1
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Zhan J, Zeher A, Huang R, Tang WK, Jenkins LM, Xia D. Conformations of Bcs1L undergoing ATP hydrolysis suggest a concerted translocation mechanism for folded iron-sulfur protein substrate. Nat Commun 2024; 15:4655. [PMID: 38821922 PMCID: PMC11143374 DOI: 10.1038/s41467-024-49029-y] [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: 10/10/2023] [Accepted: 05/20/2024] [Indexed: 06/02/2024] Open
Abstract
The human AAA-ATPase Bcs1L translocates the fully assembled Rieske iron-sulfur protein (ISP) precursor across the mitochondrial inner membrane, enabling respiratory Complex III assembly. Exactly how the folded substrate is bound to and released from Bcs1L has been unclear, and there has been ongoing debate as to whether subunits of Bcs1L act in sequence or in unison hydrolyzing ATP when moving the protein cargo. Here, we captured Bcs1L conformations by cryo-EM during active ATP hydrolysis in the presence or absence of ISP substrate. In contrast to the threading mechanism widely employed by AAA proteins in substrate translocation, subunits of Bcs1L alternate uniformly between ATP and ADP conformations without detectable intermediates that have different, co-existing nucleotide states, indicating that the subunits act in concert. We further show that the ISP can be trapped by Bcs1 when its subunits are all in the ADP-bound state, which we propose to be released in the apo form.
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Affiliation(s)
- Jingyu Zhan
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Allison Zeher
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- NIH Intramural Cryo-EM Consortium (NICE), Bethesda, MD, USA
| | - Rick Huang
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- NIH Intramural Cryo-EM Consortium (NICE), Bethesda, MD, USA
| | - Wai Kwan Tang
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Di Xia
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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2
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Zheng W, Chai P, Zhu J, Zhang K. High-resolution in situ structures of mammalian respiratory supercomplexes. Nature 2024:10.1038/s41586-024-07488-9. [PMID: 38811722 DOI: 10.1038/s41586-024-07488-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 04/30/2024] [Indexed: 05/31/2024]
Abstract
Mitochondria play a pivotal part in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane through a series of respiratory complexes1-4. Despite extensive in vitro structural studies, determining the atomic details of their molecular mechanisms in physiological states remains a major challenge, primarily because of loss of the native environment during purification. Here we directly image porcine mitochondria using an in situ cryo-electron microscopy approach. This enables us to determine the structures of various high-order assemblies of respiratory supercomplexes in their native states. We identify four main supercomplex organizations: I1III2IV1, I1III2IV2, I2III2IV2 and I2III4IV2, which potentially expand into higher-order arrays on the inner membranes. These diverse supercomplexes are largely formed by 'protein-lipids-protein' interactions, which in turn have a substantial impact on the local geometry of the surrounding membranes. Our in situ structures also capture numerous reactive intermediates within these respiratory supercomplexes, shedding light on the dynamic processes of the ubiquinone/ubiquinol exchange mechanism in complex I and the Q-cycle in complex III. Structural comparison of supercomplexes from mitochondria treated under different conditions indicates a possible correlation between conformational states of complexes I and III, probably in response to environmental changes. By preserving the native membrane environment, our approach enables structural studies of mitochondrial respiratory supercomplexes in reaction at high resolution across multiple scales, from atomic-level details to the broader subcellular context.
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Affiliation(s)
- Wan Zheng
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Pengxin Chai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jiapeng Zhu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Kai Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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3
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Hagras MA. Respiratory Complex III: A Bioengine with a Ligand-Triggered Electron-Tunneling Gating Mechanism. J Phys Chem B 2024; 128:990-1000. [PMID: 38241470 DOI: 10.1021/acs.jpcb.3c07095] [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: 01/21/2024]
Abstract
Respiratory complex III (a.k.a., the bc1 complex) plays a key role in the electron transport chain in aerobic cells. The bc1 complex exhibits multiple unique electron tunneling (ET) processes, such as ET-bifurcation at the Qo site and movement of the Rieske domain. Moreover, we previously discovered that electron tunneling in the low potential arm of the bc1 complex is regulated by a key phenylalanine residue (Phe90). The main goal of the current work is to study the dynamics of the key Phe90 residue in the electron tunneling reaction between heme bL and heme bH as a function of the occupancy of the Qo and Qi binding sites in the bc1 complex. We simulated the molecular dynamics of four model systems of respiratory complex III with different ligands bound at the Qo and Qi binding sites. In addition, we calculated the electron tunneling rate constants between heme bL and heme bH along the simulated molecular dynamics trajectories. The binding of aromatic ligands at the Qo site induces a conformational cascade that properly positions the Phe90 residue, reducing the through-space ET distance from ∼7 to ∼5.5 Å and thus enhancing the electron transfer rate between the heme bL and the heme bH redox pair. Also, the binding of aromatic ligands at the Qi site induces conformational changes that stabilize the Phe90 conformational variation from ∼1.5 to ∼0.5 Å. Hence, our molecular dynamics simulation results show an on-demand two-step conformational connection between the occupancy of the Qo and Qi binding sites and the conformational dynamics of the Phe90 residue. Additionally, our dynamic electron tunneling results confirm our previously reported findings that the Phe90 residue acts as an electron-tunneling gate or switch, controlling the electron transfer rate between the heme bL and heme bH redox systems.
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Affiliation(s)
- Muhammad A Hagras
- Department of Basic Sciences, University of Health Sciences and Pharmacy, St. Louis, Missouri 63110, United States
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4
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Esser L, Xia D. Mitochondrial Cytochrome bc1 Complex as Validated Drug Target: A Structural Perspective. Trop Med Infect Dis 2024; 9:39. [PMID: 38393128 PMCID: PMC10892539 DOI: 10.3390/tropicalmed9020039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Mitochondrial respiratory chain Complex III, also known as cytochrome bc1 complex or cyt bc1, is a validated target not only for antibiotics but also for pesticides and anti-parasitic drugs. Although significant progress has been made in understanding the mechanisms of cyt bc1 function and inhibition by using various natural and synthetic compounds, important issues remain in overcoming drug resistance in agriculture and in evading cytotoxicity in medicine. In this review, we look at these issues from a structural perspective. After a brief description of the essential and common structural features, we point out the differences among various cyt bc1 complexes of different organisms, whose structures have been determined to atomic resolution. We use a few examples of cyt bc1 structures determined via bound inhibitors to illustrate both conformational changes observed and implications to the Q-cycle mechanism of cyt bc1 function. These structures not only offer views of atomic interactions between cyt bc1 complexes and inhibitors, but they also provide explanations for drug resistance when structural details are coupled to sequence changes. Examples are provided for exploiting structural differences in evolutionarily conserved enzymes to develop antifungal drugs for selectivity enhancement, which offer a unique perspective on differential interactions that can be exploited to overcome cytotoxicity in treating human infections.
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Affiliation(s)
| | - Di Xia
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 2122C, Bethesda, MD 20892, USA
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5
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Pan Y, Zhan J, Jiang Y, Xia D, Scheuring S. A concerted ATPase cycle of the protein transporter AAA-ATPase Bcs1. Nat Commun 2023; 14:6369. [PMID: 37821516 PMCID: PMC10567702 DOI: 10.1038/s41467-023-41806-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 09/18/2023] [Indexed: 10/13/2023] Open
Abstract
Bcs1, a homo-heptameric transmembrane AAA-ATPase, facilitates folded Rieske iron-sulfur protein translocation across the inner mitochondrial membrane. Structures in different nucleotide states (ATPγS, ADP, apo) provided conformational snapshots, but the kinetics and structural transitions of the ATPase cycle remain elusive. Here, using high-speed atomic force microscopy (HS-AFM) and line scanning (HS-AFM-LS), we characterized single-molecule Bcs1 ATPase cycling. While the ATP conformation had ~5600 ms lifetime, independent of the ATP-concentration, the ADP/apo conformation lifetime was ATP-concentration dependent and reached ~320 ms at saturating ATP-concentration, giving a maximum turnover rate of 0.17 s-1. Importantly, Bcs1 ATPase cycle conformational changes occurred in concert. Furthermore, we propose that the transport mechanism involves opening the IMS gate through energetically costly straightening of the transmembrane helices, potentially driving rapid gate resealing. Overall, our results establish a concerted ATPase cycle mechanism in Bcs1, distinct from other AAA-ATPases that use a hand-over-hand mechanism.
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Affiliation(s)
- Yangang Pan
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Jingyu Zhan
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yining Jiang
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Biochemistry & Structural Biology, Cell & Developmental Biology, and Molecular Biology (BCMB) Program, Weill Cornell Graduate School of Biomedical Sciences, New York, USA
| | - Di Xia
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Simon Scheuring
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA.
- Department of Physiology & Biophysics, Weill Cornell Medical College, New York, NY, USA.
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY, USA.
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6
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Jacobs HT, Szibor M, Rathkolb B, da Silva-Buttkus P, Aguilar-Pimentel JA, Amarie OV, Becker L, Calzada-Wack J, Dragano N, Garrett L, Gerlini R, Hölter SM, Klein-Rodewald T, Kraiger M, Leuchtenberger S, Marschall S, Östereicher MA, Pfannes K, Sanz-Moreno A, Seisenberger C, Spielmann N, Stoeger C, Wurst W, Fuchs H, Hrabě de Angelis M, Gailus-Durner V. AOX delays the onset of the lethal phenotype in a mouse model of Uqcrh (complex III) disease. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166760. [PMID: 37230398 DOI: 10.1016/j.bbadis.2023.166760] [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: 03/09/2023] [Revised: 04/24/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023]
Abstract
The alternative oxidase, AOX, provides a by-pass of the cytochrome segment of the mitochondrial respiratory chain when the chain is unavailable. AOX is absent from mammals, but AOX from Ciona intestinalis is benign when expressed in mice. Although non-protonmotive, so does not contribute directly to ATP production, it has been shown to modify and in some cases rescue phenotypes of respiratory-chain disease models. Here we studied the effect of C. intestinalis AOX on mice engineered to express a disease-equivalent mutant of Uqcrh, encoding the hinge subunit of mitochondrial respiratory complex III, which results in a complex metabolic phenotype beginning at 4-5 weeks, rapidly progressing to lethality within a further 6-7 weeks. AOX expression delayed the onset of this phenotype by several weeks, but provided no long-term benefit. We discuss the significance of this finding in light of the known and hypothesized effects of AOX on metabolism, redox homeostasis, oxidative stress and cell signaling. Although not a panacea, the ability of AOX to mitigate disease onset and progression means it could be useful in treatment.
