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Yanagisawa S, Bukhari ZA, Parra KJ, Frasch WD. Eukaryotic yeast V 1-ATPase rotary mechanism insights revealed by high-resolution single-molecule studies. Front Mol Biosci 2024; 11:1269040. [PMID: 38567099 PMCID: PMC10985318 DOI: 10.3389/fmolb.2024.1269040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 02/07/2024] [Indexed: 04/04/2024] Open
Abstract
Vacuolar ATP-dependent proton pumps (V-ATPases) belong to a super-family of rotary ATPases and ATP synthases. The V1 complex consumes ATP to drive rotation of a central rotor that pumps protons across membranes via the Vo complex. Eukaryotic V-ATPases are regulated by reversible disassembly of subunit C, V1 without C, and VO. ATP hydrolysis is thought to generate an unknown rotary state that initiates regulated disassembly. Dissociated V1 is inhibited by subunit H that traps it in a specific rotational position. Here, we report the first single-molecule studies with high resolution of time and rotational position of Saccharomyces cerevisiae V1-ATPase lacking subunits H and C (V1ΔHC), which resolves previously elusive dwells and angular velocity changes. Rotation occurred in 120° power strokes separated by dwells comparable to catalytic dwells observed in other rotary ATPases. However, unique V1ΔHC rotational features included: 1) faltering power stroke rotation during the first 60°; 2) a dwell often occurring ∼45° after the catalytic dwell, which did not increase in duration at limiting MgATP; 3) a second dwell, ∼2-fold longer occurring 112° that increased in duration and occurrence at limiting MgATP; 4) limiting MgATP-dependent decreases in power stroke angular velocity where dwells were not observed. The results presented here are consistent with MgATP binding to the empty catalytic site at 112° and MgADP released at ∼45°, and provide important new insight concerning the molecular basis for the differences in rotary positions of substrate binding and product release between V-type and F-type ATPases.
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Affiliation(s)
- Seiga Yanagisawa
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Zain A. Bukhari
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Karlett J. Parra
- Department of Biochemistry and Molecular Biology, University of New Mexico School of Medicine, Albuquerque, NM, United States
| | - Wayne D. Frasch
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
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Ragunathan P, Shuyi Ng P, Singh S, Poh WH, Litty D, Kalia NP, Larsson S, Harikishore A, Rice SA, Ingham PW, Müller V, Moraski G, Miller MJ, Dick T, Pethe K, Grüber G. GaMF1.39's antibiotic efficacy and its enhanced antitubercular activity in combination with clofazimine, Telacebec, ND-011992, or TBAJ-876. Microbiol Spectr 2023; 11:e0228223. [PMID: 37982630 PMCID: PMC10715162 DOI: 10.1128/spectrum.02282-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 10/12/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE New drugs are needed to combat multidrug-resistant tuberculosis. The electron transport chain (ETC) maintains the electrochemical potential across the cytoplasmic membrane and allows the production of ATP, the energy currency of any living cell. The mycobacterial engine F-ATP synthase catalyzes the formation of ATP and has come into focus as an attractive and rich drug target. Recent deep insights into these mycobacterial F1FO-ATP synthase elements opened the door for a renaissance of structure-based target identification and inhibitor design. In this study, we present the GaMF1.39 antimycobacterial compound, targeting the rotary subunit γ of the biological engine. The compound is bactericidal, inhibits infection ex vivo, and displays enhanced anti-tuberculosis activity in combination with ETC inhibitors, which promises new strategies to shorten tuberculosis chemotherapy.
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Affiliation(s)
- Priya Ragunathan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Pearly Shuyi Ng
- Experimental Drug Development Centre, Agency for Science, Technology and Research, Singapore, Singapore
| | - Samsher Singh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building, Singapore, Singapore
| | - Wee Han Poh
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Dennis Litty
- Molecular Microbiology and Bioenergetics, Institute for Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Frankfurt, Germany
| | - Nitin Pal Kalia
- Department of Biological Sciences (Pharmacology & Toxicology), National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Simon Larsson
- Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building, Singapore, Singapore
| | - Amaravadhi Harikishore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
| | - Scott A. Rice
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Philip W. Ingham
- Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building, Singapore, Singapore
| | - Volker Müller
- Molecular Microbiology and Bioenergetics, Institute for Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Frankfurt, Germany
| | - Garrett Moraski
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Marvin J. Miller
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
- Department of Microbiology and Immunology, Georgetown University, Washington, DC, USA
| | - Kevin Pethe
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building, Singapore, Singapore
- National Centre for Infectious Diseases (NCID), Jalan Tan Tock Seng, Singapore, Singapore
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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Saw WG, Le KCM, Shin J, Kwek JHM, Wong CF, Ragunathan P, Fong TC, Müller V, Grüber G. Atomic insights of an up and down conformation of the Acinetobacter baumannii F 1 -ATPase subunit ε and deciphering the residues critical for ATP hydrolysis inhibition and ATP synthesis. FASEB J 2023; 37:e23040. [PMID: 37318822 DOI: 10.1096/fj.202300175rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/23/2023] [Accepted: 06/05/2023] [Indexed: 06/16/2023]
Abstract
The Acinetobacter baumannii F1 FO -ATP synthase (α3 :β3 :γ:δ:ε:a:b2 :c10 ), which is essential for this strictly respiratory opportunistic human pathogen, is incapable of ATP-driven proton translocation due to its latent ATPase activity. Here, we generated and purified the first recombinant A. baumannii F1 -ATPase (AbF1 -ATPase) composed of subunits α3 :β3 :γ:ε, showing latent ATP hydrolysis. A 3.0 Å cryo-electron microscopy structure visualizes the architecture and regulatory element of this enzyme, in which the C-terminal domain of subunit ε (Abε) is present in an extended position. An ε-free AbF1 -ɑβγ complex generated showed a 21.5-fold ATP hydrolysis increase, demonstrating that Abε is the major regulator of AbF1 -ATPase's latent ATP hydrolysis. The recombinant system enabled mutational studies of single amino acid substitutions within Abε or its interacting subunits β and γ, respectively, as well as C-terminal truncated mutants of Abε, providing a detailed picture of Abε's main element for the self-inhibition mechanism of ATP hydrolysis. Using a heterologous expression system, the importance of Abε's C-terminus in ATP synthesis of inverted membrane vesicles, including AbF1 FO -ATP synthases, has been explored. In addition, we are presenting the first NMR solution structure of the compact form of Abε, revealing interaction of its N-terminal β-barrel and C-terminal ɑ-hairpin domain. A double mutant of Abε highlights critical residues for Abε's domain-domain formation which is important also for AbF1 -ATPase's stability. Abε does not bind MgATP, which is described to regulate the up and down movements in other bacterial counterparts. The data are compared to regulatory elements of F1 -ATPases in bacteria, chloroplasts, and mitochondria to prevent wasting of ATP.
