1
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Žuna K, Tyschuk T, Beikbaghban T, Sternberg F, Kreiter J, Pohl EE. The 2-oxoglutarate/malate carrier extends the family of mitochondrial carriers capable of fatty acid and 2,4-dinitrophenol-activated proton transport. Acta Physiol (Oxf) 2024; 240:e14143. [PMID: 38577966 DOI: 10.1111/apha.14143] [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: 10/19/2023] [Revised: 03/06/2024] [Accepted: 03/11/2024] [Indexed: 04/06/2024]
Abstract
AIMS Metabolic reprogramming in cancer cells has been linked to mitochondrial dysfunction. The mitochondrial 2-oxoglutarate/malate carrier (OGC) has been suggested as a potential target for preventing cancer progression. Although OGC is involved in the malate/aspartate shuttle, its exact role in cancer metabolism remains unclear. We aimed to investigate whether OGC may contribute to the alteration of mitochondrial inner membrane potential by transporting protons. METHODS The expression of OGC in mouse tissues and cancer cells was investigated by PCR and Western blot analysis. The proton transport function of recombinant murine OGC was evaluated by measuring the membrane conductance (Gm) of planar lipid bilayers. OGC-mediated substrate transport was measured in proteoliposomes using 14C-malate. RESULTS OGC increases proton Gm only in the presence of natural (long-chain fatty acids, FA) or chemical (2,4-dinitrophenol) protonophores. The increase in OGC activity directly correlates with the increase in the number of unsaturated bonds of the FA. OGC substrates and inhibitors compete with FA for the same protein binding site. Arginine 90 was identified as a critical amino acid for the binding of FA, ATP, 2-oxoglutarate, and malate, which is a first step towards understanding the OGC-mediated proton transport mechanism. CONCLUSION OGC extends the family of mitochondrial transporters with dual function: (i) metabolite transport and (ii) proton transport facilitated in the presence of protonophores. Elucidating the contribution of OGC to uncoupling may be essential for the design of targeted drugs for the treatment of cancer and other metabolic diseases.
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Affiliation(s)
- Kristina Žuna
- Physiology and Biophysics, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Tatyana Tyschuk
- Physiology and Biophysics, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Taraneh Beikbaghban
- Physiology and Biophysics, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Felix Sternberg
- Physiology and Biophysics, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Jürgen Kreiter
- Physiology and Biophysics, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Elena E Pohl
- Physiology and Biophysics, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
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2
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Pyrihová E, King MS, King AC, Toleco MR, van der Giezen M, Kunji ERS. A mitochondrial carrier transports glycolytic intermediates to link cytosolic and mitochondrial glycolysis in the human gut parasite Blastocystis. eLife 2024; 13:RP94187. [PMID: 38780415 PMCID: PMC11115451 DOI: 10.7554/elife.94187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024] Open
Abstract
Stramenopiles form a clade of diverse eukaryotic organisms, including multicellular algae, the fish and plant pathogenic oomycetes, such as the potato blight Phytophthora, and the human intestinal protozoan Blastocystis. In most eukaryotes, glycolysis is a strictly cytosolic metabolic pathway that converts glucose to pyruvate, resulting in the production of NADH and ATP (Adenosine triphosphate). In contrast, stramenopiles have a branched glycolysis in which the enzymes of the pay-off phase are located in both the cytosol and the mitochondrial matrix. Here, we identify a mitochondrial carrier in Blastocystis that can transport glycolytic intermediates, such as dihydroxyacetone phosphate and glyceraldehyde-3-phosphate, across the mitochondrial inner membrane, linking the cytosolic and mitochondrial branches of glycolysis. Comparative analyses with the phylogenetically related human mitochondrial oxoglutarate carrier (SLC25A11) and dicarboxylate carrier (SLC25A10) show that the glycolytic intermediate carrier has lost its ability to transport the canonical substrates malate and oxoglutarate. Blastocystis lacks several key components of oxidative phosphorylation required for the generation of mitochondrial ATP, such as complexes III and IV, ATP synthase, and ADP/ATP carriers. The presence of the glycolytic pay-off phase in the mitochondrial matrix generates ATP, which powers energy-requiring processes, such as macromolecular synthesis, as well as NADH, used by mitochondrial complex I to generate a proton motive force to drive the import of proteins and molecules. Given its unique substrate specificity and central role in carbon and energy metabolism, the carrier for glycolytic intermediates identified here represents a specific drug and pesticide target against stramenopile pathogens, which are of great economic importance.
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Affiliation(s)
- Eva Pyrihová
- Medical Research Council Mitochondrial Biology Unit, The Keith Peters BuildingCambridgeUnited Kingdom
- University of Stavanger, Department of Chemistry, Bioscience, and Environmental EngineeringStavangerNorway
| | - Martin S King
- Medical Research Council Mitochondrial Biology Unit, The Keith Peters BuildingCambridgeUnited Kingdom
| | - Alannah C King
- Medical Research Council Mitochondrial Biology Unit, The Keith Peters BuildingCambridgeUnited Kingdom
| | - M Rey Toleco
- University of Stavanger, Department of Chemistry, Bioscience, and Environmental EngineeringStavangerNorway
| | - Mark van der Giezen
- University of Stavanger, Department of Chemistry, Bioscience, and Environmental EngineeringStavangerNorway
- Research Department Stavanger University HospitalStavangerNorway
| | - Edmund RS Kunji
- Medical Research Council Mitochondrial Biology Unit, The Keith Peters BuildingCambridgeUnited Kingdom
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3
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Jones SA, Ruprecht JJ, Crichton PG, Kunji ERS. Structural mechanisms of mitochondrial uncoupling protein 1 regulation in thermogenesis. Trends Biochem Sci 2024:S0968-0004(24)00071-9. [PMID: 38565497 DOI: 10.1016/j.tibs.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/28/2024] [Accepted: 03/08/2024] [Indexed: 04/04/2024]
Abstract
In mitochondria, the oxidation of nutrients is coupled to ATP synthesis by the generation of a protonmotive force across the mitochondrial inner membrane. In mammalian brown adipose tissue (BAT), uncoupling protein 1 (UCP1, SLC25A7), a member of the SLC25 mitochondrial carrier family, dissipates the protonmotive force by facilitating the return of protons to the mitochondrial matrix. This process short-circuits the mitochondrion, generating heat for non-shivering thermogenesis. Recent cryo-electron microscopy (cryo-EM) structures of human UCP1 have provided new molecular insights into the inhibition and activation of thermogenesis. Here, we discuss these structures, describing how purine nucleotides lock UCP1 in a proton-impermeable conformation and rationalizing potential conformational changes of this carrier in response to fatty acid activators that enable proton leak for thermogenesis.
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Affiliation(s)
- Scott A Jones
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Keith Peters Building, Cambridge, CB2 0XY, UK
| | - Jonathan J Ruprecht
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Keith Peters Building, Cambridge, CB2 0XY, UK
| | - Paul G Crichton
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Edmund R S Kunji
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Keith Peters Building, Cambridge, CB2 0XY, UK.
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4
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Kreiter J, Tyschuk T, Pohl EE. Uncoupling Protein 3 Catalyzes the Exchange of C4 Metabolites Similar to UCP2. Biomolecules 2023; 14:21. [PMID: 38254621 PMCID: PMC10813146 DOI: 10.3390/biom14010021] [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: 09/29/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Uncoupling protein 3 (UCP3) belongs to the mitochondrial carrier protein superfamily SLC25 and is abundant in brown adipose tissue (BAT), the heart, and muscles. The expression of UCP3 in tissues mainly dependent on fatty acid oxidation suggests its involvement in cellular metabolism and has drawn attention to its possible transport function beyond the transport of protons in the presence of fatty acids. Based on the high homology between UCP2 and UCP3, we hypothesized that UCP3 transports C4 metabolites similar to UCP2. To test this, we measured the transport of substrates against phosphate (32Pi) in proteoliposomes reconstituted with recombinant murine UCP3 (mUCP3). We found that mUCP3 mainly transports aspartate and sulfate but also malate, malonate, oxaloacetate, and succinate. The transport rates calculated from the exchange of 32Pi against extraliposomal aspartate and sulfate were 23.9 ± 5.8 and 17.5 ± 5.1 µmol/min/mg, respectively. Using site-directed mutagenesis, we revealed that mutation of R84 resulted in impaired aspartate/phosphate exchange, demonstrating its critical role in substrate transport. The difference in substrate preference between mUCP2 and mUCP3 may be explained by their different tissue expression patterns and biological functions in these tissues.
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Affiliation(s)
| | | | - Elena E. Pohl
- Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine, 1210 Vienna, Austria; (J.K.); (T.T.)
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5
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Goyal S, Cambronne XA. Layered mechanisms regulating the human mitochondrial NAD+ transporter SLC25A51. Biochem Soc Trans 2023; 51:1989-2004. [PMID: 38108469 PMCID: PMC10802112 DOI: 10.1042/bst20220318] [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: 09/19/2023] [Revised: 11/28/2023] [Accepted: 12/08/2023] [Indexed: 12/19/2023]
Abstract
SLC25A51 is the primary mitochondrial NAD+ transporter in humans and controls many local reactions by mediating the influx of oxidized NAD+. Intriguingly, SLC25A51 lacks several key features compared with other members in the mitochondrial carrier family, thus its molecular mechanism has been unclear. A deeper understanding would shed light on the control of cellular respiration, the citric acid cycle, and free NAD+ concentrations in mammalian mitochondria. This review discusses recent insights into the transport mechanism of SLC25A51, and in the process highlights a multitiered regulation that governs NAD+ transport. The aspects regulating SLC25A51 import activity can be categorized as contributions from (1) structural characteristics of the transporter itself, (2) its microenvironment, and (3) distinctive properties of the transported ligand. These unique mechanisms further evoke compelling new ideas for modulating the activity of this transporter, as well as new mechanistic models for the mitochondrial carrier family.
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Affiliation(s)
- Shivansh Goyal
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712
| | - Xiaolu A. Cambronne
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712
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6
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Goyal S, Paspureddi A, Lu M, Chan H, Lyons SN, Wilson CN, Niere M, Ziegler M, Cambronne XA. Dynamics of SLC25A51 reveal preference for oxidized NAD + and substrate led transport. EMBO Rep 2023; 24:e56596. [PMID: 37575034 PMCID: PMC10561365 DOI: 10.15252/embr.202256596] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 07/23/2023] [Accepted: 07/27/2023] [Indexed: 08/15/2023] Open
Abstract
SLC25A51 is a member of the mitochondrial carrier family (MCF) but lacks key residues that contribute to the mechanism of other nucleotide MCF transporters. Thus, how SLC25A51 transports NAD+ across the inner mitochondrial membrane remains unclear. To elucidate its mechanism, we use Molecular Dynamics simulations to reconstitute SLC25A51 homology models into lipid bilayers and to generate hypotheses to test. We observe spontaneous binding of cardiolipin phospholipids to three distinct sites on the exterior of SLC25A51's central pore and find that mutation of these sites impairs cardiolipin binding and transporter activity. We also observe that stable formation of the required matrix gate is controlled by a single salt bridge. We identify binding sites in SLC25A51 for NAD+ and show that its selectivity for NAD+ is guided by an electrostatic interaction between the charged nicotinamide ring in the ligand and a negatively charged patch in the pore. In turn, interaction of NAD+ with interior residue E132 guides the ligand to dynamically engage and weaken the salt bridge gate, representing a ligand-induced initiation of transport.
