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Del Dotto V, Musiani F, Baracca A, Solaini G. Variants in Human ATP Synthase Mitochondrial Genes: Biochemical Dysfunctions, Associated Diseases, and Therapies. Int J Mol Sci 2024; 25:2239. [PMID: 38396915 PMCID: PMC10889682 DOI: 10.3390/ijms25042239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Mitochondrial ATP synthase (Complex V) catalyzes the last step of oxidative phosphorylation and provides most of the energy (ATP) required by human cells. The mitochondrial genes MT-ATP6 and MT-ATP8 encode two subunits of the multi-subunit Complex V. Since the discovery of the first MT-ATP6 variant in the year 1990 as the cause of Neuropathy, Ataxia, and Retinitis Pigmentosa (NARP) syndrome, a large and continuously increasing number of inborn variants in the MT-ATP6 and MT-ATP8 genes have been identified as pathogenic. Variants in these genes correlate with various clinical phenotypes, which include several neurodegenerative and multisystemic disorders. In the present review, we report the pathogenic variants in mitochondrial ATP synthase genes and highlight the molecular mechanisms underlying ATP synthase deficiency that promote biochemical dysfunctions. We discuss the possible structural changes induced by the most common variants found in patients by considering the recent cryo-electron microscopy structure of human ATP synthase. Finally, we provide the state-of-the-art of all therapeutic proposals reported in the literature, including drug interventions targeting mitochondrial dysfunctions, allotopic gene expression- and nuclease-based strategies, and discuss their potential translation into clinical trials.
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Affiliation(s)
- Valentina Del Dotto
- Laboratory of Biochemistry and Mitochondrial Pathophysiology, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126 Bologna, Italy; (V.D.D.); (G.S.)
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40127 Bologna, Italy;
| | - Alessandra Baracca
- Laboratory of Biochemistry and Mitochondrial Pathophysiology, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126 Bologna, Italy; (V.D.D.); (G.S.)
| | - Giancarlo Solaini
- Laboratory of Biochemistry and Mitochondrial Pathophysiology, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126 Bologna, Italy; (V.D.D.); (G.S.)
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2
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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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Kabala AM, Binko K, Godard F, Charles C, Dautant A, Baranowska E, Skoczen N, Gombeau K, Bouhier M, Becker HD, Ackerman SH, Steinmetz LM, Tribouillard-Tanvier D, Kucharczyk R, di Rago JP. Assembly-dependent translation of subunits 6 (Atp6) and 9 (Atp9) of ATP synthase in yeast mitochondria. Genetics 2022; 220:iyac007. [PMID: 35100419 PMCID: PMC8893259 DOI: 10.1093/genetics/iyac007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/30/2021] [Indexed: 12/04/2022] Open
Abstract
The yeast mitochondrial ATP synthase is an assembly of 28 subunits of 17 types of which 3 (subunits 6, 8, and 9) are encoded by mitochondrial genes, while the 14 others have a nuclear genetic origin. Within the membrane domain (FO) of this enzyme, the subunit 6 and a ring of 10 identical subunits 9 transport protons across the mitochondrial inner membrane coupled to ATP synthesis in the extra-membrane structure (F1) of ATP synthase. As a result of their dual genetic origin, the ATP synthase subunits are synthesized in the cytosol and inside the mitochondrion. How they are produced in the proper stoichiometry from two different cellular compartments is still poorly understood. The experiments herein reported show that the rate of translation of the subunits 9 and 6 is enhanced in strains with mutations leading to specific defects in the assembly of these proteins. These translation modifications involve assembly intermediates interacting with subunits 6 and 9 within the final enzyme and cis-regulatory sequences that control gene expression in the organelle. In addition to enabling a balanced output of the ATP synthase subunits, these assembly-dependent feedback loops are presumably important to limit the accumulation of harmful assembly intermediates that have the potential to dissipate the mitochondrial membrane electrical potential and the main source of chemical energy of the cell.
