1
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Senoo N, Chinthapalli DK, Baile MG, Golla VK, Saha B, Oluwole AO, Ogunbona OB, Saba JA, Munteanu T, Valdez Y, Whited K, Sheridan MS, Chorev D, Alder NN, May ER, Robinson CV, Claypool SM. Functional diversity among cardiolipin binding sites on the mitochondrial ADP/ATP carrier. EMBO J 2024; 43:2979-3008. [PMID: 38839991 PMCID: PMC11251061 DOI: 10.1038/s44318-024-00132-2] [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: 07/11/2023] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 06/07/2024] Open
Abstract
Lipid-protein interactions play a multitude of essential roles in membrane homeostasis. Mitochondrial membranes have a unique lipid-protein environment that ensures bioenergetic efficiency. Cardiolipin (CL), the signature mitochondrial lipid, plays multiple roles in promoting oxidative phosphorylation (OXPHOS). In the inner mitochondrial membrane, the ADP/ATP carrier (AAC in yeast; adenine nucleotide translocator, ANT in mammals) exchanges ADP and ATP, enabling OXPHOS. AAC/ANT contains three tightly bound CLs, and these interactions are evolutionarily conserved. Here, we investigated the role of these buried CLs in AAC/ANT using a combination of biochemical approaches, native mass spectrometry, and molecular dynamics simulations. We introduced negatively charged mutations into each CL-binding site of yeast Aac2 and established experimentally that the mutations disrupted the CL interactions. While all mutations destabilized Aac2 tertiary structure, transport activity was impaired in a binding site-specific manner. Additionally, we determined that a disease-associated missense mutation in one CL-binding site in human ANT1 compromised its structure and transport activity, resulting in OXPHOS defects. Our findings highlight the conserved significance of CL in AAC/ANT structure and function, directly tied to specific lipid-protein interactions.
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Affiliation(s)
- Nanami Senoo
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Mitochondrial Phospholipid Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Dinesh K Chinthapalli
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Oxford, OX1 3QU, UK
| | - Matthew G Baile
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Vinaya K Golla
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA, 22903, USA
| | - Bodhisattwa Saha
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QU, UK
| | - Abraham O Oluwole
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Oxford, OX1 3QU, UK
| | - Oluwaseun B Ogunbona
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - James A Saba
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Teona Munteanu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Yllka Valdez
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Kevin Whited
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Macie S Sheridan
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Mitochondrial Phospholipid Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Dror Chorev
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QU, UK
| | - Nathan N Alder
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Eric R May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Oxford, OX1 3QU, UK
| | - Steven M Claypool
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Mitochondrial Phospholipid Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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2
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Senoo N, Chinthapalli DK, Baile MG, Golla VK, Saha B, Ogunbona OB, Saba JA, Munteanu T, Valdez Y, Whited K, Chorev D, Alder NN, May ER, Robinson CV, Claypool SM. Conserved cardiolipin-mitochondrial ADP/ATP carrier interactions assume distinct structural and functional roles that are clinically relevant. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.05.539595. [PMID: 37205478 PMCID: PMC10187269 DOI: 10.1101/2023.05.05.539595] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The mitochondrial phospholipid cardiolipin (CL) promotes bioenergetics via oxidative phosphorylation (OXPHOS). Three tightly bound CLs are evolutionarily conserved in the ADP/ATP carrier (AAC in yeast; adenine nucleotide translocator, ANT in mammals) which resides in the inner mitochondrial membrane and exchanges ADP and ATP to enable OXPHOS. Here, we investigated the role of these buried CLs in the carrier using yeast Aac2 as a model. We introduced negatively charged mutations into each CL-binding site of Aac2 to disrupt the CL interactions via electrostatic repulsion. While all mutations disturbing the CL-protein interaction destabilized Aac2 monomeric structure, transport activity was impaired in a pocket-specific manner. Finally, we determined that a disease-associated missense mutation in one CL-binding site in ANT1 compromised its structure and transport activity, resulting in OXPHOS defects. Our findings highlight the conserved significance of CL in AAC/ANT structure and function, directly tied to specific lipid-protein interactions.