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Affiliation(s)
- Shivansh Goyal
- Department of Molecular BiosciencesUniversity of Texas at AustinAustinTXUSA
| | | | - Mu‐Jie Lu
- Department of Molecular BiosciencesUniversity of Texas at AustinAustinTXUSA
| | - Hsin‐Ru Chan
- Department of Molecular BiosciencesUniversity of Texas at AustinAustinTXUSA
| | - Scott N Lyons
- Department of Molecular BiosciencesUniversity of Texas at AustinAustinTXUSA
| | - Crystal N Wilson
- Department of Molecular BiosciencesUniversity of Texas at AustinAustinTXUSA
| | - Marc Niere
- Department of BiomedicineUniversity of BergenBergenNorway
| | | | - Xiaolu A Cambronne
- Department of Molecular BiosciencesUniversity of Texas at AustinAustinTXUSA
- Livestrong Cancer InstituteUniversity of Texas at AustinAustinTXUSA
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7
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Kreiter J, Škulj S, Brkljača Z, Bardakji S, Vazdar M, Pohl EE. FA Sliding as the Mechanism for the ANT1-Mediated Fatty Acid Anion Transport in Lipid Bilayers. Int J Mol Sci 2023; 24:13701. [PMID: 37762012 PMCID: PMC10531397 DOI: 10.3390/ijms241813701] [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: 07/25/2023] [Revised: 08/27/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Mitochondrial adenine nucleotide translocase (ANT) exchanges ADP for ATP to maintain energy production in the cell. Its protonophoric function in the presence of long-chain fatty acids (FA) is also recognized. Our previous results imply that proton/FA transport can be best described with the FA cycling model, in which protonated FA transports the proton to the mitochondrial matrix. The mechanism by which ANT1 transports FA anions back to the intermembrane space remains unclear. Using a combined approach involving measurements of the current through the planar lipid bilayers reconstituted with ANT1, site-directed mutagenesis and molecular dynamics simulations, we show that the FA anion is first attracted by positively charged arginines or lysines on the matrix side of ANT1 before moving along the positively charged protein-lipid interface and binding to R79, where it is protonated. We show that R79 is also critical for the competitive binding of ANT1 substrates (ADP and ATP) and inhibitors (carboxyatractyloside and bongkrekic acid). The binding sites are well conserved in mitochondrial SLC25 members, suggesting a general mechanism for transporting FA anions across the inner mitochondrial membrane.
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Affiliation(s)
- Jürgen Kreiter
- Institute of Physiology, Pathophysiology, and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine, 1210 Vienna, Austria; (J.K.); (S.Š.); (S.B.)
| | - Sanja Škulj
- Institute of Physiology, Pathophysiology, and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine, 1210 Vienna, Austria; (J.K.); (S.Š.); (S.B.)
| | - Zlatko Brkljača
- Division of Organic Chemistry and Biochemistry, Rudjer Bošković Institute, 10000 Zagreb, Croatia;
| | - Sarah Bardakji
- Institute of Physiology, Pathophysiology, and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine, 1210 Vienna, Austria; (J.K.); (S.Š.); (S.B.)
| | - Mario Vazdar
- Department of Mathematics, Informatics, and Cybernetics, University of Chemistry and Technology, 166 28 Prague, Czech Republic
| | - Elena E. Pohl
- Institute of Physiology, Pathophysiology, and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine, 1210 Vienna, Austria; (J.K.); (S.Š.); (S.B.)
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8
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Hoogstraten CA, Jacobs MME, de Boer G, van de Wal MAE, Koopman WJH, Smeitink JAM, Russel FGM, Schirris TJJ. Metabolic impact of genetic and chemical ADP/ATP carrier inhibition in renal proximal tubule epithelial cells. Arch Toxicol 2023; 97:1927-1941. [PMID: 37154957 PMCID: PMC10256673 DOI: 10.1007/s00204-023-03510-7] [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: 12/05/2022] [Accepted: 04/26/2023] [Indexed: 05/10/2023]
Abstract
Mitochondrial dysfunction is pivotal in drug-induced acute kidney injury (AKI), but the underlying mechanisms remain largely unknown. Transport proteins embedded in the mitochondrial inner membrane form a significant class of potential drug off-targets. So far, most transporter-drug interactions have been reported for the mitochondrial ADP/ATP carrier (AAC). Since it remains unknown to what extent AAC contributes to drug-induced mitochondrial dysfunction in AKI, we here aimed to better understand the functional role of AAC in the energy metabolism of human renal proximal tubular cells. To this end, CRISPR/Cas9 technology was applied to generate AAC3-/- human conditionally immortalized renal proximal tubule epithelial cells. This AAC3-/- cell model was characterized with respect to mitochondrial function and morphology. To explore whether this model could provide first insights into (mitochondrial) adverse drug effects with suspicion towards AAC-mediated mechanisms, wild-type and knockout cells were exposed to established AAC inhibitors, after which cellular metabolic activity and mitochondrial respiratory capacity were measured. Two AAC3-/- clones showed a significant reduction in ADP import and ATP export rates and mitochondrial mass, without influencing overall morphology. AAC3-/- clones exhibited reduced ATP production, oxygen consumption rates and metabolic spare capacity was particularly affected, mainly in conditions with galactose as carbon source. Chemical AAC inhibition was stronger compared to genetic inhibition in AAC3-/-, suggesting functional compensation by remaining AAC isoforms in our knockout model. In conclusion, our results indicate that ciPTEC-OAT1 cells have a predominantly oxidative phenotype that was not additionally activated by switching energy source. Genetic inhibition of AAC3 particularly impacted mitochondrial spare capacity, without affecting mitochondrial morphology, suggesting an important role for AAC in maintaining the metabolic spare respiration.
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Affiliation(s)
- Charlotte A Hoogstraten
- Department of Pharmacology and Toxicology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
| | - Maaike M E Jacobs
- Department of Pharmacology and Toxicology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
| | - Guido de Boer
- Department of Pharmacology and Toxicology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
| | - Melissa A E van de Wal
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
| | - Werner J H Koopman
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
| | - Jan A M Smeitink
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
- Khondrion BV, Nijmegen, 6525 EX, The Netherlands
| | - Frans G M Russel
- Department of Pharmacology and Toxicology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands.
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands.
| | - Tom J J Schirris
- Department of Pharmacology and Toxicology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
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9
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Zítek J, King MS, Peña-Diaz P, Pyrihová E, King AC, Kunji ERS, Hampl V. The free-living flagellate Paratrimastix pyriformis uses a distinct mitochondrial carrier to balance adenine nucleotide pools. Arch Biochem Biophys 2023; 742:109638. [PMID: 37192692 PMCID: PMC10251735 DOI: 10.1016/j.abb.2023.109638] [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: 04/07/2023] [Revised: 05/12/2023] [Accepted: 05/13/2023] [Indexed: 05/18/2023]
Abstract
Paratrimastix pyriformis is a free-living flagellate thriving in low-oxygen freshwater sediments. It belongs to the group Metamonada along with human parasites, such as Giardia and Trichomonas. Like other metamonads, P. pyriformis has a mitochondrion-related organelle (MRO) which in this protist is primarily involved in one-carbon folate metabolism. The MRO contains four members of the solute carrier family 25 (SLC25) responsible for the exchange of metabolites across the mitochondrial inner membrane. Here, we characterise the function of the adenine nucleotide carrier PpMC1 by thermostability shift and transport assays. We show that it transports ATP, ADP and, to a lesser extent, AMP, but not phosphate. The carrier is distinct in function and origin from both ADP/ATP carriers and ATP-Mg/phosphate carriers, and it most likely represents a distinct class of adenine nucleotide carriers.
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Affiliation(s)
- Justyna Zítek
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, 252 50, Czech Republic
| | - Martin S King
- Medical Research Council Mitochondrial Biology Unit, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Priscila Peña-Diaz
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, 252 50, Czech Republic
| | - Eva Pyrihová
- Medical Research Council Mitochondrial Biology Unit, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom; University of Stavanger, Department of Chemistry, Bioscience, And Environmental Engineering, Richard Johnsens Gate 4, N-4021, Stavanger, Norway
| | - Alannah C King
- Medical Research Council Mitochondrial Biology Unit, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Edmund R S Kunji
- Medical Research Council Mitochondrial Biology Unit, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom.
| | - Vladimír Hampl
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, 252 50, Czech Republic.
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10
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Jones SA, Gogoi P, Ruprecht JJ, King MS, Lee Y, Zögg T, Pardon E, Chand D, Steimle S, Copeman DM, Cotrim CA, Steyaert J, Crichton PG, Moiseenkova-Bell V, Kunji ER. Structural basis of purine nucleotide inhibition of human uncoupling protein 1. SCIENCE ADVANCES 2023; 9:eadh4251. [PMID: 37256948 PMCID: PMC10413660 DOI: 10.1126/sciadv.adh4251] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/24/2023] [Indexed: 06/02/2023]
Abstract
Mitochondrial uncoupling protein 1 (UCP1) gives brown adipose tissue of mammals its specialized ability to burn calories as heat for thermoregulation. When activated by fatty acids, UCP1 catalyzes the leak of protons across the mitochondrial inner membrane, short-circuiting the mitochondrion to generate heat, bypassing ATP synthesis. In contrast, purine nucleotides bind and inhibit UCP1, regulating proton leak by a molecular mechanism that is unclear. We present the cryo-electron microscopy structure of the GTP-inhibited state of UCP1, which is consistent with its nonconducting state. The purine nucleotide cross-links the transmembrane helices of UCP1 with an extensive interaction network. Our results provide a structural basis for understanding the specificity and pH dependency of the regulatory mechanism. UCP1 has retained all of the key functional and structural features required for a mitochondrial carrier-like transport mechanism. The analysis shows that inhibitor binding prevents the conformational changes that UCP1 uses to facilitate proton leak.
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Affiliation(s)
- Scott A. Jones
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Keith Peters Building, Cambridge CB2 0XY, UK
| | - Prerana Gogoi
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, 10-124 Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5158, USA
| | - Jonathan J. Ruprecht
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Keith Peters Building, Cambridge CB2 0XY, UK
| | - Martin S. King
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Keith Peters Building, Cambridge CB2 0XY, UK
| | - Yang Lee
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Keith Peters Building, Cambridge CB2 0XY, UK
| | - Thomas Zögg
- VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Els Pardon
- VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Deepak Chand
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Keith Peters Building, Cambridge CB2 0XY, UK
| | - Stefan Steimle
- Department of Biochemistry and Biophysics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Danielle M. Copeman
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Camila A. Cotrim
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Jan Steyaert
- VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Paul G. Crichton
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Vera Moiseenkova-Bell
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, 10-124 Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5158, USA
| | - Edmund R. S. Kunji
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Keith Peters Building, Cambridge CB2 0XY, UK
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11
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Gagelin A, Largeau C, Masscheleyn S, Piel MS, Calderón-Mora D, Bouillaud F, Hénin J, Miroux B. Molecular determinants of inhibition of UCP1-mediated respiratory uncoupling. Nat Commun 2023; 14:2594. [PMID: 37147287 PMCID: PMC10162991 DOI: 10.1038/s41467-023-38219-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 04/21/2023] [Indexed: 05/07/2023] Open
Abstract
Brown adipose tissue expresses uncoupling protein 1 (UCP1), which dissipates energy as heat, making it a target for treating metabolic disorders. Here, we investigate how purine nucleotides inhibit respiration uncoupling by UCP1. Our molecular simulations predict that GDP and GTP bind UCP1 in the common substrate binding site in an upright orientation, where the base moiety interacts with conserved residues R92 and E191. We identify a triplet of uncharged residues, F88/I187/W281, forming hydrophobic contacts with nucleotides. In yeast spheroplast respiration assays, both I187A and W281A mutants increase the fatty acid-induced uncoupling activity of UCP1 and partially suppress the inhibition of UCP1 activity by nucleotides. The F88A/I187A/W281A triple mutant is overactivated by fatty acids even at high concentrations of purine nucleotides. In simulations, E191 and W281 interact with purine but not pyrimidine bases. These results provide a molecular understanding of the selective inhibition of UCP1 by purine nucleotides.