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Affiliation(s)
- Anna M Kabala
- CNRS, IBGC, University of Bordeaux, UMR 5095, F-33000 Bordeaux, France
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 01-224 Warsaw, Poland
| | - Krystyna Binko
- CNRS, IBGC, University of Bordeaux, UMR 5095, F-33000 Bordeaux, France
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 01-224 Warsaw, Poland
| | - François Godard
- CNRS, IBGC, University of Bordeaux, UMR 5095, F-33000 Bordeaux, France
| | - Camille Charles
- CNRS, IBGC, University of Bordeaux, UMR 5095, F-33000 Bordeaux, France
| | - Alain Dautant
- CNRS, IBGC, University of Bordeaux, UMR 5095, F-33000 Bordeaux, France
| | - Emilia Baranowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 01-224 Warsaw, Poland
| | - Natalia Skoczen
- CNRS, IBGC, University of Bordeaux, UMR 5095, F-33000 Bordeaux, France
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 01-224 Warsaw, Poland
| | - Kewin Gombeau
- CNRS, IBGC, University of Bordeaux, UMR 5095, F-33000 Bordeaux, France
| | - Marine Bouhier
- CNRS, IBGC, University of Bordeaux, UMR 5095, F-33000 Bordeaux, France
| | - Hubert D Becker
- UPR ‘Architecture et Réactivité de l’ARN’, CNRS, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, F-67084 Strasbourg Cedex, France
| | - Sharon H Ackerman
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48202, USA
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Stanford Genome Technology Center, Palo Alto, CA 94304, USA
| | | | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 01-224 Warsaw, Poland
| | - Jean-Paul di Rago
- CNRS, IBGC, University of Bordeaux, UMR 5095, F-33000 Bordeaux, France
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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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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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Ding Q, Kucharczyk R, Zhao W, Dautant A, Xu S, Niedzwiecka K, Su X, Giraud MF, Gombeau K, Zhang M, Xie H, Zeng C, Bouhier M, di Rago JP, Liu Z, Tribouillard-Tanvier D, Chen H. Case Report: Identification of a Novel Variant (m.8909T>C) of Human Mitochondrial ATP6 Gene and Its Functional Consequences on Yeast ATP Synthase. Life (Basel) 2020; 10:life10090215. [PMID: 32971864 PMCID: PMC7555451 DOI: 10.3390/life10090215] [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: 07/31/2020] [Revised: 09/09/2020] [Accepted: 09/17/2020] [Indexed: 11/16/2022] Open
Abstract
With the advent of next generation sequencing, the list of mitochondrial DNA (mtDNA) mutations identified in patients rapidly and continuously expands. They are frequently found in a limited number of cases, sometimes a single individual (as with the case herein reported) and in heterogeneous genetic backgrounds (heteroplasmy), which makes it difficult to conclude about their pathogenicity and functional consequences. As an organism amenable to mitochondrial DNA manipulation, able to survive by fermentation to loss-of-function mtDNA mutations, and where heteroplasmy is unstable, Saccharomyces cerevisiae is an excellent model for investigating novel human mtDNA variants, in isolation and in a controlled genetic context. We herein report the identification of a novel variant in mitochondrial ATP6 gene, m.8909T>C. It was found in combination with the well-known pathogenic m.3243A>G mutation in mt-tRNALeu. We show that an equivalent of the m.8909T>C mutation compromises yeast adenosine tri-phosphate (ATP) synthase assembly/stability and reduces the rate of mitochondrial ATP synthesis by 20-30% compared to wild type yeast. Other previously reported ATP6 mutations with a well-established pathogenicity (like m.8993T>C and m.9176T>C) were shown to have similar effects on yeast ATP synthase. It can be inferred that alone the m.8909T>C variant has the potential to compromise human health.