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Affiliation(s)
- Wuan-Geok Saw
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Khoa Cong Minh Le
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Joon Shin
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jes Hui Min Kwek
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Chui Fann Wong
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Priya Ragunathan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Tuck Choy Fong
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Volker Müller
- Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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Zharova TV, Grivennikova VG, Borisov VB. F1·Fo ATP Synthase/ATPase: Contemporary View on Unidirectional Catalysis. Int J Mol Sci 2023; 24:5417. [PMID: 36982498 PMCID: PMC10049701 DOI: 10.3390/ijms24065417] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/05/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
F1·Fo-ATP synthases/ATPases (F1·Fo) are molecular machines that couple either ATP synthesis from ADP and phosphate or ATP hydrolysis to the consumption or production of a transmembrane electrochemical gradient of protons. Currently, in view of the spread of drug-resistant disease-causing strains, there is an increasing interest in F1·Fo as new targets for antimicrobial drugs, in particular, anti-tuberculosis drugs, and inhibitors of these membrane proteins are being considered in this capacity. However, the specific drug search is hampered by the complex mechanism of regulation of F1·Fo in bacteria, in particular, in mycobacteria: the enzyme efficiently synthesizes ATP, but is not capable of ATP hydrolysis. In this review, we consider the current state of the problem of “unidirectional” F1·Fo catalysis found in a wide range of bacterial F1·Fo and enzymes from other organisms, the understanding of which will be useful for developing a strategy for the search for new drugs that selectively disrupt the energy production of bacterial cells.
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Wong CF, Saw WG, Basak S, Sano M, Ueno H, Kerk HW, Litty D, Ragunathan P, Dick T, Müller V, Noji H, Grüber G. Structural Elements Involved in ATP Hydrolysis Inhibition and ATP Synthesis of Tuberculosis and Nontuberculous Mycobacterial F-ATP Synthase Decipher New Targets for Inhibitors. Antimicrob Agents Chemother 2022; 66:e0105622. [PMID: 36445139 DOI: 10.1128/aac.01056-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The F1FO-ATP synthase is required for the viability of tuberculosis (TB) and nontuberculous mycobacteria (NTM) and has been validated as a drug target. Here, we present the cryo-EM structures of the Mycobacterium smegmatis F1-ATPase and the F1FO-ATP synthase with different nucleotide occupation within the catalytic sites and visualize critical elements for latent ATP hydrolysis and efficient ATP synthesis. Mutational studies reveal that the extended C-terminal domain (αCTD) of subunit α is the main element for the self-inhibition mechanism of ATP hydrolysis for TB and NTM bacteria. Rotational studies indicate that the transition between the inhibition state by the αCTD and the active state is a rapid process. We demonstrate that the unique mycobacterial γ-loop and subunit δ are critical elements required for ATP formation. The data underline that these mycobacterium-specific elements of α, γ, and δ are attractive targets, providing a platform for the discovery of species-specific inhibitors.
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Abstract
The F-type ATPase family of enzymes, including ATP synthases, are found ubiquitously in biological membranes. ATP synthesis from ADP and inorganic phosphate is driven by an electrochemical H+ gradient or H+ motive force, in which intramolecular rotation of F-type ATPase is generated with H+ transport across the membranes. Because this rotation is essential for energy coupling between catalysis and H+-transport, regulation of the rotation is important to adapt to environmental changes and maintain ATP concentration. Recently, a series of cryo-electron microscopy images provided detailed insights into the structure of the H+ pathway and the multiple subunit arrangement. However, the regulatory mechanism of the rotation has not been clarified. This review describes the inhibition mechanism of ATP hydrolysis in bacterial enzymes. In addition, properties of the F-type ATPase of Streptococcus mutans, which acts as a H+-pump in an acidic environment, are described. These findings may help in the development of novel antimicrobial agents.
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Frasch WD, Bukhari ZA, Yanagisawa S. F1FO ATP synthase molecular motor mechanisms. Front Microbiol 2022; 13:965620. [PMID: 36081786 PMCID: PMC9447477 DOI: 10.3389/fmicb.2022.965620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
The F-ATP synthase, consisting of F1 and FO motors connected by a central rotor and the stators, is the enzyme responsible for synthesizing the majority of ATP in all organisms. The F1 (αβ)3 ring stator contains three catalytic sites. Single-molecule F1 rotation studies revealed that ATP hydrolysis at each catalytic site (0°) precedes a power-stroke that rotates subunit-γ 120° with angular velocities that vary with rotational position. Catalytic site conformations vary relative to subunit-γ position (βE, empty; βD, ADP bound; βT, ATP-bound). During a power stroke, βE binds ATP (0°–60°) and βD releases ADP (60°–120°). Årrhenius analysis of the power stroke revealed that elastic energy powers rotation via unwinding the γ-subunit coiled-coil. Energy from ATP binding at 34° closes βE upon subunit-γ to drive rotation to 120° and forcing the subunit-γ to exchange its tether from βE to βD, which changes catalytic site conformations. In F1FO, the membrane-bound FO complex contains a ring of c-subunits that is attached to subunit-γ. This c-ring rotates relative to the subunit-a stator in response to transmembrane proton flow driven by a pH gradient, which drives subunit-γ rotation in the opposite direction to force ATP synthesis in F1. Single-molecule studies of F1FO embedded in lipid bilayer nanodisks showed that the c-ring transiently stopped F1-ATPase-driven rotation every 36° (at each c-subunit in the c10-ring of E. coli F1FO) and was able to rotate 11° in the direction of ATP synthesis. Protonation and deprotonation of the conserved carboxyl group on each c-subunit is facilitated by separate groups of subunit-a residues, which were determined to have different pKa’s. Mutations of any of any residue from either group changed both pKa values, which changed the occurrence of the 11° rotation proportionately. This supports a Grotthuss mechanism for proton translocation and indicates that proton translocation occurs during the 11° steps. This is consistent with a mechanism in which each 36° of rotation the c-ring during ATP synthesis involves a proton translocation-dependent 11° rotation of the c-ring, followed by a 25° rotation driven by electrostatic interaction of the negatively charged unprotonated carboxyl group to the positively charged essential arginine in subunit-a.
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Mendoza-Hoffmann F, Zarco-Zavala M, Ortega R, Celis-Sandoval H, Torres-Larios A, García-Trejo JJ. Evolution of the Inhibitory and Non-Inhibitory ε, ζ, and IF 1 Subunits of the F 1F O-ATPase as Related to the Endosymbiotic Origin of Mitochondria. Microorganisms 2022; 10:microorganisms10071372. [PMID: 35889091 PMCID: PMC9317440 DOI: 10.3390/microorganisms10071372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/03/2022] [Accepted: 07/03/2022] [Indexed: 12/10/2022] Open
Abstract
The F1FO-ATP synthase nanomotor synthesizes >90% of the cellular ATP of almost all living beings by rotating in the “forward” direction, but it can also consume the same ATP pools by rotating in “reverse.” To prevent futile F1FO-ATPase activity, several different inhibitory proteins or domains in bacteria (ε and ζ subunits), mitochondria (IF1), and chloroplasts (ε and γ disulfide) emerged to block the F1FO-ATPase activity selectively. In this study, we analyze how these F1FO-ATPase inhibitory proteins have evolved. The phylogeny of the α-proteobacterial ε showed that it diverged in its C-terminal side, thus losing both the inhibitory function and the ATP-binding/sensor motif that controls this inhibition. The losses of inhibitory function and the ATP-binding site correlate with an evolutionary divergence of non-inhibitory α-proteobacterial ε and mitochondrial δ subunits from inhibitory bacterial and chloroplastidic ε subunits. Here, we confirm the lack of inhibitory function of wild-type and C-terminal truncated ε subunits of P. denitrificans. Taken together, the data show that ζ evolved to replace ε as the primary inhibitor of the F1FO-ATPase of free-living α-proteobacteria. However, the ζ inhibitory function was also partially lost in some symbiotic α-proteobacteria and totally lost in some strictly parasitic α-proteobacteria such as the Rickettsiales order. Finally, we found that ζ and IF1 likely evolved independently via convergent evolution before and after the endosymbiotic origin mitochondria, respectively. This led us to propose the ε and ζ subunits as tracer genes of the pre-endosymbiont that evolved into the actual mitochondria.
