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Cimadamore-Werthein C, King MS, Lacabanne D, Pyrihová E, Jaiquel Baron S, Kunji ER. Human mitochondrial carriers of the SLC25 family function as monomers exchanging substrates with a ping-pong kinetic mechanism. EMBO J 2024; 43:3450-3465. [PMID: 38937634 PMCID: PMC11329753 DOI: 10.1038/s44318-024-00150-0] [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: 03/14/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 06/29/2024] Open
Abstract
Members of the SLC25 mitochondrial carrier family link cytosolic and mitochondrial metabolism and support cellular maintenance and growth by transporting compounds across the mitochondrial inner membrane. Their monomeric or dimeric state and kinetic mechanism have been a matter of long-standing debate. It is believed by some that they exist as homodimers and transport substrates with a sequential kinetic mechanism, forming a ternary complex where both exchanged substrates are bound simultaneously. Some studies, in contrast, have provided evidence indicating that the mitochondrial ADP/ATP carrier (SLC25A4) functions as a monomer, has a single substrate binding site, and operates with a ping-pong kinetic mechanism, whereby ADP is imported before ATP is exported. Here we reanalyze the oligomeric state and kinetic properties of the human mitochondrial citrate carrier (SLC25A1), dicarboxylate carrier (SLC25A10), oxoglutarate carrier (SLC25A11), and aspartate/glutamate carrier (SLC25A13), all previously reported to be dimers with a sequential kinetic mechanism. We demonstrate that they are monomers, except for dimeric SLC25A13, and operate with a ping-pong kinetic mechanism in which the substrate import and export steps occur consecutively. These observations are consistent with a common transport mechanism, based on a functional monomer, in which a single central substrate-binding site is alternately accessible.
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Affiliation(s)
- Camila Cimadamore-Werthein
- Medical Research Council Mitochondrial Biology Unit, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Martin S King
- Medical Research Council Mitochondrial Biology Unit, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Denis Lacabanne
- Medical Research Council Mitochondrial Biology Unit, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Eva Pyrihová
- Medical Research Council Mitochondrial Biology Unit, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Stephany Jaiquel Baron
- Medical Research Council Mitochondrial Biology Unit, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Edmund Rs Kunji
- Medical Research Council Mitochondrial Biology Unit, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom.
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2
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Horten P, Song K, Garlich J, Hardt R, Colina-Tenorio L, Horvath SE, Schulte U, Fakler B, van der Laan M, Becker T, Stuart RA, Pfanner N, Rampelt H. Identification of MIMAS, a multifunctional mega-assembly integrating metabolic and respiratory biogenesis factors of mitochondria. Cell Rep 2024; 43:113772. [PMID: 38393949 PMCID: PMC11010658 DOI: 10.1016/j.celrep.2024.113772] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/03/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The mitochondrial inner membrane plays central roles in bioenergetics and metabolism and contains several established membrane protein complexes. Here, we report the identification of a mega-complex of the inner membrane, termed mitochondrial multifunctional assembly (MIMAS). Its large size of 3 MDa explains why MIMAS has escaped detection in the analysis of mitochondria so far. MIMAS combines proteins of diverse functions from respiratory chain assembly to metabolite transport, dehydrogenases, and lipid biosynthesis but not the large established supercomplexes of the respiratory chain, ATP synthase, or prohibitin scaffold. MIMAS integrity depends on the non-bilayer phospholipid phosphatidylethanolamine, in contrast to respiratory supercomplexes whose stability depends on cardiolipin. Our findings suggest that MIMAS forms a protein-lipid mega-assembly in the mitochondrial inner membrane that integrates respiratory biogenesis and metabolic processes in a multifunctional platform.
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Affiliation(s)
- Patrick Horten
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Kuo Song
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Joshua Garlich
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Robert Hardt
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany
| | - Lilia Colina-Tenorio
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Susanne E Horvath
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Uwe Schulte
- Institute of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Bernd Fakler
- Institute of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Martin van der Laan
- Medical Biochemistry and Molecular Biology, Center for Molecular Signaling, PZMS, Faculty of Medicine, Saarland University, 66421 Homburg, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany
| | - Rosemary A Stuart
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
| | - Heike Rampelt
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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Mavridou V, King MS, Tavoulari S, Ruprecht JJ, Palmer SM, Kunji ERS. Substrate binding in the mitochondrial ADP/ATP carrier is a step-wise process guiding the structural changes in the transport cycle. Nat Commun 2022; 13:3585. [PMID: 35739110 PMCID: PMC9226169 DOI: 10.1038/s41467-022-31366-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 06/14/2022] [Indexed: 02/02/2023] Open
Abstract
Mitochondrial ADP/ATP carriers import ADP into the mitochondrial matrix and export ATP to the cytosol to fuel cellular processes. Structures of the inhibited cytoplasmic- and matrix-open states have confirmed an alternating access transport mechanism, but the molecular details of substrate binding remain unresolved. Here, we evaluate the role of the solvent-exposed residues of the translocation pathway in the process of substrate binding. We identify the main binding site, comprising three positively charged and a set of aliphatic and aromatic residues, which bind ADP and ATP in both states. Additionally, there are two pairs of asparagine/arginine residues on opposite sides of this site that are involved in substrate binding in a state-dependent manner. Thus, the substrates are directed through a series of binding poses, inducing the conformational changes of the carrier that lead to their translocation. The properties of this site explain the electrogenic and reversible nature of adenine nucleotide transport.
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Affiliation(s)
- Vasiliki Mavridou
- grid.5335.00000000121885934Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Keith Peters Building, Hills Road, Cambridge, CB2 0XY UK
| | - Martin S. King
- grid.5335.00000000121885934Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Keith Peters Building, Hills Road, Cambridge, CB2 0XY UK
| | - Sotiria Tavoulari
- grid.5335.00000000121885934Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Keith Peters Building, Hills Road, Cambridge, CB2 0XY UK
| | - Jonathan J. Ruprecht
- grid.5335.00000000121885934Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Keith Peters Building, Hills Road, Cambridge, CB2 0XY UK
| | - Shane M. Palmer
- grid.5335.00000000121885934Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Keith Peters Building, Hills Road, Cambridge, CB2 0XY UK
| | - Edmund R. S. Kunji
- grid.5335.00000000121885934Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Keith Peters Building, Hills Road, Cambridge, CB2 0XY UK
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4
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Saccharomyces cerevisiae as a Tool for Studying Mutations in Nuclear Genes Involved in Diseases Caused by Mitochondrial DNA Instability. Genes (Basel) 2021; 12:genes12121866. [PMID: 34946817 PMCID: PMC8701800 DOI: 10.3390/genes12121866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/20/2021] [Accepted: 11/23/2021] [Indexed: 01/03/2023] Open
Abstract
Mitochondrial DNA (mtDNA) maintenance is critical for oxidative phosphorylation (OXPHOS) since some subunits of the respiratory chain complexes are mitochondrially encoded. Pathological mutations in nuclear genes involved in the mtDNA metabolism may result in a quantitative decrease in mtDNA levels, referred to as mtDNA depletion, or in qualitative defects in mtDNA, especially in multiple deletions. Since, in the last decade, most of the novel mutations have been identified through whole-exome sequencing, it is crucial to confirm the pathogenicity by functional analysis in the appropriate model systems. Among these, the yeast Saccharomyces cerevisiae has proved to be a good model for studying mutations associated with mtDNA instability. This review focuses on the use of yeast for evaluating the pathogenicity of mutations in six genes, MPV17/SYM1, MRM2/MRM2, OPA1/MGM1, POLG/MIP1, RRM2B/RNR2, and SLC25A4/AAC2, all associated with mtDNA depletion or multiple deletions. We highlight the techniques used to construct a specific model and to measure the mtDNA instability as well as the main results obtained. We then report the contribution that yeast has given in understanding the pathogenic mechanisms of the mutant variants, in finding the genetic suppressors of the mitochondrial defects and in the discovery of molecules able to improve the mtDNA stability.