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Affiliation(s)
- Nanami Senoo
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Mitochondrial Phospholipid Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dinesh K. Chinthapalli
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Oxford, OX1 3QU, UK
| | - Matthew G. Baile
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Vinaya K. Golla
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Bodhisattwa Saha
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QU, UK
| | - Oluwaseun B. Ogunbona
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James A. Saba
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Teona Munteanu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yllka Valdez
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kevin Whited
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dror Chorev
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QU, UK
| | - Nathan N. Alder
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Eric R. May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Oxford, OX1 3QU, UK
| | - Steven M. Claypool
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Mitochondrial Phospholipid Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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3
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Acoba MG, Alpergin ESS, Renuse S, Fernández-Del-Río L, Lu YW, Khalimonchuk O, Clarke CF, Pandey A, Wolfgang MJ, Claypool SM. The mitochondrial carrier SFXN1 is critical for complex III integrity and cellular metabolism. Cell Rep 2021; 34:108869. [PMID: 33730581 PMCID: PMC8048093 DOI: 10.1016/j.celrep.2021.108869] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 01/18/2021] [Accepted: 02/24/2021] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial carriers (MCs) mediate the passage of small molecules across the inner mitochondrial membrane (IMM), enabling regulated crosstalk between compartmentalized reactions. Despite MCs representing the largest family of solute carriers in mammals, most have not been subjected to a comprehensive investigation, limiting our understanding of their metabolic contributions. Here, we functionally characterize SFXN1, a member of the non-canonical, sideroflexin family. We find that SFXN1, an integral IMM protein with an uneven number of transmembrane domains, is a TIM22 complex substrate. SFXN1 deficiency leads to mitochondrial respiratory chain impairments, most detrimental to complex III (CIII) biogenesis, activity, and assembly, compromising coenzyme Q levels. The CIII dysfunction is independent of one-carbon metabolism, the known primary role for SFXN1 as a mitochondrial serine transporter. Instead, SFXN1 supports CIII function by participating in heme and α-ketoglutarate metabolism. Our findings highlight the multiple ways that SFXN1-based amino acid transport impacts mitochondrial and cellular metabolic efficiency.
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Affiliation(s)
- Michelle Grace Acoba
- Department of Physiology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ebru S Selen Alpergin
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Santosh Renuse
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lucía Fernández-Del-Río
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ya-Wen Lu
- Department of Physiology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Oleh Khalimonchuk
- Department of Biochemistry and Nebraska Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA; Fred & Pamela Buffett Cancer Center, Omaha, NE 68198, USA
| | - Catherine F Clarke
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Akhilesh Pandey
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Departments of Pathology and Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Michael J Wolfgang
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Steven M Claypool
- Department of Physiology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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4
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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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5
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Hsieh YL, Chen CW, Lin WH, Li BR. Construction of the Nickel Oxide Nanocoral Structure on Microscope Slides for Total Self-Assembly-Oriented Probe Immobilization and Signal Enhancement. ACS APPLIED BIO MATERIALS 2020; 3:3304-3312. [PMID: 35025373 DOI: 10.1021/acsabm.0c00249] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Proper orientation of probes and the binding capacity of surfaces will determine the performance of bio-applications. It has been reported that immobilizing through bio-/chemical affinity is an efficient but gentle strategy to solve the above-mentioned issue. Herein, we introduce a total self-assembly approach via the strong affinity of nickel oxide (NiO) to the polyhistidine-tag (His-tag). It allows the efficient immobilizing His-tagged proteins with orientation. Furthermore, we find that the nanocoral structure can be formed after applying rapid thermal annealing at 1100 °C, which could increase the His-tagged protein binding capacity efficiently by the enhanced surface-to-volume ratio. Lastly, we demonstrate the NiO thin film with the nanocoral structure, which has great potential for universal biosensing with a wide range of biomolecules, including DNA, protein, and bacteria. Through His-tagged monomer streptavidin (His6-mSA) or His-tagged protein G (His6-protein G), the biotinylated DNA or antibody could be immobilized with proper orientation on the surface consequently to complete a sensitive biomolecule detection. Moreover, the NiO nanocoral structure has the advantages of high hydrophilicity, transmittance, and pH stability that are promising to develop into several kinds of bio-applications in the near future.