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Affiliation(s)
- Francisco Mendoza-Hoffmann
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California (UABC)—Campus Tijuana, Tijuana C.P. 22390, Baja California, Mexico
- Correspondence: (F.M.-H.); (J.J.G.-T.)
| | - Mariel Zarco-Zavala
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de Mexico C.P. 04510, Coyoacan, Mexico
| | - Raquel Ortega
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de Mexico C.P. 04510, Coyoacan, Mexico
| | - Heliodoro Celis-Sandoval
- Instituto de Fisiología Celular (IFC), Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de Mexico C.P. 04510, Coyoacan, Mexico
| | - Alfredo Torres-Larios
- Instituto de Fisiología Celular (IFC), Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de Mexico C.P. 04510, Coyoacan, Mexico
| | - José J. García-Trejo
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de Mexico C.P. 04510, Coyoacan, Mexico
- Correspondence: (F.M.-H.); (J.J.G.-T.)
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Ragunathan P, Dick T, Grüber G. Anti-Mycobacterium abscessus Activity of Tuberculosis F-ATP Synthase Inhibitor GaMF1. Antimicrob Agents Chemother 2022; 66:e0001822. [PMID: 35481752 DOI: 10.1128/aac.00018-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
New drug targets and molecules with bactericidal activity are needed against the respiratory mycobacterial pathogen Mycobacterium abscessus. Employing a lead repurposing strategy, the antituberculosis compound GaMF1 was tested against M. abscessus. Whole-cell and ATP synthesis assays demonstrated that GaMF1 inhibits growth and kills M. abscessus by targeting the F-ATP synthase. GaMF1's anti-M. abscessus activity increased in combination with clofazimine, rifabutin, or amikacin. The study expands the repertoire of anti-M. abscessus compounds targeting oxidative phosphorylation.
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Harikishore A, Saw WG, Ragunathan P, Litty D, Dick T, Müller V, Grüber G. Mutational Analysis of Mycobacterial F-ATP Synthase Subunit δ Leads to a Potent δ Enzyme Inhibitor. ACS Chem Biol 2022; 17:529-535. [PMID: 35148057 DOI: 10.1021/acschembio.1c00766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While many bacteria are able to bypass the requirement for oxidative phosphorylation when grown on carbohydrates, Mycobacterium tuberculosis is unable to do so. Differences of amino acid composition and structural features of the mycobacterial F-ATP synthase (α3:β3:γ:δ:ε:a:b:b':c9) compared to its prokaryotic or human counterparts were recently elucidated and paved avenues for the discovery of molecules interfering with various regulative mechanisms of this essential energy converter. In this context, the mycobacterial peripheral stalk subunit δ came into focus, which displays a unique N-terminal 111-amino acid extension. Here, mutants of recombinant mycobacterial subunit δ were characterized, revealing significant reduction in ATP synthesis and demonstrating essentiality of this subunit for effective catalysis. These results provided the basis for the generation of a four-feature model forming a δ receptor-based pharmacophore and to identify a potent subunit δ inhibitor DeMF1 via in silico screening. The successful targeting of the δ subunit demonstrates the potential to advance δ's flexible coupling as a new area for the development of F-ATP synthase inhibitors.
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Affiliation(s)
- Amaravadhi Harikishore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Wuan-Geok Saw
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Priya Ragunathan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Dennis Litty
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, New Jersey 07110, United States
- Medical Sciences, Hackensack Meridian School of Medicine, 123 Metro Boulevard, Nutley, New Jersey 07110, United States
- Department of Microbiology and Immunology, Georgetown University, 3900 Reservoir Road NW Medical-Dental Building, Washington, D.C. 20007, United States
| | - Volker Müller
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
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Vestergaard M, Bald D, Ingmer H. Targeting the ATP synthase in bacterial and fungal pathogens – beyond Mycobacterium tuberculosis. J Glob Antimicrob Resist 2022. [DOI: 10.1016/j.jgar.2022.01.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 01/24/2022] [Accepted: 01/30/2022] [Indexed: 11/23/2022] Open
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Yanagisawa S, Frasch WD. pH-dependent 11° F 1F O ATP synthase sub-steps reveal insight into the F O torque generating mechanism. eLife 2021; 10:70016. [PMID: 34970963 PMCID: PMC8754430 DOI: 10.7554/elife.70016] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 12/27/2021] [Indexed: 12/04/2022] Open
Abstract
Most cellular ATP is made by rotary F1FO ATP synthases using proton translocation-generated clockwise torque on the FO c-ring rotor, while F1-ATP hydrolysis can force counterclockwise rotation and proton pumping. The FO torque-generating mechanism remains elusive even though the FO interface of stator subunit-a, which contains the transmembrane proton half-channels, and the c-ring is known from recent F1FO structures. Here, single-molecule F1FO rotation studies determined that the pKa values of the half-channels differ, show that mutations of residues in these channels change the pKa values of both half-channels, and reveal the ability of FO to undergo single c-subunit rotational stepping. These experiments provide evidence to support the hypothesis that proton translocation through FO operates via a Grotthuss mechanism involving a column of single water molecules in each half-channel linked by proton translocation-dependent c-ring rotation. We also observed pH-dependent 11° ATP synthase-direction sub-steps of the Escherichia coli c10-ring of F1FO against the torque of F1-ATPase-dependent rotation that result from H+ transfer events from FO subunit-a groups with a low pKa to one c-subunit in the c-ring, and from an adjacent c-subunit to stator groups with a high pKa. These results support a mechanism in which alternating proton translocation-dependent 11° and 25° synthase-direction rotational sub-steps of the c10-ring occur to sustain F1FO ATP synthesis.