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5
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Kunji ERS, King MS, Ruprecht JJ, Thangaratnarajah C. The SLC25 Carrier Family: Important Transport Proteins in Mitochondrial Physiology and Pathology. Physiology (Bethesda) 2021; 35:302-327. [PMID: 32783608 PMCID: PMC7611780 DOI: 10.1152/physiol.00009.2020] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Members of the mitochondrial carrier family (SLC25) transport a variety of compounds across the inner membrane of mitochondria. These transport steps provide building blocks for the cell and link the pathways of the mitochondrial matrix and cytosol. An increasing number of diseases and pathologies has been associated with their dysfunction. In this review, the molecular basis of these diseases is explained based on our current understanding of their transport mechanism.
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Affiliation(s)
- Edmund R S Kunji
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Martin S King
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Jonathan J Ruprecht
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Chancievan Thangaratnarajah
- Groningen Biomolecular Sciences and Biotechnology Institute, Membrane Enzymology, University of Groningen, Groningen, The Netherlands
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6
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The mitochondrial ADP/ATP carrier exists and functions as a monomer. Biochem Soc Trans 2021; 48:1419-1432. [PMID: 32725219 PMCID: PMC7458400 DOI: 10.1042/bst20190933] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/26/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022]
Abstract
For more than 40 years, the oligomeric state of members of the mitochondrial carrier family (SLC25) has been the subject of debate. Initially, the consensus was that they were dimeric, based on the application of a large number of different techniques. However, the structures of the mitochondrial ADP/ATP carrier, a member of the family, clearly demonstrated that its structural fold is monomeric, lacking a conserved dimerisation interface. A re-evaluation of previously published data, with the advantage of hindsight, concluded that technical errors were at the basis of the earlier dimer claims. Here, we revisit this topic, as new claims for the existence of dimers of the bovine ADP/ATP carrier have emerged using native mass spectrometry of mitochondrial membrane vesicles. However, the measured mass does not agree with previously published values, and a large number of post-translational modifications are proposed to account for the difference. Contrarily, these modifications are not observed in electron density maps of the bovine carrier. If they were present, they would interfere with the structure and function of the carrier, including inhibitor and substrate binding. Furthermore, the reported mass does not account for three tightly bound cardiolipin molecules, which are consistently observed in other studies and are important stabilising factors for the transport mechanism. The monomeric carrier has all of the required properties for a functional transporter and undergoes large conformational changes that are incompatible with a stable dimerisation interface. Thus, our view that the native mitochondrial ADP/ATP carrier exists and functions as a monomer remains unaltered.
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Abstract
Members of the mitochondrial carrier family [solute carrier family 25 (SLC25)] transport nucleotides, amino acids, carboxylic acids, fatty acids, inorganic ions, and vitamins across the mitochondrial inner membrane. They are important for many cellular processes, such as oxidative phosphorylation of lipids and sugars, amino acid metabolism, macromolecular synthesis, ion homeostasis, cellular regulation, and differentiation. Here, we describe the functional elements of the transport mechanism of mitochondrial carriers, consisting of one central substrate-binding site and two gates with salt-bridge networks on either side of the carrier. Binding of the substrate during import causes three gate elements to rotate inward, forming the cytoplasmic network and closing access to the substrate-binding site from the intermembrane space. Simultaneously, three core elements rock outward, disrupting the matrix network and opening the substrate-binding site to the matrix side of the membrane. During export, substrate binding triggers conformational changes involving the same elements but operating in reverse.
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Affiliation(s)
- J J Ruprecht
- Medical Research Council Mitochondrial Biology Unit, Keith Peters Building, University of Cambridge, Cambridge CB2 0XY, United Kingdom; ,
| | - E R S Kunji
- Medical Research Council Mitochondrial Biology Unit, Keith Peters Building, University of Cambridge, Cambridge CB2 0XY, United Kingdom; ,
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8
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A Single Cysteine Residue in the Translocation Pathway of the Mitosomal ADP/ATP Carrier from Cryptosporidium parvum Confers a Broad Nucleotide Specificity. Int J Mol Sci 2020; 21:ijms21238971. [PMID: 33255957 PMCID: PMC7730227 DOI: 10.3390/ijms21238971] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/09/2020] [Accepted: 11/23/2020] [Indexed: 12/18/2022] Open
Abstract
Cryptosporidiumparvum is a clinically important eukaryotic parasite that causes the disease cryptosporidiosis, which manifests with gastroenteritis-like symptoms. The protist has mitosomes, which are organelles of mitochondrial origin that have only been partially characterized. The genome encodes a highly reduced set of transport proteins of the SLC25 mitochondrial carrier family of unknown function. Here, we have studied the transport properties of one member of the C. parvum carrier family, demonstrating that it resembles the mitochondrial ADP/ATP carrier of eukaryotes. However, this carrier has a broader substrate specificity for nucleotides, transporting adenosine, thymidine, and uridine di- and triphosphates in contrast to its mitochondrial orthologues, which have a strict substrate specificity for ADP and ATP. Inspection of the putative translocation pathway highlights a cysteine residue, which is a serine in mitochondrial ADP/ATP carriers. When the serine residue is replaced by cysteine or larger hydrophobic residues in the yeast mitochondrial ADP/ATP carrier, the substrate specificity becomes broad, showing that this residue is important for nucleotide base selectivity in ADP/ATP carriers.