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Affiliation(s)
- Yu-Ling Hsieh
- Institute of Biomedical Engineering, College of Electrical and Computer Engineering, National Chiao Tung University, 1001 University Road, Hsinchu 300, Taiwan
| | - Chien-Wei Chen
- Institute of Biomedical Engineering, College of Electrical and Computer Engineering, National Chiao Tung University, 1001 University Road, Hsinchu 300, Taiwan.,Department of Electrical and Computer Engineering, College of Electrical and Computer Engineering, National Chiao Tung University, 1001 University Road, Hsinchu 300, Taiwan
| | - Wan-Hsuan Lin
- Institute of Biomedical Engineering, College of Electrical and Computer Engineering, National Chiao Tung University, 1001 University Road, Hsinchu 300, Taiwan
| | - Bor-Ran Li
- Institute of Biomedical Engineering, College of Electrical and Computer Engineering, National Chiao Tung University, 1001 University Road, Hsinchu 300, Taiwan.,Department of Electrical and Computer Engineering, College of Electrical and Computer Engineering, National Chiao Tung University, 1001 University Road, Hsinchu 300, Taiwan.,Center for Emergent Functional Matter Science, National Chiao Tung University, 1001 University Road, Hsinchu 300, Taiwan
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6
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Calzada E, Avery E, Sam PN, Modak A, Wang C, McCaffery JM, Han X, Alder NN, Claypool SM. Phosphatidylethanolamine made in the inner mitochondrial membrane is essential for yeast cytochrome bc 1 complex function. Nat Commun 2019; 10:1432. [PMID: 30926815 PMCID: PMC6441012 DOI: 10.1038/s41467-019-09425-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 03/11/2019] [Indexed: 12/18/2022] Open
Abstract
Of the four separate PE biosynthetic pathways in eukaryotes, one occurs in the mitochondrial inner membrane (IM) and is executed by phosphatidylserine decarboxylase (Psd1). Deletion of Psd1 is lethal in mice and compromises mitochondrial function. We hypothesize that this reflects inefficient import of non-mitochondrial PE into the IM. Here, we test this by re-wiring PE metabolism in yeast by re-directing Psd1 to the outer mitochondrial membrane or the endomembrane system and show that PE can cross the IMS in both directions. Nonetheless, PE synthesis in the IM is critical for cytochrome bc1 complex (III) function and mutations predicted to disrupt a conserved PE-binding site in the complex III subunit, Qcr7, impair complex III activity similar to PSD1 deletion. Collectively, these data challenge the current dogma of PE trafficking and demonstrate that PE made in the IM by Psd1 support the intrinsic functionality of complex III.
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Affiliation(s)
- Elizabeth Calzada
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Erica Avery
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Pingdewinde N Sam
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Arnab Modak
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Chunyan Wang
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - J Michael McCaffery
- Integrated Imaging Center, Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Nathan N Alder
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Steven M Claypool
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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7
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Lu YW, Acoba MG, Selvaraju K, Huang TC, Nirujogi RS, Sathe G, Pandey A, Claypool SM. Human adenine nucleotide translocases physically and functionally interact with respirasomes. Mol Biol Cell 2017; 28:1489-1506. [PMID: 28404750 PMCID: PMC5449148 DOI: 10.1091/mbc.e17-03-0195] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 03/30/2017] [Accepted: 04/04/2017] [Indexed: 11/11/2022] Open
Abstract
A network of interactions for human adenine nucleotide translocases, required for oxidative phosphorylation, is reported. Of particular interest is an evolutionarily conserved and functionally important association with respiratory supercomplexes, which is surprising because the respirasomes of yeast and mammals are different. Members of the adenine nucleotide translocase (ANT) family exchange ADP for ATP across the mitochondrial inner membrane, an activity that is essential for oxidative phosphorylation (OXPHOS). Mutations in or dysregulation of ANTs is associated with progressive external ophthalmoplegia, cardiomyopathy, nonsyndromic intellectual disability, apoptosis, and the Warburg effect. Binding partners of human ANTs have not been systematically identified. The absence of such information has prevented a detailed molecular understanding of the assorted ANT-associated diseases, including insight into their disparate phenotypic manifestations. To fill this void, in this study, we define the interactomes of two human ANT isoforms. Analogous to its yeast counterpart, human ANTs associate with heterologous partner proteins, including the respiratory supercomplex (RSC) and other solute carriers. The evolutionarily conserved ANT–RSC association is particularly noteworthy because the composition, and thereby organization, of RSCs in yeast and human is different. Surprisingly, absence of the major ANT isoform only modestly impairs OXPHOS in HEK293 cells, indicating that the low levels of other isoforms provide functional redundancy. In contrast, pharmacological inhibition of OXPHOS expression and function inhibits ANT-dependent ADP/ATP exchange. Thus ANTs and the OXPHOS machinery physically interact and functionally cooperate to enhance ANT transport capacity and mitochondrial respiration.