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Affiliation(s)
- Seiga Yanagisawa
- 1School of Life Sciences, Arizona State University, Tempe, United States
| | - Wayne D Frasch
- School of Life Sciences, Arizona State University, Tempe, United States
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Harikishore A, Wong CF, Ragunathan P, Litty D, Müller V, Grüber G. Targeting Mycobacterial F-ATP Synthase C-Terminal α Subunit Interaction Motif on Rotary Subunit γ. Antibiotics (Basel) 2021; 10:1456. [PMID: 34943667 DOI: 10.3390/antibiotics10121456] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 12/03/2022] Open
Abstract
Mycobacteria regulate their energy (ATP) levels to sustain their survival even in stringent living conditions. Recent studies have shown that mycobacteria not only slow down their respiratory rate but also block ATP hydrolysis of the F-ATP synthase (α3:β3:γ:δ:ε:a:b:b’:c9) to maintain ATP homeostasis in situations not amenable for growth. The mycobacteria-specific α C-terminus (α533-545) has unraveled to be the major regulative of latent ATP hydrolysis. Its deletion stimulates ATPase activity while reducing ATP synthesis. In one of the six rotational states of F-ATP synthase, α533-545 has been visualized to dock deep into subunit γ, thereby blocking rotation of γ within the engine. The functional role(s) of this C-terminus in the other rotational states are not clarified yet and are being still pursued in structural studies. Based on the interaction pattern of the docked α533-545 region with subunit γ, we attempted to study the druggability of the α533-545 motif. In this direction, our computational work has led to the development of an eight-featured α533-545 peptide pharmacophore, followed by database screening, molecular docking, and pose selection, resulting in eleven hit molecules. ATP synthesis inhibition assays using recombinant ATP synthase as well as mycobacterial inverted membrane vesicles show that one of the hits, AlMF1, inhibited the mycobacterial F-ATP synthase in a micromolar range. The successful targeting of the α533-545-γ interaction motif demonstrates the potential to develop inhibitors targeting the α site to interrupt rotary coupling with ATP synthesis.
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Mizrahi V, Barry Iii CE. Hit movie reveals how a tuberculosis drug halts ATP synthesis. Nature 2021; 589:21-2. [PMID: 33299164 DOI: 10.1038/d41586-020-03406-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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Guo H, Courbon GM, Bueler SA, Mai J, Liu J, Rubinstein JL. Structure of mycobacterial ATP synthase bound to the tuberculosis drug bedaquiline. Nature 2021; 589:143-7. [PMID: 33299175 DOI: 10.1038/s41586-020-3004-3] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/21/2020] [Indexed: 01/01/2023]
Abstract
Tuberculosis-the world's leading cause of death by infectious disease-is increasingly resistant to current first-line antibiotics1. The bacterium Mycobacterium tuberculosis (which causes tuberculosis) can survive low-energy conditions, allowing infections to remain dormant and decreasing their susceptibility to many antibiotics2. Bedaquiline was developed in 2005 from a lead compound identified in a phenotypic screen against Mycobacterium smegmatis3. This drug can sterilize even latent M. tuberculosis infections4 and has become a cornerstone of treatment for multidrug-resistant and extensively drug-resistant tuberculosis1,5,6. Bedaquiline targets the mycobacterial ATP synthase3, which is an essential enzyme in the obligate aerobic Mycobacterium genus3,7, but how it binds the intact enzyme is unknown. Here we determined cryo-electron microscopy structures of M. smegmatis ATP synthase alone and in complex with bedaquiline. The drug-free structure suggests that hook-like extensions from the α-subunits prevent the enzyme from running in reverse, inhibiting ATP hydrolysis and preserving energy in hypoxic conditions. Bedaquiline binding induces large conformational changes in the ATP synthase, creating tight binding pockets at the interface of subunits a and c that explain the potency of this drug as an antibiotic for tuberculosis.
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16
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Wong CF, Grüber G. The Unique C-Terminal Extension of Mycobacterial F-ATP Synthase Subunit α Is the Major Contributor to Its Latent ATP Hydrolysis Activity. Antimicrob Agents Chemother 2020; 64:e01568-20. [PMID: 32988828 DOI: 10.1128/AAC.01568-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/16/2020] [Indexed: 01/03/2023] Open
Abstract
Mycobacterial F1Fo-ATP synthases (α3:β3:γ:δ:ε:a:b:b':c9 ) are incapable of ATP-driven proton translocation due to their latent ATPase activity. This prevents wasting of ATP and altering of the proton motive force, whose dissipation is lethal to mycobacteria. We demonstrate that the mycobacterial C-terminal extension of nucleotide-binding subunit α contributes mainly to the suppression of ATPase activity in the recombinant mycobacterial F1-ATPase. Using C-terminal deletion mutants, the regions responsible for the enzyme's latency were mapped, providing a new compound epitope.
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17
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Appetecchia F, Consalvi S, Scarpecci C, Biava M, Poce G. SAR Analysis of Small Molecules Interfering with Energy-Metabolism in Mycobacterium tuberculosis. Pharmaceuticals (Basel) 2020; 13:E227. [PMID: 32878317 PMCID: PMC7557483 DOI: 10.3390/ph13090227] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 12/13/2022] Open
Abstract
Tuberculosis remains the world's top infectious killer: it caused a total of 1.5 million deaths and 10 million people fell ill with TB in 2018. Thanks to TB diagnosis and treatment, mortality has been falling in recent years, with an estimated 58 million saved lives between 2000 and 2018. However, the emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mtb strains is a major concern that might reverse this progress. Therefore, the development of new drugs acting upon novel mechanisms of action is a high priority in the global health agenda. With the approval of bedaquiline, which targets mycobacterial energy production, and delamanid, which targets cell wall synthesis and energy production, the energy-metabolism in Mtb has received much attention in the last decade as a potential target to investigate and develop new antimycobacterial drugs. In this review, we describe potent anti-mycobacterial agents targeting the energy-metabolism at different steps with a special focus on structure-activity relationship (SAR) studies of the most advanced compound classes.
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Affiliation(s)
| | | | | | | | - Giovanna Poce
- Department of Chemistry and Technologies of Drug, Sapienza University of Rome, piazzale A. Moro 5, 00185 Rome, Italy; (F.A.); (S.C.); (C.S.); (M.B.)
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18
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Wong CF, Lau AM, Harikishore A, Saw WG, Shin J, Ragunathan P, Bhushan S, Ngan SFC, Sze SK, Bates RW, Dick T, Grüber G. A systematic assessment of mycobacterial F 1 -ATPase subunit ε's role in latent ATPase hydrolysis. FEBS J 2020; 288:818-836. [PMID: 32525613 DOI: 10.1111/febs.15440] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 05/05/2020] [Accepted: 06/03/2020] [Indexed: 12/20/2022]
Abstract
In contrast to most bacteria, the mycobacterial F1 FO -ATP synthase (α3 :β3 :γ:δ:ε:a:b:b':c9 ) does not perform ATP hydrolysis-driven proton translocation. Although subunits α, γ and ε of the catalytic F1 -ATPase component α3 :β3 :γ:ε have all been implicated in the suppression of the enzyme's ATPase activity, the mechanism remains poorly defined. Here, we brought the central stalk subunit ε into focus by generating the recombinant Mycobacterium smegmatis F1 -ATPase (MsF1 -ATPase), whose 3D low-resolution structure is presented, and its ε-free form MsF1 αβγ, which showed an eightfold ATP hydrolysis increase and provided a defined system to systematically study the segments of mycobacterial ε's suppression of ATPase activity. Deletion of four amino acids at ε's N terminus, mutant MsF1 αβγεΔ2-5 , revealed similar ATP hydrolysis as MsF1 αβγ. Together with biochemical and NMR solution studies of a single, double, triple and quadruple N-terminal ε-mutants, the importance of the first N-terminal residues of mycobacterial ε in structure stability and latency is described. Engineering ε's C-terminal mutant MsF1 αβγεΔ121 and MsF1 αβγεΔ103-121 with deletion of the C-terminal residue D121 and the two C-terminal ɑ-helices, respectively, revealed the requirement of the very C terminus for communication with the catalytic α3 β3 -headpiece and its function in ATP hydrolysis inhibition. Finally, we applied the tools developed during the study for an in silico screen to identify a novel subunit ε-targeting F-ATP synthase inhibitor.