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Affiliation(s)
- Howard T Jacobs
- Faculty of Medicine and Health Technology, FI-33014 Tampere University, Finland; Department of Environment and Genetics, La Trobe University, Melbourne, Victoria 3086, Australia.
| | - Marten Szibor
- Faculty of Medicine and Health Technology, FI-33014 Tampere University, Finland; Department of Cardiothoracic Surgery, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Friedrich Schiller University of Jena, Am Klinikum 1, 07747 Jena, Germany
| | - Birgit Rathkolb
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany; Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-University München, Feodor-Lynen Str. 25, 81377 Munich, Germany; German Center for Diabetes Research (DZD), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Patricia da Silva-Buttkus
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Juan Antonio Aguilar-Pimentel
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Oana V Amarie
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Lore Becker
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Julia Calzada-Wack
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Nathalia Dragano
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Lillian Garrett
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Raffaele Gerlini
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Sabine M Hölter
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany; Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Tanja Klein-Rodewald
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Markus Kraiger
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Stefanie Leuchtenberger
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Susan Marschall
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Manuela A Östereicher
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Kristina Pfannes
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Adrián Sanz-Moreno
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Claudia Seisenberger
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Nadine Spielmann
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Claudia Stoeger
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany; Chair of Developmental Genetics, TUM School of Life Sciences, Technische Universität München, Freising-Weihenstephan, Germany; Deutsches Institut für Neurodegenerative Erkrankungen (DZNE) Site Munich, Feodor-Lynen-Str. 17, 81377 Munich, Germany
| | - Helmut Fuchs
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Martin Hrabě de Angelis
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany; Chair of Experimental Genetics, TUM School of Life Sciences, Technische Universität München, Alte Akademie 8, 85354 Freising, Germany.
| | - Valérie Gailus-Durner
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
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7
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Borek A, Wójcik-Augustyn A, Kuleta P, Ekiert R, Osyczka A. Identification of hydrogen bonding network for proton transfer at the quinol oxidation site of Rhodobacter capsulatus cytochrome bc 1. J Biol Chem 2023; 299:105249. [PMID: 37714464 PMCID: PMC10583091 DOI: 10.1016/j.jbc.2023.105249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023] Open
Abstract
Cytochrome bc1 catalyzes electron transfer from quinol (QH2) to cytochrome c in reactions coupled to proton translocation across the energy-conserving membrane. Energetic efficiency of the catalytic cycle is secured by a two-electron and two-proton bifurcation reaction leading to oxidation of QH2 and reduction of the Rieske cluster and heme bL. The proton paths associated with this reaction remain elusive. Here, we used site-directed mutagenesis and quantum mechanical calculations to analyze the contribution of protonable side chains located at the heme bL side of the QH2 oxidation site in Rhodobacter capsulatus cytochrome bc1. We observe that the proton path is effectively switched off when H276 and E295 are simultaneously mutated to the nonprotonable residues in the H276F/E295V double mutant. The two single mutants, H276F or E295V, are less efficient but still transfer protons at functionally relevant rates. Natural selection exposed two single mutations, N279S and M154T, that restored the functional proton transfers in H276F/E295V. Quantum mechanical calculations indicated that H276F/E295V traps the side chain of Y147 in a position distant from QH2, whereas either N279S or M154T induce local changes releasing Y147 from that position. This shortens the distance between the protonable groups of Y147 and D278 and/or increases mobility of the Y147 side chain, which makes Y147 efficient in transferring protons from QH2 toward D278 in H276F/E295V. Overall, our study identified an extended hydrogen bonding network, build up by E295, H276, D278, and Y147, involved in efficient proton removal from QH2 at the heme bL side of QH2 oxidation site.
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Affiliation(s)
- Arkadiusz Borek
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Anna Wójcik-Augustyn
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Patryk Kuleta
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Robert Ekiert
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Artur Osyczka
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland.
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8
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Wang JY, Zhang LH, Hong YH, Cai LN, Storey KB, Zhang JY, Zhang SS, Yu DN. How Does Mitochondrial Protein-Coding Gene Expression in Fejervarya kawamurai (Anura: Dicroglossidae) Respond to Extreme Temperatures? Animals (Basel) 2023; 13:3015. [PMID: 37835622 PMCID: PMC10571990 DOI: 10.3390/ani13193015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/22/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023] Open
Abstract
Unusual climates can lead to extreme temperatures. Fejervarya kawamurai, one of the most prevalent anurans in the paddy fields of tropical and subtropical regions in Asia, is sensitive to climate change. The present study focuses primarily on a single question: how do the 13 mitochondrial protein-coding genes (PCGs) respond to extreme temperature change compared with 25 °C controls? Thirty-eight genes including an extra tRNA-Met gene were identified and sequenced from the mitochondrial genome of F. kawamurai. Evolutionary relationships were assessed within the Dicroglossidae and showed that Dicroglossinae is monophyletic and F. kawamurai is a sister group to the clade of (F. multistriata + F. limnocharis). Transcript levels of mitochondrial genes in liver were also evaluated to assess responses to 24 h exposure to low (2 °C and 4 °C) or high (40 °C) temperatures. Under 2 °C, seven genes showed significant changes in liver transcript levels, among which transcript levels of ATP8, ND1, ND2, ND3, ND4, and Cytb increased, respectively, and ND5 decreased. However, exposure to 4 °C for 24 h was very different in that the expressions of ten mitochondrial protein-coding genes, except ND1, ND3, and Cytb, were significantly downregulated. Among them, the transcript level of ND5 was most significantly downregulated, decreasing by 0.28-fold. Exposure to a hot environment at 40 °C for 24 h resulted in a marked difference in transcript responses with strong upregulation of eight genes, ranging from a 1.52-fold increase in ND4L to a 2.18-fold rise in Cytb transcript levels, although COI and ND5 were reduced to 0.56 and 0.67, respectively, compared with the controls. Overall, these results suggest that at 4 °C, F. kawamurai appears to have entered a hypometabolic state of hibernation, whereas its mitochondrial oxidative phosphorylation was affected at both 2 °C and 40 °C. The majority of mitochondrial PCGs exhibited substantial changes at all three temperatures, indicating that frogs such as F. kawamurai that inhabit tropical or subtropical regions are susceptible to ambient temperature changes and can quickly employ compensating adjustments to proteins involved in the mitochondrial electron transport chain.
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Affiliation(s)
- Jing-Yan Wang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Li-Hua Zhang
- Taishun County Forestry Bureau, Wenzhou 325000, China
| | - Yue-Huan Hong
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Ling-Na Cai
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Jia-Yong Zhang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Shu-Sheng Zhang
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
- Zhejiang Wuyanling National Nature Reserve, Wenzhou 325500, China
| | - Dan-Na Yu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
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9
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Lamb IM, Okoye IC, Mather MW, Vaidya AB. Unique Properties of Apicomplexan Mitochondria. Annu Rev Microbiol 2023; 77:541-560. [PMID: 37406344 DOI: 10.1146/annurev-micro-032421-120540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
Apicomplexan parasites constitute more than 6,000 species infecting a wide range of hosts. These include important pathogens such as those causing malaria and toxoplasmosis. Their evolutionary emergence coincided with the dawn of animals. Mitochondrial genomes of apicomplexan parasites have undergone dramatic reduction in their coding capacity, with genes for only three proteins and ribosomal RNA genes present in scrambled fragments originating from both strands. Different branches of the apicomplexans have undergone rearrangements of these genes, with Toxoplasma having massive variations in gene arrangements spread over multiple copies. The vast evolutionary distance between the parasite and the host mitochondria has been exploited for the development of antiparasitic drugs, especially those used to treat malaria, wherein inhibition of the parasite mitochondrial respiratory chain is selectively targeted with little toxicity to the host mitochondria. We describe additional unique characteristics of the parasite mitochondria that are being investigated and provide greater insights into these deep-branching eukaryotic pathogens.
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Affiliation(s)
- Ian M Lamb
- Center for Molecular Parasitology, Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA;
| | - Ijeoma C Okoye
- Center for Molecular Parasitology, Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA;
| | - Michael W Mather
- Center for Molecular Parasitology, Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA;
| | - Akhil B Vaidya
- Center for Molecular Parasitology, Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA;
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10
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Esser L, Zhou F, Zeher A, Wu W, Huang R, Yu CA, Lane KD, Wellems TE, Xia D. Structure of complex III with bound antimalarial agent CK-2-68 provides insights into selective inhibition of Plasmodium cytochrome bc 1 complexes. J Biol Chem 2023; 299:104860. [PMID: 37236355 PMCID: PMC10404626 DOI: 10.1016/j.jbc.2023.104860] [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: 12/19/2022] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Among the various components of the protozoan Plasmodium mitochondrial respiratory chain, only Complex III is a validated cellular target for antimalarial drugs. The compound CK-2-68 was developed to specifically target the alternate NADH dehydrogenase of the malaria parasite respiratory chain, but the true target for its antimalarial activity has been controversial. Here, we report the cryo-EM structure of mammalian mitochondrial Complex III bound with CK-2-68 and examine the structure-function relationships of the inhibitor's selective action on Plasmodium. We show that CK-2-68 binds specifically to the quinol oxidation site of Complex III, arresting the motion of the iron-sulfur protein subunit, which suggests an inhibition mechanism similar to that of Pf-type Complex III inhibitors such as atovaquone, stigmatellin, and UHDBT. Our results shed light on the mechanisms of observed resistance conferred by mutations, elucidate the molecular basis of the wide therapeutic window of CK-2-68 for selective action of Plasmodium vs. host cytochrome bc1, and provide guidance for future development of antimalarials targeting Complex III.
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Affiliation(s)
- Lothar Esser
- Laboratory of Cell Biology, Center for Cancer Research National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Fei Zhou
- Laboratory of Cell Biology, Center for Cancer Research National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Allison Zeher
- Laboratory of Cell Biology, Center for Cancer Research National Cancer Institute, NIH, Bethesda, Maryland, USA; NIH Intramural Cryo-EM Consortium (NICE), Bethesda, Maryland, USA
| | - Weimin Wu
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, NIH, Frederick, Maryland, USA
| | - Rick Huang
- Laboratory of Cell Biology, Center for Cancer Research National Cancer Institute, NIH, Bethesda, Maryland, USA; NIH Intramural Cryo-EM Consortium (NICE), Bethesda, Maryland, USA
| | - Chang-An Yu
- Department of Biochemistry, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Kristin D Lane
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Thomas E Wellems
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Di Xia
- Laboratory of Cell Biology, Center for Cancer Research National Cancer Institute, NIH, Bethesda, Maryland, USA.
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11
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Lu X, Vandenhole M, Tsakireli D, Pergantis SA, Vontas J, Jonckheere W, Van Leeuwen T. Increased metabolism in combination with the novel cytochrome b target-site mutation L258F confers cross-resistance between the Q o inhibitors acequinocyl and bifenazate in Tetranychus urticae. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 192:105411. [PMID: 37105638 DOI: 10.1016/j.pestbp.2023.105411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 06/19/2023]
Abstract
Acequinocyl and bifenazate are potent acaricides acting at the Qo site of complex III of the electron transport chain, but frequent applications of these acaricides have led to the development of resistance in spider mites. Target-site resistance caused by mutations in the conserved cd1- and ef-helices of the Qo pocket of cytochrome b has been elucidated as the main resistance mechanism. We therefore monitored Qo pocket mutations in European field populations of Tetranychus urticae and uncovered a new mutation, L258F. The role of this mutation was validated by revealing patterns of maternal inheritance and by the independently replicated introgression in an unrelated susceptible genetic background. However, the parental strain exhibited higher resistance levels than conferred by the mutation alone in isogenic lines, especially for acequinocyl, implying the involvement of strong additional resistance mechanisms. This was confirmed by revealing a polygenic inheritance pattern with classical genetic crosses and via synergism experiments. Therefore, a genome-wide expression analysis was conducted that identified a number of highly overexpressed detoxification genes, including many P450s. Functional expression revealed that the P450 CYP392A11 can metabolize bifenazate by hydroxylation of the ring structure. In conclusion, the novel cytochrome b target-site mutation L258F was uncovered in a recently collected field strain and its role in acequinocyl and bifenazate resistance was validated. However, the high level of resistance in this strain is most likely caused by a combination of target-site resistance and P450-based increased detoxification, potentially acting in synergism.
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Affiliation(s)
- Xueping Lu
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Coupure Links 653, Ghent University, B-9000 Ghent, Belgium.
| | - Marilou Vandenhole
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Coupure Links 653, Ghent University, B-9000 Ghent, Belgium.
| | - Dimitra Tsakireli
- Laboratory of Pesticide Science, Department of Crop Science, Agricultural University of Athens, 75 Iera Odos Street, GR-11855 Athens, Greece; Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology, Hellas, 100 N. Plastira Street, GR-700 13 Heraklion, Crete, Greece.
| | - Spiros A Pergantis
- Environmental Chemical Processes Laboratory, Department of Chemistry, University of Crete, Voutes Campus, 70013 Heraklion, Crete, Greece.
| | - John Vontas
- Laboratory of Pesticide Science, Department of Crop Science, Agricultural University of Athens, 75 Iera Odos Street, GR-11855 Athens, Greece; Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology, Hellas, 100 N. Plastira Street, GR-700 13 Heraklion, Crete, Greece.
| | - Wim Jonckheere
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Coupure Links 653, Ghent University, B-9000 Ghent, Belgium.
| | - Thomas Van Leeuwen
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Coupure Links 653, Ghent University, B-9000 Ghent, Belgium.