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Affiliation(s)
- Ya-Wen Lu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
| | - Michelle Grace Acoba
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
| | - Kandasamy Selvaraju
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
| | - Tai-Chung Huang
- McKusick-Nathans Institute of Genetic Medicine, Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185.,Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University Cancer Center, Taipei 10051, Taiwan
| | - Raja S Nirujogi
- McKusick-Nathans Institute of Genetic Medicine, Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
| | - Gajanan Sathe
- McKusick-Nathans Institute of Genetic Medicine, Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
| | - Steven M Claypool
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
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8
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Lu YW, Galbraith L, Herndon JD, Lu YL, Pras-Raves M, Vervaart M, Van Kampen A, Luyf A, Koehler CM, McCaffery JM, Gottlieb E, Vaz FM, Claypool SM. Defining functional classes of Barth syndrome mutation in humans. Hum Mol Genet 2016; 25:1754-70. [PMID: 26908608 PMCID: PMC4986330 DOI: 10.1093/hmg/ddw046] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/08/2016] [Accepted: 02/15/2016] [Indexed: 11/13/2022] Open
Abstract
The X-linked disease Barth syndrome (BTHS) is caused by mutations in TAZ; TAZ is the main determinant of the final acyl chain composition of the mitochondrial-specific phospholipid, cardiolipin. To date, a detailed characterization of endogenous TAZ has only been performed in yeast. Further, why a given BTHS-associated missense mutation impairs TAZ function has only been determined in a yeast model of this human disease. Presently, the detailed characterization of yeast tafazzin harboring individual BTHS mutations at evolutionarily conserved residues has identified seven distinct loss-of-function mechanisms caused by patient-associated missense alleles. However, whether the biochemical consequences associated with individual mutations also occur in the context of human TAZ in a validated mammalian model has not been demonstrated. Here, utilizing newly established monoclonal antibodies capable of detecting endogenous TAZ, we demonstrate that mammalian TAZ, like its yeast counterpart, is localized to the mitochondrion where it adopts an extremely protease-resistant fold, associates non-integrally with intermembrane space-facing membranes and assembles in a range of complexes. Even though multiple isoforms are expressed at the mRNA level, only a single polypeptide that co-migrates with the human isoform lacking exon 5 is expressed in human skin fibroblasts, HEK293 cells, and murine heart and liver mitochondria. Finally, using a new genome-edited mammalian BTHS cell culture model, we demonstrate that the loss-of-function mechanisms for two BTHS alleles that represent two of the seven functional classes of BTHS mutation as originally defined in yeast, are the same when modeled in human TAZ.
