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Panja C, Niedzwiecka K, Baranowska E, Poznanski J, Kucharczyk R. Analysis of MT-ATP8 gene variants reported in patients by modeling in silico and in yeast model organism. Sci Rep 2023; 13:9972. [PMID: 37340059 DOI: 10.1038/s41598-023-36637-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 06/07/2023] [Indexed: 06/22/2023] Open
Abstract
Defects in ATP synthase functioning due to the substitutions in its two mitochondrially encoded subunits a and 8 lead to untreatable mitochondrial diseases. Defining the character of variants in genes encoding these subunits is challenging due to their low frequency, heteroplasmy of mitochondrial DNA in patients' cells and polymorphisms of mitochondrial genome. We successfully used yeast S. cerevisiae as a model to study the effects of variants in MT-ATP6 gene and our research led to understand how eight amino acid residues substitutions impact the proton translocation through the channel formed by subunit a and c-ring of ATP synthase at the molecular level. Here we applied this approach to study the effects of the m.8403T>C variant in MT-ATP8 gene. The biochemical data from yeast mitochondria indicate that equivalent mutation is not detrimental for the yeast enzyme functioning. The structural analysis of substitutions in subunit 8 introduced by m.8403T>C and five other variants in MT-ATP8 provides indications about the role of subunit 8 in the membrane domain of ATP synthase and potential structural consequences of substitutions in this subunit.
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Affiliation(s)
- Chiranjit Panja
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Katarzyna Niedzwiecka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Emilia Baranowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jaroslaw Poznanski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
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Baranowska E, Niedzwiecka K, Panja C, Charles C, Dautant A, Poznanski J, di Rago JP, Tribouillard-Tanvier D, Kucharczyk R. Probing the pathogenicity of patient-derived variants of MT-ATP6 in yeast. Dis Model Mech 2023; 16:307138. [PMID: 37083953 PMCID: PMC10151828 DOI: 10.1242/dmm.049783] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 02/28/2023] [Indexed: 04/22/2023] Open
Abstract
The list of mitochondrial DNA (mtDNA) variants detected in individuals with neurodegenerative diseases is constantly growing. Evaluating their functional consequences and pathogenicity is not easy, especially when they are found in only a limited number of patients together with wild-type mtDNA (heteroplasmy). Owing to its amenability to mitochondrial genetic transformation and incapacity to stably maintain heteroplasmy, and the strong evolutionary conservation of the proteins encoded in mitochondria, Saccharomyces cerevisiae provides a convenient model to investigate the functional consequences of human mtDNA variants. We herein report the construction and energy-transducing properties of yeast models of eight MT-ATP6 gene variants identified in patients with various disorders: m.8843T>C, m.8950G>A, m.9016A>G, m.9025G>A, m.9029A>G, m.9058A>G, m.9139G>A and m.9160T>C. Significant defect in growth dependent on respiration and deficits in ATP production were observed in yeast models of m.8950G>A, m.9025G>A and m.9029A>G, providing evidence of pathogenicity for these variants. Yeast models of the five other variants showed very mild, if any, effect on mitochondrial function, suggesting that the variants do not have, at least alone, the potential to compromise human health.