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Affiliation(s)
- Qiuju Ding
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing 211166, China; (Q.D.); (W.Z.); (S.X.); (M.Z.); (H.X.); (C.Z.); (Z.L.)
| | - Róża Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 00090 Warsaw, Poland; (R.K.); (K.N.)
| | - Weiwei Zhao
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing 211166, China; (Q.D.); (W.Z.); (S.X.); (M.Z.); (H.X.); (C.Z.); (Z.L.)
| | - Alain Dautant
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux, CNRS, UMR 5095, F-33000 Bordeaux, France; (A.D.); (X.S.); (M.-F.G.); (K.G.); (M.B.); (J.-P.d.R.)
| | - Shutian Xu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing 211166, China; (Q.D.); (W.Z.); (S.X.); (M.Z.); (H.X.); (C.Z.); (Z.L.)
| | - Katarzyna Niedzwiecka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 00090 Warsaw, Poland; (R.K.); (K.N.)
| | - Xin Su
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux, CNRS, UMR 5095, F-33000 Bordeaux, France; (A.D.); (X.S.); (M.-F.G.); (K.G.); (M.B.); (J.-P.d.R.)
| | - Marie-France Giraud
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux, CNRS, UMR 5095, F-33000 Bordeaux, France; (A.D.); (X.S.); (M.-F.G.); (K.G.); (M.B.); (J.-P.d.R.)
| | - Kewin Gombeau
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux, CNRS, UMR 5095, F-33000 Bordeaux, France; (A.D.); (X.S.); (M.-F.G.); (K.G.); (M.B.); (J.-P.d.R.)
| | - Mingchao Zhang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing 211166, China; (Q.D.); (W.Z.); (S.X.); (M.Z.); (H.X.); (C.Z.); (Z.L.)
| | - Honglang Xie
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing 211166, China; (Q.D.); (W.Z.); (S.X.); (M.Z.); (H.X.); (C.Z.); (Z.L.)
| | - Caihong Zeng
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing 211166, China; (Q.D.); (W.Z.); (S.X.); (M.Z.); (H.X.); (C.Z.); (Z.L.)
| | - Marine Bouhier
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux, CNRS, UMR 5095, F-33000 Bordeaux, France; (A.D.); (X.S.); (M.-F.G.); (K.G.); (M.B.); (J.-P.d.R.)
| | - Jean-Paul di Rago
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux, CNRS, UMR 5095, F-33000 Bordeaux, France; (A.D.); (X.S.); (M.-F.G.); (K.G.); (M.B.); (J.-P.d.R.)
| | - Zhihong Liu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing 211166, China; (Q.D.); (W.Z.); (S.X.); (M.Z.); (H.X.); (C.Z.); (Z.L.)
| | - Déborah Tribouillard-Tanvier
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux, CNRS, UMR 5095, F-33000 Bordeaux, France; (A.D.); (X.S.); (M.-F.G.); (K.G.); (M.B.); (J.-P.d.R.)
- Institut national de la santé et de la recherche médicale, 75000 Paris, France
- Correspondence: (D.T.-T.); (H.C.)
| | - Huimei Chen
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing 211166, China; (Q.D.); (W.Z.); (S.X.); (M.Z.); (H.X.); (C.Z.); (Z.L.)
- Correspondence: (D.T.-T.); (H.C.)
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8
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Su X, Dautant A, Godard F, Bouhier M, Zoladek T, Kucharczyk R, di Rago JP, Tribouillard-Tanvier D. Molecular Basis of the Pathogenic Mechanism Induced by the m.9191T>C Mutation in Mitochondrial ATP6 Gene. Int J Mol Sci 2020; 21:ijms21145083. [PMID: 32708436 PMCID: PMC7404254 DOI: 10.3390/ijms21145083] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/10/2020] [Accepted: 07/16/2020] [Indexed: 12/15/2022] Open
Abstract
Probing the pathogenicity and functional consequences of mitochondrial DNA (mtDNA) mutations from patient’s cells and tissues is difficult due to genetic heteroplasmy (co-existence of wild type and mutated mtDNA in cells), occurrence of numerous mtDNA polymorphisms, and absence of methods for genetically transforming human mitochondria. Owing to its good fermenting capacity that enables survival to loss-of-function mtDNA mutations, its amenability to mitochondrial genome manipulation, and lack of heteroplasmy, Saccharomyces cerevisiae is an excellent model for studying and resolving the molecular bases of human diseases linked to mtDNA in a controlled genetic background. Using this model, we previously showed that a pathogenic mutation in mitochondrial ATP6 gene (m.9191T>C), that converts a highly conserved leucine residue into proline in human ATP synthase subunit a (aL222P), severely compromises the assembly of yeast ATP synthase and reduces by 90% the rate of mitochondrial ATP synthesis. Herein, we report the isolation of intragenic suppressors of this mutation. In light of recently described high resolution structures of ATP synthase, the results indicate that the m.9191T>C mutation disrupts a four α-helix bundle in subunit a and that the leucine residue it targets indirectly optimizes proton conduction through the membrane domain of ATP synthase.