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Affiliation(s)
- Ya-Wen Lu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185, USA
| | - Laura Galbraith
- Cancer Research UK, The Beatson Institute for Cancer Research, Glasgow G61 1BD, UK
| | - Jenny D Herndon
- Department of Chemistry and Biochemistry, Molecular Biology Institute, and Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA 90095-1569, USA
| | - Ya-Lin Lu
- Division of Biology and Biomedical Sciences, Graduate School of Arts and Sciences, Washington University, St. Louis, MO 63130-4899, USA
| | - Mia Pras-Raves
- Departments of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases and
| | - Martin Vervaart
- Departments of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases and
| | - Antoine Van Kampen
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, Amsterdam, The Netherlands and
| | - Angela Luyf
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, Amsterdam, The Netherlands and
| | - Carla M Koehler
- Department of Chemistry and Biochemistry, Molecular Biology Institute, and Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA 90095-1569, USA
| | - J Michael McCaffery
- Integrated Imaging Center, Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Eyal Gottlieb
- Cancer Research UK, The Beatson Institute for Cancer Research, Glasgow G61 1BD, UK
| | - Frederic M Vaz
- Departments of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases and
| | - Steven M Claypool
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185, USA,
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9
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Baile MG, Sathappa M, Lu YW, Pryce E, Whited K, McCaffery JM, Han X, Alder NN, Claypool SM. Unremodeled and remodeled cardiolipin are functionally indistinguishable in yeast. J Biol Chem 2013; 289:1768-78. [PMID: 24285538 DOI: 10.1074/jbc.m113.525733] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
After biosynthesis, an evolutionarily conserved acyl chain remodeling process generates a final highly homogeneous and yet tissue-specific molecular form of the mitochondrial lipid cardiolipin. Hence, cardiolipin molecules in different organisms, and even different tissues within the same organism, contain a distinct collection of attached acyl chains. This observation is the basis for the widely accepted paradigm that the acyl chain composition of cardiolipin is matched to the unique mitochondrial demands of a tissue. For this hypothesis to be correct, cardiolipin molecules with different acyl chain compositions should have distinct functional capacities, and cardiolipin that has been remodeled should promote cardiolipin-dependent mitochondrial processes better than its unremodeled form. However, functional disparities between different molecular forms of cardiolipin have never been established. Here, we interrogate this simple but crucial prediction utilizing the best available model to do so, Saccharomyces cerevisiae. Specifically, we compare the ability of unremodeled and remodeled cardiolipin, which differ markedly in their acyl chain composition, to support mitochondrial activities known to require cardiolipin. Surprisingly, defined changes in the acyl chain composition of cardiolipin do not alter either mitochondrial morphology or oxidative phosphorylation. Importantly, preventing cardiolipin remodeling initiation in yeast lacking TAZ1, an ortholog of the causative gene in Barth syndrome, ameliorates mitochondrial dysfunction. Thus, our data do not support the prevailing hypothesis that unremodeled cardiolipin is functionally distinct from remodeled cardiolipin, at least for the functions examined, suggesting alternative physiological roles for this conserved pathway.
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Affiliation(s)
- Matthew G Baile
- From the Department of Physiology, The Johns Hopkins School of Medicine, Baltimore, Maryland 21205
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10
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Baile MG, Whited K, Claypool SM. Deacylation on the matrix side of the mitochondrial inner membrane regulates cardiolipin remodeling. Mol Biol Cell 2013; 24:2008-20. [PMID: 23637464 PMCID: PMC3681703 DOI: 10.1091/mbc.e13-03-0121] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Our understanding of the clinically relevant tafazzin-mediated cardiolipin (CL) remodeling pathway is incomplete. In this study, a new trafficking step required for CL remodeling has been identified. Further, it is demonstrated that flux through this CL remodeling pathway is controlled by the strength of the mitochondrial electrochemical gradient. The mitochondrial-specific lipid cardiolipin (CL) is required for numerous processes therein. After its synthesis on the matrix-facing leaflet of the inner membrane (IM), CL undergoes acyl chain remodeling to achieve its final form. In yeast, this process is completed by the transacylase tafazzin, which associates with intermembrane space (IMS)-facing membrane leaflets. Mutations in TAZ1 result in the X-linked cardiomyopathy Barth syndrome. Amazingly, despite this clear pathophysiological association, the physiological importance of CL remodeling is unresolved. In this paper, we show that the lipase initiating CL remodeling, Cld1p, is associated with the matrix-facing leaflet of the mitochondrial IM. Thus monolysocardiolipin generated by Cld1p must be transported to IMS-facing membrane leaflets to gain access to tafazzin, identifying a previously unknown step required for CL remodeling. Additionally, we show that Cld1p is the major site of regulation in CL remodeling; and that, like CL biosynthesis, CL remodeling is augmented in growth conditions requiring mitochondrially produced energy. However, unlike CL biosynthesis, dissipation of the mitochondrial membrane potential stimulates CL remodeling, identifying a novel feedback mechanism linking CL remodeling to oxidative phosphorylation capacity.