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Affiliation(s)
- Chui-Fann Wong
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Aik-Meng Lau
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Amaravadhi Harikishore
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Wuan-Geok Saw
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Joon Shin
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Priya Ragunathan
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Shashi Bhushan
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore City, Singapore
| | - So-Fong Cam Ngan
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Roderick W Bates
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore City, Singapore.,Department of Medical Sciences, Hackensack Meridian School of Medicine at Seton Hall University, Nutley, NJ, USA
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
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19
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Hotra A, Ragunathan P, Ng PS, Seankongsuk P, Harikishore A, Sarathy JP, Saw W, Lakshmanan U, Sae‐Lao P, Kalia NP, Shin J, Kalyanasundaram R, Anbarasu S, Parthasarathy K, Pradeep CN, Makhija H, Dröge P, Poulsen A, Tan JHL, Pethe K, Dick T, Bates RW, Grüber G. Discovery of a Novel Mycobacterial F‐ATP Synthase Inhibitor and its Potency in Combination with Diarylquinolines. Angew Chem Int Ed Engl 2020; 59:13295-13304. [DOI: 10.1002/anie.202002546] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Indexed: 01/08/2023]
Affiliation(s)
- Adam Hotra
- School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link Singapore 637371 Republic of Singapore
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
- Nanyang Institute of Technology in Health and Medicine Interdisciplinary Graduate School Nanyang Technological University Republic of Singapore
| | - Priya Ragunathan
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
| | - Pearly Shuyi Ng
- Experimental Drug Development Centre Agency for Science Technology and Research, A*STAR 10 Biopolis Road Singapore 138670 Republic of Singapore
| | - Pattarakiat Seankongsuk
- School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link Singapore 637371 Republic of Singapore
| | - Amaravadhi Harikishore
- School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link Singapore 637371 Republic of Singapore
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
| | - Jickky Palmae Sarathy
- Department of Microbiology and Immunology Yong Loo Lin School of Medicine National University of Singapore 14 Medical Drive Singapore 117599 Republic of Singapore
| | - Wuan‐Geok Saw
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
| | - Umayal Lakshmanan
- Experimental Drug Development Centre Agency for Science Technology and Research, A*STAR 10 Biopolis Road Singapore 138670 Republic of Singapore
| | - Patcharaporn Sae‐Lao
- School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link Singapore 637371 Republic of Singapore
| | - Nitin Pal Kalia
- Lee Kong Chian School of Medicine Nanyang Technological University Experimental Medicine Building Republic of Singapore
| | - Joon Shin
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
| | - Revathy Kalyanasundaram
- Centre for Drug Discovery and Development Sathyabama Institute of Science and Technology Chennai 600119 India
| | - Sivaraj Anbarasu
- Centre for Drug Discovery and Development Sathyabama Institute of Science and Technology Chennai 600119 India
| | - Krupakar Parthasarathy
- Centre for Drug Discovery and Development Sathyabama Institute of Science and Technology Chennai 600119 India
| | - Chaudhari Namrata Pradeep
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
| | - Harshyaa Makhija
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
| | - Peter Dröge
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
| | - Anders Poulsen
- Experimental Drug Development Centre Agency for Science Technology and Research, A*STAR 10 Biopolis Road Singapore 138670 Republic of Singapore
| | - Jocelyn Hui Ling Tan
- Experimental Drug Development Centre Agency for Science Technology and Research, A*STAR 10 Biopolis Road Singapore 138670 Republic of Singapore
| | - Kevin Pethe
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
- Lee Kong Chian School of Medicine Nanyang Technological University Experimental Medicine Building Republic of Singapore
| | - Thomas Dick
- Department of Microbiology and Immunology Yong Loo Lin School of Medicine National University of Singapore 14 Medical Drive Singapore 117599 Republic of Singapore
- Center for Discovery and Innovation Hackensack Meridian Health 340 Kingsland Street Nutley NJ 07110 USA
| | - Roderick W. Bates
- School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link Singapore 637371 Republic of Singapore
| | - Gerhard Grüber
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
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20
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Hotra A, Ragunathan P, Ng PS, Seankongsuk P, Harikishore A, Sarathy JP, Saw W, Lakshmanan U, Sae‐Lao P, Kalia NP, Shin J, Kalyanasundaram R, Anbarasu S, Parthasarathy K, Pradeep CN, Makhija H, Dröge P, Poulsen A, Tan JHL, Pethe K, Dick T, Bates RW, Grüber G. Discovery of a Novel Mycobacterial F‐ATP Synthase Inhibitor and its Potency in Combination with Diarylquinolines. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Adam Hotra
- School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link Singapore 637371 Republic of Singapore
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
- Nanyang Institute of Technology in Health and Medicine Interdisciplinary Graduate School Nanyang Technological University Republic of Singapore
| | - Priya Ragunathan
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
| | - Pearly Shuyi Ng
- Experimental Drug Development Centre Agency for Science Technology and Research, A*STAR 10 Biopolis Road Singapore 138670 Republic of Singapore
| | - Pattarakiat Seankongsuk
- School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link Singapore 637371 Republic of Singapore
| | - Amaravadhi Harikishore
- School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link Singapore 637371 Republic of Singapore
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
| | - Jickky Palmae Sarathy
- Department of Microbiology and Immunology Yong Loo Lin School of Medicine National University of Singapore 14 Medical Drive Singapore 117599 Republic of Singapore
| | - Wuan‐Geok Saw
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
| | - Umayal Lakshmanan
- Experimental Drug Development Centre Agency for Science Technology and Research, A*STAR 10 Biopolis Road Singapore 138670 Republic of Singapore
| | - Patcharaporn Sae‐Lao
- School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link Singapore 637371 Republic of Singapore
| | - Nitin Pal Kalia
- Lee Kong Chian School of Medicine Nanyang Technological University Experimental Medicine Building Republic of Singapore
| | - Joon Shin
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
| | - Revathy Kalyanasundaram
- Centre for Drug Discovery and Development Sathyabama Institute of Science and Technology Chennai 600119 India
| | - Sivaraj Anbarasu
- Centre for Drug Discovery and Development Sathyabama Institute of Science and Technology Chennai 600119 India
| | - Krupakar Parthasarathy
- Centre for Drug Discovery and Development Sathyabama Institute of Science and Technology Chennai 600119 India
| | - Chaudhari Namrata Pradeep
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
| | - Harshyaa Makhija
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
| | - Peter Dröge
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
| | - Anders Poulsen
- Experimental Drug Development Centre Agency for Science Technology and Research, A*STAR 10 Biopolis Road Singapore 138670 Republic of Singapore