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Affiliation(s)
- Xin Su
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux, 1 Rue Camille Saint-Saëns, 33077 Bordeaux, France; (X.S.); (A.D.); (F.G.); (M.B.); (J.-P.d.R.)
| | - Alain Dautant
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux, 1 Rue Camille Saint-Saëns, 33077 Bordeaux, France; (X.S.); (A.D.); (F.G.); (M.B.); (J.-P.d.R.)
| | - François Godard
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux, 1 Rue Camille Saint-Saëns, 33077 Bordeaux, France; (X.S.); (A.D.); (F.G.); (M.B.); (J.-P.d.R.)
| | - Marine Bouhier
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux, 1 Rue Camille Saint-Saëns, 33077 Bordeaux, France; (X.S.); (A.D.); (F.G.); (M.B.); (J.-P.d.R.)
| | - Teresa Zoladek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; (T.Z.); (R.K.)
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; (T.Z.); (R.K.)
| | - Jean-Paul di Rago
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux, 1 Rue Camille Saint-Saëns, 33077 Bordeaux, France; (X.S.); (A.D.); (F.G.); (M.B.); (J.-P.d.R.)
| | - Déborah Tribouillard-Tanvier
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux, 1 Rue Camille Saint-Saëns, 33077 Bordeaux, France; (X.S.); (A.D.); (F.G.); (M.B.); (J.-P.d.R.)
- Correspondence:
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9
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Kucharczyk R, Dautant A, Gombeau K, Godard F, Tribouillard-Tanvier D, di Rago JP. The pathogenic MT-ATP6 m.8851T>C mutation prevents proton movements within the n-side hydrophilic cleft of the membrane domain of ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:562-572. [PMID: 31181185 DOI: 10.1016/j.bbabio.2019.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 04/12/2019] [Accepted: 06/02/2019] [Indexed: 12/14/2022]
Abstract
Dozens of pathogenic mutations have been localized in the mitochondrial gene (MT-ATP6) that encodes the subunit a of ATP synthase. The subunit a together with a ring of identical subunits c moves protons across the mitochondrial inner membrane coupled to rotation of the subunit c-ring and ATP synthesis. One of these mutations, m.8851T>C, has been associated with bilateral striatal lesions of childhood (BSLC), a group of rare neurological disorders characterized by symmetric degeneration of the corpus striatum. It converts a highly conserved tryptophan residue into arginine at position 109 of subunit a (aW109R). We previously showed that an equivalent thereof in Saccharomyces cerevisiae (aW126R) severely impairs by an unknown mechanism the functioning of ATP synthase without any visible assembly/stability defect. Herein we show that ATP synthase function was recovered to varying degree by replacing the mutant arginine residue 126 with methionine, lysine or glycine or by replacing with methionine an arginine residue present at position 169 of subunit a (aR169). In recently described atomic structures of yeast ATP synthase, aR169 is at the center of a hydrophilic cleft along which protons are transported from the subunit c-ring to the mitochondrial matrix, in the proximity of the two residues known from a long time to be essential to the activity of FO (aR176 and cE59). We provide evidence that the aW126R change is responsible for electrostatic and steric hindrance that enables aR169 to engage in a salt bridge with cE59. As a result, aR176 cannot interact properly with cE5 and ATP synthase fails to effectively move protons across the mitochondrial membrane. In addition to insight into the pathogenic mechanism induced by the m.8851T>C mutation, the present study brings interesting information about the role of specific residues of subunit a in the energy-transducing activity of ATP synthase.