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Affiliation(s)
- Matthew G Baile
- Department of Physiology, Johns Hopkins School of Medicine, Baltimore, MD 21205-2185, USA
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11
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Whited K, Baile MG, Currier P, Claypool SM. Seven functional classes of Barth syndrome mutation. Hum Mol Genet 2012; 22:483-92. [PMID: 23100323 DOI: 10.1093/hmg/dds447] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Patients with Barth syndrome (BTHS), a rare X-linked disease, suffer from skeletal and cardiomyopathy and bouts of cyclic neutropenia. The causative gene encodes tafazzin, a transacylase, which is the major determinant of the final acyl chain composition of the mitochondrial-specific phospholipid, CL. In addition to numerous frame shift and splice-site mutations, 36 missense mutations have been associated with BTHS. Previously, we established a BTHS-mutant panel in the yeast Saccharomyces cerevisiae that successfully models 18/21 conserved pathogenic missense mutations and defined the loss-of-function mechanism associated with a subset of the mutant tafazzins. Here, we report the biochemical and cell biological characterization of the rest of the yeast BTHS-mutant panel and in so doing identify three additional modes of tafazzin dysfunction. The largest group of mutant tafazzins is catalytically null, two mutants encode hypomorphic alleles, and another two mutants are temperature sensitive. Additionally, we have expanded the defects associated with previously characterized matrix-mislocalized-mutant tafazzins to include the rapid degradation of aggregation-prone polypeptides that correctly localize to the mitochondrial IMS. In sum, our in-depth characterization of the yeast BTHS-mutant panel has identified seven functional classes of BTHS mutation.
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Affiliation(s)
- Kevin Whited
- Department of Physiology, Johns Hopkins School of Medicine, Baltimore, MD 21205-2185, USA
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12
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Claypool SM, Whited K, Srijumnong S, Han X, Koehler CM. Barth syndrome mutations that cause tafazzin complex lability. ACTA ACUST UNITED AC 2011; 192:447-62. [PMID: 21300850 PMCID: PMC3101092 DOI: 10.1083/jcb.201008177] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Deficits in mitochondrial function result in many human diseases. The X-linked disease Barth syndrome (BTHS) is caused by mutations in the tafazzin gene TAZ1. Its product, Taz1p, participates in the metabolism of cardiolipin, the signature phospholipid of mitochondria. In this paper, a yeast BTHS mutant tafazzin panel is established, and 18 of the 21 tested BTHS missense mutations cannot functionally replace endogenous tafazzin. Four BTHS mutant tafazzins expressed at low levels are degraded by the intermembrane space AAA (i-AAA) protease, suggesting misfolding of the mutant polypeptides. Paradoxically, each of these mutant tafazzins assembles in normal protein complexes. Furthermore, in the absence of the i-AAA protease, increased expression and assembly of two of the BTHS mutants improve their function. However, the BTHS mutant complexes are extremely unstable and accumulate as insoluble aggregates when disassembled in the absence of the i-AAA protease. Thus, the loss of function for these BTHS mutants results from the inherent instability of the mutant tafazzin complexes.
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Affiliation(s)
- Steven M Claypool
- Department of Physiology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
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13
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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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14
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Claypool SM, Oktay Y, Boontheung P, Loo JA, Koehler CM. Cardiolipin defines the interactome of the major ADP/ATP carrier protein of the mitochondrial inner membrane. ACTA ACUST UNITED AC 2008; 182:937-50. [PMID: 18779372 PMCID: PMC2528576 DOI: 10.1083/jcb.200801152] [Citation(s) in RCA: 238] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Defined mutations in the mitochondrial ADP/ATP carrier (AAC) are associated with certain types of progressive external ophthalmoplegia. AAC is required for oxidative phosphorylation (OXPHOS), and dysregulation of AAC has been implicated in apoptosis. Little is known about the AAC interactome, aside from a known requirement for the phospholipid cardiolipin (CL) and that it is thought to function as a homodimer. Using a newly developed dual affinity tag, we demonstrate that yeast AAC2 physically participates in several protein complexes of distinct size and composition. The respiratory supercomplex and several smaller AAC2-containing complexes, including other members of the mitochondrial carrier family, are identified here. In the absence of CL, most of the defined interactions are destabilized or undetectable. The absence of CL and/or AAC2 results in distinct yet additive alterations in respiratory supercomplex structure and respiratory function. Thus, a single lipid can significantly alter the functional interactome of an individual protein.