| | - Jocelyn Hui Ling Tan
- Experimental Drug Development Centre Agency for Science Technology and Research, A*STAR 10 Biopolis Road Singapore 138670 Republic of Singapore
| | - Kevin Pethe
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
- Lee Kong Chian School of Medicine Nanyang Technological University Experimental Medicine Building Republic of Singapore
| | - Thomas Dick
- Department of Microbiology and Immunology Yong Loo Lin School of Medicine National University of Singapore 14 Medical Drive Singapore 117599 Republic of Singapore
- Center for Discovery and Innovation Hackensack Meridian Health 340 Kingsland Street Nutley NJ 07110 USA
| | - Roderick W. Bates
- School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link Singapore 637371 Republic of Singapore
| | - Gerhard Grüber
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
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21
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Foo CS, Pethe K, Lupien A. Oxidative Phosphorylation—an Update on a New, Essential Target Space for Drug Discovery in Mycobacterium tuberculosis. Applied Sciences 2020; 10:2339. [DOI: 10.3390/app10072339] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
New drugs with new mechanisms of action are urgently required to tackle the global tuberculosis epidemic. Following the FDA-approval of the ATP synthase inhibitor bedaquiline (Sirturo®), energy metabolism has become the subject of intense focus as a novel pathway to exploit for tuberculosis drug development. This enthusiasm stems from the fact that oxidative phosphorylation (OxPhos) and the maintenance of the transmembrane electrochemical gradient are essential for the viability of replicating and non-replicating Mycobacterium tuberculosis (M. tb), the etiological agent of human tuberculosis (TB). Therefore, new drugs targeting this pathway have the potential to shorten TB treatment, which is one of the major goals of TB drug discovery. This review summarises the latest and key findings regarding the OxPhos pathway in M. tb and provides an overview of the inhibitors targeting various components. We also discuss the potential of new regimens containing these inhibitors, the flexibility of this pathway and, consequently, the complexity in targeting it. Lastly, we discuss opportunities and future directions of this drug target space.
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22
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Saw WG, Wong CF, Dick T, Grüber G. Overexpression, purification, enzymatic and microscopic characterization of recombinant mycobacterial F-ATP synthase. Biochem Biophys Res Commun 2019; 522:374-380. [PMID: 31761325 DOI: 10.1016/j.bbrc.2019.11.098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 11/15/2019] [Indexed: 01/16/2023]
Abstract
The F-ATP synthase is an essential enzyme in mycobacteria, including the pathogenic Mycobacterium tuberculosis. Several new compounds in the TB-drug pipeline target the F-ATP synthase. In light of the importance and pharmacological attractiveness of this novel antibiotic target, tools have to be developed to generate a recombinant mycobacterial F1FO ATP synthase to achieve atomic insight and mutants for mechanistic and regulatory understanding as well as structure-based drug design. Here, we report the first genetically engineered, purified and enzymatically active recombinant M. smegmatis F1FO ATP synthase. The projected 2D- and 3D structures of the recombinant enzyme derived from negatively stained electron micrographs are presented. Furthermore, the first 2D projections from cryo-electron images are revealed, paving the way for an atomic resolution structure determination.
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Affiliation(s)
- Wuan-Geok Saw
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
| | - Chui-Fann Wong
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Gerhard Grüber
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.
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23
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Kamariah N, Ragunathan P, Shin J, Saw WG, Wong CF, Dick T, Grüber G. Unique structural and mechanistic properties of mycobacterial F-ATP synthases: Implications for drug design. Prog Biophys Mol Biol 2020; 152:64-73. [PMID: 31743686 DOI: 10.1016/j.pbiomolbio.2019.11.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/25/2019] [Accepted: 11/13/2019] [Indexed: 12/31/2022]
Abstract
The causative agent of Tuberculosis (TB) Mycobacterium tuberculosis (Mtb) encounters unfavourable environmental conditions in the lungs, including nutrient limitation, low oxygen tensions and/or low/high pH values. These harsh conditions in the host triggers Mtb to enter a dormant state in which the pathogen does not replicate and uses host-derived fatty acids instead of carbohydrates as an energy source. Independent to the energy source, the bacterium's energy currency ATP is generated by oxidative phosphorylation, in which the F1FO-ATP synthase uses the proton motive force generated by the electron transport chain. This catalyst is essential in Mtb and inhibition by the diarylquinoline class of drugs like Bedaquilline, TBAJ-587, TBAJ-876 or squaramides demonstrated that this engine is an attractive target in TB drug discovery. A special feature of the mycobacterial F-ATP synthase is its inability to establish a significant proton gradient during ATP hydrolysis, and its latent ATPase activity, to prevent energy waste and to control the membrane potential. Recently, unique epitopes of mycobacterial F1FO-ATP synthase subunits absent in their prokaryotic or mitochondrial counterparts have been identified to contribute to the regulation of the low ATPase activity. Most recent structural insights into individual subunits, the F1 domain or the entire mycobacterial enzyme added to the understanding of mechanisms, regulation and differences of the mycobacterial F1FO-ATP synthase compared to other bacterial and eukaryotic engines. These novel insights provide the basis for the design of new compounds targeting this engine and even novel regimens for multidrug resistant TB.
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24
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Saw WG, Wu ML, Ragunathan P, Biuković G, Lau AM, Shin J, Harikishore A, Cheung CY, Hards K, Sarathy JP, Bates RW, Cook GM, Dick T, Grüber G. Disrupting coupling within mycobacterial F-ATP synthases subunit ε causes dysregulated energy production and cell wall biosynthesis. Sci Rep 2019; 9:16759. [PMID: 31727946 DOI: 10.1038/s41598-019-53107-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 10/28/2019] [Indexed: 11/23/2022] Open
Abstract
The dynamic interaction of the N- and C-terminal domains of mycobacterial F-ATP synthase subunit ε is proposed to contribute to efficient coupling of H+-translocation and ATP synthesis. Here, we investigate crosstalk between both subunit ε domains by introducing chromosomal atpC missense mutations in the C-terminal helix 2 of ε predicted to disrupt inter domain and subunit ε-α crosstalk and therefore coupling. The ε mutant εR105A,R111A,R113A,R115A (ε4A) showed decreased intracellular ATP, slower growth rates and lower molar growth yields on non-fermentable carbon sources. Cellular respiration and metabolism were all accelerated in the mutant strain indicative of dysregulated oxidative phosphorylation. The ε4A mutant exhibited an altered colony morphology and was hypersusceptible to cell wall-acting antimicrobials suggesting defective cell wall biosynthesis. In silico screening identified a novel mycobacterial F-ATP synthase inhibitor disrupting ε’s coupling activity demonstrating the potential to advance this regulation as a new area for mycobacterial F-ATP synthase inhibitor development.