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12
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Havens J, Su T, Wang Q, Yu CA, Yu L, Durham B, Millett F. Photoinduced electron transfer in cytochrome bc 1: Dynamics of rotation of the Iron-sulfur protein during bifurcated electron transfer from ubiquinol to cytochrome c 1 and cytochrome b L. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148957. [PMID: 36709837 DOI: 10.1016/j.bbabio.2023.148957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 01/12/2023] [Accepted: 01/20/2023] [Indexed: 01/27/2023]
Abstract
The electron transfer reactions within wild-type Rhodobacter sphaeroides cytochrome bc1 (cyt bc1) were studied using a binuclear ruthenium complex to rapidly photooxidize cyt c1. When cyt c1, the iron‑sulfur center Fe2S2, and cyt bH were reduced before the reaction, photooxidation of cyt c1 led to electron transfer from Fe2S2 to cyt c1 with a rate constant of ka = 80,000 s-1, followed by bifurcated reduction of both Fe2S2 and cyt bL by QH2 in the Qo site with a rate constant of k2 = 3000 s-1. The resulting Q then traveled from the Qo site to the Qi site and oxidized one equivalent each of cyt bL and cyt bH with a rate constant of k3 = 340 s-1. The rate constant ka was decreased in a nonlinear fashion by a factor of 53 as the viscosity was increased to 13.7. A mechanism that is consistent with the effect of viscosity involves rotational diffusion of the iron‑sulfur protein from the b state with reduced Fe2S2 close to cyt bL to one or more intermediate states, followed by rotation to the final c1 state with Fe2S2 close to cyt c1, and rapid electron transfer to cyt c1.
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Affiliation(s)
- Jeffrey Havens
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States of America; Vaccines and Therapeutics Division, Chemical and Biological Technologies, Defense Threat Reduction Agency, Fort Belvoir, VA 22060, United States of America
| | - Ting Su
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, United States of America; ABclonal Technology Woburn, MA 01801, United States of America
| | - Qiyu Wang
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, United States of America; Vesigen Therapeutics Cambridge, MA 02139, United States of America
| | - Chang-An Yu
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, United States of America
| | - Linda Yu
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, United States of America
| | - Bill Durham
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States of America
| | - Francis Millett
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States of America.
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13
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Zhan J, Xia D. Bcs1, a novel target for fungicide. Front Chem 2023; 11:1146753. [PMID: 36993815 PMCID: PMC10040684 DOI: 10.3389/fchem.2023.1146753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/03/2023] [Indexed: 03/14/2023] Open
Abstract
The mitochondrial respiratory chain has long been a primary target for the development of fungicides for its indispensable role in various cellular functions including energy metabolism. Over the years, a wide range of natural and synthetic fungicides and pesticides targeting the respiratory chain complexes have been discovered or developed and used in agriculture and in medicine, which brought considerable economic gains but was also accompanied by the emergence of resistance to these compounds. To delay and overcome the onset of resistance, novel targets for fungicides development are actively being pursued. Mitochondrial AAA protein Bcs1 is necessary for the biogenesis of respiratory chain Complex III, also known as cyt bc1 complex, by delivering the last essential iron-sulfur protein subunit in its folded form to the cyt bc1 precomplex. Although no report on the phenotypes of knock-out Bcs1 has been reported in animals, pathogenic Bcs1 mutations cause Complex III deficiency and respiratory growth defects, which makes it a promising new target for the development of fungicides. Recent Cryo-EM and X-ray structures of mouse and yeast Bcs1 revealed the basic oligomeric states of Bcs1, shed light on the translocation mechanism of its substrate ISP, and provided the basis for structure-based drug design. This review summarizes the recent progress made on understanding the structure and function of Bcs1, proposes the use of Bcs1 as an antifungal target, and provides novel prospects for fungicides design by targeting Bcs1.
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14
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Wieferig JP, Kühlbrandt W. Analysis of the conformational heterogeneity of the Rieske iron-sulfur protein in complex III 2 by cryo-EM. IUCRJ 2023; 10:27-37. [PMID: 36598500 PMCID: PMC9812224 DOI: 10.1107/s2052252522010570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
Movement of the Rieske domain of the iron-sulfur protein is essential for intramolecular electron transfer within complex III2 (CIII2) of the respiratory chain as it bridges a gap in the cofactor chain towards the electron acceptor cytochrome c. We present cryo-EM structures of CIII2 from Yarrowia lipolytica at resolutions up to 2.0 Å under different conditions, with different redox states of the cofactors of the high-potential chain. All possible permutations of three primary positions were observed, indicating that the two halves of the dimeric complex act independently. Addition of the substrate analogue decylubiquinone to CIII2 with a reduced high-potential chain increased the occupancy of the Qo site. The extent of Rieske domain interactions through hydrogen bonds to the cytochrome b and cytochrome c1 subunits varied depending on the redox state and substrate. In the absence of quinols, the reduced Rieske domain interacted more closely with cytochrome b and cytochrome c1 than in the oxidized state. Upon addition of the inhibitor antimycin A, the heterogeneity of the cd1-helix and ef-loop increased, which may be indicative of a long-range effect on the Rieske domain.
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Affiliation(s)
- Jan-Philip Wieferig
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
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15
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Zara V, De Blasi G, Ferramosca A. Assembly of the Multi-Subunit Cytochrome bc1 Complex in the Yeast Saccharomyces cerevisiae. Int J Mol Sci 2022; 23:ijms231810537. [PMID: 36142449 PMCID: PMC9502982 DOI: 10.3390/ijms231810537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/29/2022] Open
Abstract
The cytochrome bc1 complex is an essential component of the mitochondrial respiratory chain of the yeast Saccharomyces cerevisiae. It is composed of ten protein subunits, three of them playing an important role in electron transfer and proton pumping across the inner mitochondrial membrane. Cytochrome b, the central component of this respiratory complex, is encoded by the mitochondrial genome, whereas all the other subunits are of nuclear origin. The assembly of all these subunits into the mature and functional cytochrome bc1 complex is therefore a complicated process which requires the participation of several chaperone proteins. It has been found that the assembly process of the mitochondrial bc1 complex proceeds through the formation of distinct sub-complexes in an ordered sequence. Most of these sub-complexes have been thoroughly characterized, and their molecular compositions have also been defined. This study critically analyses the results obtained so far and highlights new possible areas of investigation.
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16
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Wang L, Yang Z, He X, Pu S, Yang C, Wu Q, Zhou Z, Cen X, Zhao H. Mitochondrial protein dysfunction in pathogenesis of neurological diseases. Front Mol Neurosci 2022; 15:974480. [PMID: 36157077 PMCID: PMC9489860 DOI: 10.3389/fnmol.2022.974480] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/08/2022] [Indexed: 11/21/2022] Open
Abstract
Mitochondria are essential organelles for neuronal function and cell survival. Besides the well-known bioenergetics, additional mitochondrial roles in calcium signaling, lipid biogenesis, regulation of reactive oxygen species, and apoptosis are pivotal in diverse cellular processes. The mitochondrial proteome encompasses about 1,500 proteins encoded by both the nuclear DNA and the maternally inherited mitochondrial DNA. Mutations in the nuclear or mitochondrial genome, or combinations of both, can result in mitochondrial protein deficiencies and mitochondrial malfunction. Therefore, mitochondrial quality control by proteins involved in various surveillance mechanisms is critical for neuronal integrity and viability. Abnormal proteins involved in mitochondrial bioenergetics, dynamics, mitophagy, import machinery, ion channels, and mitochondrial DNA maintenance have been linked to the pathogenesis of a number of neurological diseases. The goal of this review is to give an overview of these pathways and to summarize the interconnections between mitochondrial protein dysfunction and neurological diseases.
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Affiliation(s)
- Liang Wang
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu, China
| | - Ziyun Yang
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu, China
- School of Life Sciences, Guangxi Normal University, Guilin, China
- Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China
- Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Xiumei He
- School of Life Sciences, Guangxi Normal University, Guilin, China
- Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China
- Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Shiming Pu
- School of Life Sciences, Guangxi Normal University, Guilin, China
- Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China
- Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Cheng Yang
- School of Life Sciences, Guangxi Normal University, Guilin, China
- Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China
- Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Qiong Wu
- School of Life Sciences, Guangxi Normal University, Guilin, China
- Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China
- Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Zuping Zhou
- Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China
- Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Xiaobo Cen
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu, China
| | - Hongxia Zhao
- School of Life Sciences, Guangxi Normal University, Guilin, China
- Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China
- Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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17
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Meyer EH, Letts JA, Maldonado M. Structural insights into the assembly and the function of the plant oxidative phosphorylation system. THE NEW PHYTOLOGIST 2022; 235:1315-1329. [PMID: 35588181 DOI: 10.1111/nph.18259] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/05/2022] [Indexed: 05/23/2023]
Abstract
One of the key functions of mitochondria is the production of ATP to support cellular metabolism and growth. The last step of mitochondrial ATP synthesis is performed by the oxidative phosphorylation (OXPHOS) system, an ensemble of protein complexes embedded in the inner mitochondrial membrane. In the last 25 yr, many structures of OXPHOS complexes and supercomplexes have been resolved in yeast, mammals, and bacteria. However, structures of plant OXPHOS enzymes only became available very recently. In this review, we highlight the plant-specific features revealed by the recent structures and discuss how they advance our understanding of the function and assembly of plant OXPHOS complexes. We also propose new hypotheses to be tested and discuss older findings to be re-evaluated. Further biochemical and structural work on the plant OXPHOS system will lead to a deeper understanding of plant respiration and its regulation, with significant agricultural, environmental, and societal implications.
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Affiliation(s)
- Etienne H Meyer
- Institute of Plant Physiology, Martin-Luther-University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany
| | - James A Letts
- Department of Molecular and Cellular Biology, University of California-Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Maria Maldonado
- Department of Molecular and Cellular Biology, University of California-Davis, One Shields Avenue, Davis, CA, 95616, USA
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18
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Amporndanai K, Pinthong N, O’Neill PM, Hong WD, Amewu RK, Pidathala C, Berry NG, Leung SC, Ward SA, Biagini GA, Hasnain SS, Antonyuk SV. Targeting the Ubiquinol-Reduction (Q i) Site of the Mitochondrial Cytochrome bc1 Complex for the Development of Next Generation Quinolone Antimalarials. BIOLOGY 2022; 11:biology11081109. [PMID: 35892964 PMCID: PMC9330653 DOI: 10.3390/biology11081109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/11/2022] [Accepted: 07/18/2022] [Indexed: 11/16/2022]
Abstract
Antimalarials targeting the ubiquinol-oxidation (Qo) site of the Plasmodium falciparum bc1 complex, such as atovaquone, have become less effective due to the rapid emergence of resistance linked to point mutations in the Qo site. Recent findings showed a series of 2-aryl quinolones mediate inhibitions of this complex by binding to the ubiquinone-reduction (Qi) site, which offers a potential advantage in circumventing drug resistance. Since it is essential to understand how 2-aryl quinolone lead compounds bind within the Qi site, here we describe the co-crystallization and structure elucidation of the bovine cytochrome bc1 complex with three different antimalarial 4(1H)-quinolone sub-types, including two 2-aryl quinolone derivatives and a 3-aryl quinolone analogue for comparison. Currently, no structural information is available for Plasmodial cytochrome bc1. Our crystallographic studies have enabled comparison of an in-silico homology docking model of P. falciparum with the mammalian's equivalent, enabling an examination of how binding compares for the 2- versus 3-aryl analogues. Based on crystallographic and computational modeling, key differences in human and P. falciparum Qi sites have been mapped that provide new insights that can be exploited for the development of next-generation antimalarials with greater selective inhibitory activity against the parasite bc1 with improved antimalarial properties.
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Affiliation(s)
- Kangsa Amporndanai
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK; (K.A.); (N.P.); (S.S.H.)
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Nattapon Pinthong
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK; (K.A.); (N.P.); (S.S.H.)
- Department of Protozoology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Paul M. O’Neill
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
- Correspondence: (P.M.O.); (S.V.A.); Tel.: +44-(0)-1517955145 (S.V.A.); +44-(0)-1517943552 (P.M.O.)
| | - W. David Hong
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
| | - Richard K. Amewu
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
- Department of Chemistry, School of Physical and Mathematical Sciences, University of Ghana, Accra P.O. Box LG 586, Ghana
| | - Chandrakala Pidathala
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
- Composite Interceptive Med-Science Laboratories Pvt. Ltd., Bengaluru 60099, Karnataka, India
| | - Neil G. Berry
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
| | - Suet C. Leung
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
| | - Stephen A. Ward
- Centre for Drugs and Diagnostics, Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK; (S.A.W.); (G.A.B.)
| | - Giancarlo A. Biagini
- Centre for Drugs and Diagnostics, Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK; (S.A.W.); (G.A.B.)