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Affiliation(s)
- Roza Kucharczyk
- Institut de Biochimie et Génétique Cellulaires of CNRS, Bordeaux University, 1 Rue Camille Saint-Saëns, Bordeaux 33077 cedex, France; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
| | - Alain Dautant
- Institut de Biochimie et Génétique Cellulaires of CNRS, Bordeaux University, 1 Rue Camille Saint-Saëns, Bordeaux 33077 cedex, France
| | - Kewin Gombeau
- Institut de Biochimie et Génétique Cellulaires of CNRS, Bordeaux University, 1 Rue Camille Saint-Saëns, Bordeaux 33077 cedex, France
| | - François Godard
- Institut de Biochimie et Génétique Cellulaires of CNRS, Bordeaux University, 1 Rue Camille Saint-Saëns, Bordeaux 33077 cedex, France
| | - Déborah Tribouillard-Tanvier
- Institut de Biochimie et Génétique Cellulaires of CNRS, Bordeaux University, 1 Rue Camille Saint-Saëns, Bordeaux 33077 cedex, France
| | - Jean-Paul di Rago
- Institut de Biochimie et Génétique Cellulaires of CNRS, Bordeaux University, 1 Rue Camille Saint-Saëns, Bordeaux 33077 cedex, France.
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10
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Kucharczyk R, Dautant A, Godard F, Tribouillard-Tanvier D, di Rago JP. Functional investigation of an universally conserved leucine residue in subunit a of ATP synthase targeted by the pathogenic m.9176 T>G mutation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1860:52-59. [PMID: 30414414 DOI: 10.1016/j.bbabio.2018.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/06/2018] [Accepted: 11/07/2018] [Indexed: 01/10/2023]
Abstract
Protons are transported from the mitochondrial matrix to the intermembrane space of mitochondria during the transfer of electrons to oxygen and shuttled back to the matrix by the a subunit and a ring of identical c subunits across the membrane domain (FO) of ATP synthase, which is coupled to ATP synthesis. A mutation (m.9176 T > G) of the mitochondrial ATP6 gene that replaces an universally conserved leucine residue into arginine at amino acid position 217 of human subunit a (aL217R) has been associated to NARP (Neuropathy, Ataxia and Retinitis Pigmentosa) and MILS (Maternally Inherited Leigh's Syndrome) diseases. We previously showed that an equivalent thereof in Saccharomyces cerevisiae (aL237R) severely impairs subunit a assembly/stability and decreases by >90% the rate of mitochondrial ATP synthesis. Herein we identified three spontaneous first-site intragenic suppressors (aR237M, aR237T and aR237S) that fully restore ATP synthase assembly. However, mitochondrial ATP synthesis rate was only partially recovered (40-50% vs wild type yeast). In light of recently described high-resolution yeast ATP synthase structures, the detrimental consequences of the aL237R change can be explained by steric and electrostatic hindrance with the universally conserved subunit a arginine residue (aR176) that is essential to FO activity. aL237 together with three other nearby hydrophobic residues have been proposed to prevent ion shortage between two physically separated hydrophilic pockets within the FO. Our results suggest that aL237 favors subunit c-ring rotation by optimizing electrostatic interaction between aR176 and an acidic residue in subunit c (cE59) known to be essential also to the activity of FO.
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Affiliation(s)
- Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
| | - Alain Dautant
- Institut de Biochimie et Génétique Cellulaires, CNRS-Bordeaux University (UMR5095), 1 Rue Camille Saint-Saëns, Bordeaux 33077 cedex, France
| | - François Godard
- Institut de Biochimie et Génétique Cellulaires, CNRS-Bordeaux University (UMR5095), 1 Rue Camille Saint-Saëns, Bordeaux 33077 cedex, France
| | - Déborah Tribouillard-Tanvier
- Institut de Biochimie et Génétique Cellulaires, CNRS-Bordeaux University (UMR5095), 1 Rue Camille Saint-Saëns, Bordeaux 33077 cedex, France
| | - Jean-Paul di Rago
- Institut de Biochimie et Génétique Cellulaires, CNRS-Bordeaux University (UMR5095), 1 Rue Camille Saint-Saëns, Bordeaux 33077 cedex, France..