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25
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Kamariah N, Huber RG, Nartey W, Bhushan S, Bond PJ, Grüber G. Structure and subunit arrangement of Mycobacterial F1FO ATP synthase and novel features of the unique mycobacterial subunit δ. J Struct Biol 2019; 207:199-208. [DOI: 10.1016/j.jsb.2019.05.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/21/2019] [Accepted: 05/23/2019] [Indexed: 02/08/2023]
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26
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Zhang AT, Montgomery MG, Leslie AGW, Cook GM, Walker JE. The structure of the catalytic domain of the ATP synthase from Mycobacterium smegmatis is a target for developing antitubercular drugs. Proc Natl Acad Sci U S A 2019; 116:4206-11. [PMID: 30683723 DOI: 10.1073/pnas.1817615116] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The crystal structure of the F1-catalytic domain of the adenosine triphosphate (ATP) synthase has been determined from Mycobacterium smegmatis which hydrolyzes ATP very poorly. The structure of the α3β3-component of the catalytic domain is similar to those in active F1-ATPases in Escherichia coli and Geobacillus stearothermophilus However, its ε-subunit differs from those in these two active bacterial F1-ATPases as an ATP molecule is not bound to the two α-helices forming its C-terminal domain, probably because they are shorter than those in active enzymes and they lack an amino acid that contributes to the ATP binding site in active enzymes. In E. coli and G. stearothermophilus, the α-helices adopt an "up" state where the α-helices enter the α3β3-domain and prevent the rotor from turning. The mycobacterial F1-ATPase is most similar to the F1-ATPase from Caldalkalibacillus thermarum, which also hydrolyzes ATP poorly. The βE-subunits in both enzymes are in the usual "open" conformation but appear to be occupied uniquely by the combination of an adenosine 5'-diphosphate molecule with no magnesium ion plus phosphate. This occupation is consistent with the finding that their rotors have been arrested at the same point in their rotary catalytic cycles. These bound hydrolytic products are probably the basis of the inhibition of ATP hydrolysis. It can be envisaged that specific as yet unidentified small molecules might bind to the F1 domain in Mycobacterium tuberculosis, prevent ATP synthesis, and inhibit the growth of the pathogen.
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27
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Abstract
H+-FOF1-ATP synthase (F-ATPase, F-type ATPase, FOF1 complex) catalyzes ATP synthesis from ADP and inorganic phosphate in eubacteria, mitochondria, chloroplasts, and some archaea. ATP synthesis is powered by the transmembrane proton transport driven by the proton motive force (PMF) generated by the respiratory or photosynthetic electron transport chains. When the PMF is decreased or absent, ATP synthase catalyzes the reverse reaction, working as an ATP-dependent proton pump. The ATPase activity of the enzyme is regulated by several mechanisms, of which the most conserved is the non-competitive inhibition by the MgADP complex (ADP-inhibition). When ADP binds to the catalytic site without phosphate, the enzyme may undergo conformational changes that lock bound ADP, resulting in enzyme inactivation. PMF can induce release of inhibitory ADP and reactivate ATP synthase; the threshold PMF value required for enzyme reactivation might exceed the PMF for ATP synthesis. Moreover, membrane energization increases the catalytic site affinity to phosphate, thereby reducing the probability of ADP binding without phosphate and preventing enzyme transition to the ADP-inhibited state. Besides phosphate, oxyanions (e.g., sulfite and bicarbonate), alcohols, lauryldimethylamine oxide, and a number of other detergents can weaken ADP-inhibition and increase ATPase activity of the enzyme. In this paper, we review the data on ADP-inhibition of ATP synthases from different organisms and discuss the in vivo role of this phenomenon and its relationship with other regulatory mechanisms, such as ATPase activity inhibition by subunit ε and nucleotide binding in the noncatalytic sites of the enzyme. It should be noted that in Escherichia coli enzyme, ADP-inhibition is relatively weak and rather enhanced than prevented by phosphate.
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Affiliation(s)
- A S Lapashina
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - B A Feniouk
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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Bogdanović N, Sundararaman L, Kamariah N, Tyagi A, Bhushan S, Ragunathan P, Shin J, Dick T, Grüber G. Structure and function of Mycobacterium-specific components of F-ATP synthase subunits α and ε. J Struct Biol 2018; 204:420-434. [PMID: 30342092 DOI: 10.1016/j.jsb.2018.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/08/2018] [Accepted: 10/16/2018] [Indexed: 01/21/2023]
Abstract
The Mycobacterium tuberculosis (Mtb) F1FO-ATP synthase (α3:β3:γ:δ:ε:a:b:b':c9) is an essential enzyme that supplies energy for both the aerobic growing and the hypoxic dormant stage of the mycobacterial life cycle. Employing the heterologous F-ATP synthase model system αchi3:β3:γ we showed previously, that transfer of the C-terminal domain (CTD) of Mtb subunit α (Mtα514-549) to a standard F-ATP synthase α subunit suppresses ATPase activity. Here we determined the 3D reconstruction from electron micrographs of the αchi3:β3:γ complex reconstituted with the Mtb subunit ε (Mtε), which has been shown to crosstalk with the CTD of Mtα. Together with the first solution shape of Mtb subunit α (Mtα), derived from solution X-ray scattering, the structural data visualize the extended C-terminal stretch of the mycobacterial subunit α. In addition, Mtε mutants MtεR62L, MtεE87A, Mtε6-121, and Mtε1-120, reconstituted with αchi3:β3:γ provided insight into their role in coupling and in trapping inhibiting MgADP. NMR solution studies of MtεE87A gave insights into how this residue contributes to stability and crosstalk between the N-terminal domain (NTD) and the CTD of Mtε. Analyses of the N-terminal mutant Mtε6-121 highlight the differences of the NTD of mycobacterial subunit ε to the well described Geobacillus stearothermophilus or Escherichia coli counterparts. These data are discussed in context of a crosstalk between the very N-terminal amino acids of Mtε and the loop region of one c subunit of the c-ring turbine for coupling of proton-translocation and ATP synthesis activity.
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Affiliation(s)
- Nebojša Bogdanović
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Lavanya Sundararaman
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Neelagandan Kamariah
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Anu Tyagi
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Shashi Bhushan
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore; NTU Institute of Structural Biology, Nanyang Technological University, Republic of Singapore
| | - Priya Ragunathan
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Joon Shin
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Thomas Dick
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Republic of Singapore; Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, 225 Warren Street, Newark, NJ 07103, USA
| | - Gerhard Grüber
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore.