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Affiliation(s)
- Emilia Baranowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02106 Warsaw, Poland
| | - Katarzyna Niedzwiecka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02106 Warsaw, Poland
| | - Chiranjit Panja
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02106 Warsaw, Poland
| | - Camille Charles
- University of Bordeaux, Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France
| | - Alain Dautant
- University of Bordeaux, Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France
| | - Jarosław Poznanski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02106 Warsaw, Poland
| | - Jean-Paul di Rago
- University of Bordeaux, Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France
| | - Déborah Tribouillard-Tanvier
- University of Bordeaux, Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02106 Warsaw, Poland
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Baranowska E, Niedzwiecka K, Panja C, Charles C, Dautant A, di Rago JP, Tribouillard-Tanvier D, Kucharczyk R. Molecular basis of diseases induced by the mitochondrial DNA mutation m.9032 T > C. Hum Mol Genet 2022; 32:1313-1323. [PMID: 36434790 PMCID: PMC10077503 DOI: 10.1093/hmg/ddac292] [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: 09/05/2022] [Revised: 11/08/2022] [Accepted: 11/22/2022] [Indexed: 11/28/2022] Open
Abstract
The mitochondrial DNA mutation m.9032 T > C was previously identified in patients presenting with NARP (Neuropathy Ataxia Retinitis Pigmentosa). Their clinical features had a maternal transmission and patient's cells showed a reduced oxidative phosphorylation capacity, elevated reactive oxygen species (ROS) production and hyperpolarization of the mitochondrial inner membrane, providing evidence that m.9032 T > C is truly pathogenic. This mutation leads to replacement of a highly conserved leucine residue with proline at position 169 of ATP synthase subunit a (L169P). This protein and a ring of identical c-subunits (c-ring) move protons through the mitochondrial inner membrane coupled to ATP synthesis. We herein investigated the consequences of m.9032 T > C on ATP synthase in a strain of Saccharomyces cerevisiae with an equivalent mutation (L186P). The mutant enzyme assembled correctly but was mostly inactive as evidenced by a > 95% drop in the rate of mitochondrial ATP synthesis and absence of significant ATP-driven proton pumping across the mitochondrial membrane. Intragenic suppressors selected from L186P yeast restoring ATP synthase function to varying degrees (30-70%) were identified at the original mutation site (L186S) or in another position of the subunit a (H114Q, I118T). In light of atomic structures of yeast ATP synthase recently described, we conclude from these results that m.9032 T > C disrupts proton conduction between the external side of the membrane and the c-ring, and that H114Q and I118T enable protons to access the c-ring through a modified pathway.
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Affiliation(s)
- Emilia Baranowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Katarzyna Niedzwiecka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Chiranjit Panja
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Camille Charles
- Univ. Bordeaux, CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Alain Dautant
- Univ. Bordeaux, CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | | | | | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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Tribouillard-Tanvier D, Dautant A, Godard F, Charles C, Panja C, di Rago JP, Kucharczyk R. Creation of Yeast Models for Evaluating the Pathogenicity of Mutations in the Human Mitochondrial Gene MT-ATP6 and Discovering Therapeutic Molecules. Methods Mol Biol 2022; 2497:221-242. [PMID: 35771445 DOI: 10.1007/978-1-0716-2309-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Numerous diseases in humans have been associated with mutations of the mitochondrial genome (mtDNA). This genome encodes 13 protein subunits of complexes involved in oxidative phosphorylation (OXPHOS), a process that provides aerobic eukaryotes with the energy-rich adenosine triphosphate molecule (ATP). Mutations of the mtDNA may therefore have dramatic consequences especially in tissues and organs with high energy demand. Evaluating the pathogenicity of these mutations may be difficult because they often affect only a fraction of the numerous copies of the mitochondrial genome (up to several thousands in a single cell), which is referred to as heteroplasmy. Furthermore, due to its exposure to reactive oxygen species (ROS) produced in mitochondria, the mtDNA is prone to mutations, and some may be simply neutral polymorphisms with no detrimental consequences on human health. Another difficulty is the absence of methods for genetically transforming human mitochondria. Face to these complexities, the yeast Saccharomyces cerevisiae provides a convenient model for investigating the consequences of human mtDNA mutations in a defined genetic background. Owing to its good fermentation capacity, it can survive the loss of OXPHOS, its mitochondrial genome can be manipulated, and genetic heterogeneity in its mitochondria is unstable. Taking advantage of these unique attributes, we herein describe a method we have developed for creating yeast models of mitochondrial ATP6 gene mutations detected in patients, to determine how they impact OXPHOS. Additionally, we describe how these models can be used to discover molecules with therapeutic potential.