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Affiliation(s)
- Antoine Gagelin
- Université Paris Cité, Laboratoire de Biochimie Théorique CNRS UPR9080, Paris, 75005, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, 75005, France
| | - Corentin Largeau
- Université Paris Cité, Laboratoire de Biochimie Théorique CNRS UPR9080, Paris, 75005, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, 75005, France
- Université Paris Cité, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires CNRS UMR7099, Paris, 75005, France
| | - Sandrine Masscheleyn
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, 75005, France
- Université Paris Cité, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires CNRS UMR7099, Paris, 75005, France
| | - Mathilde S Piel
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, 75005, France
- Université Paris Cité, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires CNRS UMR7099, Paris, 75005, France
| | - Daniel Calderón-Mora
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, 75005, France
- Université Paris Cité, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires CNRS UMR7099, Paris, 75005, France
| | - Frédéric Bouillaud
- Université Paris Cité, Institut Cochin, Inserm U1016, CNRS UMR8104, Paris, 75014, France
| | - Jérôme Hénin
- Université Paris Cité, Laboratoire de Biochimie Théorique CNRS UPR9080, Paris, 75005, France.
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, 75005, France.
| | - Bruno Miroux
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, 75005, France.
- Université Paris Cité, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires CNRS UMR7099, Paris, 75005, France.
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12
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Salam MAE, Salama K, Selim YMM, Saad M, Rady R, Alawbathani S, Schroeder S, Elmonem MA, Elkhateeb N. Three siblings with variable degrees of neuromuscular involvement and congenital sideroblastic anemia: A peculiar phenotype and a surprise genotypic explanation. Ann Hum Genet 2023. [PMID: 36916508 DOI: 10.1111/ahg.12505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/22/2023] [Accepted: 02/26/2023] [Indexed: 03/16/2023]
Abstract
INTRODUCTION Congenital sideroblastic anemias (CSAs) are a group of inherited bone-marrow disorders manifesting with erythroid hyperplasia and ineffective erythropoiesis. METHODS We describe a detailed clinical and genetic characterization of three siblings with CSA. RESULTS Two of them had limb-girdle myopathy and global developmental delay. The two elder siblings performed allogenic hematopoietic stem-cell transplantation 5 and 3 years prior with stabilization of the hematological features. Exome sequencing in the non-transplanted sibling revealed a novel homozygous nonsense variant in SLC25A38 gene NM_017875.2:c.559C > T; p.(Arg187*) causing autosomal-recessive sideroblastic anemia type-2, and a second homozygous pathogenic previously reported variant in GMPPB gene NM_013334.3:c.458C > T; p.(Thr153Ile) causing autosomal-recessive muscular dystrophy-dystroglycanopathy type B14. With the established diagnosis, hematopoietic stem cell transplantation is now being scheduled for the youngest sibling, and a trial therapy with acetylcholine esterase inhibitors was started for the two neurologically affected patients with partial clinical improvement. CONCLUSION This family emphasizes the importance of whole-exome sequencing for familial cases with complex phenotypes and vague neurological manifestations.
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Affiliation(s)
- Mai Abd El Salam
- Department of Pediatrics (Pediatric Hematology Unit), Kasr Alainy Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Khaled Salama
- Department of Pediatrics (Pediatric Hematology Unit), Kasr Alainy Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Yasmeen M M Selim
- Department of Pediatrics (Pediatric Hematology Unit), Kasr Alainy Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mariam Saad
- Department of Pediatrics (Pediatric Hematology Unit), Kasr Alainy Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Rasha Rady
- Department of Pediatrics (Pediatric Hematology Unit), Kasr Alainy Faculty of Medicine, Cairo University, Cairo, Egypt
| | | | | | - Mohamed A Elmonem
- Department of Clinical and Chemical Pathology, Kasr Alainy Faculty of Medicine, Cairo University, Cairo, Egypt.,Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt
| | - Nour Elkhateeb
- Department of Pediatrics (Pediatric Neurology and Metabolic Medicine Unit), Kasr Alainy Faculty of Medicine, Cairo University, Cairo, Egypt.,Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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13
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Identification and Functional Analysis of Two Mitoferrins, CsMIT1 and CsMIT2, Participating in Iron Homeostasis in Cucumber. Int J Mol Sci 2023; 24:ijms24055050. [PMID: 36902490 PMCID: PMC10003640 DOI: 10.3390/ijms24055050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/09/2023] Open
Abstract
Mitochondria are one of the major iron sinks in plant cells. Mitochondrial iron accumulation involves the action of ferric reductase oxidases (FRO) and carriers located in the inner mitochondrial membrane. It has been suggested that among these transporters, mitoferrins (mitochondrial iron transporters, MITs) belonging to the mitochondrial carrier family (MCF) function as mitochondrial iron importers. In this study, two cucumber proteins, CsMIT1 and CsMIT2, with high homology to Arabidopsis, rice and yeast MITs were identified and characterized. CsMIT1 and CsMIT2 were expressed in all organs of the two-week-old seedlings. Under Fe-limited conditions as well as Fe excess, the mRNA levels of CsMIT1 and CsMIT2 were altered, suggesting their regulation by iron availability. Analyses using Arabidopsis protoplasts confirmed the mitochondrial localization of cucumber mitoferrins. Expression of CsMIT1 and CsMIT2 restored the growth of the Δmrs3Δmrs4 mutant (defective in mitochondrial Fe transport), but not in mutants sensitive to other heavy metals. Moreover, the altered cytosolic and mitochondrial Fe concentrations, observed in the Δmrs3Δmrs4 strain, were recovered almost to the levels of WT yeast by expressing CsMIT1 or CsMIT2. These results indicate that cucumber proteins are involved in the iron transport from the cytoplasm to the mitochondria.
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14
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Miniero DV, Gambacorta N, Spagnoletta A, Tragni V, Loizzo S, Nicolotti O, Pierri CL, De Palma A. New Insights Regarding Hemin Inhibition of the Purified Rat Brain 2-Oxoglutarate Carrier and Relationships with Mitochondrial Dysfunction. J Clin Med 2022; 11:7519. [PMID: 36556135 PMCID: PMC9785169 DOI: 10.3390/jcm11247519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
A kinetic analysis of the transport assays on the purified rat brain 2-oxoglutarate/malate carrier (OGC) was performed starting from our recent results reporting about a competitive inhibitory behavior of hemin, a physiological porphyrin derivative, on the OGC reconstituted in an active form into proteoliposomes. The newly provided transport data and the elaboration of the kinetic equations show evidence that hemin exerts a mechanism of partially competitive inhibition, coupled with the formation of a ternary complex hemin-carrier substrate, when hemin targets the OGC from the matrix face. A possible interpretation of the provided kinetic analysis, which is supported by computational studies, could indicate the existence of a binding region responsible for the inhibition of the OGC and supposedly involved in the regulation of OGC activity. The proposed regulatory binding site is located on OGC mitochondrial matrix loops, where hemin could establish specific interactions with residues involved in the substrate recognition and/or conformational changes responsible for the translocation of mitochondrial carrier substrates. The regulatory binding site would be placed about 6 Å below the substrate binding site of the OGC, facing the mitochondrial matrix, and would allow the simultaneous binding of hemin and 2-oxoglutarate or malate to different regions of the carrier. Overall, the presented experimental and computational analyses help to shed light on the possible existence of the hemin-carrier substrate ternary complex, confirming the ability of the OGC to bind porphyrin derivatives, and in particular hemin, with possible consequences for the mitochondrial redox state mediated by the malate/aspartate shuttle led by the mitochondrial carriers OGC and AGC.
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Affiliation(s)
- Daniela Valeria Miniero
- Department of Biosciences, Biotechnologies and Environment, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70125 Bari, Italy
| | - Nicola Gambacorta
- Department of Pharmacy-Pharmaceutical Sciences, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70125 Bari, Italy
| | - Anna Spagnoletta
- ENEA Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Trisaia Research Centre, S.S. 106 Jonica, Km 419,500, 75026 Rotondella (MT), Italy
| | - Vincenzo Tragni
- Department of Pharmacy-Pharmaceutical Sciences, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70125 Bari, Italy
| | - Stefano Loizzo
- Department of Cardiovascular, Endocrine-Metabolic Diseases and Aging, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Roma, Italy
| | - Orazio Nicolotti
- Department of Pharmacy-Pharmaceutical Sciences, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70125 Bari, Italy
| | - Ciro Leonardo Pierri
- Department of Pharmacy-Pharmaceutical Sciences, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70125 Bari, Italy
| | - Annalisa De Palma
- Department of Biosciences, Biotechnologies and Environment, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70125 Bari, Italy
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15
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Tavoulari S, Lacabanne D, Thangaratnarajah C, Kunji ERS. Pathogenic variants of the mitochondrial aspartate/glutamate carrier causing citrin deficiency. Trends Endocrinol Metab 2022; 33:539-553. [PMID: 35725541 PMCID: PMC7614230 DOI: 10.1016/j.tem.2022.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/26/2022] [Accepted: 05/19/2022] [Indexed: 12/22/2022]
Abstract
Citrin deficiency is a pan-ethnic and highly prevalent mitochondrial disease with three different stages: neonatal intrahepatic cholestasis (NICCD), a relatively mild adaptation stage, and type II citrullinemia in adulthood (CTLN2). The cause is the absence or dysfunction of the calcium-regulated mitochondrial aspartate/glutamate carrier 2 (AGC2/SLC25A13), also called citrin, which imports glutamate into the mitochondrial matrix and exports aspartate to the cytosol. In citrin deficiency, these missing transport steps lead to impairment of the malate-aspartate shuttle, gluconeogenesis, amino acid homeostasis, and the urea cycle. In this review, we describe the geological spread and occurrence of citrin deficiency, the metabolic consequences and use our current knowledge of the structure to predict the impact of the known pathogenic mutations on the calcium-regulatory and transport mechanism of citrin.
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Affiliation(s)
- Sotiria Tavoulari
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Denis Lacabanne
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Chancievan Thangaratnarajah
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Edmund R S Kunji
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.
