wong
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
| | - Ho Sing Lo
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
| | - Samir Benlekbir
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Canada
| | - Liwen Jiang
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, China.,CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Wilson Chun Yu Lau
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
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Shi M, Gao J, Zhang MQ. Web3DMol: interactive protein structure visualization based on WebGL. Nucleic Acids Res 2019; 45:W523-W527. [PMID: 28482028 PMCID: PMC5570197 DOI: 10.1093/nar/gkx383] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/26/2017] [Indexed: 11/24/2022] Open
Abstract
A growing number of web-based databases and tools for protein research are being developed. There is now a widespread need for visualization tools to present the three-dimensional (3D) structure of proteins in web browsers. Here, we introduce our 3D modeling program—Web3DMol—a web application focusing on protein structure visualization in modern web browsers. Users submit a PDB identification code or select a PDB archive from their local disk, and Web3DMol will display and allow interactive manipulation of the 3D structure. Featured functions, such as sequence plot, fragment segmentation, measure tool and meta-information display, are offered for users to gain a better understanding of protein structure. Easy-to-use APIs are available for developers to reuse and extend Web3DMol. Web3DMol can be freely accessed at http://web3dmol.duapp.com/, and the source code is distributed under the MIT license.
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Affiliation(s)
- Maoxiang Shi
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Juntao Gao
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Michael Q Zhang
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Department of Automation, Tsinghua University, Beijing 100084, China.,Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080-3021, USA
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Bahuguna A, Rawat DS. An overview of new antitubercular drugs, drug candidates, and their targets. Med Res Rev 2019; 40:263-292. [PMID: 31254295 DOI: 10.1002/med.21602] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 12/15/2022]
Abstract
The causative agent of tuberculosis (TB), Mycobacterium tuberculosis and more recently totally drug-resistant strains of M. tuberculosis, display unique mechanisms to survive in the host. A four-drug treatment regimen was introduced 40 years ago but the emergence of multidrug-resistance and more recently TDR necessitates the identification of new targets and drugs for the cure of M. tuberculosis infection. The current efforts in the drug development process are insufficient to completely eradicate the TB epidemic. For almost five decades the TB drug development process remained stagnant. The last 10 years have made sudden progress giving some new and highly promising drugs including bedaquiline, delamanid, and pretomanid. Many of the candidates are repurposed compounds, which were developed to treat other infections but later, exhibited anti-TB properties also. Each class of drug has a specific target and a definite mode of action. These targets are either involved in cell wall biosynthesis, protein synthesis, DNA/RNA synthesis, or metabolism. This review discusses recent progress in the discovery of newly developed and Food and Drug Administration approved drugs as well as repurposed drugs, their targets, mode of action, drug-target interactions, and their structure-activity relationship.
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Affiliation(s)
| | - Diwan S Rawat
- Department of Chemistry, University of Delhi, Delhi, India
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45
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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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Salifu EY, Agoni C, Olotu FA, Dokurugu YM, Soliman MES. Halting ionic shuttle to disrupt the synthetic machinery-Structural and molecular insights into the inhibitory roles of Bedaquiline towards Mycobacterium tuberculosis ATP synthase in the treatment of tuberculosis. J Cell Biochem 2019; 120:16108-16119. [PMID: 31125144 DOI: 10.1002/jcb.28891] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/26/2019] [Accepted: 03/15/2019] [Indexed: 12/31/2022]
Abstract
Therapeutic targeting of the adenosine triphosphate (ATP) machinery of Mycobacterium tuberculosis (Mtb) has recently presented a potent and alternative measure to halt the pathogenesis of tuberculosis. This has been potentiated by the development of bedaquiline (BDQ), a novel small molecule inhibitor that selectively inhibits mycobacterial F1 Fo -ATP synthase by targeting its rotor c-ring, resulting in the disruption of ATP synthesis and consequential cell death. Although the structural resolution of the mycobacterial C9 ring in co`mplex with BDQ provided the first-hand detail of BDQ interaction at the c-ring region of the ATP synthase, there still remains a need to obtain essential and dynamic insights into the mechanistic activity of this drug molecule towards crucial survival machinery of Mtb. As such, for the first time, we report an atomistic model to describe the structural dynamics that explicate the experimentally reported antagonistic features of BDQ in halting ion shuttling by the mycobacterial c-ring, using molecular dynamics simulation and the Molecular Mechanics/Poisson-Boltzmann Surface Area methods. Results showed that BDQ exhibited a considerably high ΔG while it specifically maintained high-affinity interactions with Glu65B and Asp32B , blocking their crucial roles in proton binding and shuttling, which is required for ATP synthesis. Moreover, the bulky nature of BDQ induced a rigid and compact conformation of the rotor c-ring, which impedes the essential rotatory motion that drives ion exchange and shuttling. In addition, the binding affinity of a BDQ molecule was considerably increased by the complementary binding of another BDQ molecule, which indicates that an increase in BDQ molecule enhances inhibitory potency against Mtb ATP synthase. Taken together, findings provide atomistic perspectives into the inhibitory mechanisms of BDQ coupled with insights that could enhance the structure-based design of novel ATP synthase inhibitors towards the treatment of tuberculosis.