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK; (K.A.); (N.P.); (S.S.H.)
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK; (K.A.); (N.P.); (S.S.H.)
- Correspondence: (P.M.O.); (S.V.A.); Tel.: +44-(0)-1517955145 (S.V.A.); +44-(0)-1517943552 (P.M.O.)
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19
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Mendes D, Peixoto F, Oliveira MM, Andrade PB, Videira RA. Mitochondria research and neurodegenerative diseases: on the track to understanding the biological world of high complexity. Mitochondrion 2022; 65:67-79. [PMID: 35623557 DOI: 10.1016/j.mito.2022.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/20/2022] [Accepted: 05/22/2022] [Indexed: 12/18/2022]
Abstract
From the simple unicellular eukaryote to the highly complex multicellular organism like Human, mitochondrion emerges as a ubiquitous player to ensure the organism's functionality. It is popularly known as "the powerhouse of the cell" by its key role in ATP generation. However, our understanding of the physiological relevance of mitochondria is being challenged by data obtained in different fields. In this review, a short history of the mitochondria research field is presented, stressing the findings and questions that allowed the knowledge advances, and put mitochondrion as the main player of safeguarding organism life as well as a key to solve the puzzle of the neurodegenerative diseases.
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Affiliation(s)
- Daniela Mendes
- REQUIMTE/LAQV, Laboratory of Pharmacognosy, Department of Chemistry, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, no 228, Porto 4050-313, Portugal
| | - Francisco Peixoto
- Chemistry Center - Vila Real (CQ-VR), Biological and Environment Department, School of Life and Environmental Sciences, University of Trás-os-Montes e Alto Douro, UTAD, P.O. Box 1013, 5001-801 Vila Real, Portugal
| | - Maria M Oliveira
- Chemistry Center - Vila Real (CQ-VR), Chemistry Department, School of Life and Environmental Sciences, University of Trás-os-Montes e Alto Douro, UTAD, P.O. Box 1013, 5001-801 Vila Real, Portugal
| | - Paula B Andrade
- REQUIMTE/LAQV, Laboratory of Pharmacognosy, Department of Chemistry, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, no 228, Porto 4050-313, Portugal
| | - Romeu A Videira
- REQUIMTE/LAQV, Laboratory of Pharmacognosy, Department of Chemistry, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, no 228, Porto 4050-313, Portugal.
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20
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Wang Y, Chi H, Xu F, He Z, Li Z, Wu F, Li Y, Zhang G, Peng X, Yu S, Yang J, Zhang W, Yang X. Cadmium chloride-induced apoptosis of HK-2 cells via interfering with mitochondrial respiratory chain. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 236:113494. [PMID: 35413622 DOI: 10.1016/j.ecoenv.2022.113494] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 04/02/2022] [Accepted: 04/04/2022] [Indexed: 06/14/2023]
Abstract
Cadmium could induce cell apoptosis, probably related to the dysfunction of the mitochondrial respiratory chain. The human renal proximal tubule (HK-2) was used to explore the mechanism of mitochondrial respiratory chain dysfunction during apoptosis induced by cadmium chloride (CdCl2). Cell viability was evaluated by cell proliferation assay and different concentrations of 60, 80 and 100 μM were selected to evaluate the mitochondrial toxicity of CdCl2 respectively. Under the CdCl2 treatment for 24 h, the mitochondrial reactive oxygen species (ROS) of HK-2 cells increased and the superoxide dismutase (SOD) activity was inhibited at the above three concentrations separately. Both ATP content and mitochondrial membrane potential decreased significantly at 100 μM concentration. The levels of procaspase-3 and Bcl-2 had fallen in a concentration-dependent manner and Bax was significantly increased at 60, 80 and 100 μM concentration compared with no CdCl2 treatment respectively, which activated the mitochondrial apoptosis pathway. N-acetyl-cysteine (NAC) could partially resist CdCl2-induced cell apoptosis, while myxothiazol (Myx) promoted the process. Mitochondria relative alterations manifested as inhibition of complex III and V. In addition, both the quantity of mitochondrial coenzyme Q-binding protein CoQ10 homolog B (CoQ10B) and cytochrome c (Cyt c) had decreased significantly. Taken together, CdCl2 induced HK-2 apoptosis due to the mitochondrial respiratory chain dysfunction by reducing the CoQ10B level, offering a novel evaluating indicator for the environmental toxicity of CdCl2.
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Affiliation(s)
- Yan Wang
- Department of public health and preventive medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, PR China
| | - Huiqin Chi
- Food Safety and Health Research Center, Guangdong Provincial Key Laboratory of Tropical Disease Research, Guangdong, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, PR China
| | - Feifei Xu
- Food Safety and Health Research Center, Guangdong Provincial Key Laboratory of Tropical Disease Research, Guangdong, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, PR China
| | - Zhini He
- Food Safety and Health Research Center, Guangdong Provincial Key Laboratory of Tropical Disease Research, Guangdong, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, PR China
| | - Ziyin Li
- Food Safety and Health Research Center, Guangdong Provincial Key Laboratory of Tropical Disease Research, Guangdong, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, PR China
| | - Fan Wu
- Department of public health and preventive medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, PR China
| | - Yueqi Li
- Department of public health and preventive medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, PR China
| | - Gaoqiang Zhang
- Department of public health and preventive medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, PR China
| | - Xinyue Peng
- Department of public health and preventive medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, PR China
| | - Susu Yu
- Department of public health and preventive medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, PR China
| | - Jiani Yang
- Department of public health and preventive medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, PR China
| | - Wenjuan Zhang
- Department of public health and preventive medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, PR China.
| | - Xingfen Yang
- Food Safety and Health Research Center, Guangdong Provincial Key Laboratory of Tropical Disease Research, Guangdong, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, PR China.
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21
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Yang D, Qi X, Zhou X, Li Z, Zhou H, Fan Z. Synthesis of potent antifungal 3,4-dichloroisothiazole-based strobilurins with both direct fungicidal activity and systemic acquired resistance. RSC Med Chem 2022; 13:429-435. [PMID: 35647548 PMCID: PMC9020617 DOI: 10.1039/d1md00402f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 01/21/2022] [Indexed: 01/26/2023] Open
Abstract
To continue our efforts to discover novel fungicide lead structures, a series of 3,4-dichloroisothiazole-based-strobilurin derivatives were synthesized and characterized. In vitro bioassay screening with 9 different plant pathogens suggested that the linker between 3,4-dichloroisothiazole and the pharmacophore played a critical role in fungicidal potency and scope. Among these, compound 2a with a cis-methoxy oxime ether as a linker was a better active compound. Further modification of 2a, 4a and 6a by replacement of carboxylic ester with a carboxamide led to the best active compound 7a in this study. In vivo bioassay screening and verification indicated that compounds 1c and 7a displayed the best efficacy against wheat white powder (Erysiphe graminis) and corn rust (Puccinia sorghi Schw). In addition, compound 7a was validated by upregulating salicylic acid (SA) signaling and reactive oxygen species (ROS)-related gene expression. A potent lead compound with a broad spectrum of fungicidal and systemic acquired resistance activity has been discovered by bridging 3,4-dichloroisothiazole and the strobilurin pharmacophore with various linkers.
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Affiliation(s)
- Dongyan Yang
- Innovative Institute for Plant Health, School of Chemistry and Chemical Engineering, Zhongkai University of Agriculture and EngineeringNo. 24, Dongsha Road, Haizhu DistrictGuangzhouGuangdong 510225PR China,State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai UniversityNo. 94, Weijin RoadTianjin 300071P. R. China,Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai UniversityNo. 94, Weijin RoadTianjin 300071P. R. China
| | - Xin Qi
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai UniversityNo. 94, Weijin RoadTianjin 300071P. R. China,Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai UniversityNo. 94, Weijin RoadTianjin 300071P. R. China
| | - Xinhua Zhou
- Innovative Institute for Plant Health, School of Chemistry and Chemical Engineering, Zhongkai University of Agriculture and EngineeringNo. 24, Dongsha Road, Haizhu DistrictGuangzhouGuangdong 510225PR China
| | - Zhengming Li
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai UniversityNo. 94, Weijin RoadTianjin 300071P. R. China,Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai UniversityNo. 94, Weijin RoadTianjin 300071P. R. China
| | - Hongjun Zhou
- Innovative Institute for Plant Health, School of Chemistry and Chemical Engineering, Zhongkai University of Agriculture and EngineeringNo. 24, Dongsha Road, Haizhu DistrictGuangzhouGuangdong 510225PR China
| | - Zhijin Fan
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai UniversityNo. 94, Weijin RoadTianjin 300071P. R. China,Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai UniversityNo. 94, Weijin RoadTianjin 300071P. R. China
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22
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Zhou L, Maldonado M, Padavannil A, Guo F, Letts JA. Structures of Tetrahymena's respiratory chain reveal the diversity of eukaryotic core metabolism. Science 2022; 376:831-839. [PMID: 35357889 DOI: 10.1126/science.abn7747] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Respiration is a core biological energy-converting process whose last steps are carried out by a chain of multi-subunit complexes in the inner mitochondrial membrane. To probe the functional and structural diversity of eukaryotic respiration, we examined the respiratory chain of the ciliate Tetrahymena thermophila (Tt). Using cryo-electron microscopy on a mixed sample, we solved structures of a supercomplex between Tt-complex I (CI) and Tt-CIII2 (Tt-SC I+III2) and a structure of Tt-CIV2. Tt-SC I+III2 (~2.3 MDa) is a curved assembly with structural and functional symmetry breaking. Tt-CIV2 is a ~2.7 MDa dimer with over 52 subunits per protomer, including mitochondrial carriers and a TIM83-TIM133-like domain. Our structural and functional study of the T. thermophila respiratory chain reveals divergence in key components of eukaryotic respiration, expanding our understanding of core metabolism.
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Affiliation(s)
- Long Zhou
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - María Maldonado
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Abhilash Padavannil
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Fei Guo
- BIOEM Facility, University of California, Davis, CA 95616, USA
| | - James A Letts
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
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23
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Vercellino I, Sazanov LA. The assembly, regulation and function of the mitochondrial respiratory chain. Nat Rev Mol Cell Biol 2022; 23:141-161. [PMID: 34621061 DOI: 10.1038/s41580-021-00415-0] [Citation(s) in RCA: 249] [Impact Index Per Article: 124.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2021] [Indexed: 02/08/2023]
Abstract
The mitochondrial oxidative phosphorylation system is central to cellular metabolism. It comprises five enzymatic complexes and two mobile electron carriers that work in a mitochondrial respiratory chain. By coupling the oxidation of reducing equivalents coming into mitochondria to the generation and subsequent dissipation of a proton gradient across the inner mitochondrial membrane, this electron transport chain drives the production of ATP, which is then used as a primary energy carrier in virtually all cellular processes. Minimal perturbations of the respiratory chain activity are linked to diseases; therefore, it is necessary to understand how these complexes are assembled and regulated and how they function. In this Review, we outline the latest assembly models for each individual complex, and we also highlight the recent discoveries indicating that the formation of larger assemblies, known as respiratory supercomplexes, originates from the association of the intermediates of individual complexes. We then discuss how recent cryo-electron microscopy structures have been key to answering open questions on the function of the electron transport chain in mitochondrial respiration and how supercomplexes and other factors, including metabolites, can regulate the activity of the single complexes. When relevant, we discuss how these mechanisms contribute to physiology and outline their deregulation in human diseases.
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Affiliation(s)
- Irene Vercellino
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Leonid A Sazanov
- Institute of Science and Technology Austria, Klosterneuburg, Austria.