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16
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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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17
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Bertholet AM, Natale AM, Bisignano P, Suzuki J, Fedorenko A, Hamilton J, Brustovetsky T, Kazak L, Garrity R, Chouchani ET, Brustovetsky N, Grabe M, Kirichok Y. Mitochondrial uncouplers induce proton leak by activating AAC and UCP1. Nature 2022; 606:180-187. [PMID: 35614225 PMCID: PMC9646675 DOI: 10.1038/s41586-022-04747-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/08/2022] [Indexed: 11/08/2022]
Abstract
Mitochondria generate heat due to H+ leak (IH) across their inner membrane1. IH results from the action of long-chain fatty acids on uncoupling protein 1 (UCP1) in brown fat2-6 and ADP/ATP carrier (AAC) in other tissues1,7-9, but the underlying mechanism is poorly understood. As evidence of pharmacological activators of IH through UCP1 and AAC is lacking, IH is induced by protonophores such as 2,4-dinitrophenol (DNP) and cyanide-4-(trifluoromethoxy) phenylhydrazone (FCCP)10,11. Although protonophores show potential in combating obesity, diabetes and fatty liver in animal models12-14, their clinical potential for treating human disease is limited due to indiscriminately increasing H+ conductance across all biological membranes10,11 and adverse side effects15. Here we report the direct measurement of IH induced by DNP, FCCP and other common protonophores and find that it is dependent on AAC and UCP1. Using molecular structures of AAC, we perform a computational analysis to determine the binding sites for protonophores and long-chain fatty acids, and find that they overlap with the putative ADP/ATP-binding site. We also develop a mathematical model that proposes a mechanism of uncoupler-dependent IH through AAC. Thus, common protonophoric uncouplers are synthetic activators of IH through AAC and UCP1, paving the way for the development of new and more specific activators of these two central mediators of mitochondrial bioenergetics.
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Affiliation(s)
- Ambre M Bertholet
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA
- Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Andrew M Natale
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Paola Bisignano
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Junji Suzuki
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA
| | - Andriy Fedorenko
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA
| | - James Hamilton
- Department of Pharmacology and Toxicology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Tatiana Brustovetsky
- Department of Pharmacology and Toxicology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Lawrence Kazak
- Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Ryan Garrity
- Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Edward T Chouchani
- Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Nickolay Brustovetsky
- Department of Pharmacology and Toxicology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Michael Grabe
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
| | - Yuriy Kirichok
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA.
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18
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Shi X, Reinstadler B, Shah H, To TL, Byrne K, Summer L, Calvo SE, Goldberger O, Doench JG, Mootha VK, Shen H. Combinatorial GxGxE CRISPR screen identifies SLC25A39 in mitochondrial glutathione transport linking iron homeostasis to OXPHOS. Nat Commun 2022; 13:2483. [PMID: 35513392 PMCID: PMC9072411 DOI: 10.1038/s41467-022-30126-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 04/18/2022] [Indexed: 12/18/2022] Open
Abstract
The SLC25 carrier family consists of 53 transporters that shuttle nutrients and co-factors across mitochondrial membranes. The family is highly redundant and their transport activities coupled to metabolic state. Here, we use a pooled, dual CRISPR screening strategy that knocks out pairs of transporters in four metabolic states - glucose, galactose, OXPHOS inhibition, and absence of pyruvate - designed to unmask the inter-dependence of these genes. In total, we screen 63 genes in four metabolic states, corresponding to 2016 single and pair-wise genetic perturbations. We recover 19 gene-by-environment (GxE) interactions and 9 gene-by-gene (GxG) interactions. One GxE interaction hit illustrates that the fitness defect in the mitochondrial folate carrier (SLC25A32) KO cells is genetically buffered in galactose due to a lack of substrate in de novo purine biosynthesis. GxG analysis highlights a buffering interaction between the iron transporter SLC25A37 (A37) and the poorly characterized SLC25A39 (A39). Mitochondrial metabolite profiling, organelle transport assays, and structure-guided mutagenesis identify A39 as critical for mitochondrial glutathione (GSH) import. Functional studies reveal that A39-mediated glutathione homeostasis and A37-mediated mitochondrial iron uptake operate jointly to support mitochondrial OXPHOS. Our work underscores the value of studying family-wide genetic interactions across different metabolic environments.
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Affiliation(s)
- Xiaojian Shi
- Cellular and Molecular Physiology Department, Yale School of Medicine, New Haven, CT, USA
- Systems Biology Institute, Yale West Campus, West Haven, CT, USA
| | - Bryn Reinstadler
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Hardik Shah
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Tsz-Leung To
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Katie Byrne
- Cellular and Molecular Physiology Department, Yale School of Medicine, New Haven, CT, USA
- Systems Biology Institute, Yale West Campus, West Haven, CT, USA
| | - Luanna Summer
- Cellular and Molecular Physiology Department, Yale School of Medicine, New Haven, CT, USA
- Systems Biology Institute, Yale West Campus, West Haven, CT, USA
| | - Sarah E Calvo
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Olga Goldberger
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Vamsi K Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Hongying Shen
- Cellular and Molecular Physiology Department, Yale School of Medicine, New Haven, CT, USA.
- Systems Biology Institute, Yale West Campus, West Haven, CT, USA.
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19
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Mechanistic Insights into Multiple-step Transport of Mitochondrial ADP/ATP Carrier. Comput Struct Biotechnol J 2022; 20:1829-1840. [PMID: 35521544 PMCID: PMC9046947 DOI: 10.1016/j.csbj.2022.03.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 03/28/2022] [Accepted: 03/28/2022] [Indexed: 01/02/2023] Open
Abstract
The ADP/ATP carrier (AAC) is crucial for mitochondrial functions by importing ADP and exporting ATP across the inner mitochondrial membrane. However, the mechanism of highly specific ADP recognition and transport by AAC remains largely elusive. In this work, spontaneous ADP binding process to the ground c-state AAC was investigated through rigorous molecular dynamics simulations of over 31 microseconds in total. With improved simulation strategy, we have successfully identified a highly specific ADP binding site in the upper region of the cavity, and this site exhibits selectivity for ADP over ATP based on free-energy calculations. Sequence analyses on adenine nucleotide transporters also suggest that this subgroup uses the upper region of the cavity, rather than the previously proposed central binding site located at the bottom of the cavity to discriminate their substrates. Identification of the new site unveils the unusually high substrate specificity of AAC and explains the dependence of transport on the flexibility between anti and syn glycosidic conformers of ADP. Moreover, this new site together with the central site supports early biochemical findings. In light of these early findings, our simulations described a multi-step model in which the carrier uses different sites for substrate attraction, recognition and conformational transition. These results provide new insights into the transport mechanism of AAC and other adenine nucleotide transporters.
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20
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Uncoupling Proteins and Regulated Proton Leak in Mitochondria. Int J Mol Sci 2022; 23:ijms23031528. [PMID: 35163451 PMCID: PMC8835771 DOI: 10.3390/ijms23031528] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 01/26/2022] [Indexed: 12/17/2022] Open
Abstract
Higher concentration of protons in the mitochondrial intermembrane space compared to the matrix results in an electrochemical potential causing the back flux of protons to the matrix. This proton transport can take place through ATP synthase complex (leading to formation of ATP) or can occur via proton transporters of the mitochondrial carrier superfamily and/or membrane lipids. Some mitochondrial proton transporters, such as uncoupling proteins (UCPs), transport protons as their general regulating function; while others are symporters or antiporters, which use the proton gradient as a driving force to co-transport other substrates across the mitochondrial inner membrane (such as phosphate carrier, a symporter; or aspartate/glutamate transporter, an antiporter). Passage (or leakage) of protons across the inner membrane to matrix from any route other than ATP synthase negatively impacts ATP synthesis. The focus of this review is on regulated proton transport by UCPs. Recent findings on the structure and function of UCPs, and the related research methodologies, are also critically reviewed. Due to structural similarity of members of the mitochondrial carrier superfamily, several of the known structural features are potentially expandable to all members. Overall, this report provides a brief, yet comprehensive, overview of the current knowledge in the field.
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21
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Pardo B, Herrada-Soler E, Satrústegui J, Contreras L, del Arco A. AGC1 Deficiency: Pathology and Molecular and Cellular Mechanisms of the Disease. Int J Mol Sci 2022; 23:528. [PMID: 35008954 PMCID: PMC8745132 DOI: 10.3390/ijms23010528] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 02/01/2023] Open
Abstract
AGC1/Aralar/Slc25a12 is the mitochondrial carrier of aspartate-glutamate, the regulatory component of the NADH malate-aspartate shuttle (MAS) that transfers cytosolic redox power to neuronal mitochondria. The deficiency in AGC1/Aralar leads to the human rare disease named "early infantile epileptic encephalopathy 39" (EIEE 39, OMIM # 612949) characterized by epilepsy, hypotonia, arrested psychomotor neurodevelopment, hypo myelination and a drastic drop in brain aspartate (Asp) and N-acetylaspartate (NAA). Current evidence suggest that neurons are the main brain cell type expressing Aralar. However, paradoxically, glial functions such as myelin and Glutamine (Gln) synthesis are markedly impaired in AGC1 deficiency. Herein, we discuss the role of the AGC1/Aralar-MAS pathway in neuronal functions such as Asp and NAA synthesis, lactate use, respiration on glucose, glutamate (Glu) oxidation and other neurometabolic aspects. The possible mechanism triggering the pathophysiological findings in AGC1 deficiency, such as epilepsy and postnatal hypomyelination observed in humans and mice, are also included. Many of these mechanisms arise from findings in the aralar-KO mice model that extensively recapitulate the human disease including the astroglial failure to synthesize Gln and the dopamine (DA) mishandling in the nigrostriatal system. Epilepsy and DA mishandling are a direct consequence of the metabolic defect in neurons due to AGC1/Aralar deficiency. However, the deficits in myelin and Gln synthesis may be a consequence of neuronal affectation or a direct effect of AGC1/Aralar deficiency in glial cells. Further research is needed to clarify this question and delineate the transcellular metabolic fluxes that control brain functions. Finally, we discuss therapeutic approaches successfully used in AGC1-deficient patients and mice.
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Affiliation(s)
- Beatriz Pardo
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (E.H.-S.); (J.S.); (L.C.)
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid (UAM)-Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain;
- Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Eduardo Herrada-Soler
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (E.H.-S.); (J.S.); (L.C.)
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid (UAM)-Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain;
- Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Jorgina Satrústegui
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (E.H.-S.); (J.S.); (L.C.)
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid (UAM)-Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain;
- Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Laura Contreras
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (E.H.-S.); (J.S.); (L.C.)
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid (UAM)-Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain;
- Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Araceli del Arco
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid (UAM)-Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain;
- Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Centro Regional de Investigaciones Biomédicas, Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla La Mancha, 45071 Toledo, Spain
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22
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Dietz JV, Fox JL, Khalimonchuk O. Down the Iron Path: Mitochondrial Iron Homeostasis and Beyond. Cells 2021; 10:cells10092198. [PMID: 34571846 PMCID: PMC8468894 DOI: 10.3390/cells10092198] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 12/20/2022] Open
Abstract
Cellular iron homeostasis and mitochondrial iron homeostasis are interdependent. Mitochondria must import iron to form iron–sulfur clusters and heme, and to incorporate these cofactors along with iron ions into mitochondrial proteins that support essential functions, including cellular respiration. In turn, mitochondria supply the cell with heme and enable the biogenesis of cytosolic and nuclear proteins containing iron–sulfur clusters. Impairment in cellular or mitochondrial iron homeostasis is deleterious and can result in numerous human diseases. Due to its reactivity, iron is stored and trafficked through the body, intracellularly, and within mitochondria via carefully orchestrated processes. Here, we focus on describing the processes of and components involved in mitochondrial iron trafficking and storage, as well as mitochondrial iron–sulfur cluster biogenesis and heme biosynthesis. Recent findings and the most pressing topics for future research are highlighted.