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Affiliation(s)
- Steven M Claypool
- Department of Chemistry and Biochemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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Claypool SM, Boontheung P, McCaffery JM, Loo JA, Koehler CM. The cardiolipin transacylase, tafazzin, associates with two distinct respiratory components providing insight into Barth syndrome. Mol Biol Cell 2008; 19:5143-55. [PMID: 18799610 DOI: 10.1091/mbc.e08-09-0896] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Mutations in the mitochondrial cardiolipin (CL) transacylase, tafazzin (Taz1p), result in the X-linked cardioskeletal myopathy, Barth syndrome (BTHS). The mitochondria of BTHS patients exhibit variable respiratory defects and abnormal cristae ultrastructure. The biochemical basis for these observations is unknown. In the absence of its target phospholipid, CL, a very large Taz1p complex is missing, whereas several discrete smaller complexes are still observed. None of the identified Taz1p complexes represents Taz1p homodimers. Instead, yeast Taz1p physically assembles in several protein complexes of distinct size and composition. The ATP synthase and AAC2, both required for oxidative phosphorylation, are identified in separate stable Taz1p complexes. In the absence of CL, each interaction is still detected albeit in reduced abundance compared with when CL is present. Taz1p is not necessary for the normal expression of AAC2 or ATP synthase subunits or assembly of their respective complexes. In contrast, the largest Taz1p complex requires assembled ATP synthase and CL. Mitochondria in Delta taz1 yeast, similar to ATP synthase oligomer mutants, exhibit altered cristae morphology even though ATP synthase oligomer formation is unaffected. Thus, the Taz1p interactome defined here provides novel insight into the variable respiratory defects and morphological abnormalities observed in mitochondria of BTHS patients.
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Affiliation(s)
- Steven M Claypool
- Department of Chemistry and Biochemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1569, USA
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Abstract
About 10% to 15% of the nuclear genes of eukaryotic organisms encode mitochondrial proteins. These proteins are synthesized in the cytosol and recognized by receptors on the surface of mitochondria. Translocases in the outer and inner membrane of mitochondria mediate the import and intramitochondrial sorting of these proteins; ATP and the membrane potential are used as energy sources. Chaperones and auxiliary factors assist in the folding and assembly of mitochondrial proteins into their native, three-dimensional structures. This review summarizes the present knowledge on the import and sorting of mitochondrial precursor proteins, with a special emphasis on unresolved questions and topics of current research.
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Affiliation(s)
- Walter Neupert
- Institut für Physiologische Chemie, Universität München, 81377 München, Germany.
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Gubbens J, Vader P, Damen JMA, O'Flaherty MC, Slijper M, de Kruijff B, de Kroon AIPM. Probing the Membrane Interface-Interacting Proteome Using Photoactivatable Lipid Cross-Linkers. J Proteome Res 2007; 6:1951-62. [PMID: 17375948 DOI: 10.1021/pr060561a] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To analyze proteins interacting at the membrane interface, a phospholipid analogue was used with a photoactivatable headgroup (ASA-DLPE, N-(4-azidosalicylamidyl)-1,2-dilauroyl-sn-glycero-3-phosphoethanolamine) for selective cross-linking. The peripheral membrane protein cytochrome c from the inner mitochondrial membrane was rendered carbonate wash-resistant by cross-linking to ASA-DLPE in a model membrane system, validating our approach. Cross-link products of cytochrome c and its precursor apocytochrome c were demonstrated by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and were specifically detected by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), taking advantage of the intrinsic UV absorbance of the cross-linker. Application of the method to inner mitochondrial membranes from Saccharomyces cerevisae revealed cross-link products of both exogenously added apocytochrome c and endogenous proteins with molecular weights around 34 and 72 kDa. Liquid chromatograpy (LC)-MS/MS was performed to identify these proteins, resulting in a list of candidate proteins potentially cross-linked at the membrane interface. The approach described here provides methodology for capturing phospholipid-protein interactions in their native environment of the biomembrane using modern proteomics techniques.