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24
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Chojnacka KJ, Elancheliyan P, Mussulini BHM, Mohanraj K, Callegari S, Gosk A, Banach T, Góral T, Szczepanowska K, Rehling P, Serwa RA, Chacińska A. Ovarian carcinoma immunoreactive antigen-like protein 2 (OCIAD2) is a novel complex III specific assembly factor in mitochondria. Mol Biol Cell 2022; 33:ar29. [PMID: 35080992 PMCID: PMC9250361 DOI: 10.1091/mbc.e21-03-0143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Assembly of the dimeric complex III (CIII2) in the mitochondrial inner membrane is an intricate process in which several accessory proteins are involved as assembly factors. Despite numerous studies, this process has yet to be fully understood. Here we report the identification of human OCIAD2 (ovarian carcinoma immunoreactive antigen–like protein 2) as an assembly factor for CIII2. OCIAD2 was found to be deregulated in several carcinomas and also in some neurogenerative disorders; however, its nonpathological role had not been elucidated. We have shown that OCIAD2 localizes to mitochondria and interacts with electron transport chain (ETC) proteins. Complete loss of OCIAD2 using gene editing in HEK293 cells resulted in abnormal mitochondrial morphology, a substantial decrease of both CIII2 and supercomplex III2+IV, and a reduction in CIII enzymatic activity. Identification of OCIAD2 as a protein required for assembly of functional CIII2 provides a new insight into the biogenesis and architecture of the ETC. Elucidating the mechanism of OCIAD2 action is important both for the understanding of cellular metabolism and for an understanding of its role in malignant transformation.
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Affiliation(s)
| | | | | | - Karthik Mohanraj
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw, Poland
| | - Sylvie Callegari
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Cellular Biochemistry, University Medical Center Göttingen, 37073, Göttingen, Germany
| | - Aleksandra Gosk
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Tomasz Banach
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw, Poland
| | - Tomasz Góral
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Karolina Szczepanowska
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw, Poland
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, 37073, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Germany.,Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Remigiusz Adam Serwa
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw, Poland
| | - Agnieszka Chacińska
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw, Poland
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25
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Manoj KM, Gideon DA, Jaeken L. Interaction of membrane-embedded cytochrome b-complexes with quinols: Classical Q-cycle and murburn model. Cell Biochem Funct 2022; 40:118-126. [PMID: 35026863 DOI: 10.1002/cbf.3682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/03/2021] [Accepted: 12/14/2021] [Indexed: 01/07/2023]
Abstract
We recently proposed a diffusible reactive (oxygen) species (DRS/DROS) based function for cytochrome b complexes (CBC) and quinones (Q)/quinols (QH2 ) in the murburn model of bioenergetics. This proposal is in direct conflict with the classical purview of Q-cycle. Via extensive analyses of the structure-function correlations of membrane-quinones/quinols and proteins, we present qualitative and quantitative arguments to infer that the classical model cannot explain the energetics, kinetics, mechanism and probabilistic considerations. Therefore, it is proposed that Q-cycle is neither necessary nor feasible at CBCs. In contrast, we substantiate that the murburn model explains: (a) crucial structural data of CBCs, (b) why quinones/quinols are utilized in bioenergetic membranes, (c) how trans-membrane potential is generated owing to effective charge separation at CBCs, (d) mobility data of O2 , DRS, Q/QH2 , and (e) utility of other reaction/membrane components. Further, the murburn model also accommodates the absence of quinones in anaerobic Archaea, wherein methanophenazines are prevalent. The work mandates that the textbooks and research agendas are refreshed to reflect the new perception. SIGNIFICANCE: The current article must be seen as a critical and detailed analysis of the role and working mechanism of quinone (Q) /quinols (QH2 ) in bioenergetic membranes. In the classical model, QH2 are perceived as highly mobile electron-transport agents that bind and donate electrons to cytochrome b complexes (CBCs), using sophisticated electronic circuitries, in order to recycle Q and pump protons. The classical perception sees radicals (such as Q*-, O2 *-, etc., also called diffusible reactive species, DRS) as wasteful or toxic (patho) physiological manifestations. It is highlighted herein that QH2 has low mobility and matrix has little protons to pump. New insights from the structural analyses of diverse CBCs and quinols, in conjunction with murburn reaction thermodynamics suggest that the electrons from substrates/quinols are effectively utilized via DRS. This perception fits into a much broader analysis of 1 and 2 electron transfers in overall redox metabolism, as recently brought out by the murburn model, wherein DRS are considered obligatory ingredients of physiology. Thus, the findings mandate a reorientation in the pertinent research field.
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Affiliation(s)
- Kelath Murali Manoj
- Biochemistry, Satyamjayatu: The Science & Ethics Foundation, Palakkad, India
| | | | - Laurent Jaeken
- Karel de Grote University College, Antwerp University Association, Campus Hoboken, Hoboken, Belgium
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26
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27
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Chen CL, Kang PT, Zhang L, Xiao K, Zweier JL, Chilian WM, Chen YR. Reperfusion mediates heme impairment with increased protein cysteine sulfonation of mitochondrial complex III in the post-ischemic heart. J Mol Cell Cardiol 2021; 161:23-38. [PMID: 34331972 PMCID: PMC8629835 DOI: 10.1016/j.yjmcc.2021.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 07/08/2021] [Accepted: 07/21/2021] [Indexed: 11/19/2022]
Abstract
A serious consequence of myocardial ischemia-reperfusion injury (I/R) is oxidative damage, which causes mitochondrial dysfunction. The cascading ROS can propagate and potentially induce heme bleaching and protein cysteine sulfonation (PrSO3H) of the mitochondrial electron transport chain. Herein we studied the mechanism of I/R-mediated irreversible oxidative injury of complex III in mitochondria from rat hearts subjected to 30-min of ischemia and 24-h of reperfusion in vivo. In the I/R region, the catalytic activity of complex III was significantly impaired. Spectroscopic analysis indicated that I/R mediated the destruction of hemes b and c + c1 in the mitochondria, supporting I/R-mediated complex III impairment. However, no significant impairment of complex III activity and heme damage were observed in mitochondria from the risk region of rat hearts subjected only to 30-min ischemia, despite a decreased state 3 respiration. In the I/R mitochondria, carbamidomethylated C122/C125 of cytochrome c1 via alkylating complex III with a down regulation of HCCS was exclusively detected, supporting I/R-mediated thioether defect of heme c1. LC-MS/MS analysis showed that I/R mitochondria had intensely increased complex III PrSO3H levels at the C236 ligand of the [2Fe2S] cluster of the Rieske iron‑sulfur protein (uqcrfs1), thus impairing the electron transport activity. MS analysis also indicated increased PrSO3H of the hinge protein at C65 and of cytochrome c1 at C140 and C220, which are confined in the intermembrane space. MS analysis also showed that I/R extensively enhanced the PrSO3H of the core 1 (uqcrc1) and core 2 (uqcrc2) subunits in the matrix compartment, thus supporting the conclusion that complex III releases ROS to both sides of the inner membrane during reperfusion. Analysis of ischemic mitochondria indicated a modest reduction from the basal level of complex III PrSO3H detected in the mitochondria of sham control hearts, suggesting that the physiologic hyperoxygenation and ROS overproduction during reperfusion mediated the enhancement of complex III PrSO3H. In conclusion, reperfusion-mediated heme damage with increased PrSO3H controls oxidative injury to complex III and aggravates mitochondrial dysfunction in the post-ischemic heart.
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Affiliation(s)
- Chwen-Lih Chen
- Department of Integrative Medical Sciences, College of Medicine, Northeast Ohio Medical University, Rootstown, OH 44272, United States of America
| | - Patrick T Kang
- Department of Integrative Medical Sciences, College of Medicine, Northeast Ohio Medical University, Rootstown, OH 44272, United States of America
| | - Liwen Zhang
- Campus Chemical Instrument Center, Proteomics and Mass Spectrometry Facility, The Ohio State University, Columbus, OH 43210, United States of America
| | - Kunhong Xiao
- Department of Pharmacology and Chemical Biology and Biomedical Mass Spectrometry Center, University of Pittsburgh, PA 15261, United States of America
| | - Jay L Zweier
- Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, United States of America
| | - William M Chilian
- Department of Integrative Medical Sciences, College of Medicine, Northeast Ohio Medical University, Rootstown, OH 44272, United States of America
| | - Yeong-Renn Chen
- Department of Integrative Medical Sciences, College of Medicine, Northeast Ohio Medical University, Rootstown, OH 44272, United States of America.
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28
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Pacheco R, Quezada SA, Kalergis AM, Becker MI, Ferreira J, De Ioannes AE. Allergens of the urushiol family promote mitochondrial dysfunction by inhibiting the electron transport at the level of cytochromes b and chemically modify cytochrome c 1. Biol Res 2021; 54:35. [PMID: 34711292 PMCID: PMC8554850 DOI: 10.1186/s40659-021-00357-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/06/2021] [Indexed: 11/10/2022] Open
Abstract
Background Urushiols are pro-electrophilic haptens that cause severe contact dermatitis mediated by CD8+ effector T-cells and downregulated by CD4+ T-cells. However, the molecular mechanism by which urushiols stimulate innate immunity in the initial stages of this allergic reaction is poorly understood. Here we explore the sub-cellular mechanisms by which urushiols initiate the allergic response. Results Electron microscopy observations of mouse ears exposed to litreol (3-n-pentadecyl-10-enyl-catechol]) showed keratinocytes containing swollen mitochondria with round electron-dense inclusion bodies in the matrix. Biochemical analyses of sub-mitochondrial fractions revealed an inhibitory effect of urushiols on electron flow through the mitochondrial respiratory chain, which requires both the aliphatic and catecholic moieties of these allergens. Moreover, urushiols extracted from poison ivy/oak (mixtures of 3-n-pentadecyl-8,11,13 enyl/3-n-heptadecyl-8,11 enyl catechol) exerted a higher inhibitory effect on mitochondrial respiration than did pentadecyl catechol or litreol, indicating that the higher number of unsaturations in the aliphatic chain, stronger the allergenicity of urushiols. Furthermore, the analysis of radioactive proteins isolated from mitochondria incubated with 3H-litreol, indicated that this urushiol was bound to cytochrome c1. According to the proximity of cytochromes c1 and b, functional evidence indicated the site of electron flow inhibition was within complex III, in between cytochromes bL (cyt b566) and bH (cyt b562). Conclusion Our data provide functional and molecular evidence indicating that the interruption of the mitochondrial electron transport chain constitutes an important mechanism by which urushiols initiates the allergic response. Thus, mitochondria may constitute a source of cellular targets for generating neoantigens involved in the T-cell mediated allergy induced by urushiols. Supplementary Information The online version contains supplementary material available at 10.1186/s40659-021-00357-z.
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Affiliation(s)
- Rodrigo Pacheco
- Laboratorio de Neuroinmunología, Fundación Ciencia & Vida, Santiago, Chile. .,Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile.
| | - Sergio A Quezada
- Cancer Immunology Unit, University College London (UCL) Cancer Institute, London, England, UK
| | - Alexis M Kalergis
- Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica, Santiago, Chile
| | - María Inés Becker
- Fundación Ciencia y Tecnología para el Desarrollo (FUCITED), Santiago, Chile.,Department of Research and Development, Biosonda Corporation, Santiago, Chile.,Faculty of Physical and Mathematical Sciences, Department of Chemical Engineering, Biotechnology and Materials, Universidad de Chile, Santiago, Chile
| | - Jorge Ferreira
- Faculty of Medicine, Institute of Biomedical Sciences, Molecular and Clinical Pharmacology Program, Universidad de Chile, Santiago, Chile
| | - Alfredo E De Ioannes
- Department of Research and Development, Biosonda Corporation, Santiago, Chile.,Faculty of Physical and Mathematical Sciences, Department of Chemical Engineering, Biotechnology and Materials, Universidad de Chile, Santiago, Chile.,Faculty of Medicine, Institute of Biomedical Sciences, Molecular and Clinical Pharmacology Program, Universidad de Chile, Santiago, Chile
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29
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Sindhu T, Debnath P. Cytochrome bc1-aa3 oxidase supercomplex as emerging and potential drug target against tuberculosis. Curr Mol Pharmacol 2021; 15:380-392. [PMID: 34602044 DOI: 10.2174/1874467214666210928152512] [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: 11/16/2020] [Revised: 03/26/2021] [Accepted: 06/06/2021] [Indexed: 11/22/2022]
Abstract
The cytochrome bc1-aa3 supercomplex plays an essential role in the cellular respiratory system of Mycobacterium Tuberculosis. It transfers electrons from menaquinol to cytochrome aa3 (Complex IV) via cytochrome bc1 (Complex III), which reduces the oxygen. The electron transfer from a variety of donors into oxygen through the respiratory electron transport chain is essential to pump protons across the membrane creating an electrochemical transmembrane gradient (proton motive force, PMF) that regulates the synthesis of ATP via the oxidative phosphorylation process. Cytochrome bc1-aa3 supercomplex in M. tuberculosis is, therefore, a major drug target for antibiotic action. In recent years, several respiratory chain components have been targeted for developing new candidate drugs, illustrating the therapeutic potential of obstructing energy conversion of M. tuberculosis. The recently available cryo-EM structure of mycobacterial cytochrome bc1-aa3 supercomplex with open and closed conformations has opened new avenues for understanding its structure and function for developing more effective, new therapeutics against pulmonary tuberculosis. In this review, we discuss the role and function of several components, subunits, and drug targeting elements of the supercomplex cytochrome bc1-aa3, and its potential inhibitors in detail.