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Affiliation(s)
| | - Alain Dautant
- Univ. Bordeaux, CNRS, IBGC, UMR 5095, Bordeaux, France
| | | | | | - Chiranjit Panja
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
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Nesci S, Trombetti F, Pagliarani A, Ventrella V, Algieri C, Tioli G, Lenaz G. Molecular and Supramolecular Structure of the Mitochondrial Oxidative Phosphorylation System: Implications for Pathology. Life (Basel) 2021; 11:242. [PMID: 33804034 PMCID: PMC7999509 DOI: 10.3390/life11030242] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 02/07/2023] Open
Abstract
Under aerobic conditions, mitochondrial oxidative phosphorylation (OXPHOS) converts the energy released by nutrient oxidation into ATP, the currency of living organisms. The whole biochemical machinery is hosted by the inner mitochondrial membrane (mtIM) where the protonmotive force built by respiratory complexes, dynamically assembled as super-complexes, allows the F1FO-ATP synthase to make ATP from ADP + Pi. Recently mitochondria emerged not only as cell powerhouses, but also as signaling hubs by way of reactive oxygen species (ROS) production. However, when ROS removal systems and/or OXPHOS constituents are defective, the physiological ROS generation can cause ROS imbalance and oxidative stress, which in turn damages cell components. Moreover, the morphology of mitochondria rules cell fate and the formation of the mitochondrial permeability transition pore in the mtIM, which, most likely with the F1FO-ATP synthase contribution, permeabilizes mitochondria and leads to cell death. As the multiple mitochondrial functions are mutually interconnected, changes in protein composition by mutations or in supercomplex assembly and/or in membrane structures often generate a dysfunctional cascade and lead to life-incompatible diseases or severe syndromes. The known structural/functional changes in mitochondrial proteins and structures, which impact mitochondrial bioenergetics because of an impaired or defective energy transduction system, here reviewed, constitute the main biochemical damage in a variety of genetic and age-related diseases.
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Affiliation(s)
- Salvatore Nesci
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, 40064 Ozzano Emilia, Italy; (F.T.); (V.V.); (C.A.)
| | - Fabiana Trombetti
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, 40064 Ozzano Emilia, Italy; (F.T.); (V.V.); (C.A.)
| | - Alessandra Pagliarani
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, 40064 Ozzano Emilia, Italy; (F.T.); (V.V.); (C.A.)
| | - Vittoria Ventrella
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, 40064 Ozzano Emilia, Italy; (F.T.); (V.V.); (C.A.)
| | - Cristina Algieri
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, 40064 Ozzano Emilia, Italy; (F.T.); (V.V.); (C.A.)
| | - Gaia Tioli
- Department of Biomedical and Neuromotor Sciences, Alma Mater Studiorum University of Bologna, 40138 Bologna, Italy;
| | - Giorgio Lenaz
- Department of Biomedical and Neuromotor Sciences, Alma Mater Studiorum University of Bologna, 40138 Bologna, Italy;
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Su X, Dautant A, Rak M, Godard F, Ezkurdia N, Bouhier M, Bietenhader M, Mueller DM, Kucharczyk R, di Rago JP, Tribouillard-Tanvier D. The pathogenic m.8993 T > G mutation in mitochondrial ATP6 gene prevents proton release from the subunit c-ring rotor of ATP synthase. Hum Mol Genet 2021; 30:381-392. [PMID: 33600551 DOI: 10.1093/hmg/ddab043] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/26/2021] [Accepted: 01/26/2021] [Indexed: 02/05/2023] Open
Abstract
The human ATP synthase is an assembly of 29 subunits of 18 different types, of which only two (a and 8) are encoded in the mitochondrial genome. Subunit a, together with an oligomeric ring of c-subunit (c-ring), forms the proton pathway responsible for the transport of protons through the mitochondrial inner membrane, coupled to rotation of the c-ring and ATP synthesis. Neuromuscular diseases have been associated to a number of mutations in the gene encoding subunit a, ATP6. The most common, m.8993 T > G, leads to replacement of a strictly conserved leucine residue with arginine (aL156R). We previously showed that the equivalent mutation (aL173R) dramatically compromises respiratory growth of Saccharomyces cerevisiae and causes a 90% drop in the rate of mitochondrial ATP synthesis. Here, we isolated revertants from the aL173R strain that show improved respiratory growth. Four first-site reversions at codon 173 (aL173M, aL173S, aL173K and aL173W) and five second-site reversions at another codon (aR169M, aR169S, aA170P, aA170G and aI216S) were identified. Based on the atomic structures of yeast ATP synthase and the biochemical properties of the revertant strains, we propose that the aL173R mutation is responsible for unfavorable electrostatic interactions that prevent the release of protons from the c-ring into a channel from which protons move from the c-ring to the mitochondrial matrix. The results provide further evidence that yeast aL173 (and thus human aL156) optimizes the exit of protons from ATP synthase, but is not essential despite its strict evolutionary conservation.