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Affiliation(s)
- Elliasu Y Salifu
- Molecular Bio-computation and Drug Design Laboratory, Discipline of Pharmaceutical Chemistry, University of KwaZulu-Natal, Westville Campus, Durban, South Africa
| | - Clement Agoni
- Molecular Bio-computation and Drug Design Laboratory, Discipline of Pharmaceutical Chemistry, University of KwaZulu-Natal, Westville Campus, Durban, South Africa
| | - Fisayo A Olotu
- Molecular Bio-computation and Drug Design Laboratory, Discipline of Pharmaceutical Chemistry, University of KwaZulu-Natal, Westville Campus, Durban, South Africa
| | - Yussif M Dokurugu
- College of Pharmacy & Pharmaceutical Sciences, Institute of Public Health, Florida Agricultural & Mechanical University, Tallahassee, Florida
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, Discipline of Pharmaceutical Chemistry, University of KwaZulu-Natal, Westville Campus, Durban, South Africa
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Krah A, Marzinek JK, Bond PJ. Insights into water accessible pathways and the inactivation mechanism of proton translocation by the membrane-embedded domain of V-type ATPases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:1004-1010. [DOI: 10.1016/j.bbamem.2019.02.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 01/29/2019] [Accepted: 02/27/2019] [Indexed: 01/25/2023]
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Abstract
F1Fo ATP synthases produce most of the ATP in the cell. F-type ATP synthases have been investigated for more than 50 years, but a full understanding of their molecular mechanisms has become possible only with the recent structures of complete, functionally competent complexes determined by electron cryo-microscopy (cryo-EM). High-resolution cryo-EM structures offer a wealth of unexpected new insights. The catalytic F1 head rotates with the central γ-subunit for the first part of each ATP-generating power stroke. Joint rotation is enabled by subunit δ/OSCP acting as a flexible hinge between F1 and the peripheral stalk. Subunit a conducts protons to and from the c-ring rotor through two conserved aqueous channels. The channels are separated by ∼6 Å in the hydrophobic core of Fo, resulting in a strong local field that generates torque to drive rotary catalysis in F1. The structure of the chloroplast F1Fo complex explains how ATPase activity is turned off at night by a redox switch. Structures of mitochondrial ATP synthase dimers indicate how they shape the inner membrane cristae. The new cryo-EM structures complete our picture of the ATP synthases and reveal the unique mechanism by which they transform an electrochemical membrane potential into biologically useful chemical energy.
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Affiliation(s)
- Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt, Germany;
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Krasnoselska GO, Meier T. Purification and Reconstitution of Ilyobacter tartaricus ATP Synthase. Methods Mol Biol 2019; 1805:51-71. [PMID: 29971712 DOI: 10.1007/978-1-4939-8556-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
F-type adenosine triphosphate (ATP) synthase is a membrane-bound macromolecular complex, which is responsible for the synthesis of ATP, the universal energy source in living cells. This enzyme uses the proton- or sodium-motive force to power ATP synthesis by a unique rotary mechanism and can also operate in reverse, ATP hydrolysis, to generate ion gradients across membranes. The F1Fo-ATP synthases from bacteria consist of eight different structural subunits, forming a complex of ∼550 kDa in size. In the bacterium Ilyobacter tartaricus the ATP synthase has the stoichiometry α3β3γδεab2c11. This chapter describes a wet-lab working protocol for the purification of several tens of milligrams of pure, heterologously (E. coli-)produced I. tartaricus Na+-driven F1Fo-ATP synthase and its subsequent efficient reconstitution into proteoliposomes. The methods are useful for a broad range of subsequent biochemical and biotechnological applications.
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Affiliation(s)
- Ganna O Krasnoselska
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Thomas Meier
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
- Department of Life Sciences, Imperial College London, London, UK.
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Sielaff H, Yanagisawa S, Frasch WD, Junge W, Börsch M. Structural Asymmetry and Kinetic Limping of Single Rotary F-ATP Synthases. Molecules 2019; 24:E504. [PMID: 30704145 PMCID: PMC6384691 DOI: 10.3390/molecules24030504] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 12/12/2022] Open
Abstract
F-ATP synthases use proton flow through the FO domain to synthesize ATP in the F₁ domain. In Escherichia coli, the enzyme consists of rotor subunits γεc10 and stator subunits (αβ)₃δab₂. Subunits c10 or (αβ)₃ alone are rotationally symmetric. However, symmetry is broken by the b₂ homodimer, which together with subunit δa, forms a single eccentric stalk connecting the membrane embedded FO domain with the soluble F₁ domain, and the central rotating and curved stalk composed of subunit γε. Although each of the three catalytic binding sites in (αβ)₃ catalyzes the same set of partial reactions in the time average, they might not be fully equivalent at any moment, because the structural symmetry is broken by contact with b₂δ in F₁ and with b₂a in FO. We monitored the enzyme's rotary progression during ATP hydrolysis by three single-molecule techniques: fluorescence video-microscopy with attached actin filaments, Förster resonance energy transfer between pairs of fluorescence probes, and a polarization assay using gold nanorods. We found that one dwell in the three-stepped rotary progression lasting longer than the other two by a factor of up to 1.6. This effect of the structural asymmetry is small due to the internal elastic coupling.
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Affiliation(s)
- Hendrik Sielaff
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, 07743 Jena, Germany.
| | - Seiga Yanagisawa
- School of Life Sciences, Arizona State University, Tempe, Arizona, AZ 85287, USA.
| | - Wayne D Frasch
- School of Life Sciences, Arizona State University, Tempe, Arizona, AZ 85287, USA.
| | - Wolfgang Junge
- Department of Biology & Chemistry, University of Osnabrück, 49076 Osnabrück, Germany.
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, 07743 Jena, Germany.
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