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Martin JL, Ishmukhametov R, Spetzler D, Hornung T, Frasch WD. Elastic coupling power stroke mechanism of the F 1-ATPase molecular motor. Proc Natl Acad Sci U S A 2018; 115:5750-5. [PMID: 29760063 DOI: 10.1073/pnas.1803147115] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The angular velocity profile of the 120° F1-ATPase power stroke was resolved as a function of temperature from 16.3 to 44.6 °C using a ΔμATP = -31.25 kBT at a time resolution of 10 μs. Angular velocities during the first 60° of the power stroke (phase 1) varied inversely with temperature, resulting in negative activation energies with a parabolic dependence. This is direct evidence that phase 1 rotation derives from elastic energy (spring constant, κ = 50 kBT·rad-2). Phase 2 of the power stroke had an enthalpic component indicating that additional energy input occurred to enable the γ-subunit to overcome energy stored by the spring after rotating beyond its 34° equilibrium position. The correlation between the probability distribution of ATP binding to the empty catalytic site and the negative Ea values of the power stroke during phase 1 suggests that this additional energy is derived from the binding of ATP to the empty catalytic site. A second torsion spring (κ = 150 kBT·rad-2; equilibrium position, 90°) was also evident that mitigated the enthalpic cost of phase 2 rotation. The maximum ΔGǂ was 22.6 kBT, and maximum efficiency was 72%. An elastic coupling mechanism is proposed that uses the coiled-coil domain of the γ-subunit rotor as a torsion spring during phase 1, and then as a crankshaft driven by ATP-binding-dependent conformational changes during phase 2 to drive the power stroke.
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Krah A, Zarco-Zavala M, McMillan DGG. Insights into the regulatory function of the ɛ subunit from bacterial F-type ATP synthases: a comparison of structural, biochemical and biophysical data. Open Biol 2018; 8:170275. [PMID: 29769322 PMCID: PMC5990651 DOI: 10.1098/rsob.170275] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 04/24/2018] [Indexed: 01/07/2023] Open
Abstract
ATP synthases catalyse the formation of ATP, the most common chemical energy storage unit found in living cells. These enzymes are driven by an electrochemical ion gradient, which allows the catalytic evolution of ATP by a binding change mechanism. Most ATP synthases are capable of catalysing ATP hydrolysis to varying degrees, and to prevent wasteful ATP hydrolysis, bacteria and mitochondria have regulatory mechanisms such as ADP inhibition. Additionally, ɛ subunit inhibition has also been described in three bacterial systems, Escherichia coli, Bacillus PS3 and Caldalkalibacillus thermarum TA2.A1. Previous studies suggest that the ɛ subunit is capable of undergoing an ATP-dependent conformational change from the ATP hydrolytic inhibitory 'extended' conformation to the ATP-induced non-inhibitory 'hairpin' conformation. A recently published crystal structure of the F1 domain of the C. thermarum TA2.A1 F1Fo ATP synthase revealed a mutant ɛ subunit lacking the ability to bind ATP in a hairpin conformation. This is a surprising observation considering it is an organism that performs no ATP hydrolysis in vivo, and appears to challenge the current dogma on the regulatory role of the ɛ subunit. This has prompted a re-examination of present knowledge of the ɛ subunits role in different organisms. Here, we compare published biochemical, biophysical and structural data involving ɛ subunit-mediated ATP hydrolysis regulation in a variety of organisms, concluding that the ɛ subunit from the bacterial F-type ATP synthases is indeed capable of regulating ATP hydrolysis activity in a wide variety of bacteria, making it a potentially valuable drug target, but its exact role is still under debate.
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Affiliation(s)
- Alexander Krah
- School of Computational Sciences, Korea Institute for Advanced Study, 85 Hoegiro Dongdaemun-gu, Seoul 02455, Republic of Korea
| | - Mariel Zarco-Zavala
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Duncan G G McMillan
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, Delft 2629 HZ, The Netherlands
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Iqbal IK, Bajeli S, Akela AK, Kumar A. Bioenergetics of Mycobacterium: An Emerging Landscape for Drug Discovery. Pathogens 2018; 7:E24. [PMID: 29473841 PMCID: PMC5874750 DOI: 10.3390/pathogens7010024] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 01/29/2018] [Accepted: 01/31/2018] [Indexed: 11/16/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) exhibits remarkable metabolic flexibility that enables it to survive a plethora of host environments during its life cycle. With the advent of bedaquiline for treatment of multidrug-resistant tuberculosis, oxidative phosphorylation has been validated as an important target and a vulnerable component of mycobacterial metabolism. Exploiting the dependence of Mtb on oxidative phosphorylation for energy production, several components of this pathway have been targeted for the development of new antimycobacterial agents. This includes targeting NADH dehydrogenase by phenothiazine derivatives, menaquinone biosynthesis by DG70 and other compounds, terminal oxidase by imidazopyridine amides and ATP synthase by diarylquinolines. Importantly, oxidative phosphorylation also plays a critical role in the survival of persisters. Thus, inhibitors of oxidative phosphorylation can synergize with frontline TB drugs to shorten the course of treatment. In this review, we discuss the oxidative phosphorylation pathway and development of its inhibitors in detail.
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Affiliation(s)
- Iram Khan Iqbal
- Council of Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh 160036, India.
| | - Sapna Bajeli
- Council of Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh 160036, India.
| | - Ajit Kumar Akela
- Council of Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh 160036, India.
| | - Ashwani Kumar
- Council of Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh 160036, India.
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Joon S, Ragunathan P, Sundararaman L, Nartey W, Kundu S, Manimekalai MSS, Bogdanović N, Dick T, Grüber G. The NMR solution structure of Mycobacterium tuberculosis F-ATP synthase subunit ε provides new insight into energy coupling inside the rotary engine. FEBS J 2018; 285:1111-1128. [PMID: 29360236 DOI: 10.1111/febs.14392] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 11/30/2017] [Accepted: 01/18/2018] [Indexed: 11/27/2022]
Abstract
Mycobacterium tuberculosis (Mt) F1 F0 ATP synthase (α3 :β3 :γ:δ:ε:a:b:b':c9 ) is essential for the viability of growing and nongrowing persister cells of the pathogen. Here, we present the first NMR solution structure of Mtε, revealing an N-terminal β-barrel domain (NTD) and a C-terminal domain (CTD) composed of a helix-loop-helix with helix 1 and -2 being shorter compared to their counterparts in other bacteria. The C-terminal amino acids are oriented toward the NTD, forming a domain-domain interface between the NTD and CTD. The Mtε structure provides a novel mechanistic model of coupling c-ring- and ε rotation via a patch of hydrophobic residues in the NTD and residues of the CTD to the bottom of the catalytic α3 β3 -headpiece. To test our model, genome site-directed mutagenesis was employed to introduce amino acid changes in these two parts of the epsilon subunit. Inverted vesicle assays show that these mutations caused an increase in ATP hydrolysis activity and a reduction in ATP synthesis. The structural and enzymatic data are discussed in light of the transition mechanism of a compact and extended state of Mtε, which provides the inhibitory effects of this coupling subunit inside the rotary engine. Finally, the employment of these data with molecular docking shed light into the second binding site of the drug Bedaquiline. DATABASE Structural data are available in the PDB under the accession number 5YIO.
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Affiliation(s)
- Shin Joon
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Priya Ragunathan
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Lavanya Sundararaman
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Wilson Nartey
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Subhashri Kundu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Nebojša Bogdanović
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Thomas Dick
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA
| | - Gerhard Grüber
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
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