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Affiliation(s)
- Jonathan V. Dietz
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA;
| | - Jennifer L. Fox
- Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC 29424, USA;
| | - Oleh Khalimonchuk
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA;
- Nebraska Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA
- Fred and Pamela Buffett Cancer Center, Omaha, NE 68198, USA
- Correspondence:
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23
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The Interaction of Hemin, a Porphyrin Derivative, with the Purified Rat Brain 2-Oxoglutarate Carrier. Biomolecules 2021; 11:biom11081175. [PMID: 34439841 PMCID: PMC8393474 DOI: 10.3390/biom11081175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/26/2022] Open
Abstract
The mitochondrial 2-oxoglutarate carrier (OGC), isolated and purified from rat brain mitochondria, was reconstituted into proteoliposomes to study the interaction with hemin, a porphyrin derivative, which may result from the breakdown of heme-containing proteins and plays a key role in several metabolic pathways. By kinetic approaches, on the basis of the single binding centre gated pore mechanism, we analyzed the effect of hemin on the transport rate of OGC in uptake and efflux experiments in proteoliposomes reconstituted in the presence of the substrate 2-oxoglutarate. Overall, our experimental data fit the hypothesis that hemin operates a competitive inhibition in the 0.5-10 µM concentration range. As a consequence of the OGC inhibition, the malate/aspartate shuttle might be impaired, causing an alteration of mitochondrial function. Hence, considering that the metabolism of porphyrins implies both cytoplasmic and mitochondrial processes, OGC may participate in the regulation of porphyrin derivatives availability and the related metabolic pathways that depend on them (such as oxidative phosphorylation and apoptosis). For the sake of clarity, a simplified model based on induced-fit molecular docking supported the in vitro transport assays findings that hemin was as good as 2-oxoglutarate to bind the carrier by engaging specific ionic hydrogen bond interactions with a number of key residues known for participating in the similarly located mitochondrial carrier substrate binding site.
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24
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Finlayson J, Barakati N, Langlais PR, Funk J, Zapata Bustos R, Coletta DK, Luo M, Willis WT, Mandarino LJ. Site-specific acetylation of adenine nucleotide translocase 1 at lysine 23 in human muscle. Anal Biochem 2021; 630:114319. [PMID: 34332952 DOI: 10.1016/j.ab.2021.114319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/14/2021] [Accepted: 07/28/2021] [Indexed: 12/01/2022]
Abstract
Evidence suggests acetylation of human adenine nucleotide translocase 1 (ANT1) at lysine 23 (Lys23) reduces binding of ADP. Lys23 contributes to the positive charge that facilitates this interaction. This study was undertaken to characterize ANT1 abundance and acetylation by a novel method using small amounts of human skeletal muscle biopsies. Lysates of whole muscle or mitochondria from the same tissue were prepared from needle biopsies of vastus lateralis muscle of healthy volunteers. Lysed proteins were resolved on gels, the section containing ANT1 (surrounding 30 Kd) was excised, digested with trypsin, spiked with labeled unacetylated and acetylated synthetic standard peptides and analyzed by mass spectrometry. Natural logarithm transformation of data linearized ion intensities over a 10-fold range of peptide mass. Coefficients of variation ranged from 7 to 30% for ANT1 abundance and Lys23 acetylation. In three volunteers, ANT1 content was 8.36 ± 0.33 nmol/g wet weight muscle and 0.64 ± 0.05 nmol/mg mitochondria, so mitochondrial content was 13.3 ± 2.4 mg mitochondria per gram muscle. Acetylation of Lys23 averaged 14.3 ± 4.2% and 4.87 ± 1.84% in whole muscle and mitochondria, respectively. This assay makes it possible to assess effects of acetylation on the function of ANT1 in human muscle.
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Affiliation(s)
- Jean Finlayson
- Division of Endocrinology, Department of Medicine, University of Arizona, Tucson, AZ, USA; Center for Disparities in Diabetes, Obesity, and Metabolism, University of Arizona Health Science, Tucson, AZ, USA
| | - Neusha Barakati
- Division of Endocrinology, Department of Medicine, University of Arizona, Tucson, AZ, USA; Center for Disparities in Diabetes, Obesity, and Metabolism, University of Arizona Health Science, Tucson, AZ, USA
| | - Paul R Langlais
- Division of Endocrinology, Department of Medicine, University of Arizona, Tucson, AZ, USA; Center for Disparities in Diabetes, Obesity, and Metabolism, University of Arizona Health Science, Tucson, AZ, USA
| | - Janet Funk
- Division of Endocrinology, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Rocio Zapata Bustos
- Division of Endocrinology, Department of Medicine, University of Arizona, Tucson, AZ, USA; Center for Disparities in Diabetes, Obesity, and Metabolism, University of Arizona Health Science, Tucson, AZ, USA
| | - Dawn K Coletta
- Division of Endocrinology, Department of Medicine, University of Arizona, Tucson, AZ, USA; Center for Disparities in Diabetes, Obesity, and Metabolism, University of Arizona Health Science, Tucson, AZ, USA; Department of Physiology, University of Arizona, Tucson, AZ, USA
| | - Moulun Luo
- Division of Endocrinology, Department of Medicine, University of Arizona, Tucson, AZ, USA; Center for Disparities in Diabetes, Obesity, and Metabolism, University of Arizona Health Science, Tucson, AZ, USA
| | - Wayne T Willis
- Division of Endocrinology, Department of Medicine, University of Arizona, Tucson, AZ, USA; Center for Disparities in Diabetes, Obesity, and Metabolism, University of Arizona Health Science, Tucson, AZ, USA
| | - Lawrence J Mandarino
- Division of Endocrinology, Department of Medicine, University of Arizona, Tucson, AZ, USA; Center for Disparities in Diabetes, Obesity, and Metabolism, University of Arizona Health Science, Tucson, AZ, USA.
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25
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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: 63] [Impact Index Per Article: 21.0] [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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26
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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: 14] [Impact Index Per Article: 4.7] [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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27
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Pasquadibisceglie A, Polticelli F. Computational studies of the mitochondrial carrier family SLC25. Present status and future perspectives. BIO-ALGORITHMS AND MED-SYSTEMS 2021. [DOI: 10.1515/bams-2021-0018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
The members of the mitochondrial carrier family, also known as solute carrier family 25 (SLC25), are transmembrane proteins involved in the translocation of a plethora of small molecules between the mitochondrial intermembrane space and the matrix. These transporters are characterized by three homologous domains structure and a transport mechanism that involves the transition between different conformations. Mutations in regions critical for these transporters’ function often cause several diseases, given the crucial role of these proteins in the mitochondrial homeostasis. Experimental studies can be problematic in the case of membrane proteins, in particular concerning the characterization of the structure–function relationships. For this reason, computational methods are often applied in order to develop new hypotheses or to support/explain experimental evidence. Here the computational analyses carried out on the SLC25 members are reviewed, describing the main techniques used and the outcome in terms of improved knowledge of the transport mechanism. Potential future applications on this protein family of more recent and advanced in silico methods are also suggested.
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Affiliation(s)
| | - Fabio Polticelli
- Department of Sciences , Roma Tre University , Rome , Italy
- National Institute of Nuclear Physics, Roma Tre Section , Rome , Italy
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28
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Willis W, Willis E, Kuzmiak-Glancy S, Kras K, Hudgens J, Barakati N, Stern J, Mandarino L. Oxidative phosphorylation K 0.5ADP in vitro depends on substrate oxidative capacity: Insights from a luciferase-based assay to evaluate ADP kinetic parameters. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148430. [PMID: 33887230 DOI: 10.1016/j.bbabio.2021.148430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/30/2021] [Accepted: 04/07/2021] [Indexed: 12/21/2022]
Abstract
The K0.5ADP of oxidative phosphorylation (OxPhos) identifies the cytosolic ADP concentration which elicits one-half the maximum OxPhos rate. This kinetic parameter is commonly measured to assess mitochondrial metabolic control sensitivity. Here we describe a luciferase-based assay to evaluate the ADP kinetic parameters of mitochondrial ATP production from OxPhos, adenylate kinase (AK), and creatine kinase (CK). The high sensitivity, reproducibility, and throughput of the microplate-based assay enabled a comprehensive kinetic assessment of all three pathways in mitochondria isolated from mouse liver, kidney, heart, and skeletal muscle. Carboxyatractyloside titrations were also performed with the assay to estimate the flux control strength of the adenine nucleotide translocase (ANT) over OxPhos in human skeletal muscle mitochondria. ANT flux control coefficients were 0.91 ± 0.07, 0.83 ± 0.06, and 0.51 ± 0.07 at ADP concentrations of 6.25, 12.5, and 25 μM, respectively, an [ADP] range which spanned the K0.5ADP. The oxidative capacity of substrate combinations added to drive OxPhos was found to dramatically influence ADP kinetics in mitochondria from several tissues. In mouse skeletal muscle ten different substrate combinations elicited a 7-fold range of OxPhos Vmax, which correlated positively (R2 = 0.963) with K0.5ADP values ranging from 2.3 ± 0.2 μM to 11.9 ± 0.6 μM. We propose that substrate-enhanced capacity to generate the protonmotive force increases the OxPhos K0.5ADP because flux control at ANT increases, thus K0.5ADP rises toward the dissociation constant, KdADP, of ADP-ANT binding. The findings are discussed in the context of top-down metabolic control analysis.
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Affiliation(s)
- Wayne Willis
- Department of Medicine, Division of Endocrinology, University of Arizona, Tucson, AZ, United States; Center for Disparities in Diabetes, Obesity, and Metabolism, University of Arizona, Tucson, AZ, United States.
| | - Elizabeth Willis
- College of Medicine, University of Kentucky, Lexington, KY, United States
| | - Sarah Kuzmiak-Glancy
- Department of Kinesiology, University of Maryland, College Park, MD, United States
| | - Katon Kras
- Department of Medicine, Division of Endocrinology, University of Arizona, Tucson, AZ, United States
| | - Jamie Hudgens
- College of Pharmacy, Midwestern University, Glendale, AZ, United States
| | - Neusha Barakati
- Department of Medicine, Division of Endocrinology, University of Arizona, Tucson, AZ, United States
| | - Jennifer Stern
- Department of Medicine, Division of Endocrinology, University of Arizona, Tucson, AZ, United States; Center for Disparities in Diabetes, Obesity, and Metabolism, University of Arizona, Tucson, AZ, United States
| | - Lawrence Mandarino
- Department of Medicine, Division of Endocrinology, University of Arizona, Tucson, AZ, United States; Center for Disparities in Diabetes, Obesity, and Metabolism, University of Arizona, Tucson, AZ, United States
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29
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Tonazzi A, Giangregorio N, Console L, Palmieri F, Indiveri C. The Mitochondrial Carnitine Acyl-carnitine Carrier (SLC25A20): Molecular Mechanisms of Transport, Role in Redox Sensing and Interaction with Drugs. Biomolecules 2021; 11:biom11040521. [PMID: 33807231 PMCID: PMC8066319 DOI: 10.3390/biom11040521] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 12/22/2022] Open
Abstract
The SLC25A20 transporter, also known as carnitine acyl-carnitine carrier (CAC), catalyzes the transport of short, medium and long carbon chain acyl-carnitines across the mitochondrial inner membrane in exchange for carnitine. The 30-year story of the protein responsible for this function started with its purification from rat liver mitochondria. Even though its 3D structure is not yet available, CAC is one of the most deeply characterized transport proteins of the inner mitochondrial membrane. Other than functional, kinetic and mechanistic data, post-translational modifications regulating the transport activity of CAC have been revealed. CAC interactions with drugs or xenobiotics relevant to human health and toxicology and the response of the carrier function to dietary compounds have been discovered. Exploiting combined approaches of site-directed mutagenesis with chemical targeting and bioinformatics, a large set of data on structure/function relationships have been obtained, giving novel information on the molecular mechanism of the transport catalyzed by this protein.