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9
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Senoo N, Kandasamy S, Ogunbona OB, Baile MG, Lu Y, Claypool SM. Cardiolipin, conformation, and respiratory complex-dependent oligomerization of the major mitochondrial ADP/ATP carrier in yeast. SCIENCE ADVANCES 2020; 6:eabb0780. [PMID: 32923632 PMCID: PMC7455186 DOI: 10.1126/sciadv.abb0780] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 07/08/2020] [Indexed: 05/30/2023]
Abstract
The phospholipid cardiolipin has pleiotropic structural and functional roles that are collectively essential for mitochondrial biology. Yet, the molecular details of how this lipid supports the structure and function of proteins and protein complexes are poorly understood. To address this property of cardiolipin, we use the mitochondrial adenosine 5'-diphosphate/adenosine 5'-triphosphate carrier (Aac) as a model. Here, we have determined that cardiolipin is critical for both the tertiary and quaternary assembly of the major yeast Aac isoform Aac2 as well as its conformation. Notably, these cardiolipin-provided structural roles are separable. In addition, we show that multiple copies of Aac2 engage in shared complexes that are largely dependent on the presence of assembled respiratory complexes III and IV or respiratory supercomplexes. Intriguingly, the assembly state of Aac2 is sensitive to its transport-related conformation. Together, these results expand our understanding of the numerous structural roles provided by cardiolipin for mitochondrial membrane proteins.
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10
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Abstract
Saccharomyces cerevisiae is one of the most popular expression systems for eukaryotic membrane proteins. Here, we describe protocols for the expression and purification of mitochondrial membrane proteins developed in our laboratory during the last 15 years. To optimize their expression in a functional form, different promoter systems as well as codon-optimization and complementation strategies were established. Purification approaches were developed which remove the membrane protein from the affinity column by specific proteolytic cleavage rather than by elution. This strategy has several important advantages, most notably improving the purity of the sample, as contaminants stay bound to the column, thus eliminating the need for a secondary purification step, such as size exclusion chromatography. This strategy also avoids dilution of the sample, which would occur as a consequence of elution, precluding the need for concentration steps, and thus preventing detergent concentration.
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Affiliation(s)
- Martin S King
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Edmund R S Kunji
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
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11
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Ogunbona OB, Claypool SM. Emerging Roles in the Biogenesis of Cytochrome c Oxidase for Members of the Mitochondrial Carrier Family. Front Cell Dev Biol 2019; 7:3. [PMID: 30766870 PMCID: PMC6365663 DOI: 10.3389/fcell.2019.00003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 01/10/2019] [Indexed: 12/11/2022] Open
Abstract
The mitochondrial carrier family (MCF) is a group of transport proteins that are mostly localized to the inner mitochondrial membrane where they facilitate the movement of various solutes across the membrane. Although these carriers represent potential targets for therapeutic application and are repeatedly associated with human disease, research on the MCF has not progressed commensurate to their physiologic and pathophysiologic importance. Many of the 53 MCF members in humans are orphans and lack known transport substrates. Even for the relatively well-studied members of this family, such as the ADP/ATP carrier and the uncoupling protein, there exist fundamental gaps in our understanding of their biological roles including a clear rationale for the existence of multiple isoforms. Here, we briefly review this important family of mitochondrial carriers, provide a few salient examples of their diverse metabolic roles and disease associations, and then focus on an emerging link between several distinct MCF members, including the ADP/ATP carrier, and cytochrome c oxidase biogenesis. As the ADP/ATP carrier is regarded as the paradigm of the entire MCF, its newly established role in regulating translation of the mitochondrial genome highlights that we still have a lot to learn about these metabolite transporters.
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Affiliation(s)
- Oluwaseun B. Ogunbona
- Department of Physiology, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
- Department of Pathology & Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA, United States
| | - Steven M. Claypool
- Department of Physiology, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
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The transport mechanism of the mitochondrial ADP/ATP carrier. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:2379-93. [PMID: 27001633 DOI: 10.1016/j.bbamcr.2016.03.015] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/15/2016] [Accepted: 03/16/2016] [Indexed: 12/18/2022]
Abstract
The mitochondrial ADP/ATP carrier imports ADP from the cytosol and exports ATP from the mitochondrial matrix, which are key transport steps for oxidative phosphorylation in eukaryotic organisms. The transport protein belongs to the mitochondrial carrier family, a large transporter family in the inner membrane of mitochondria. It is one of the best studied members of the family and serves as a paradigm for the molecular mechanism of mitochondrial carriers. Structurally, the carrier consists of three homologous domains, each composed of two transmembrane α-helices linked with a loop and short α-helix on the matrix side. The transporter cycles between a cytoplasmic and matrix state in which a central substrate binding site is alternately accessible to these compartments for binding of ADP or ATP. On both the cytoplasmic and matrix side of the carrier are networks consisting of three salt bridges each. In the cytoplasmic state, the matrix salt bridge network is formed and the cytoplasmic network is disrupted, opening the central substrate binding site to the intermembrane space and cytosol, whereas the converse occurs in the matrix state. In the transport cycle, tighter substrate binding in the intermediate states allows the interconversion of conformations by lowering the energy barrier for disruption and formation of these networks, opening and closing the carrier to either side of the membrane in an alternating way. Conversion between cytoplasmic and matrix states might require the simultaneous rotation of three domains around a central translocation pathway, constituting a unique mechanism among transport proteins. This article is part of a Special Issue entitled: Mitochondrial Channels edited by Pierre Sonveaux, Pierre Maechler and Jean-Claude Martinou.
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Uncoupling protein 1 binds one nucleotide per monomer and is stabilized by tightly bound cardiolipin. Proc Natl Acad Sci U S A 2015; 112:6973-8. [PMID: 26038550 DOI: 10.1073/pnas.1503833112] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Uncoupling protein 1 (UCP1) catalyzes fatty acid-activated, purine nucleotide-sensitive proton leak across the mitochondrial inner membrane of brown adipose tissue to produce heat, and could help combat obesity and metabolic disease in humans. Studies over the last 30 years conclude that the protein is a dimer, binding one nucleotide molecule per two proteins, and unlike the related mitochondrial ADP/ATP carrier, does not bind cardiolipin. Here, we have developed novel methods to purify milligram amounts of UCP1 from native sources by using covalent chromatography that, unlike past methods, allows the protein to be prepared in defined conditions, free of excess detergent and lipid. Assessment of purified preparations by TLC reveal that UCP1 retains tightly bound cardiolipin, with a lipid phosphorus content equating to three molecules per protein, like the ADP/ATP carrier. Cardiolipin stabilizes UCP1, as demonstrated by reconstitution experiments and thermostability assays, indicating that the lipid has an integral role in the functioning of the protein, similar to other mitochondrial carriers. Furthermore, we find that UCP1 is not dimeric but monomeric, as indicated by size exclusion analysis, and has a ligand titration profile in isothermal calorimetric measurements that clearly shows that one nucleotide binds per monomer. These findings reveal the fundamental composition of UCP1, which is essential for understanding the mechanism of the protein. Our assessment of the properties of UCP1 indicate that it is not unique among mitochondrial carriers and so is likely to use a common exchange mechanism in its primary function in brown adipose tissue mitochondria.