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Affiliation(s)
- Thangaraj Sindhu
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka. India
| | - Pal Debnath
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka. India
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30
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Koumpoura CL, Robert A, Athanassopoulos CM, Baltas M. Antimalarial Inhibitors Targeting Epigenetics or Mitochondria in Plasmodium falciparum: Recent Survey upon Synthesis and Biological Evaluation of Potential Drugs against Malaria. Molecules 2021; 26:molecules26185711. [PMID: 34577183 PMCID: PMC8467436 DOI: 10.3390/molecules26185711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 12/01/2022] Open
Abstract
Despite many efforts, malaria remains among the most problematic infectious diseases worldwide, mainly due to the development of drug resistance by P. falciparum. Over the past decade, new essential pathways have been emerged to fight against malaria. Among them, epigenetic processes and mitochondrial metabolism appear to be important targets. This review will focus on recent evolutions concerning worldwide efforts to conceive, synthesize and evaluate new drug candidates interfering selectively and efficiently with these two targets and pathways. The focus will be on compounds/scaffolds that possess biological/pharmacophoric properties on DNA methyltransferases and HDAC’s for epigenetics, and on cytochrome bc1 and dihydroorotate dehydrogenase for mitochondrion.
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Affiliation(s)
- Christina L. Koumpoura
- CNRS, LCC (Laboratoire de Chimie de Coordination), Université de Toulouse, UPS, INPT, Inserm ERL 1289, 205 Route de Narbonne, BP 44099, CEDEX 4, F-31077 Toulouse, France; (C.L.K.); (A.R.)
| | - Anne Robert
- CNRS, LCC (Laboratoire de Chimie de Coordination), Université de Toulouse, UPS, INPT, Inserm ERL 1289, 205 Route de Narbonne, BP 44099, CEDEX 4, F-31077 Toulouse, France; (C.L.K.); (A.R.)
| | | | - Michel Baltas
- CNRS, LCC (Laboratoire de Chimie de Coordination), Université de Toulouse, UPS, INPT, Inserm ERL 1289, 205 Route de Narbonne, BP 44099, CEDEX 4, F-31077 Toulouse, France; (C.L.K.); (A.R.)
- Correspondence:
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31
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Brischigliaro M, Frigo E, Corrà S, De Pittà C, Szabò I, Zeviani M, Costa R. Modelling of BCS1L-related human mitochondrial disease in Drosophila melanogaster. J Mol Med (Berl) 2021; 99:1471-1485. [PMID: 34274978 PMCID: PMC8455400 DOI: 10.1007/s00109-021-02110-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 06/04/2021] [Accepted: 06/29/2021] [Indexed: 11/09/2022]
Abstract
Mutations in BCS1L are the most frequent cause of human mitochondrial disease linked to complex III deficiency. Different forms of BCS1L-related diseases and more than 20 pathogenic alleles have been reported to date. Clinical symptoms are highly heterogenous, and multisystem involvement is often present, with liver and brain being the most frequently affected organs. BCS1L encodes a mitochondrial AAA + -family member with essential roles in the latest steps in the biogenesis of mitochondrial respiratory chain complex III. Since Bcs1 has been investigated mostly in yeast and mammals, its function in invertebrates remains largely unknown. Here, we describe the phenotypical, biochemical and metabolic consequences of Bcs1 genetic manipulation in Drosophila melanogaster. Our data demonstrate the fundamental role of Bcs1 in complex III biogenesis in invertebrates and provide novel, reliable models for BCS1L-related human mitochondrial diseases. These models recapitulate several features of the human disorders, collectively pointing to a crucial role of Bcs1 and, in turn, of complex III, in development, organismal fitness and physiology of several tissues.
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Affiliation(s)
| | - Elena Frigo
- Department of Biology, University of Padova, Padova, Italy
| | - Samantha Corrà
- Department of Biology, University of Padova, Padova, Italy
| | | | - Ildikò Szabò
- Department of Biology, University of Padova, Padova, Italy
| | - Massimo Zeviani
- Department of Neurosciences, University of Padova, Padova, Italy
| | - Rodolfo Costa
- Department of Biology, University of Padova, Padova, Italy. .,Italian National Research Council (CNR) Institute of Neuroscience, Padova, Italy.
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32
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In Silico Modeling of the Mitochondrial Pumping Complexes with Markov State Models. Methods Mol Biol 2021. [PMID: 34060059 DOI: 10.1007/978-1-0716-1266-8_31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The mechanism of proton pumping by the mitochondrial electron transport chain complexes is still enigmatic after decades of research. Recently, there has been interest in in silico Markov state models to model the mitochondrial pumping complexes at the microscopic level, and this chapter describes the methods of constructing and simulating such models.
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Esmaili M, Eldeeb MA, Moosavi-Movahedi AA. Current Developments in Native Nanometric Discoidal Membrane Bilayer Formed by Amphipathic Polymers. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1771. [PMID: 34361157 PMCID: PMC8308186 DOI: 10.3390/nano11071771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/27/2021] [Accepted: 06/30/2021] [Indexed: 12/18/2022]
Abstract
Unlike cytosolic proteins, membrane proteins (MPs) are embedded within the plasma membrane and the lipid bilayer of intracellular organelles. MPs serve in various cellular processes and account for over 65% of the current drug targets. The development of membrane mimetic systems such as bicelles, short synthetic polymers or amphipols, and membrane scaffold proteins (MSP)-based nanodiscs has facilitated the accommodation of synthetic lipids to stabilize MPs, yet the preparation of these membrane mimetics remains detergent-dependent. Bio-inspired synthetic polymers present an invaluable tool for excision and liberation of superstructures of MPs and their surrounding annular lipid bilayer in the nanometric discoidal assemblies. In this article, we discuss the significance of self-assembling process in design of biomimetic systems, review development of multiple series of amphipathic polymers and the significance of these polymeric "belts" in biomedical research in particular in unraveling the structures, dynamics and functions of several high-value membrane protein targets.
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Affiliation(s)
- Mansoore Esmaili
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Mohamed A. Eldeeb
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada;
- Department of Chemistry, Faculty of Science, Cairo University, Cairo 12613, Egypt
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34
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Capitanio G, Papa F, Papa S. The allosteric protein interactions in the proton-motive function of mammalian redox enzymes of the respiratory chain. Biochimie 2021; 189:1-12. [PMID: 34097987 DOI: 10.1016/j.biochi.2021.05.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/17/2021] [Accepted: 05/31/2021] [Indexed: 12/22/2022]
Abstract
Insight into mammalian respiratory complexes defines the role of allosteric protein interactions in their proton-motive activity. In cytochrome c oxidase (CxIV) conformational change of subunit I, caused by O2 binding to heme a32+-CuB+ and reduction, and stereochemical transitions coupled to oxidation/reduction of heme a and CuA, combined with electrostatic effects, determine the proton pumping activity. In ubiquinone-cytochrome c oxidoreductase (CxIII) conformational movement of Fe-S protein between cytochromes b and c1 is the key element of the proton-motive activity. In NADH-ubiquinone oxidoreductase (CxI) ubiquinone binding and reduction result in conformational changes of subunits in the quinone reaction structure which initiate proton pumping.
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Affiliation(s)
- Giuseppe Capitanio
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari "Aldo Moro", 70124, Bari, Italy.
| | - Francesco Papa
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari "Aldo Moro", 70124, Bari, Italy.
| | - Sergio Papa
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari "Aldo Moro", 70124, Bari, Italy; Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121, Napoli, Italy.
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35
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Bendre AD, Peters PJ, Kumar J. Recent Insights into the Structure and Function of Mycobacterial Membrane Proteins Facilitated by Cryo-EM. J Membr Biol 2021; 254:321-341. [PMID: 33954837 PMCID: PMC8099146 DOI: 10.1007/s00232-021-00179-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 03/23/2021] [Indexed: 12/26/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is one of the deadliest pathogens encountered by humanity. Over the decades, its characteristic membrane organization and composition have been understood. However, there is still limited structural information and mechanistic understanding of the constituent membrane proteins critical for drug discovery pipelines. Recent advances in single-particle cryo-electron microscopy and cryo-electron tomography have provided the much-needed impetus towards structure determination of several vital Mtb membrane proteins whose structures were inaccessible via X-ray crystallography and NMR. Important insights into membrane composition and organization have been gained via a combination of electron tomography and biochemical and biophysical assays. In addition, till the time of writing this review, 75 new structures of various Mtb proteins have been reported via single-particle cryo-EM. The information obtained from these structures has improved our understanding of the mechanisms of action of these proteins and the physiological pathways they are associated with. These structures have opened avenues for structure-based drug design and vaccine discovery programs that might help achieve global-TB control. This review describes the structural features of selected membrane proteins (type VII secretion systems, Rv1819c, Arabinosyltransferase, Fatty Acid Synthase, F-type ATP synthase, respiratory supercomplex, ClpP1P2 protease, ClpB disaggregase and SAM riboswitch), their involvement in physiological pathways, and possible use as a drug target. Tuberculosis is a deadly disease caused by Mycobacterium tuberculosis. The Cryo-EM and tomography have simplified the understanding of the mycobacterial membrane organization. Some proteins are located in the plasma membrane; some span the entire envelope, while some, like MspA, are located in the mycomembrane. Cryo-EM has made the study of such membrane proteins feasible.
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Affiliation(s)
- Ameya D Bendre
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University Campus, Ganeshkhind, Pune, Maharashtra, 411007, India
| | - Peter J Peters
- The Maastricht Multimodal Molecular Imaging Institute (M4I), Division of Nanoscopy, Maastricht University, Maastricht, The Netherlands
| | - Janesh Kumar
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University Campus, Ganeshkhind, Pune, Maharashtra, 411007, India.
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36
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Le Vasseur M, Friedman J, Jost M, Xu J, Yamada J, Kampmann M, Horlbeck MA, Salemi MR, Phinney BS, Weissman JS, Nunnari J. Genome-wide CRISPRi screening identifies OCIAD1 as a prohibitin client and regulatory determinant of mitochondrial Complex III assembly in human cells. eLife 2021; 10:67624. [PMID: 34034859 PMCID: PMC8154037 DOI: 10.7554/elife.67624] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/10/2021] [Indexed: 01/01/2023] Open
Abstract
Dysfunction of the mitochondrial electron transport chain (mETC) is a major cause of human mitochondrial diseases. To identify determinants of mETC function, we screened a genome-wide human CRISPRi library under oxidative metabolic conditions with selective inhibition of mitochondrial Complex III and identified ovarian carcinoma immunoreactive antigen (OCIA) domain-containing protein 1 (OCIAD1) as a Complex III assembly factor. We find that OCIAD1 is an inner mitochondrial membrane protein that forms a complex with supramolecular prohibitin assemblies. Our data indicate that OCIAD1 is required for maintenance of normal steady-state levels of Complex III and the proteolytic processing of the catalytic subunit cytochrome c1 (CYC1). In OCIAD1 depleted mitochondria, unprocessed CYC1 is hemylated and incorporated into Complex III. We propose that OCIAD1 acts as an adaptor within prohibitin assemblies to stabilize and/or chaperone CYC1 and to facilitate its proteolytic processing by the IMMP2L protease.