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Affiliation(s)
- Annamaria Tonazzi
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Via Orabona 4, 70126 Bari, Italy; (A.T.); (N.G.)
| | - Nicola Giangregorio
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Via Orabona 4, 70126 Bari, Italy; (A.T.); (N.G.)
| | - Lara Console
- Unit of Biochemistry and Molecular Biotechnology, Department DiBEST (Biologia, Ecologia, Scienze della Terra), University of Calabria, Via P. Bucci 4C, 87036 Arcavacata di Rende, Italy;
| | - Ferdinando Palmieri
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Via Orabona 4, 70126 Bari, Italy; (A.T.); (N.G.)
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70125 Bari, Italy
- Correspondence: (F.P.); (C.I.); Tel.: +39-080-544-3323 (F.P.); Tel.: +39-0984-492939 (C.I.)
| | - Cesare Indiveri
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Via Orabona 4, 70126 Bari, Italy; (A.T.); (N.G.)
- Unit of Biochemistry and Molecular Biotechnology, Department DiBEST (Biologia, Ecologia, Scienze della Terra), University of Calabria, Via P. Bucci 4C, 87036 Arcavacata di Rende, Italy;
- Correspondence: (F.P.); (C.I.); Tel.: +39-080-544-3323 (F.P.); Tel.: +39-0984-492939 (C.I.)
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30
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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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31
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Tragni V, Cotugno P, De Grassi A, Massari F, Di Ronzo F, Aresta AM, Zambonin C, Sanzani SM, Ippolito A, Pierri CL. Targeting mitochondrial metabolite transporters in Penicillium expansum for reducing patulin production. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 158:158-181. [PMID: 33250320 DOI: 10.1016/j.plaphy.2020.07.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/30/2020] [Accepted: 07/13/2020] [Indexed: 06/12/2023]
Abstract
There is an increasing need of alternative treatments to control fungal infection and consequent mycotoxin accumulation in harvested fruits and vegetables. Indeed, only few biological targets of antifungal agents have been characterized and can be used for limiting fungal spread from decayed fruits/vegetables to surrounding healthy ones during storage. On this concern, a promising target of new antifungal treatments may be represented by mitochondrial proteins due to some species-specific functions played by mitochondria in fungal morphogenesis, drug resistance and virulence. One of the most studied mycotoxins is patulin produced by several species of Penicillium and Aspergillus genera. Patulin is toxic to many biological systems including bacteria, higher plants and animalia. Although precise biochemical mechanisms of patulin toxicity in humans are not completely clarified, its high presence in fresh and processed apple fruits and other apple-based products makes necessary developing a strategy for limiting its presence/accumulation. Patulin biosynthetic pathway consists of an enzymatic cascade, whose first step is represented by the synthesis of 6-methylsalicylic acid, obtained from the condensation of one acetyl-CoA molecule with three malonyl-CoA molecules. The most abundant acetyl-CoA precursor is represented by citrate produced by mitochondria. In the present investigation we report about the possibility to control patulin production through the inhibition of mitochondrial/peroxisome transporters involved in the export of acetyl-CoA precursors from mitochondria and/or peroxisomes, with specific reference to the predicted P. expansum mitochondrial Ctp1p, DTC, Sfc1p, Oac1p and peroxisomal PXN carriers.
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Affiliation(s)
- Vincenzo Tragni
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126, Bari, Italy
| | - Pietro Cotugno
- Biology Department, University of Bari Aldo Moro, Via Amendola 165/A, 70126, Bari, Italy
| | - Anna De Grassi
- Laboratory of Biochemistry, Molecular and Structural Biology, Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125, Bari, Italy; BROWSer S.r.l. (https://browser-bioinf.com/) c/o, Department of Biosciences, Biotechnologies, Biopharmaceutics, University "Aldo Moro" of Bari, Via E. Orabona, 4, 70126, Bari, Italy
| | - Federica Massari
- Biology Department, University of Bari Aldo Moro, Via Amendola 165/A, 70126, Bari, Italy
| | - Francesco Di Ronzo
- Laboratory of Biochemistry, Molecular and Structural Biology, Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125, Bari, Italy
| | - Antonella Maria Aresta
- Chemistry Department, University of Bari Aldo Moro, Via Amendola 165/A, 70126, Bari, Italy
| | - Carlo Zambonin
- Chemistry Department, University of Bari Aldo Moro, Via Amendola 165/A, 70126, Bari, Italy
| | | | - Antonio Ippolito
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126, Bari, Italy.
| | - Ciro Leonardo Pierri
- Laboratory of Biochemistry, Molecular and Structural Biology, Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125, Bari, Italy; BROWSer S.r.l. (https://browser-bioinf.com/) c/o, Department of Biosciences, Biotechnologies, Biopharmaceutics, University "Aldo Moro" of Bari, Via E. Orabona, 4, 70126, Bari, Italy.
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32
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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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33
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Barreto P, Couñago RM, Arruda P. Mitochondrial uncoupling protein-dependent signaling in plant bioenergetics and stress response. Mitochondrion 2020; 53:109-120. [DOI: 10.1016/j.mito.2020.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/06/2020] [Accepted: 05/14/2020] [Indexed: 12/15/2022]
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34
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Jezierska S, Claus S, Van Bogaert INA. Identification and importance of mitochondrial citrate carriers and ATP citrate lyase for glycolipid production in Starmerella bombicola. Appl Microbiol Biotechnol 2020; 104:6235-6248. [PMID: 32474798 DOI: 10.1007/s00253-020-10702-z] [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] [Received: 03/16/2020] [Revised: 05/19/2020] [Accepted: 05/24/2020] [Indexed: 09/16/2023]
Abstract
Starmerella bombicola is a non-conventional yeast commercially used as a microbial cell factory for sophorolipid production. Sophorolipids are glycolipid biosurfactants composed of a glucose disaccharide sophorose and a fatty acid. In de novo sophorolipid synthesis, the fatty acid moiety is derived from the fatty acid synthesis (FAS) complex; therefore, the yeast's lipid metabolism plays a crucial role in sophorolipid biosynthesis. As a fatty acid precursor, citric acid is a key primary metabolite that connects carbohydrate and lipid metabolism, and in S. bombicola, it also has a regulatory effect on sophorolipid composition and productivity. We aimed to identify the mitochondrial transporters involved in citrate shuttling and the ATP citrate lyase (Acl), the enzyme that converts citric acid into acetyl-CoA. Subsequently, we studied their role in the citric acid shuttle and glycolipid synthesis and the potential of citrate metabolism as a genetic manipulation target for increased glycolipid synthesis. Bioinformatics analyses predicted 32 mitochondrial carriers of which two were identified as citrate transporters, named SbCtp1 and SbYhm2. Deletion of these mitochondrial carriers led to a lesser sophorolipid yield and a shift in the lactonic/acidic sophorolipid ratio. However, only the knockout of SbYhm2 caused a decrease of citric and an increase of malic acid extracellular concentrations. Additionally, deletion of SbAcl1 had a negative effect on S. bombicola's specific growth rate and sophorolipid synthesis and contributed to extra- and intracellular citric acid accumulation. Unexpectedly, SbAcl1 overexpression also decreased glycolipid production.Key Points• Starmerella bombicola is an industrially relevant microbial cell factory for biosurfactant production.• There are 32 predicted mitochondrial carriers in S. bombicola.• Citrate mitochondrial carriers SbYhm2 and SbCtp1 are essential for glycolipid synthesis in S. bombicola.• Deletion of SbAcl1 negatively affects growth and sophorolipid production in S. bombicola. Graphical abstract.
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Affiliation(s)
- Sylwia Jezierska
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Silke Claus
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Inge N A Van Bogaert
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
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Gao F, Voncken F, Colasante C. The mitochondrial phosphate carrier TbMCP11 is essential for mitochondrial function in the procyclic form of Trypanosoma brucei. Mol Biochem Parasitol 2020; 237:111275. [PMID: 32353560 DOI: 10.1016/j.molbiopara.2020.111275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/02/2020] [Accepted: 03/24/2020] [Indexed: 01/24/2023]
Abstract
Conserved amongst all eukaryotes is a family of mitochondrial carrier proteins (SLC25A) responsible for the import of various solutes across the inner mitochondrial membrane. We previously reported that the human parasite Trypanosoma brucei possesses 26 SLC25A proteins (TbMCPs) amongst which two, TbMCP11 and TbMCP8, were predicted to function as phosphate importers. The transport of inorganic phosphate into the mitochondrion is a prerequisite to drive ATP synthesis by substrate level and oxidative phosphorylation and thus crucial for cell viability. In this paper we describe the functional characterization of TbMCP11. In procyclic form T. brucei, the RNAi of TbMCP11 blocked ATP synthesis on mitochondrial substrates, caused a drop of the mitochondrial oxygen consumption and drastically reduced cell viability. The functional complementation in yeast and mitochondrial swelling experiments suggested a role for TbMCP11 as inorganic phosphate carrier. Interestingly, procyclic form T. brucei cells in which TbMCP11 was depleted displayed an inability to either replicate or divide the kinetoplast DNA, which resulted in a severe cytokinesis defect.
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Affiliation(s)
- Fei Gao
- Department of Neuroscience, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0AH, United Kingdom
| | - Frank Voncken
- Department of Biomedical Sciences, School of Life Sciences, University of Hull, Cottingham Road, Hull, HU6 7RX, United Kingdom
| | - Claudia Colasante
- Institute for Anatomy and Cell Biology, Division of Medical Cell Biology, Aulweg 123, University of Giessen, 35392, Giessen, Germany.
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Genetic compensation in a stable slc25a46 mutant zebrafish: A case for using F0 CRISPR mutagenesis to study phenotypes caused by inherited disease. PLoS One 2020; 15:e0230566. [PMID: 32208444 PMCID: PMC7092968 DOI: 10.1371/journal.pone.0230566] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 03/03/2020] [Indexed: 12/22/2022] Open
Abstract
A phenomenon of genetic compensation is commonly observed when an organism with a disease-bearing mutation shows incomplete penetrance of the disease phenotype. Such incomplete phenotypic penetrance, or genetic compensation, is more commonly found in stable knockout models, rather than transient knockdown models. As such, these incidents present a challenge for the disease modeling field, although a deeper understanding of genetic compensation may also hold the key for novel therapeutic interventions. In our study we created a knockout model of slc25a46 gene, which is a recently discovered important player in mitochondrial dynamics, and deleterious mutations in which are known to cause peripheral neuropathy, optic atrophy and cerebellar ataxia. We report a case of genetic compensation in a stable slc25a46 homozygous zebrafish mutant (hereafter referred as “mutant”), in contrast to a penetrant disease phenotype in the first generation (F0) slc25a46 mosaic mutant (hereafter referred as “crispant”), generated with CRISPR/Cas-9 technology. We show that the crispant phenotype is specific and rescuable. By performing mRNA sequencing, we define significant changes in slc25a46 mutant’s gene expression profile, which are largely absent in crispants. We find that among the most significantly altered mRNAs, anxa6 gene stands out as a functionally relevant player in mitochondrial dynamics. We also find that our genetic compensation case does not arise from mechanisms driven by mutant mRNA decay. Our study contributes to the growing evidence of the genetic compensation phenomenon and presents novel insights about Slc25a46 function. Furthermore, our study provides the evidence for the efficiency of F0 CRISPR screens for disease candidate genes, which may be used to advance the field of functional genetics.