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Booty LM, King MS, Thangaratnarajah C, Majd H, James AM, Kunji ERS, Murphy MP. The mitochondrial dicarboxylate and 2-oxoglutarate carriers do not transport glutathione. FEBS Lett 2015; 589:621-8. [PMID: 25637873 PMCID: PMC4332691 DOI: 10.1016/j.febslet.2015.01.027] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 01/19/2015] [Accepted: 01/20/2015] [Indexed: 01/23/2023]
Abstract
Glutathione carries out vital protective roles within mitochondria, but is synthesised in the cytosol. Previous studies have suggested that the mitochondrial dicarboxylate and 2-oxoglutarate carriers were responsible for glutathione uptake. We set out to characterise the putative glutathione transport by using fused membrane vesicles of Lactococcus lactis overexpressing the dicarboxylate and 2-oxoglutarate carriers. Although transport of the canonical substrates could be measured readily, an excess of glutathione did not compete for substrate uptake nor could transport of glutathione be measured directly. Thus these mitochondrial carriers do not transport glutathione and the identity of the mitochondrial glutathione transporter remains unknown.
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Affiliation(s)
- Lee M Booty
- Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Martin S King
- Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Chancievan Thangaratnarajah
- Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Homa Majd
- Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Andrew M James
- Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Edmund R S Kunji
- Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK.
| | - Michael P Murphy
- Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK.
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15
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Monné M, Palmieri F. Antiporters of the mitochondrial carrier family. CURRENT TOPICS IN MEMBRANES 2014; 73:289-320. [PMID: 24745987 DOI: 10.1016/b978-0-12-800223-0.00008-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The eukaryotic transport protein family SLC25 consists of mitochondrial carriers (MCs) that are recognized on the sequence level by a threefold repeated and conserved signature motif. The majority of MCs characterized so far catalyzes strict exchanges of substrates across the mitochondrial inner membrane. The substrates are nucleotides, metabolic intermediates, and cofactors that are required in cytoplasmic and matrix metabolism. This review summarizes and discusses the current knowledge of the antiport mechanism(s) of MCs that has been deduced from determining transport characteristics and by analyzing structural, sequence, and mutagenesis data. The mode of transport varies among different MCs with respect to how the substrate translocation depends on the electrical and pH gradients across the mitochondrial inner membrane, for example, the ADP/ATP carrier is electrogenic (electrophoretic), the GTP/GDP carrier is dependent on the pH gradient, the aspartate/glutamate carrier is dependent on both, and the oxoglutarate/malate carrier is independent of them. The structure of the bovine ADP/ATP carrier consists of a six-transmembrane α-helix bundle with a pseudo-threefold symmetry and a closed matrix gate. By using this structure as a template in homology modeling, residues engaged in substrate binding and the formation of a cytoplasmic gate in MCs have been proposed. The functional importance of the residues of the binding site, the matrix, and the cytoplasmic gates is supported by transport activities of different MCs with single point mutations. Cumulative evidence has been used to postulate a general transport mechanism for MCs.
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Affiliation(s)
- Magnus Monné
- Department of Biosciences, Biotechnology and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari, Bari, Italy; Department of Sciences, University of Basilicata, Potenza, Italy
| | - Ferdinando Palmieri
- Department of Biosciences, Biotechnology and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari, Bari, Italy.
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Giangregorio N, Console L, Tonazzi A, Palmieri F, Indiveri C. Identification of amino acid residues underlying the antiport mechanism of the mitochondrial carnitine/acylcarnitine carrier by site-directed mutagenesis and chemical labeling. Biochemistry 2014; 53:6924-33. [PMID: 25325845 DOI: 10.1021/bi5009112] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The mitochondrial carnitine/acylcarnitine carrier catalyzes the transport of carnitine and acylcarnitines by antiport as well as by uniport with a rate slower than the rate of antiport. The mechanism of antiport resulting from coupling of two opposed uniport reactions was investigated by site-directed mutagenesis. The transport reaction was followed as [(3)H]carnitine uptake in or efflux from proteoliposomes reconstituted with the wild type or mutants, in the presence or absence of a countersubstrate. The ratio between the antiport and uniport rates for the wild type was 3.0 or 2.5, using the uptake or efflux procedure, respectively. This ratio did not vary substantially in mutants H29A, K35R, G121A, E132A, K135A, R178A, D179E, E191A, K194A, K234A, and E288A. A ratio of 1.0 was measured for mutant K35A, indicating a loss of antiport function by this mutant. Ratios of >1.0 but significantly lower than that of the wild type were measured for mutants D32A, K97A, and D231A, indicating the involvement of these residues in the antiport mechanism. To investigate the role of the countersubstrate in the conformational changes underlying the transport reaction, the m-state of the transporter (opened toward the matrix side) was specifically labeled with N-ethylmaleimide while the c-state of the carrier (opened toward the cytosolic side) was labeled with fluorescein maleimide. The labeling results indicated that the addition of an external substrate, on one hand, reduced the amount of protein in the m-state and, on the other, increased the protein fraction in the c-state. This substrate-induced conformational change was abolished in the protein lacking K35, pointing to the role of this residue as a sensor in the mechanism of the antiport reaction.
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Affiliation(s)
- Nicola Giangregorio
- CNR Institute of Biomembranes and Bioenergetics , via Amendola 165/A, 70126 Bari, Italy
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17
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Abstract
Lipid composition is expected to play an important role in modulating membrane enzyme activity, in particular if the substrates are themselves lipid molecules. A paradigmatic case is FAAH (fatty acid amide hydrolase), an enzyme critical in terminating endocannabinoid signalling and an important therapeutic target. In the present study, using a combined experimental and computational approach, we show that membrane lipids modulate the structure, subcellular localization and activity of FAAH. We report that the FAAH dimer is stabilized by the lipid bilayer and shows a higher membrane-binding affinity and enzymatic activity within membranes containing both cholesterol and the natural FAAH substrate AEA (anandamide). Additionally, co-localization of cholesterol, AEA and FAAH in mouse neuroblastoma cells suggests a mechanism through which cholesterol increases the substrate accessibility of FAAH.
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18
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Adenine nucleotide translocase, mitochondrial stress, and degenerative cell death. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2013; 2013:146860. [PMID: 23970947 PMCID: PMC3732615 DOI: 10.1155/2013/146860] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 06/14/2013] [Accepted: 06/24/2013] [Indexed: 12/18/2022]
Abstract
Mitochondria are intracellular organelles involved in ATP synthesis, apoptosis, calcium signaling, metabolism, and the synthesis of critical metabolic cofactors. Mitochondrial dysfunction is associated with age-related degenerative diseases. How mitochondrial dysfunction causes cell degeneration is not well understood. Recent studies have shown that mutations in the adenine nucleotide translocase (Ant) cause aging-dependent degenerative cell death (DCD) in yeast, which is sequentially manifested by inner membrane stress, mitochondrial DNA (mtDNA) loss, and progressive loss of cell viability. Ant is an abundant protein primarily involved in ADP/ATP exchange across the mitochondrial inner membrane. It also mediates basal proton leak and regulates the mitochondrial permeability transition pore. Missense mutations in the human Ant1 cause several degenerative diseases which are commonly manifested by fractional mtDNA deletions. Multiple models have been proposed to explain the Ant1-induced pathogenesis. Studies from yeast have suggested that in addition to altered nucleotide transport properties, the mutant proteins cause a global stress on the inner membrane. The mutant proteins likely interfere with general mitochondrial biogenesis in a dominant-negative manner, which secondarily destabilizes mtDNA. More recent work revealed that the Ant-induced DCD is suppressed by reduced cytosolic protein synthesis. This finding suggests a proteostatic crosstalk between mitochondria and the cytosol, which may play an important role for cell survival during aging.