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Affiliation(s)
- Maxence Le Vasseur
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, Davis, United States
| | - Jonathan Friedman
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, Davis, United States.,Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Marco Jost
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, United States.,Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, United States
| | - Jiawei Xu
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, Davis, United States
| | - Justin Yamada
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, Davis, United States
| | - Martin Kampmann
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, United States.,Institute for Neurodegenerative Diseases and Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, United States.,Chan-Zuckerberg Biohub, San Francisco, United States
| | - Max A Horlbeck
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, United States
| | - Michelle R Salemi
- Proteomics Core Facility, University of California, Davis, Davis, United States
| | - Brett S Phinney
- Proteomics Core Facility, University of California, Davis, Davis, United States
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, United States.,Whitehead Institute, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Jodi Nunnari
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, Davis, United States
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37
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Needs HI, Protasoni M, Henley JM, Prudent J, Collinson I, Pereira GC. Interplay between Mitochondrial Protein Import and Respiratory Complexes Assembly in Neuronal Health and Degeneration. Life (Basel) 2021; 11:432. [PMID: 34064758 PMCID: PMC8151517 DOI: 10.3390/life11050432] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/27/2021] [Accepted: 05/02/2021] [Indexed: 12/14/2022] Open
Abstract
The fact that >99% of mitochondrial proteins are encoded by the nuclear genome and synthesised in the cytosol renders the process of mitochondrial protein import fundamental for normal organelle physiology. In addition to this, the nuclear genome comprises most of the proteins required for respiratory complex assembly and function. This means that without fully functional protein import, mitochondrial respiration will be defective, and the major cellular ATP source depleted. When mitochondrial protein import is impaired, a number of stress response pathways are activated in order to overcome the dysfunction and restore mitochondrial and cellular proteostasis. However, prolonged impaired mitochondrial protein import and subsequent defective respiratory chain function contributes to a number of diseases including primary mitochondrial diseases and neurodegeneration. This review focuses on how the processes of mitochondrial protein translocation and respiratory complex assembly and function are interlinked, how they are regulated, and their importance in health and disease.
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Affiliation(s)
- Hope I. Needs
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; (H.I.N.); (J.M.H.)
| | - Margherita Protasoni
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; (M.P.); (J.P.)
| | - Jeremy M. Henley
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; (H.I.N.); (J.M.H.)
- Centre for Neuroscience and Regenerative Medicine, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Julien Prudent
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; (M.P.); (J.P.)
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; (H.I.N.); (J.M.H.)
| | - Gonçalo C. Pereira
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; (M.P.); (J.P.)
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38
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Sarewicz M, Pintscher S, Bujnowicz Ł, Wolska M, Artur Osyczka. The High-Spin Heme b L Mutant Exposes Dominant Reaction Leading to the Formation of the Semiquinone Spin-Coupled to the [2Fe-2S] + Cluster at the Q o Site of Rhodobacter capsulatus Cytochrome bc 1. Front Chem 2021; 9:658877. [PMID: 34026724 PMCID: PMC8138165 DOI: 10.3389/fchem.2021.658877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/19/2021] [Indexed: 11/13/2022] Open
Abstract
Cytochrome bc 1 (mitochondrial complex III) catalyzes electron transfer from quinols to cytochrome c and couples this reaction with proton translocation across lipid membrane; thus, it contributes to the generation of protonmotive force used for the synthesis of ATP. The energetic efficiency of the enzyme relies on a bifurcation reaction taking place at the Qo site which upon oxidation of ubiquinol directs one electron to the Rieske 2Fe2S cluster and the other to heme b L. The molecular mechanism of this reaction remains unclear. A semiquinone spin-coupled to the reduced 2Fe2S cluster (SQo-2Fe2S) was identified as a state associated with the operation of the Qo site. To get insights into the mechanism of the formation of this state, we first constructed a mutant in which one of the histidine ligands of the iron ion of heme b L Rhodobacter capsulatus cytochrome bc 1 was replaced by asparagine (H198N). This converted the low-spin, low-potential heme into the high-spin, high-potential species which is unable to support enzymatic turnover. We performed a comparative analysis of redox titrations of antimycin-supplemented bacterial photosynthetic membranes containing native enzyme and the mutant. The titrations revealed that H198N failed to generate detectable amounts of SQo-2Fe2S under neither equilibrium (in dark) nor nonequilibrium (in light), whereas the native enzyme generated clearly detectable SQo-2Fe2S in light. This provided further support for the mechanism in which the back electron transfer from heme b L to a ubiquinone bound at the Qo site is mainly responsible for the formation of semiquinone trapped in the SQo-2Fe2S state in R. capusulatus cytochrome bc 1.
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Affiliation(s)
- Marcin Sarewicz
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Sebastian Pintscher
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Łukasz Bujnowicz
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Małgorzata Wolska
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Artur Osyczka
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
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39
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Vanoni MA. Iron-sulfur flavoenzymes: the added value of making the most ancient redox cofactors and the versatile flavins work together. Open Biol 2021; 11:210010. [PMID: 33947244 PMCID: PMC8097209 DOI: 10.1098/rsob.210010] [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] [Indexed: 11/24/2022] Open
Abstract
Iron-sulfur (Fe-S) flavoproteins form a broad and growing class of complex, multi-domain and often multi-subunit proteins coupling the most ancient cofactors (the Fe-S clusters) and the most versatile coenzymes (the flavin coenzymes, FMN and FAD). These enzymes catalyse oxidoreduction reactions usually acting as switches between donors of electron pairs and acceptors of single electrons, and vice versa. Through selected examples, the enzymes' structure−function relationships with respect to rate and directionality of the electron transfer steps, the role of the apoprotein and its dynamics in modulating the electron transfer process will be discussed.
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Affiliation(s)
- Maria Antonietta Vanoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
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40
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Bernardi P. Looking Back to the Future of Mitochondrial Research. Front Physiol 2021; 12:682467. [PMID: 33995132 PMCID: PMC8119648 DOI: 10.3389/fphys.2021.682467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 04/12/2021] [Indexed: 12/03/2022] Open
Affiliation(s)
- Paolo Bernardi
- Department of Biomedical Sciences, University of Padova, Padova, Italy
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41
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Kell DB. A protet-based, protonic charge transfer model of energy coupling in oxidative and photosynthetic phosphorylation. Adv Microb Physiol 2021; 78:1-177. [PMID: 34147184 DOI: 10.1016/bs.ampbs.2021.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Textbooks of biochemistry will explain that the otherwise endergonic reactions of ATP synthesis can be driven by the exergonic reactions of respiratory electron transport, and that these two half-reactions are catalyzed by protein complexes embedded in the same, closed membrane. These views are correct. The textbooks also state that, according to the chemiosmotic coupling hypothesis, a (or the) kinetically and thermodynamically competent intermediate linking the two half-reactions is the electrochemical difference of protons that is in equilibrium with that between the two bulk phases that the coupling membrane serves to separate. This gradient consists of a membrane potential term Δψ and a pH gradient term ΔpH, and is known colloquially as the protonmotive force or pmf. Artificial imposition of a pmf can drive phosphorylation, but only if the pmf exceeds some 150-170mV; to achieve in vivo rates the imposed pmf must reach 200mV. The key question then is 'does the pmf generated by electron transport exceed 200mV, or even 170mV?' The possibly surprising answer, from a great many kinds of experiment and sources of evidence, including direct measurements with microelectrodes, indicates it that it does not. Observable pH changes driven by electron transport are real, and they control various processes; however, compensating ion movements restrict the Δψ component to low values. A protet-based model, that I outline here, can account for all the necessary observations, including all of those inconsistent with chemiosmotic coupling, and provides for a variety of testable hypotheses by which it might be refined.
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Affiliation(s)
- Douglas B Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative, Biology, University of Liverpool, Liverpool, United Kingdom; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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42
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Burska D, Stiburek L, Krizova J, Vanisova M, Martinek V, Sladkova J, Zamecnik J, Honzik T, Zeman J, Hansikova H, Tesarova M. Homozygous missense mutation in UQCRC2 associated with severe encephalomyopathy, mitochondrial complex III assembly defect and activation of mitochondrial protein quality control. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166147. [PMID: 33865955 DOI: 10.1016/j.bbadis.2021.166147] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/31/2021] [Accepted: 04/12/2021] [Indexed: 01/02/2023]
Abstract
The mitochondrial respiratory chain (MRC) complex III (CIII) associates with complexes I and IV (CI and CIV) into supercomplexes. We identified a novel homozygous missense mutation (c.665G>C; p.Gly222Ala) in UQCRC2 coding for structural subunit Core 2 in a patient with severe encephalomyopathy. The structural data suggest that the Gly222Ala exchange might result in an altered spatial arrangement in part of the UQCRC2 subunit, which could impact specific protein-protein interactions. Accordingly, we have found decreased levels of CIII and accumulation of CIII-specific subassemblies comprising MT-CYB, UQCRB, UQCRQ, UQCR10 and CYC1 subunits, but devoid of UQCRC1, UQCRC2, and UQCRFS1 in the patient's fibroblasts. The lack of UQCRC1 subunit-containing subassemblies could result from an impaired interaction with mutant UQCRC2Gly222Ala and subsequent degradation of both subunits by mitochondrial proteases. Indeed, we show an elevated amount of matrix CLPP protease, suggesting the activation of the mitochondrial protein quality control machinery in UQCRC2Gly222Ala fibroblasts. In line with growing evidence, we observed a rate-limiting character of CIII availability for the supercomplex formation, accompanied by a diminished amount of CI. Furthermore, we found impaired electron flux between CI and CIII in skeletal muscle and fibroblasts of the UQCRC2Gly222Ala patient. The ectopic expression of wild-type UQCRC2 in patient cells rescued maximal respiration rate, demonstrating the deleterious effect of the mutation on MRC. Our study expands the phenotypic spectrum of human disease caused by CIII Core protein deficiency, provides insight into the assembly pathway of human CIII, and supports the requirement of assembled CIII for a proper accumulation of CI.
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Affiliation(s)
- Daniela Burska
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, General University Hospital, Prague, Czech Republic
| | - Lukas Stiburek
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, General University Hospital, Prague, Czech Republic
| | - Jana Krizova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, General University Hospital, Prague, Czech Republic
| | - Marie Vanisova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, General University Hospital, Prague, Czech Republic
| | - Vaclav Martinek
- Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jana Sladkova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, General University Hospital, Prague, Czech Republic
| | - Josef Zamecnik
- Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine, Charles University, Motol University Hospital, Prague, Czech Republic
| | - Tomas Honzik
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, General University Hospital, Prague, Czech Republic
| | - Jiri Zeman
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, General University Hospital, Prague, Czech Republic
| | - Hana Hansikova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, General University Hospital, Prague, Czech Republic
| | - Marketa Tesarova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, General University Hospital, Prague, Czech Republic.
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Crofts AR. The modified Q-cycle: A look back at its development and forward to a functional model. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148417. [PMID: 33745972 DOI: 10.1016/j.bbabio.2021.148417] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/28/2021] [Accepted: 03/11/2021] [Indexed: 11/25/2022]
Abstract
On looking back at a lifetime of research, it is interesting to see, in the light of current progress, how things came to be, and to speculate on how things might be. I am delighted in the context of the Mitchell prize to have that excuse to present this necessarily personal view of developments in areas of my interests. I have focused on the Q-cycle and a few examples showing wider ramifications, since that had been the main interest of the lab in the 20 years since structures became available, - a watershed event in determining our molecular perspective. I have reviewed the evidence for our model for the mechanism of the first electron transfer of the bifurcated reaction at the Qo-site, which I think is compelling. In reviewing progress in understanding the second electron transfer, I have revisited some controversies to justify important conclusions which appear, from the literature, not to have been taken seriously. I hope this does not come over as nitpicking. The conclusions are important to the final section in which I develop an internally consistent mechanism for turnovers of the complex leading to a state similar to that observed in recent rapid-mix/freeze-quench experiments, reported three years ago. The final model is necessarily speculative but is open to test.