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The SLC25 Mitochondrial Carrier Family: Structure and Mechanism. Trends Biochem Sci 2019; 45:244-258. [PMID: 31787485 PMCID: PMC7611774 DOI: 10.1016/j.tibs.2019.11.001] [Citation(s) in RCA: 167] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/30/2019] [Accepted: 11/01/2019] [Indexed: 12/27/2022]
Abstract
Members of the mitochondrial carrier family (SLC25) provide the transport steps for amino acids, carboxylic acids, fatty acids, cofactors, inorganic ions, and nucleotides across the mitochondrial inner membrane and are crucial for many cellular processes. Here, we use new insights into the transport mechanism of the mitochondrial ADP/ATP carrier to examine the structure and function of other mitochondrial carriers. They all have a single substrate-binding site and two gates, which are present on either side of the membrane and involve salt-bridge networks. Transport is likely to occur by a common mechanism, in which the coordinated movement of six structural elements leads to the alternating opening and closing of the matrix or cytoplasmic side of the carriers.
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Zheng F, Colasante C, Voncken F. Characterisation of a mitochondrial iron transporter of the pathogen Trypanosoma brucei. Mol Biochem Parasitol 2019; 233:111221. [DOI: 10.1016/j.molbiopara.2019.111221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 09/10/2019] [Accepted: 09/13/2019] [Indexed: 12/25/2022]
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39
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Dynamics and interactions of AAC3 in DPC are not functionally relevant. Nat Struct Mol Biol 2019; 25:745-747. [PMID: 30177758 DOI: 10.1038/s41594-018-0127-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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40
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Ruprecht JJ, Kunji ER. Structural changes in the transport cycle of the mitochondrial ADP/ATP carrier. Curr Opin Struct Biol 2019; 57:135-144. [PMID: 31039524 PMCID: PMC6700394 DOI: 10.1016/j.sbi.2019.03.029] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 03/15/2019] [Accepted: 03/20/2019] [Indexed: 11/27/2022]
Abstract
The mitochondrial ADP/ATP carrier, also called adenine nucleotide translocase, accomplishes one of the most important transport activities in eukaryotic cells, importing ADP into the mitochondrial matrix for ATP synthesis, and exporting ATP to fuel cellular activities. In the transport cycle, the carrier changes between a cytoplasmic and matrix state, in which the central substrate binding site is alternately accessible to these compartments. A structure of a cytoplasmic state was known, but recently, a structure of a matrix-state in complex with bongkrekic acid was solved. Comparison of the two states explains the function of highly conserved sequence features and reveals that the transport mechanism is unique, involving the coordinated movement of six dynamic elements around a central translocation pathway.
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Affiliation(s)
- Jonathan J Ruprecht
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK.
| | - Edmund Rs Kunji
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK.
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41
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Giangregorio N, Tonazzi A, Console L, Pistillo M, Scalera V, Indiveri C. Tryptophan 224 of the rat mitochondrial carnitine/acylcarnitine carrier is crucial for the antiport mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:708-716. [PMID: 31340138 DOI: 10.1016/j.bbabio.2019.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 07/06/2019] [Accepted: 07/18/2019] [Indexed: 01/14/2023]
Abstract
The mitochondrial carnitine/acylcarnitine carrier (CACT) catalyzes an antiport of carnitine and acylcarnitines and also a uniport reaction with a rate of about one tenth with respect to the antiport rate. The antiport process results from the coupling of the two uniport reactions in opposite directions. In this mechanism, the transition of the carrier from the outward open conformation to the inward open one (or vice versa) is much faster for the carrier-substrate complex than for the unbound carrier. To investigate the molecular determinants that couple the binding of the substrate with the conformational transitions, site directed mutagenesis has been employed. The antiport or the uniport reaction was followed as [3H]carnitine uptake in or efflux from proteoliposomes reconstituted with the WT or Trp mutants of the rat CACT. Substitution of each the three Trp residues led to different results. Nearly no variations were observed upon substitution of W192 and/or W296 with Ala. While, substantial alteration of the transport function was observed in the mutants W224A, W224Y and W224F. Mutation of W224 led to the loss of the antiport function while the uniport function was unaltered. In these mutants impairment of the substrate affinity on the external side was also observed. The data highlights that W224 is involved in the coupling of the substrate binding with the matrix gate opening. The experimental data are in line with predictions by homology modeling of the CACT in its cytosolic (c-state) or matrix (m-state) opened conformations.
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Affiliation(s)
- Nicola Giangregorio
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, via Amendola 165/A, 70126 Bari, Italy
| | - Annamaria Tonazzi
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, via Amendola 165/A, 70126 Bari, Italy
| | - Lara Console
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, Via P. Bucci 4C, 87036 Arcavacata di Rende, Italy
| | - Mariella Pistillo
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, via Orabona 4, 70126 Bari, Italy
| | - Vito Scalera
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, via Orabona 4, 70126 Bari, Italy
| | - Cesare Indiveri
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, Via P. Bucci 4C, 87036 Arcavacata di Rende, Italy.
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42
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Vigani G, Solti ÏDM, Thomine SB, Philippar K. Essential and Detrimental - an Update on Intracellular Iron Trafficking and Homeostasis. PLANT & CELL PHYSIOLOGY 2019; 60:1420-1439. [PMID: 31093670 DOI: 10.1093/pcp/pcz091] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/06/2019] [Indexed: 05/22/2023]
Abstract
Chloroplasts, mitochondria and vacuoles represent characteristic organelles of the plant cell, with a predominant function in cellular metabolism. Chloroplasts are the site of photosynthesis and therefore basic and essential for photoautotrophic growth of plants. Mitochondria produce energy during respiration and vacuoles act as internal waste and storage compartments. Moreover, chloroplasts and mitochondria are sites for the biosynthesis of various compounds of primary and secondary metabolism. For photosynthesis and energy generation, the internal membranes of chloroplasts and mitochondria are equipped with electron transport chains. To perform proper electron transfer and several biosynthetic functions, both organelles contain transition metals and here iron is by far the most abundant. Although iron is thus essential for plant growth and development, it becomes toxic when present in excess and/or in its free, ionic form. The harmful effect of the latter is caused by the generation of oxidative stress. As a consequence, iron transport and homeostasis have to be tightly controlled during plant growth and development. In addition to the corresponding transport and homeostasis proteins, the vacuole plays an important role as an intracellular iron storage and release compartment at certain developmental stages. In this review, we will summarize current knowledge on iron transport and homeostasis in chloroplasts, mitochondria and vacuoles. In addition, we aim to integrate the physiological impact of intracellular iron homeostasis on cellular and developmental processes.
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Affiliation(s)
- Gianpiero Vigani
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, via Quarello 15/A, Turin I, Italy
| | - Ï Dï M Solti
- Department of Plant Physiology and Molecular Plant Biology, E�tv�s Lor�nd University, Budapest H, Hungary
| | - Sï Bastien Thomine
- Institut de Biologie Int�grative de la Cellule, CNRS, Avenue de la Terrasse, Gif-sur-Yvette, France
| | - Katrin Philippar
- Plant Biology, Center for Human- and Molecular Biology (ZHMB), Saarland University, Campus A2.4, Saarbr�cken D, Germany
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43
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Yi Q, Li Q, Yao S, Chen Y, Guan MX, Cang X. Molecular dynamics simulations on apo ADP/ATP carrier shed new lights on the featured motif of the mitochondrial carriers. Mitochondrion 2019; 47:94-102. [PMID: 31129042 DOI: 10.1016/j.mito.2019.05.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 04/30/2019] [Accepted: 05/20/2019] [Indexed: 02/04/2023]
Abstract
The ADP/ATP carrier (AAC) is a transporter responsible for the equal molar exchange of cytosolic ADP and ATP synthesized within mitochondrial matrix across the mitochondrial membrane. Its primary structure consists of three homologous repeats, and each repeat contains a conserved motif that is shared by all members of the mitochondrial carrier family (MCF). Although these MCF motif residues cluster together in the crystal structure of AAC, detailed analyses on the interactions among the motif residues are still limited. In the present study, all-atom molecular dynamics (MD) simulations of up to 10 μs have been carried out on AAC, and interactions and structural dynamics of the MCF motif residues have been specifically investigated. Our simulations have revealed: i) a very asymmetrical electrostatic network at the bottom of the pocket of apo AAC, ii) the asymmetrical interactions between the Pro kink region and the [YWF][KR] G motif in three repeats, iii) the role of the conserved Arg residues in stabilizing the C-ends of the odd-numbered helices, iv) the structural change of the [YWF][KR] G motif and its potential involvement in substrate translocation process. Our results highlight the asymmetry of the MCF residues in the three repeats, which might contribute to the ability of the carriers to transport the asymmetrical substrates. Our observations provide microscopic basis for further research on the translocation mechanism of mitochondrial carriers.
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Affiliation(s)
- Qiuzi Yi
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, China; Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Qiang Li
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, China; Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Shihao Yao
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, China; Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Ye Chen
- School of Information and Electric Engineering, China University of Mining and Technology, Xuzhou, Jiangsu 221008, China
| | - Min-Xin Guan
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, China; Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Xiaohui Cang
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, China; Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.
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44
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Ruprecht JJ, King MS, Zögg T, Aleksandrova AA, Pardon E, Crichton PG, Steyaert J, Kunji ERS. The Molecular Mechanism of Transport by the Mitochondrial ADP/ATP Carrier. Cell 2019; 176:435-447.e15. [PMID: 30611538 PMCID: PMC6349463 DOI: 10.1016/j.cell.2018.11.025] [Citation(s) in RCA: 176] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 09/25/2018] [Accepted: 11/16/2018] [Indexed: 11/30/2022]
Abstract
Mitochondrial ADP/ATP carriers transport ADP into the mitochondrial matrix for ATP synthesis, and ATP out to fuel the cell, by cycling between cytoplasmic-open and matrix-open states. The structure of the cytoplasmic-open state is known, but it has proved difficult to understand the transport mechanism in the absence of a structure in the matrix-open state. Here, we describe the structure of the matrix-open state locked by bongkrekic acid bound in the ADP/ATP-binding site at the bottom of the central cavity. The cytoplasmic side of the carrier is closed by conserved hydrophobic residues, and a salt bridge network, braced by tyrosines. Glycine and small amino acid residues allow close-packing of helices on the matrix side. Uniquely, the carrier switches between states by rotation of its three domains about a fulcrum provided by the substrate-binding site. Because these features are highly conserved, this mechanism is likely to apply to the whole mitochondrial carrier family. Video Abstract
Structure of the matrix-open state of the mitochondrial ADP/ATP carrier solved The inhibitor bongkrekic acid locks the state by occupying the substrate-binding site Conformational changes during transport are highly dynamic, using six mobile elements Roles of all conserved sequence features in mitochondrial carriers are now explained
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Affiliation(s)
- Jonathan J Ruprecht
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK.
| | - Martin S King
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Thomas Zögg
- VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Antoniya A Aleksandrova
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA
| | - Els Pardon
- VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Paul G Crichton
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Jan Steyaert
- VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Edmund R S Kunji
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK.