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19
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Crichton PG, Harding M, Ruprecht JJ, Lee Y, Kunji ERS. Lipid, detergent, and Coomassie Blue G-250 affect the migration of small membrane proteins in blue native gels: mitochondrial carriers migrate as monomers not dimers. J Biol Chem 2013; 288:22163-73. [PMID: 23744064 PMCID: PMC3724668 DOI: 10.1074/jbc.m113.484329] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Blue native gel electrophoresis is a popular method for the determination of the oligomeric state of membrane proteins. Studies using this technique have reported that mitochondrial carriers are dimeric (composed of two ∼32-kDa monomers) and, in some cases, can form physiologically relevant associations with other proteins. Here, we have scrutinized the behavior of the yeast mitochondrial ADP/ATP carrier AAC3 in blue native gels. We find that the apparent mass of AAC3 varies in a detergent- and lipid-dependent manner (from ∼60 to ∼130 kDa) that is not related to changes in the oligomeric state of the protein, but reflects differences in the associated detergent-lipid micelle and Coomassie Blue G-250 used in this technique. Higher oligomeric state species are only observed under less favorable solubilization conditions, consistent with aggregation of the protein. Calibration with an artificial covalent AAC3 dimer indicates that the mass observed for solubilized AAC3 and other mitochondrial carriers corresponds to a monomer. Size exclusion chromatography of purified AAC3 in dodecyl maltoside under blue native gel-like conditions shows that the mass of the monomer is ∼120 kDa, but appears smaller on gels (∼60 kDa) due to the unusually high amount of bound negatively charged dye, which increases the electrophoretic mobility of the protein-detergent-dye micelle complex. Our results show that bound lipid, detergent, and Coomassie stain alter the behavior of mitochondrial carriers on gels, which is likely to be true for other small membrane proteins where the associated lipid-detergent micelle is large when compared with the mass of the protein.
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Affiliation(s)
- Paul G Crichton
- Mitochondrial Biology Unit, Medical Research Council, Hills Road, Cambridge CB2 0XY, United Kingdom
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20
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Rey M, Forest E, Pelosi L. Exploring the conformational dynamics of the bovine ADP/ATP carrier in mitochondria. Biochemistry 2012; 51:9727-35. [PMID: 23136955 DOI: 10.1021/bi300759x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mitochondrial ADP/ATP carrier catalyzes the transport of ADP and ATP across the mitochondrial inner membrane by switching between two different conformations. They can be blocked by two inhibitors: carboxyatractyloside (CATR) and bongkrekic acid (BA). Our understanding of the ADP/ATP transport process is largely based on analysis of structural differences between the individual inhibited states. The X-ray crystallographic three-dimensional structure of bovine ADP/ATP carrier isoform 1 (bAnc1p) complexed with CATR was determined, but the structure of the BA-carrier complex remains unknown. We recently investigated the conformational dynamics of bAnc1p in detergent solution using hydrogen/deuterium exchange and mass spectrometry (HDX-MS). This study shed light on some features of ADP/ATP translocation, but the mechanism itself and the organization of bAnc1p in the membrane required further investigation. This paper describes the first study of bAnc1p in the mitochondria on the whole-protein scale using HDX-MS. Membrane-embedded bAnc1p was deuterated and purified under HDX-MS-compatible conditions. Our results for the carrier in the mitochondrial inner membrane differed from those published for the carrier in a detergent solution. These differences were mainly in the upper half of the cavity that globally showed a limited H/D exchange whatever the complex analyzed and at the level of the matrix loops that were less accessible to the solvent in the BA-carrier complex than in the CATR-carrier complex. They are discussed with respect to published data for bAnc1p and have provided new insights into the conformation of the matrix loops of the bovine carrier in complex with BA in mitochondria.
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Affiliation(s)
- Martial Rey
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Direction des Sciences du Vivant (DSV), Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), Laboratoire de Biologie à Grande Echelle (BGE), Grenoble F-38054, France
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21
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Yeast mitochondrial interactosome model: metabolon membrane proteins complex involved in the channeling of ADP/ATP. Int J Mol Sci 2012; 13:1858-1885. [PMID: 22408429 PMCID: PMC3291998 DOI: 10.3390/ijms13021858] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 01/20/2012] [Accepted: 01/31/2012] [Indexed: 01/06/2023] Open
Abstract
The existence of a mitochondrial interactosome (MI) has been currently well established in mammalian cells but the exact composition of this super-complex is not precisely known, and its organization seems to be different from that in yeast. One major difference is the absence of mitochondrial creatine kinase (MtCK) in yeast, unlike that described in the organization model of MI, especially in cardiac, skeletal muscle and brain cells. The aim of this review is to provide a detailed description of different partner proteins involved in the synergistic ADP/ATP transport across the mitochondrial membranes in the yeast Saccharomyces cerevisiae and to propose a new mitochondrial interactosome model. The ADP/ATP (Aacp) and inorganic phosphate (PiC) carriers as well as the VDAC (or mitochondrial porin) catalyze the import and export of ADP, ATP and Pi across the mitochondrial membranes. Aacp and PiC, which appear to be associated with the ATP synthase, consist of two nanomotors (F0, F1) under specific conditions and form ATP synthasome. Identification and characterization of such a complex were described for the first time by Pedersen and co-workers in 2003.
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22
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Watzke N, Diekert K, Obrdlik P. Electrophysiology of respiratory chain complexes and the ADP-ATP exchanger in native mitochondrial membranes. Biochemistry 2010; 49:10308-18. [PMID: 20958090 DOI: 10.1021/bi1011755] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transport of protons and solutes across mitochondrial membranes is essential for many physiological processes. However, neither the proton-pumping respiratory chain complexes nor the mitochondrial secondary active solute transport proteins have been characterized electrophysiologically in their native environment. In this study, solid-supported membrane (SSM) technology was applied for electrical measurements of respiratory chain complexes CI, CII, CIII, and CIV, the F(O)F(1)-ATPase/synthase (CV), and the adenine nucleotide translocase (ANT) in inner membranes of pig heart mitochondria. Specific substrates and inhibitors were used to validate the different assays, and the corresponding K(0.5) and IC(50) values were in good agreement with previously published results obtained with other methods. In combined measurements of CI-CV, it was possible to detect oxidative phosphorylation (OXPHOS), to measure differential effects of the uncoupler carbonyl cyanide m-chlorophenylhydrazone (CCCP) on the respective protein activities, and to determine the corresponding IC(50) values. Moreover, the measurements revealed a tight functional coupling of CI and CIII. Coenzyme Q (CoQ) analogues decylubiquinone (DBQ) and idebenone (Ide) stimulated the CII- and CIII-specific electrical currents but had inverse effects on CI-CIII activity. In summary, the results describe the electrophysiological and pharmacological properties of respiratory chain complexes, OXPHOS, and ANT in native mitochondrial membranes and demonstrate that SSM-based electrophysiology provides new insights into a complex molecular mechanism of the respiratory chain and the associated transport proteins. Besides, the SSM-based approach is suited for highly sensitive and specific testing of diverse respiratory chain modulators such as inhibitors, CoQ analogues, and uncoupling agents.
