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Grayson C, Faerman B, Koufos O, Mailloux RJ. Fatty acid oxidation drives mitochondrial hydrogen peroxide production by α-ketoglutarate dehydrogenase. J Biol Chem 2024; 300:107159. [PMID: 38479602 PMCID: PMC10997840 DOI: 10.1016/j.jbc.2024.107159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/29/2024] [Accepted: 03/06/2024] [Indexed: 04/07/2024] Open
Abstract
In the present study, we examined the mitochondrial hydrogen peroxide (mH2O2) generating capacity of α-ketoglutarate dehydrogenase (KGDH) and compared it to components of the electron transport chain using liver mitochondria isolated from male and female C57BL6N mice. We show for the first time there are some sex dimorphisms in the production of mH2O2 by electron transport chain complexes I and III when mitochondria are fueled with different substrates. However, in our investigations into these sex effects, we made the unexpected and compelling discovery that 1) KGDH serves as a major mH2O2 supplier in male and female liver mitochondria and 2) KGDH can form mH2O2 when liver mitochondria are energized with fatty acids but only when malate is used to prime the Krebs cycle. Surprisingly, 2-keto-3-methylvaleric acid (KMV), a site-specific inhibitor for KGDH, nearly abolished mH2O2 generation in both male and female liver mitochondria oxidizing palmitoyl-carnitine. KMV inhibited mH2O2 production in liver mitochondria from male and female mice oxidizing myristoyl-, octanoyl-, or butyryl-carnitine as well. S1QEL 1.1 (S1) and S3QEL 2 (S3), compounds that inhibit reactive oxygen species generation by complexes I and III, respectively, without interfering with OxPhos and respiration, had a negligible effect on the rate of mH2O2 production when pyruvate or acyl-carnitines were used as fuels. However, inclusion of KMV in reaction mixtures containing S1 and/or S3 almost abolished mH2O2 generation. Together, our findings suggest KGDH is the main mH2O2 generator in liver mitochondria, even when fatty acids are used as fuel.
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Affiliation(s)
- Cathryn Grayson
- The School of Human Nutrition, Faculty of Agricultural and Environmental Sciences, McGill University, Quebec, Canada
| | - Ben Faerman
- The School of Human Nutrition, Faculty of Agricultural and Environmental Sciences, McGill University, Quebec, Canada
| | - Olivia Koufos
- The School of Human Nutrition, Faculty of Agricultural and Environmental Sciences, McGill University, Quebec, Canada
| | - Ryan J Mailloux
- The School of Human Nutrition, Faculty of Agricultural and Environmental Sciences, McGill University, Quebec, Canada.
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2
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Meinhold S, Zdanowicz R, Giese C, Glockshuber R. Dimerization of a 5-kDa domain defines the architecture of the 5-MDa gammaproteobacterial pyruvate dehydrogenase complex. Sci Adv 2024; 10:eadj6358. [PMID: 38324697 PMCID: PMC10849603 DOI: 10.1126/sciadv.adj6358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 01/11/2024] [Indexed: 02/09/2024]
Abstract
The Escherichia coli pyruvate dehydrogenase complex (PDHc) is a ~5 MDa assembly of the catalytic subunits pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3). The PDHc core is a cubic complex of eight E2 homotrimers. Homodimers of the peripheral subunits E1 and E3 associate with the core by binding to the peripheral subunit binding domain (PSBD) of E2. Previous reports indicated that 12 E1 dimers and 6 E3 dimers bind to the 24-meric E2 core. Using an assembly arrested E2 homotrimer (E23), we show that two of the three PSBDs in the E23 dimerize, that each PSBD dimer cooperatively binds two E1 dimers, and that E3 dimers only bind to the unpaired PSBD in E23. This mechanism is preserved in wild-type PDHc, with an E1 dimer:E2 monomer:E3 dimer stoichiometry of 16:24:8. The conserved PSBD dimer interface indicates that PSBD dimerization is the previously unrecognized architectural determinant of gammaproteobacterial PDHc megacomplexes.