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Affiliation(s)
- Xin Su
- University Bordeaux, CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Alain Dautant
- University Bordeaux, CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Malgorzata Rak
- University Bordeaux, CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - François Godard
- University Bordeaux, CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Nahia Ezkurdia
- University Bordeaux, CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Marine Bouhier
- University Bordeaux, CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | | | - David M Mueller
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University, 3333 Green Bay Rd, North Chicago, IL, 60064, USA
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 00090 Warsaw, Poland
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Nesci S, Pagliarani A, Algieri C, Trombetti F. Mitochondrial F-type ATP synthase: multiple enzyme functions revealed by the membrane-embedded F O structure. Crit Rev Biochem Mol Biol 2020; 55:309-321. [PMID: 32580582 DOI: 10.1080/10409238.2020.1784084] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Of the two main sectors of the F-type ATP synthase, the membrane-intrinsic FO domain is the one which, during evolution, has undergone the highest structural variations and changes in subunit composition. The FO complexity in mitochondria is apparently related to additional enzyme functions that lack in bacterial and thylakoid complexes. Indeed, the F-type ATP synthase has the main bioenergetic role to synthesize ATP by exploiting the electrochemical gradient built by respiratory complexes. The FO membrane domain, essential in the enzyme machinery, also participates in the bioenergetic cost of synthesizing ATP and in the formation of the cristae, thus contributing to mitochondrial morphology. The recent enzyme involvement in a high-conductance channel, which forms in the inner mitochondrial membrane and promotes the mitochondrial permeability transition, highlights a new F-type ATP synthase role. Point mutations which cause amino acid substitutions in FO subunits produce mitochondrial dysfunctions and lead to severe pathologies. The FO variability in different species, pointed out by cryo-EM analysis, mirrors the multiple enzyme functions and opens a new scenario in mitochondrial biology.
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Affiliation(s)
- Salvatore Nesci
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | | | - Cristina Algieri
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Fabiana Trombetti
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
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Trombetti F, Pagliarani A, Ventrella V, Algieri C, Nesci S. Crucial aminoacids in the F O sector of the F 1F O-ATP synthase address H + across the inner mitochondrial membrane: molecular implications in mitochondrial dysfunctions. Amino Acids 2019; 51:579-587. [PMID: 30798467 DOI: 10.1007/s00726-019-02710-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/09/2019] [Indexed: 12/14/2022]
Abstract
The eukaryotic F1FO-ATP synthase/hydrolase activity is coupled to H+ translocation through the inner mitochondrial membrane. According to a recent model, two asymmetric H+ half-channels in the a subunit translate a transmembrane vertical H+ flux into the rotor rotation required for ATP synthesis/hydrolysis. Along the H+ pathway, conserved aminoacid residues, mainly glutamate, address H+ both in the downhill and uphill transmembrane movements to synthesize or hydrolyze ATP, respectively. Point mutations responsible for these aminoacid changes affect H+ transfer through the membrane and, as a cascade, result in mitochondrial dysfunctions and related pathologies. The involvement of specific aminoacid residues in driving H+ along their transmembrane pathway within a subunit, sustained by the literature and calculated data, leads to depict a model consistent with some mitochondrial disorders.
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Affiliation(s)
- Fabiana Trombetti
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, BO, Italy
| | - Alessandra Pagliarani
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, BO, Italy.
| | - Vittoria Ventrella
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, BO, Italy
| | - Cristina Algieri
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, BO, Italy
| | - Salvatore Nesci
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, BO, Italy
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