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Affiliation(s)
- Natalie Watzke
- IonGate Biosciences GmbH, Industriepark Hoechst, Frankfurt am Main, Germany
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23
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Kunji ERS, Crichton PG. Mitochondrial carriers function as monomers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:817-31. [PMID: 20362544 DOI: 10.1016/j.bbabio.2010.03.023] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Revised: 03/05/2010] [Accepted: 03/25/2010] [Indexed: 10/19/2022]
Abstract
Mitochondrial carriers link biochemical pathways in the mitochondrial matrix and cytosol by transporting metabolites, inorganic ions, nucleotides and cofactors across the mitochondrial inner membrane. Uncoupling proteins that dissipate the proton electrochemical gradient also belong to this protein family. For almost 35 years the general consensus has been that mitochondrial carriers are dimeric in structure and function. This view was based on data from inhibitor binding studies, small-angle neutron scattering, electron microscopy, differential tagging/affinity chromatography, size-exclusion chromatography, analytical ultracentrifugation, native gel electrophoresis, cross-linking experiments, tandem-fusions, negative dominance studies and mutagenesis. However, the structural folds of the ADP/ATP carriers were found to be monomeric, lacking obvious dimerisation interfaces. Subsequently, the yeast ADP/ATP carrier was demonstrated to function as a monomer. Here, we revisit the data that have been published in support of a dimeric state of mitochondrial carriers. Our analysis shows that when critical factors are taken into account, the monomer is the only plausible functional form of mitochondrial carriers. We propose a transport model based on the monomer, in which access to a single substrate binding site is controlled by two flanking salt bridge networks, explaining uniport and strict exchange of substrates.
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Affiliation(s)
- Edmund R S Kunji
- The Medical Research Council, Mitochondrial Biology Unit, Hills Road, Cambridge, CB2 0XY, UK.
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24
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Nury H, Blesneac I, Ravaud S, Pebay-Peyroula E. Structural approaches of the mitochondrial carrier family. Methods Mol Biol 2010; 654:105-117. [PMID: 20665263 DOI: 10.1007/978-1-60761-762-4_6] [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: 05/29/2023]
Abstract
The transport of solutes across the inner mitochondrial membrane is highly selective and necessitates membrane proteins mainly from the mitochondrial carrier family (MCF). These carriers are required for the transport of a variety of metabolites implicated in all the important processes occurring within the mitochondrial matrix. Due to its high abundance, the ADP/ATP carrier (AAC) is the member of the family that was studied most. It is the first mitochondrial carrier for which a high-resolution X-ray structure is known. The carrier was crystallized in the presence of a strong inhibitor, the carboxyatractyloside (CATR). The structure gives an insight not only into the overall fold of mitochondrial carriers in general but also into atomic details of the AAC in a conformation that is open toward the intermembrane space (IMS). Molecular dynamics simulations indicate the first events occurring to the carrier after the binding of ADP. A careful analysis of the primary sequences of all the carriers in light with the structure highlights properties of the protein that are related to the substrate.
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Affiliation(s)
- Hugues Nury
- Institut Pasteur, Unit if Structural Dynamics of Macromolecules, CNRS, URA 2185, Paris, France
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25
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Suppression of mitochondrial DNA instability of autosomal dominant forms of progressive external ophthalmoplegia-associated ANT1 mutations in Podospora anserina. Genetics 2009; 183:861-71. [PMID: 19687137 DOI: 10.1534/genetics.109.107813] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Maintenance and expression of mitochondrial DNA (mtDNA) are essential for the cell and the organism. In humans, several mutations in the adenine nucleotide translocase gene ANT1 are associated with multiple mtDNA deletions and autosomal dominant forms of progressive external ophthalmoplegia (adPEO). The mechanisms underlying the mtDNA instability are still obscure. A current hypothesis proposes that these pathogenic mutations primarily uncouple the mitochondrial inner membrane, which secondarily causes mtDNA instability. Here we show that the three adPEO-associated mutations equivalent to A114P, L98P, and V289M introduced into the Podospora anserina ANT1 ortholog dominantly cause severe growth defects, decreased reactive oxygen species production (ROS), decreased mitochondrial inner membrane potential (Deltapsi), and accumulation of large-scale mtDNA deletions leading to premature death. Interestingly, we show that, at least for the adPEO-type M106P and A121P mutant alleles, the associated mtDNA instability cannot be attributed only to a reduced membrane potential or to an increased ROS level since it can be suppressed without restoration of the Deltapsi or modification of the ROS production. Suppression of mtDNA instability due to the M106P and A121P mutations was obtained by an allele of the rmp1 gene involved in nucleo-mitochondrial cross- talk and also by an allele of the AS1 gene encoding a cytosolic ribosomal protein. In contrast, the mtDNA instability caused by the S296M mutation was not suppressed by these alleles.
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26
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Claypool SM. Cardiolipin, a critical determinant of mitochondrial carrier protein assembly and function. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:2059-68. [PMID: 19422785 DOI: 10.1016/j.bbamem.2009.04.020] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Revised: 03/31/2009] [Accepted: 04/28/2009] [Indexed: 10/20/2022]
Abstract
The ability of phospholipids to act as determinants of membrane protein structure and function is probably best exemplified by cardiolipin (CL), the signature phospholipid of mitochondria. Early efforts to reconstitute individual respiratory complexes and members of the mitochondrial carrier family, most notably the ADP/ATP carrier (AAC), often demonstrated the importance of CL. Over the past decade, the significance of CL in the organization of components of the electron transport chain into higher order assemblies, termed respiratory supercomplexes, has been established. Another protein required for oxidative phosphorylation, AAC, has received comparatively little attention likely stemming from the fact that AACs were thought to function in isolation as either homodimers or monomers. Recently however, AACs have been demonstrated to interact with the respiratory supercomplex, other members of the mitochondrial carrier family, and the TIM23 translocon. Interestingly, many if not all of these interactions depend on CL. As the paradigm for the mitochondrial carrier family, these discoveries with AAC suggest that other members of this large group of important proteins may be more gregarious than anticipated. Moreover, it is proposed that AAC and perhaps additional members of the mitochondrial carrier family might represent downstream targets of pathological states involving alterations in CL.
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Affiliation(s)
- Steven M Claypool
- Department of Physiology, Johns Hopkins Medical School, MD 21205, USA.