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Affiliation(s)
- Jacob Gubbens
- Department Biochemistry of Membranes, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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Chevrollier A, Loiseau D, Gautier F, Malthièry Y, Stepien G. ANT2 expression under hypoxic conditions produces opposite cell-cycle behavior in 143B and HepG2 cancer cells. Mol Carcinog 2005; 42:1-8. [PMID: 15486956 DOI: 10.1002/mc.20059] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Under hypoxic conditions, mitochondrial ATP production ceases, leaving cells entirely dependent on their glycolytic metabolism. The cytoplasmic and intramitochondrial ATP/ADP ratios, partly controlled by the adenine nucleotide translocator (ANT), are drastically modified. In dividing and growing cells that have a predominantly glycolytic metabolism, the ANT isoform 2, which has kinetic properties allowing ATP import into mitochondria, is over-expressed in comparison to control cells. We studied the cellular metabolic and proliferative response to hypoxia in two transformed human cell lines with different metabolic backgrounds: HepG2 and 143B, and in their rho(o) derivatives, i.e., cells with no mitochondrial DNA. Transformed 143B and rho(o) cells continued their proliferation whereas HepG2 cells, with a more differentiated phenotype, arrested their cell-cycle at the G(1)/S checkpoint. Hypoxia induced an increase in glycolytic activity, correlated to an induction of VEGF and hexokinase II (HK II) expression. Thus, according to their tumorigenicity, transformed cells may adopt one of two distinct behaviors to support hypoxic stress, i.e., proliferation or quiescence. Our study links the constitutive glycolytic activity and ANT2 expression levels of transformed cells with the loss of cell-cycle control after oxygen deprivation. ATP import by ANT2 allows cells to maintain their mitochondrial integrity while acquiring insensitivity to any alterations in the proteins involved in oxidative phosphorylation. This loss of cell dependence on oxidative metabolism is an important factor in the development of tumors.
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Affiliation(s)
- Arnaud Chevrollier
- INSERM E0018, Laboratoire de Biochimie et Biologie Moléculaire, CHU, Angers, France
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Pebay-Peyroula E, Dahout-Gonzalez C, Kahn R, Trézéguet V, Lauquin GJM, Brandolin G. Structure of mitochondrial ADP/ATP carrier in complex with carboxyatractyloside. Nature 2003; 426:39-44. [PMID: 14603310 DOI: 10.1038/nature02056] [Citation(s) in RCA: 744] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2003] [Accepted: 09/15/2003] [Indexed: 02/04/2023]
Abstract
ATP, the principal energy currency of the cell, fuels most biosynthetic reactions in the cytoplasm by its hydrolysis into ADP and inorganic phosphate. Because resynthesis of ATP occurs in the mitochondrial matrix, ATP is exported into the cytoplasm while ADP is imported into the matrix. The exchange is accomplished by a single protein, the ADP/ATP carrier. Here we have solved the bovine carrier structure at a resolution of 2.2 A by X-ray crystallography in complex with an inhibitor, carboxyatractyloside. Six alpha-helices form a compact transmembrane domain, which, at the surface towards the space between inner and outer mitochondrial membranes, reveals a deep depression. At its bottom, a hexapeptide carrying the signature of nucleotide carriers (RRRMMM) is located. Our structure, together with earlier biochemical results, suggests that transport substrates bind to the bottom of the cavity and that translocation results from a transient transition from a 'pit' to a 'channel' conformation.
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Affiliation(s)
- Eva Pebay-Peyroula
- Institut de Biologie Structurale, UMR 5075 CEA-CNRS-Université Joseph Fourier, 41 rue Jules Horowitz, F-38027, Grenoble cedex 1, France.
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