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Affiliation(s)
- Antony R Crofts
- Department of Biochemistry, 417 Roger Adams Laboratory, 600 South Mathews Avenue, Urbana, IL 61801, United States of America
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44
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Maclean AE, Bridges HR, Silva MF, Ding S, Ovciarikova J, Hirst J, Sheiner L. Complexome profile of Toxoplasma gondii mitochondria identifies divergent subunits of respiratory chain complexes including new subunits of cytochrome bc1 complex. PLoS Pathog 2021; 17:e1009301. [PMID: 33651838 PMCID: PMC7987180 DOI: 10.1371/journal.ppat.1009301] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 03/23/2021] [Accepted: 01/11/2021] [Indexed: 12/30/2022] Open
Abstract
The mitochondrial electron transport chain (mETC) and F1Fo-ATP synthase are of central importance for energy and metabolism in eukaryotic cells. The Apicomplexa, important pathogens of humans causing diseases such as toxoplasmosis and malaria, depend on their mETC in every known stage of their complicated life cycles. Here, using a complexome profiling proteomic approach, we have characterised the Toxoplasma mETC complexes and F1Fo-ATP synthase. We identified and assigned 60 proteins to complexes II, IV and F1Fo-ATP synthase of Toxoplasma, of which 16 have not been identified previously. Notably, our complexome profile elucidates the composition of the Toxoplasma complex III, the target of clinically used drugs such as atovaquone. We identified two new homologous subunits and two new parasite-specific subunits, one of which is broadly conserved in myzozoans. We demonstrate all four proteins are essential for complex III stability and parasite growth, and show their depletion leads to decreased mitochondrial potential, supporting their assignment as complex III subunits. Our study highlights the divergent subunit composition of the apicomplexan mETC and F1Fo-ATP synthase complexes and sets the stage for future structural and drug discovery studies.
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Affiliation(s)
- Andrew E. Maclean
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
| | - Hannah R. Bridges
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Mariana F. Silva
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
- Institute of Biomedical Sciences, Federal University of Uberlândia, Uberlândia, Brazil
| | - Shujing Ding
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Jana Ovciarikova
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
| | - Judy Hirst
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Lilach Sheiner
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
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Sarewicz M, Pintscher S, Pietras R, Borek A, Bujnowicz Ł, Hanke G, Cramer WA, Finazzi G, Osyczka A. Catalytic Reactions and Energy Conservation in the Cytochrome bc1 and b6f Complexes of Energy-Transducing Membranes. Chem Rev 2021; 121:2020-2108. [PMID: 33464892 PMCID: PMC7908018 DOI: 10.1021/acs.chemrev.0c00712] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Indexed: 12/16/2022]
Abstract
This review focuses on key components of respiratory and photosynthetic energy-transduction systems: the cytochrome bc1 and b6f (Cytbc1/b6f) membranous multisubunit homodimeric complexes. These remarkable molecular machines catalyze electron transfer from membranous quinones to water-soluble electron carriers (such as cytochromes c or plastocyanin), coupling electron flow to proton translocation across the energy-transducing membrane and contributing to the generation of a transmembrane electrochemical potential gradient, which powers cellular metabolism in the majority of living organisms. Cytsbc1/b6f share many similarities but also have significant differences. While decades of research have provided extensive knowledge on these enzymes, several important aspects of their molecular mechanisms remain to be elucidated. We summarize a broad range of structural, mechanistic, and physiological aspects required for function of Cytbc1/b6f, combining textbook fundamentals with new intriguing concepts that have emerged from more recent studies. The discussion covers but is not limited to (i) mechanisms of energy-conserving bifurcation of electron pathway and energy-wasting superoxide generation at the quinol oxidation site, (ii) the mechanism by which semiquinone is stabilized at the quinone reduction site, (iii) interactions with substrates and specific inhibitors, (iv) intermonomer electron transfer and the role of a dimeric complex, and (v) higher levels of organization and regulation that involve Cytsbc1/b6f. In addressing these topics, we point out existing uncertainties and controversies, which, as suggested, will drive further research in this field.
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Affiliation(s)
- Marcin Sarewicz
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Sebastian Pintscher
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Rafał Pietras
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Arkadiusz Borek
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Łukasz Bujnowicz
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Guy Hanke
- School
of Biological and Chemical Sciences, Queen
Mary University of London, London E1 4NS, U.K.
| | - William A. Cramer
- Department
of Biological Sciences, Purdue University, West Lafayette, Indiana 47907 United States
| | - Giovanni Finazzi
- Laboratoire
de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National Recherche Scientifique,
Commissariat Energie Atomique et Energies Alternatives, Institut National
Recherche l’agriculture, l’alimentation et l’environnement, 38054 Grenoble Cedex 9, France
| | - Artur Osyczka
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
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46
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The road to the structure of the mitochondrial respiratory chain supercomplex. Biochem Soc Trans 2021; 48:621-629. [PMID: 32311046 PMCID: PMC7200630 DOI: 10.1042/bst20190930] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 03/30/2020] [Accepted: 03/31/2020] [Indexed: 01/04/2023]
Abstract
The four complexes of the mitochondrial respiratory chain are critical for ATP production in most eukaryotic cells. Structural characterisation of these complexes has been critical for understanding the mechanisms underpinning their function. The three proton-pumping complexes, Complexes I, III and IV associate to form stable supercomplexes or respirasomes, the most abundant form containing 80 subunits in mammals. Multiple functions have been proposed for the supercomplexes, including enhancing the diffusion of electron carriers, providing stability for the complexes and protection against reactive oxygen species. Although high-resolution structures for Complexes III and IV were determined by X-ray crystallography in the 1990s, the size of Complex I and the supercomplexes necessitated advances in sample preparation and the development of cryo-electron microscopy techniques. We now enjoy structures for these beautiful complexes isolated from multiple organisms and in multiple states and together they provide important insights into respiratory chain function and the role of the supercomplex. While we as non-structural biologists use these structures for interpreting our own functional data, we need to remind ourselves that they stand on the shoulders of a large body of previous structural studies, many of which are still appropriate for use in understanding our results. In this mini-review, we discuss the history of respiratory chain structural biology studies leading to the structures of the mammalian supercomplexes and beyond.
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47
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Synthesis and fungicidal activity of methyl (E)-1-(2-((E)-2-methoxy-1-(methoxyimino)-2-oxoethyl)benzyl)-2-(1-arylidene)hydrazine-1-carboxylates †‡. Mol Divers 2021; 26:801-813. [PMID: 33548013 DOI: 10.1007/s11030-021-10187-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/18/2021] [Indexed: 10/22/2022]
Abstract
To discover novel strobilurin fungicides, a series of methyl (E)-1-(2-((E)-2-methoxy-1-(methoxy-imino)-2-oxoethyl)benzyl)-2-(1-arylidene)hydrazine-1-carboxylates were designed based on the principle of biologically active splicing and the receptor target structure. The fungicidal activity results show that this class of compounds has excellent fungicidal activity, especially against S. sclerotiorum (Lib.) deBary, wheat white powder and puccinia polysora. The result of structure-activity relationship implied that the introduction of t-butyl in the side chain facilitates the hydrophobic interaction between the compound and the active site. The electrostatic effect of the substituents on the benzene ring is also a key factor affecting such activities. Among them, the compound I-1 not only showed a fungicidal effect comparable to that of kresoxim-methyl in vivo, but also had an excellent inhibitory effect on spore germination of P. oryzae Cav in vitro, which indicated that it could be used as a potential commercial fungicide for plant disease control.
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48
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Hayward JA, Rajendran E, Zwahlen SM, Faou P, van Dooren GG. Divergent features of the coenzyme Q:cytochrome c oxidoreductase complex in Toxoplasma gondii parasites. PLoS Pathog 2021; 17:e1009211. [PMID: 33524071 PMCID: PMC7877769 DOI: 10.1371/journal.ppat.1009211] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 02/11/2021] [Accepted: 12/03/2020] [Indexed: 11/19/2022] Open
Abstract
The mitochondrion is critical for the survival of apicomplexan parasites. Several major anti-parasitic drugs, such as atovaquone and endochin-like quinolones, act through inhibition of the mitochondrial electron transport chain at the coenzyme Q:cytochrome c oxidoreductase complex (Complex III). Despite being an important drug target, the protein composition of Complex III of apicomplexan parasites has not been elucidated. Here, we undertake a mass spectrometry-based proteomic analysis of Complex III in the apicomplexan Toxoplasma gondii. Along with canonical subunits that are conserved across eukaryotic evolution, we identify several novel or highly divergent Complex III components that are conserved within the apicomplexan lineage. We demonstrate that one such subunit, which we term TgQCR11, is critical for parasite proliferation, mitochondrial oxygen consumption and Complex III activity, and establish that loss of this protein leads to defects in Complex III integrity. We conclude that the protein composition of Complex III in apicomplexans differs from that of the mammalian hosts that these parasites infect.
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Affiliation(s)
- Jenni A. Hayward
- Research School of Biology, Australian National University, Canberra, Australia
| | - Esther Rajendran
- Research School of Biology, Australian National University, Canberra, Australia
| | - Soraya M. Zwahlen
- Research School of Biology, Australian National University, Canberra, Australia
| | - Pierre Faou
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Giel G. van Dooren
- Research School of Biology, Australian National University, Canberra, Australia
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49
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Pagacz J, Broniec A, Wolska M, Osyczka A, Borek A. ROS signaling capacity of cytochrome bc 1: Opposing effects of adaptive and pathogenic mitochondrial mutations. Free Radic Biol Med 2021; 163:243-254. [PMID: 33352219 DOI: 10.1016/j.freeradbiomed.2020.12.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/07/2020] [Accepted: 12/12/2020] [Indexed: 01/06/2023]
Abstract
Cytochrome bc1, also known as mitochondrial complex III, is considered to be one of the important producers of reactive oxygen species (ROS) in living organisms. Under physiological conditions, a certain level of ROS produced by mitochondrial electron transport chain (ETC) might be beneficial and take part in cellular signaling. However, elevated levels of ROS might exhibit negative effects, resulting in cellular damage. It is well known that inhibiting the electron flow within mitochondrial complex III leads to high production of ROS. However, superoxide production by cytochrome bc1 in a non-inhibited system remained controversial. Here, we propose a novel method for ROS detection in ETC hybrid system in solution comprising bacterial cytochrome bc1 and mitochondrial complex IV. We clearly show that non-inhibited cytochrome bc1 generates ROS and that adaptive and pathogenic mitochondrial mutations suppress and enhance ROS production, respectively. We also noted that cytochrome bc1 produces ROS in a rate-dependent manner and that the mechanism of ROS generation changes according to the rate of operation of the enzyme. This dependency has not yet been reported, but seems to be crucial when discussing ROS signaling originating from mitochondria.
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Affiliation(s)
- Jakub Pagacz
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Agnieszka Broniec
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Małgorzata Wolska
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Artur Osyczka
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Arkadiusz Borek
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland.
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50
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Maldonado M, Guo F, Letts JA. Atomic structures of respiratory complex III 2, complex IV, and supercomplex III 2-IV from vascular plants. eLife 2021; 10:e62047. [PMID: 33463523 PMCID: PMC7815315 DOI: 10.7554/elife.62047] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/25/2020] [Indexed: 12/11/2022] Open
Abstract
Mitochondrial complex III (CIII2) and complex IV (CIV), which can associate into a higher-order supercomplex (SC III2+IV), play key roles in respiration. However, structures of these plant complexes remain unknown. We present atomic models of CIII2, CIV, and SC III2+IV from Vigna radiata determined by single-particle cryoEM. The structures reveal plant-specific differences in the MPP domain of CIII2 and define the subunit composition of CIV. Conformational heterogeneity analysis of CIII2 revealed long-range, coordinated movements across the complex, as well as the motion of CIII2's iron-sulfur head domain. The CIV structure suggests that, in plants, proton translocation does not occur via the H channel. The supercomplex interface differs significantly from that in yeast and bacteria in its interacting subunits, angle of approach and limited interactions in the mitochondrial matrix. These structures challenge long-standing assumptions about the plant complexes and generate new mechanistic hypotheses.
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Affiliation(s)
- Maria Maldonado
- Department of Molecular and Cellular Biology, University of California DavisDavisUnited States
| | - Fei Guo
- Department of Molecular and Cellular Biology, University of California DavisDavisUnited States
- BIOEM Facility, University of California DavisDavisUnited States
| | - James A Letts
- Department of Molecular and Cellular Biology, University of California DavisDavisUnited States
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