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45
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Jain A, Dashner ZS, Connolly EL. Mitochondrial Iron Transporters (MIT1 and MIT2) Are Essential for Iron Homeostasis and Embryogenesis in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2019; 10:1449. [PMID: 31850005 PMCID: PMC6889801 DOI: 10.3389/fpls.2019.01449] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 10/17/2019] [Indexed: 05/08/2023]
Abstract
Iron (Fe) is an essential nutrient for virtually all organisms, where it functions in critical electron transfer processes, like those involved in respiration. Photosynthetic organisms have special requirements for Fe due to its importance in photosynthesis. While the importance of Fe for mitochondria- and chloroplast-localized processes is clear, our understanding of the molecular mechanisms that underlie the trafficking of Fe to these compartments is not complete. Here, we describe the Arabidopsis mitochondrial iron transporters, MIT1 and MIT2, that belong to the mitochondrial carrier family (MCF) of transport proteins. MIT1 and MIT2 display considerable homology with known mitochondrial Fe transporters of other organisms. Expression of MIT1 or MIT2 rescues the phenotype of the yeast mrs3mrs4 mutant, which is defective in mitochondrial iron transport. Although the Arabidopsis mit1 and mit2 single mutants do not show any significant visible phenotypes, the double mutant mit1mit2 displays embryo lethality. Analysis of a mit1 -- /mit2 + - line revealed that MIT1 and MIT2 are essential for iron acquisition by mitochondria and proper mitochondrial function. In addition, loss of MIT function results in mislocalization of Fe, which in turn causes upregulation of the root high affinity Fe uptake pathway. Thus, MIT1 and MIT2 are required for the maintenance of both mitochondrial and whole plant Fe homeostasis, which, in turn, is important for the proper growth and development of the plant.
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Affiliation(s)
- Anshika Jain
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
| | - Zachary S. Dashner
- Department of Plant Science, The Pennsylvania State University, University Park, PA, United States
| | - Erin L. Connolly
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
- Department of Plant Science, The Pennsylvania State University, University Park, PA, United States
- *Correspondence: Erin L. Connolly,
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46
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Harborne SPD, Kunji ERS. Calcium-regulated mitochondrial ATP-Mg/P i carriers evolved from a fusion of an EF-hand regulatory domain with a mitochondrial ADP/ATP carrier-like domain. IUBMB Life 2018; 70:1222-1232. [PMID: 30281880 PMCID: PMC6283063 DOI: 10.1002/iub.1931] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/19/2018] [Accepted: 07/19/2018] [Indexed: 02/02/2023]
Abstract
The mitochondrial ATP-Mg/Pi carrier is responsible for the calcium-dependent regulation of adenosine nucleotide concentrations in the mitochondrial matrix, which allows mitochondria to respond to changing energy requirements of the cell. The carrier is expressed in mitochondria of fungi, plants and animals and belongs to the family of mitochondrial carriers. The carrier is unusual as it consists of three separate domains: (i) an N-terminal regulatory domain with four calcium-binding EF-hands similar to calmodulin, (ii) a loop domain containing an amphipathic α-helix and (iii) a mitochondrial carrier domain related to the mitochondrial ADP/ATP carrier. This striking example of three domains coming together from different origins to provide new functions represents an interesting quirk of evolution. In this review, we outline how the carrier was identified and how its physiological role was established with a focus on human isoforms. We exploit the sequence and structural information of the domains to explore the similarities and differences to their closest counterparts; mitochondrial ADP/ATP carriers and proteins with four EF-hands. We discuss how their combined function has led to a mechanism for calcium-regulated transport of adenosine nucleotides. Finally, we compare the ATP-Mg/Pi carrier with the mitochondrial aspartate/glutamate carrier, the only other mitochondrial carrier regulated by calcium, and we will argue that they have arisen by convergent rather than divergent evolution. © 2018 The Authors. IUBMB Life published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 70(12):1222-1232, 2018.
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Affiliation(s)
- Steven P. D. Harborne
- School of Biomedical Sciences and Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Edmund R. S. Kunji
- Medical Research Council Mitochondrial Biology UnitUniversity of CambridgeCambridgeCB2 0XYUK
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47
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King MS, Crichton PG, Ruprecht JJ, Kunji ERS. Concerns with yeast mitochondrial ADP/ATP carrier's integrity in DPC. Nat Struct Mol Biol 2018; 25:747-749. [PMID: 30177757 DOI: 10.1038/s41594-018-0125-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Martin S King
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Paul G Crichton
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jonathan J Ruprecht
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Edmund R S Kunji
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
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48
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Chipot C, Dehez F, Schnell JR, Zitzmann N, Pebay-Peyroula E, Catoire LJ, Miroux B, Kunji ERS, Veglia G, Cross TA, Schanda P. Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies. Chem Rev 2018; 118:3559-3607. [PMID: 29488756 PMCID: PMC5896743 DOI: 10.1021/acs.chemrev.7b00570] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Indexed: 12/25/2022]
Abstract
Membrane proteins perform a host of vital cellular functions. Deciphering the molecular mechanisms whereby they fulfill these functions requires detailed biophysical and structural investigations. Detergents have proven pivotal to extract the protein from its native surroundings. Yet, they provide a milieu that departs significantly from that of the biological membrane, to the extent that the structure, the dynamics, and the interactions of membrane proteins in detergents may considerably vary, as compared to the native environment. Understanding the impact of detergents on membrane proteins is, therefore, crucial to assess the biological relevance of results obtained in detergents. Here, we review the strengths and weaknesses of alkyl phosphocholines (or foscholines), the most widely used detergent in solution-NMR studies of membrane proteins. While this class of detergents is often successful for membrane protein solubilization, a growing list of examples points to destabilizing and denaturing properties, in particular for α-helical membrane proteins. Our comprehensive analysis stresses the importance of stringent controls when working with this class of detergents and when analyzing the structure and dynamics of membrane proteins in alkyl phosphocholine detergents.
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Affiliation(s)
- Christophe Chipot
- SRSMC, UMR 7019 Université de Lorraine CNRS, Vandoeuvre-les-Nancy F-54500, France
- Laboratoire
International Associé CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-les-Nancy F-54506, France
- Department
of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - François Dehez
- SRSMC, UMR 7019 Université de Lorraine CNRS, Vandoeuvre-les-Nancy F-54500, France
- Laboratoire
International Associé CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-les-Nancy F-54506, France
| | - Jason R. Schnell
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Nicole Zitzmann
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | | | - Laurent J. Catoire
- Laboratory
of Biology and Physico-Chemistry of Membrane Proteins, Institut de Biologie Physico-Chimique (IBPC), UMR
7099 CNRS, Paris 75005, France
- University
Paris Diderot, Paris 75005, France
- PSL
Research University, Paris 75005, France
| | - Bruno Miroux
- Laboratory
of Biology and Physico-Chemistry of Membrane Proteins, Institut de Biologie Physico-Chimique (IBPC), UMR
7099 CNRS, Paris 75005, France
- University
Paris Diderot, Paris 75005, France
- PSL
Research University, Paris 75005, France
| | - Edmund R. S. Kunji
- Medical
Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Gianluigi Veglia
- Department
of Biochemistry, Molecular Biology, and Biophysics, and Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Timothy A. Cross
- National
High Magnetic Field Laboratory, Florida
State University, Tallahassee, Florida 32310, United States
| | - Paul Schanda
- Université
Grenoble Alpes, CEA, CNRS, IBS, Grenoble F-38000, France
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49
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Colasante C, Zheng F, Kemp C, Voncken F. A plant-like mitochondrial carrier family protein facilitates mitochondrial transport of di- and tricarboxylates in Trypanosoma brucei. Mol Biochem Parasitol 2018; 221:36-51. [PMID: 29581011 DOI: 10.1016/j.molbiopara.2018.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 02/22/2018] [Accepted: 03/21/2018] [Indexed: 12/31/2022]
Abstract
The procyclic form of the human parasite Trypanosoma brucei harbors one single, large mitochondrion containing all tricarboxylic acid (TCA) cycle enzymes and respiratory chain complexes present also in higher eukaryotes. Metabolite exchange among subcellular compartments such as the cytoplasm, the mitochondrion, and the peroxisomes is crucial for redox homeostasis and for metabolic pathways whose enzymes are dispersed among different organelles. In higher eukaryotes, mitochondrial carrier family (MCF) proteins transport TCA-cycle intermediates across the inner mitochondrial membrane. Previously, we identified several MCF members that are essential for T. brucei survival. Among these, only one MCF protein, TbMCP12, potentially could transport dicarboxylates and tricarboxylates. Here, we conducted phylogenetic and sequence analyses and functionally characterised TbMCP12 in vivo. Our results suggested that similarly to its homologues in plants, TbMCP12 transports both dicarboxylates and tricarboxylates across the mitochondrial inner membrane. Deleting this carrier in T. brucei was not lethal, while its overexpression was deleterious. Our results suggest that the intracellular abundance of TbMCP12 is an important regulatory element for the NADPH balance and mitochondrial ATP-production.
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Affiliation(s)
- Claudia Colasante
- Institute for Anatomy and Cell Biology, Division of Medical Cell Biology, Aulweg 123, University of Giessen, 35392, Giessen, Germany.
| | - Fuli Zheng
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, 1 Xue Yuan Road, Fu Zhou, Fujian, PR China
| | - Cordula Kemp
- Department of Biomedical Sciences, School of Life Sciences, University of Hull, Cottingham Road, Hull, HU6 7RX, United Kingdom
| | - Frank Voncken
- Department of Biomedical Sciences, School of Life Sciences, University of Hull, Cottingham Road, Hull, HU6 7RX, United Kingdom
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50
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Christenson ET, Gallegos AS, Banerjee A. In vitro reconstitution, functional dissection, and mutational analysis of metal ion transport by mitoferrin-1. J Biol Chem 2018; 293:3819-3828. [PMID: 29305420 DOI: 10.1074/jbc.m117.817478] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/21/2017] [Indexed: 01/01/2023] Open
Abstract
Iron is universally important to cellular metabolism, and mitoferrin-1 and -2 have been proposed to be the iron importers of mitochondria, the cell's assembly plant of heme and iron-sulfur clusters. These iron-containing prosthetic groups are critical for a host of physiological processes ranging from oxygen transport and energy consumption to maintaining protein structural integrity. Mitoferrin-1 (Mfrn1) belongs to the mitochondrial carrier (MC) family and is atypical given its putative metallic cargo; most MCs transport nucleotides, amino acids, or other small- to medium-size metabolites. Despite the clear importance of Mfrn1 in iron utilization, its transport activity has not been demonstrated unambiguously. To bridge this knowledge gap, we have purified recombinant Mfrn1 under non-denaturing conditions and probed its metal ion-binding and transport functions. Isothermal titration calorimetry indicates that Mfrn1 has micromolar affinity for Fe(II), Mn(II), Co(II), and Ni(II). Mfrn1 was incorporated into defined liposomes, and iron transport was reconstituted in vitro, demonstrating that Mfrn1 can transport iron. Mfrn1 can also transport manganese, cobalt, copper, and zinc but discriminates against nickel. Experiments with candidate ligands for cellular labile iron reveal that Mfrn1 transports free iron and not a chelated iron complex and selects against alkali divalent ions. Extensive mutagenesis identified multiple residues that are crucial for metal binding, transport activity, or both. There is a clear abundance of residues with side chains that can coordinate first-row transition metal ions, suggesting that these could form primary or auxiliary metal-binding sites during the transport process.
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Affiliation(s)
- Eric T Christenson
- From the Unit on Structural and Chemical Biology of Membrane Proteins, Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Austin S Gallegos
- From the Unit on Structural and Chemical Biology of Membrane Proteins, Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Anirban Banerjee
- From the Unit on Structural and Chemical Biology of Membrane Proteins, Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
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