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27
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Johnston JM, Khalid S, Sansom MSP. Conformational dynamics of the mitochondrial ADP/ATP carrier: a simulation study. Mol Membr Biol 2009; 25:506-17. [PMID: 18988066 DOI: 10.1080/09687680802459271] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The mitochondrial ADP/ATP carrier is a six helix bundle membrane transport protein, which couples the exit of ATP from the mitochondrial matrix to the entry of ADP. Extended (4x20 ns) molecular dynamics simulations of the carrier, in the presence and absence of bound inhibitor (carboxyatractyloside), have been used to explore the conformational dynamics of the protein in a lipid bilayer environment, in the presence and absence of the carboxyatractyloside inhibitor. The dynamic flexibility (measured as conformational drift and fluctuations) of the protein is reduced in the presence of bound inhibitor. Proline residues in transmembrane helices H1, H3 and H5 appear to form dynamic hinges. Fluctuations in inter-helix salt bridges are also observed over the time course of the simulations. Inhibitor-protein and lipid-protein interactions have been characterised in some detail. Overall, the simulations support a transport mechanism in which flexibility about the proline hinges enables a transition between a 'closed' and an 'open' pore-like state of the carrier protein.
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28
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Stuart RA. Chapter 11 Supercomplex organization of the yeast respiratory chain complexes and the ADP/ATP carrier proteins. Methods Enzymol 2009; 456:191-208. [PMID: 19348890 DOI: 10.1016/s0076-6879(08)04411-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The enzymes involved in mitochondrial oxidative phosphorylation (OXPHOS) are coassembled into higher ordered supercomplexes within the mitochondrial inner membrane. The cytochrome bc(1)-cytochrome c oxidase (COX) supercomplex is formed by the coassociation of the two electron transport chain complexes, the cytochrome bc(1) (cytochrome c reductase) and the COX complex. Recent evidence indicates that a diversity in the populations of the cytochrome bc(1)-COX supercomplexes exists within the mitochondria, because different subpopulations of this supercomplex have been shown to further interact with distinct partner complexes (e.g., the TIM23 machinery and also the Shy1/Cox14 proteins). By use of native gel electrophoresis and affinity purification approaches, the abundant ADP/ATP carrier protein (AAC) isoform in the yeast Saccharomyces cerevisiae, the Aac2 isoform, has recently been found to also exist in physical association with the cytochrome bc(1)-COX supercomplex and its associated TIM23 machinery. The AAC proteins play a central role in cellular metabolism, because they facilitate the exchange of ADP and ATP across the mitochondrial inner membrane. The method used to analyze the cytochrome bc(1)-COX-AAC supercomplex and to affinity purify the Aac2 isoform and its associating proteins from S. cerevisiae mitochondria will be outlined in this chapter.
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Affiliation(s)
- Rosemary A Stuart
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA
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29
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Nury H, Manon F, Arnou B, le Maire M, Pebay-Peyroula E, Ebel C. Mitochondrial Bovine ADP/ATP Carrier in Detergent Is Predominantly Monomeric but Also Forms Multimeric Species. Biochemistry 2008; 47:12319-31. [DOI: 10.1021/bi801053m] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hugues Nury
- CEA, DSV, and CNRS and Université Joseph Fourier, Institut de Biologie Structurale, 41 rue Jules Horowitz, F-38027, Grenoble, France, Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, Université Bordeaux 2, F-33077 Bordeaux Cedex, France, and CEA, Institut de Biologie et Technologies de Saclay, and CNRS URA 2096 and Université Paris-Sud 11, LRA 17V, F-91191 Gif-sur-Yvette, France
| | - Florence Manon
- CEA, DSV, and CNRS and Université Joseph Fourier, Institut de Biologie Structurale, 41 rue Jules Horowitz, F-38027, Grenoble, France, Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, Université Bordeaux 2, F-33077 Bordeaux Cedex, France, and CEA, Institut de Biologie et Technologies de Saclay, and CNRS URA 2096 and Université Paris-Sud 11, LRA 17V, F-91191 Gif-sur-Yvette, France
| | - Bertrand Arnou
- CEA, DSV, and CNRS and Université Joseph Fourier, Institut de Biologie Structurale, 41 rue Jules Horowitz, F-38027, Grenoble, France, Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, Université Bordeaux 2, F-33077 Bordeaux Cedex, France, and CEA, Institut de Biologie et Technologies de Saclay, and CNRS URA 2096 and Université Paris-Sud 11, LRA 17V, F-91191 Gif-sur-Yvette, France
| | - Marc le Maire
- CEA, DSV, and CNRS and Université Joseph Fourier, Institut de Biologie Structurale, 41 rue Jules Horowitz, F-38027, Grenoble, France, Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, Université Bordeaux 2, F-33077 Bordeaux Cedex, France, and CEA, Institut de Biologie et Technologies de Saclay, and CNRS URA 2096 and Université Paris-Sud 11, LRA 17V, F-91191 Gif-sur-Yvette, France
| | - Eva Pebay-Peyroula
- CEA, DSV, and CNRS and Université Joseph Fourier, Institut de Biologie Structurale, 41 rue Jules Horowitz, F-38027, Grenoble, France, Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, Université Bordeaux 2, F-33077 Bordeaux Cedex, France, and CEA, Institut de Biologie et Technologies de Saclay, and CNRS URA 2096 and Université Paris-Sud 11, LRA 17V, F-91191 Gif-sur-Yvette, France
| | - Christine Ebel
- CEA, DSV, and CNRS and Université Joseph Fourier, Institut de Biologie Structurale, 41 rue Jules Horowitz, F-38027, Grenoble, France, Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, Université Bordeaux 2, F-33077 Bordeaux Cedex, France, and CEA, Institut de Biologie et Technologies de Saclay, and CNRS URA 2096 and Université Paris-Sud 11, LRA 17V, F-91191 Gif-sur-Yvette, France
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30
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Trézéguet V, Pélosi L, Lauquin GJM, Brandolin G. The mitochondrial ADP/ATP carrier: functional and structural studies in the route of elucidating pathophysiological aspects. J Bioenerg Biomembr 2008; 40:435-43. [PMID: 18979193 DOI: 10.1007/s10863-008-9178-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2008] [Accepted: 07/23/2008] [Indexed: 01/21/2023]
Abstract
The mitochondrial ADP/ATP carrier plays a central role in aerobic cell energetics by providing to the cytosol the ATP generated by oxidative phosphorylation. Though discovered around 40 years ago owing to the existence of unique inhibitors and in spite of numerous experimental approaches, this carrier, which stands as a model of the mitochondrial solute carriers keeps some long-standing mystery. There are still open challenging questions among them the precise ADP/ATP transport mechanism, the functional oligomeric state of the carrier and relationships between human ADP/ATP carrier dysfunctioning and pathologies. Deciphering the 3D structure of this carrier afforded a considerable progress of the knowledge but requires now additional data focused on molecular dynamics from this static picture. State of the art in this topic is reviewed and debated in this paper in view of better comprehending origin of the discrepancies in these questions and, finally, the multiple physiological roles of this carrier in eukaryotic cell economy.