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Affiliation(s)
| | | | - Christoph Giese
- ETH Zürich, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
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3
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Plokhikh KS, Nesterov SV, Chesnokov YM, Rogov AG, Kamyshinsky RA, Vasiliev AL, Yaguzhinsky LS, Vasilov RG. Association of 2-oxoacid dehydrogenase complexes with respirasomes in mitochondria. FEBS J 2024; 291:132-141. [PMID: 37789611 DOI: 10.1111/febs.16965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 08/14/2023] [Accepted: 09/29/2023] [Indexed: 10/05/2023]
Abstract
In the present study, cryo-electron tomography was used to investigate the localization of 2-oxoacid dehydrogenase complexes (OADCs) in cardiac mitochondria and mitochondrial inner membrane samples. Two classes of ordered OADC inner cores with different symmetries were distinguished and their quaternary structures modeled. One class corresponds to pyruvate dehydrogenase complexes and the other to dehydrogenase complexes of α-ketoglutarate and branched-chain α-ketoacids. OADCs were shown to be localized in close proximity to membrane-embedded respirasomes, as observed both in densely packed lamellar cristae of cardiac mitochondria and in ruptured mitochondrial samples where the dense packing is absent. This suggests the specificity of the OADC-respirasome interaction, which allows localized NADH/NAD+ exchange between OADCs and complex I of the respiratory chain. The importance of this local coupling is based on OADCs being the link between respiration, glycolysis and amino acid metabolism. The coupling of these basic metabolic processes can vary in different tissues and conditions and may be involved in the development of various pathologies. The present study shows that this important and previously missing parameter of mitochondrial complex coupling can be successfully assessed using cryo-electron tomography.
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Affiliation(s)
- Konstantin S Plokhikh
- Kurchatov Complex of NBICS-Technologies, National Research Center Kurchatov Institute, Moscow, Russia
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russia
| | - Semen V Nesterov
- Kurchatov Complex of NBICS-Technologies, National Research Center Kurchatov Institute, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Yuriy M Chesnokov
- Kurchatov Complex of NBICS-Technologies, National Research Center Kurchatov Institute, Moscow, Russia
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russia
| | - Anton G Rogov
- Kurchatov Complex of NBICS-Technologies, National Research Center Kurchatov Institute, Moscow, Russia
| | - Roman A Kamyshinsky
- Kurchatov Complex of NBICS-Technologies, National Research Center Kurchatov Institute, Moscow, Russia
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russia
| | - Aleksandr L Vasiliev
- Kurchatov Complex of NBICS-Technologies, National Research Center Kurchatov Institute, Moscow, Russia
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Lev S Yaguzhinsky
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Belozersky Research Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Russia
| | - Raif G Vasilov
- Kurchatov Complex of NBICS-Technologies, National Research Center Kurchatov Institute, Moscow, Russia
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Sundermeyer L, Folkerts JG, Lückel B, Mack C, Baumgart M, Bott M. Cellular localization of the hybrid pyruvate/2-oxoglutarate dehydrogenase complex in the actinobacterium Corynebacterium glutamicum. Microbiol Spectr 2023; 11:e0266823. [PMID: 37754766 PMCID: PMC10581250 DOI: 10.1128/spectrum.02668-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/05/2023] [Indexed: 09/28/2023] Open
Abstract
For many bacterial proteins, specific localizations within the cell have been demonstrated, but enzymes involved in central metabolism are usually considered to be homogenously distributed within the cytoplasm. Here, we provide an example for a spatially defined localization of a unique enzyme complex found in actinobacteria, the hybrid pyruvate/2-oxoglutarate dehydrogenase complex (PDH-ODH). In non-actinobacterial cells, PDH and ODH form separate multienzyme complexes of megadalton size composed of three different subunits, E1, E2, and E3. The actinobacterial PDH-ODH complex is composed of four subunits, AceE (E1p), AceF (E2p), Lpd (E3), and OdhA (E1oE2o). Using fluorescence microscopy, we observed that in Corynebacterium glutamicum, all four subunits are co-localized in distinct spots at the cell poles, and in larger cells, additional spots are present at mid-cell. These results further confirm the existence of the hybrid complex. The unphosporylated OdhI protein, which binds to OdhA and inhibits ODH activity, was co-localized with OdhA at the poles, whereas phosphorylated OdhI, which does not bind OdhA, was distributed in the entire cytoplasm. Isocitrate dehydrogenase and glutamate dehydrogenase, both metabolically linked to ODH, were evenly distributed in the cytoplasm. Based on the available structural data for individual PDH-ODH subunits, a novel supramolecular architecture of the hybrid complex differing from classical PDH and ODH complexes has to be postulated. Our results suggest that localization at the poles or at mid-cell is most likely caused by nucleoid exclusion and results in a spatially organized metabolism in actinobacteria, with consequences yet to be studied. IMPORTANCE Enzymes involved in the central metabolism of bacteria are usually considered to be distributed within the entire cytoplasm. Here, we provide an example for a spatially defined localization of a unique enzyme complex of actinobacteria, the hybrid pyruvate dehydrogenase/2-oxoglutarate dehydrogenase (PDH-ODH) complex composed of four different subunits. Using fusions with mVenus or mCherry and fluorescence microscopy, we show that all four subunits are co-localized in distinct spots at the cell poles, and in larger cells, additional spots were observed at mid-cell. These results clearly support the presence of the hybrid PDH-ODH complex and suggest a similar localization in other actinobacteria. The observation of a defined spatial localization of an enzyme complex catalyzing two key reactions of central metabolism poses questions regarding possible consequences for the availability of substrates and products within the cell and other bacterial enzyme complexes showing similar behavior.