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Affiliation(s)
- Véronique Trézéguet
- Laboratoire de Physiologie Moléculaire et Cellulaire, Institut de Biochimie et Génétique Cellulaires-UMR 5095, CNRS-Université Bordeaux2, Bordeaux Cedex, France.
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31
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Kunji ERS, Harding M, Butler PJG, Akamine P. Determination of the molecular mass and dimensions of membrane proteins by size exclusion chromatography. Methods 2008; 46:62-72. [PMID: 18952172 DOI: 10.1016/j.ymeth.2008.10.020] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Revised: 10/09/2008] [Accepted: 10/16/2008] [Indexed: 11/18/2022] Open
Abstract
Size exclusion chromatography is an established technique for the determination of hydrodynamic volumes of proteins or protein complexes. When applied to membrane proteins, the contribution of the detergent micelle, which is required to keep the protein soluble in the aqueous phase, needs to be determined to obtain accurate measurements for the protein. In a detergent series, in which the detergents differ only by the length of the alkyl chain, the contribution of the detergent micelle to the hydrodynamic volume is variable, whereas the contribution of the protein is constant. By using this approach, several parameters of membrane proteins can be estimated by extrapolation, such as the radius at the midpoint of the membrane, the average radius, the Stokes radius, and the excluded volume. The molecular mass of the protein can be determined by two independent measurements that arise from the behaviour of the free detergent micelle and protein-detergent micelle during size exclusion chromatography and the determination of the detergent-protein ratio. Determining the dimensions of protein-detergent micelles may facilitate membrane protein purification and crystallization by defining the accessibility of the protein surface.
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Affiliation(s)
- Edmund R S Kunji
- The Medical Research Council, Dunn Human Nutrition Unit, Hills Road, Cambridge CB2 0XY, UK.
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32
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Farina F, Alberti A, Breuil N, Bolotin-Fukuhara M, Pinto M, Culetto E. Differential expression pattern of the four mitochondrial adenine nucleotide transporter ant genes and their roles during the development of Caenorhabditis elegans. Dev Dyn 2008; 237:1668-81. [PMID: 18498090 DOI: 10.1002/dvdy.21578] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The adenine nucleotide transporter (ANT) mediates exchange of cytosolic ADP and mitochondrial ATP. Although most species contain more than one ANT family member, it is not known whether their roles in developmental processes are redundant or specific. Here, we show that the Caenorhabditis elegans genome encodes four candidate ant genes (ant-1.1, ant-1.2, ant-1.3, and ant-1.4). We have investigated their spatiotemporal expression patterns and discovered that, whereas ANT-1.1 is a ubiquitously expressed mitochondrial protein, the other three ANT proteins show a restricted range of cell type expression. Moreover, only the disruption of ant-1.1 function, through RNA interference (RNAi), gives a mutant phenotype. Most of the ant-1.1(RNAi) mutant embryos arrest before the morphogenesis stage. Furthermore, ant-1.1 is also required postembryonically because RNAi mutants exhibit small size and life-span extension. Our results suggest that ant-1.1 is the only ant gene strictly required for embryonic and postembryonic development in C. elegans.
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Affiliation(s)
- Francesca Farina
- Université Paris-Sud 11, CNRS UMR8621, Institut de Génétique et Microbiologie, Orsay Cedex, France
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Dienhart MK, Stuart RA. The yeast Aac2 protein exists in physical association with the cytochrome bc1-COX supercomplex and the TIM23 machinery. Mol Biol Cell 2008; 19:3934-43. [PMID: 18614795 DOI: 10.1091/mbc.e08-04-0402] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The ADP/ATP carrier (AAC) proteins play a central role in cellular metabolism as they facilitate the exchange of ADP and ATP across the mitochondrial inner membrane. We present evidence here that in yeast (Saccharomyces cerevisiae) mitochondria the abundant Aac2 isoform exists in physical association with the cytochrome c reductase (cytochrome bc(1))-cytochrome c oxidase (COX) supercomplex and its associated TIM23 machinery. Using a His-tagged Aac2 derivative and affinity purification studies, we also demonstrate here that the Aac2 isoform can be affinity-purified with other AAC proteins. Copurification of the Aac2 protein with the TIM23 machinery can occur independently of its association with the fully assembled cytochrome bc(1)-COX supercomplex. In the absence of the Aac2 protein, the assembly of the cytochrome bc(1)-COX supercomplex is perturbed, whereby a decrease in the III(2)-IV(2) assembly state relative to the III(2)-IV form is observed. We propose that the association of the Aac2 protein with the cytochrome bc(1)-COX supercomplex is important for the function of the OXPHOS complexes and for the assembly of the COX complex. The physiological implications of the association of AAC with the cytochrome bc(1)-COX-TIM23 supercomplex are also discussed.
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Affiliation(s)
- Mary K Dienhart
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
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Current awareness on yeast. Yeast 2008. [DOI: 10.1002/yea.1458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Clémençon B, Rey M, Dianoux AC, Trézéguet V, Lauquin GJM, Brandolin G, Pelosi L. Structure-function relationships of the C-terminal end of the Saccharomyces cerevisiae ADP/ATP carrier isoform 2. J Biol Chem 2008; 283:11218-25. [PMID: 18299327 DOI: 10.1074/jbc.m709565200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The adenine nucleotide carrier (Ancp) catalyzes the transport of ADP and ATP across the mitochondrial inner membrane, thus playing an essential role in the cellular energy metabolism. Two regions of Anc2p from Saccharomyces cerevisiae are specifically photolabeled using a photoactivable ADP derivative; they are the central matrix loop, m2, and the C-terminal end. To get more insights into the structure-function relationships of the C-terminal region during nucleotide transport, we have developed two independent approaches. In the first we have deleted the last eight amino acids of Anc2p (Anc2pDeltaCter) and demonstrated that the C-terminal end of Anc2p plays an essential role in yeast growth on a non-fermentable carbon source. This resulted from impaired nucleotide binding properties of the Anc2pDeltaCter variant in line with conversion of ADP binding sites from high to low affinity. In the second we probed the ligand-induced conformational changes of Anc2p C-terminal end (i) by assessing its accessibility to anti-C-terminal antibodies and (ii) by measuring intrinsic fluorescence changes of an Anc2p mutant containing only one tryptophan residue located at its C-terminal end (Anc2p3Y-u). We show that the C-terminal region is no further accessible to antibodies when Anc2p binds non-transportable analogues of ADP. Besides, Trp-316 fluorescence is highly increased upon ligand binding, suggesting large conformational changes. Taken together, our results highlight the involvement of the Anc2p C-terminal region in nucleotide recognition, binding, and transport.
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Affiliation(s)
- Benjamin Clémençon
- Laboratoire de Biochimie et Biophysique des Systè Intégrés, Institut de Recherches en Technologies et Sciences du Vivant, UMR 5092 CNRS-Commissariat à l'Energie Atomique-Université Joseph Fourier, F-38054 Grenoble cedex 9, France
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