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Affiliation(s)
- Lea Sundermeyer
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Jan-Gerrit Folkerts
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Benita Lückel
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Christina Mack
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Meike Baumgart
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Michael Bott
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Jülich, Germany
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Yang L, Wagner T, Mechaly A, Boyko A, Bruch EM, Megrian D, Gubellini F, Alzari PM, Bellinzoni M. High resolution cryo-EM and crystallographic snapshots of the actinobacterial two-in-one 2-oxoglutarate dehydrogenase. Nat Commun 2023; 14:4851. [PMID: 37563123 PMCID: PMC10415282 DOI: 10.1038/s41467-023-40253-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 07/19/2023] [Indexed: 08/12/2023] Open
Abstract
Actinobacteria possess unique ways to regulate the oxoglutarate metabolic node. Contrary to most organisms in which three enzymes compose the 2-oxoglutarate dehydrogenase complex (ODH), actinobacteria rely on a two-in-one protein (OdhA) in which both the oxidative decarboxylation and succinyl transferase steps are carried out by the same polypeptide. Here we describe high-resolution cryo-EM and crystallographic snapshots of representative enzymes from Mycobacterium smegmatis and Corynebacterium glutamicum, showing that OdhA is an 800-kDa homohexamer that assembles into a three-blade propeller shape. The obligate trimeric and dimeric states of the acyltransferase and dehydrogenase domains, respectively, are critical for maintaining the overall assembly, where both domains interact via subtle readjustments of their interfaces. Complexes obtained with substrate analogues, reaction products and allosteric regulators illustrate how these domains operate. Furthermore, we provide additional insights into the phosphorylation-dependent regulation of this enzymatic machinery by the signalling protein OdhI.
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Affiliation(s)
- Lu Yang
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
- Wuhan Institute of Biological Products Co. Ltd., Wuhan, 430207, PR China
| | - Tristan Wagner
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
- Microbial Metabolism Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, D-28359, Bremen, Germany
| | - Ariel Mechaly
- Institut Pasteur, Université Paris Cité, Plateforme de Cristallographie, F-75015, Paris, France
| | - Alexandra Boyko
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
- BostonGene, Yerevan, Armenia
| | - Eduardo M Bruch
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
- Sanofi, In vitro Biology, Integrated Drug Discovery, 350 Water St, Cambridge, MA, 02141, USA
| | - Daniela Megrian
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
| | - Francesca Gubellini
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
| | - Pedro M Alzari
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
| | - Marco Bellinzoni
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France.
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Hevler JF, Albanese P, Cabrera-Orefice A, Potter A, Jankevics A, Misic J, Scheltema RA, Brandt U, Arnold S, Heck AJR. MRPS36 provides a structural link in the eukaryotic 2-oxoglutarate dehydrogenase complex. Open Biol 2023; 13:220363. [PMID: 36854377 PMCID: PMC9974300 DOI: 10.1098/rsob.220363] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
The tricarboxylic acid cycle is the central pathway of energy production in eukaryotic cells and plays a key part in aerobic respiration throughout all kingdoms of life. One of the pivotal enzymes in this cycle is 2-oxoglutarate dehydrogenase complex (OGDHC), which generates NADH by oxidative decarboxylation of 2-oxoglutarate to succinyl-CoA. OGDHC is a megadalton protein complex originally thought to be assembled from three catalytically active subunits (E1o, E2o, E3). In fungi and animals, however, the protein MRPS36 has more recently been proposed as a putative additional component. Based on extensive cross-linking mass spectrometry data supported by phylogenetic analyses, we provide evidence that MRPS36 is an important member of the eukaryotic OGDHC, with no prokaryotic orthologues. Comparative sequence analysis and computational structure predictions reveal that, in contrast with bacteria and archaea, eukaryotic E2o does not contain the peripheral subunit-binding domain (PSBD), for which we propose that MRPS36 evolved as an E3 adaptor protein, functionally replacing the PSBD. We further provide a refined structural model of the complete eukaryotic OGDHC of approximately 3.45 MDa with novel mechanistic insights.
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Affiliation(s)
- Johannes F. Hevler
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Pascal Albanese
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Alfredo Cabrera-Orefice
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Alisa Potter
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Andris Jankevics
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Jelena Misic
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Richard A. Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Ulrich Brandt
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Susanne Arnold
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
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