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11
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Skoczeń N, Dautant A, Binko K, Godard F, Bouhier M, Su X, Lasserre JP, Giraud MF, Tribouillard-Tanvier D, Chen H, di Rago JP, Kucharczyk R. Molecular basis of diseases caused by the mtDNA mutation m.8969G>A in the subunit a of ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:602-611. [PMID: 29778688 DOI: 10.1016/j.bbabio.2018.05.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/04/2018] [Accepted: 05/15/2018] [Indexed: 01/03/2023]
Abstract
The ATP synthase which provides aerobic eukaryotes with ATP, organizes into a membrane-extrinsic catalytic domain, where ATP is generated, and a membrane-embedded FO domain that shuttles protons across the membrane. We previously identified a mutation in the mitochondrial MT-ATP6 gene (m.8969G>A) in a 14-year-old Chinese female who developed an isolated nephropathy followed by brain and muscle problems. This mutation replaces a highly conserved serine residue into asparagine at amino acid position 148 of the membrane-embedded subunit a of ATP synthase. We showed that an equivalent of this mutation in yeast (aS175N) prevents FO-mediated proton translocation. Herein we identified four first-site intragenic suppressors (aN175D, aN175K, aN175I, and aN175T), which, in light of a recently published atomic structure of yeast FO indicates that the detrimental consequences of the original mutation result from the establishment of hydrogen bonds between aN175 and a nearby glutamate residue (aE172) that was proposed to be critical for the exit of protons from the ATP synthase towards the mitochondrial matrix. Interestingly also, we found that the aS175N mutation can be suppressed by second-site suppressors (aP12S, aI171F, aI171N, aI239F, and aI200M), of which some are very distantly located (by 20-30 Å) from the original mutation. The possibility to compensate through long-range effects the aS175N mutation is an interesting observation that holds promise for the development of therapeutic molecules.
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Affiliation(s)
- Natalia Skoczeń
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33077 Bordeaux, France
| | - Alain Dautant
- CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33077 Bordeaux, France; Université de Bordeaux, IBGC, UMR 5095, F-33077 Bordeaux, France
| | - Krystyna Binko
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33077 Bordeaux, France
| | - François Godard
- CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33077 Bordeaux, France; Université de Bordeaux, IBGC, UMR 5095, F-33077 Bordeaux, France
| | - Marine Bouhier
- CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33077 Bordeaux, France; Université de Bordeaux, IBGC, UMR 5095, F-33077 Bordeaux, France
| | - Xin Su
- Nanjing University School of Medicine, Nanjing, Jiangsu, China; Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Jean-Paul Lasserre
- CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33077 Bordeaux, France; Université de Bordeaux, IBGC, UMR 5095, F-33077 Bordeaux, France
| | - Marie-France Giraud
- CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33077 Bordeaux, France; Université de Bordeaux, IBGC, UMR 5095, F-33077 Bordeaux, France
| | - Déborah Tribouillard-Tanvier
- CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33077 Bordeaux, France; Université de Bordeaux, IBGC, UMR 5095, F-33077 Bordeaux, France
| | - Huimei Chen
- Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Jean-Paul di Rago
- CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33077 Bordeaux, France; Université de Bordeaux, IBGC, UMR 5095, F-33077 Bordeaux, France.
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
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12
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Dautant A, Meier T, Hahn A, Tribouillard-Tanvier D, di Rago JP, Kucharczyk R. ATP Synthase Diseases of Mitochondrial Genetic Origin. Front Physiol 2018; 9:329. [PMID: 29670542 PMCID: PMC5893901 DOI: 10.3389/fphys.2018.00329] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 03/15/2018] [Indexed: 01/30/2023] Open
Abstract
Devastating human neuromuscular disorders have been associated to defects in the ATP synthase. This enzyme is found in the inner mitochondrial membrane and catalyzes the last step in oxidative phosphorylation, which provides aerobic eukaryotes with ATP. With the advent of structures of complete ATP synthases, and the availability of genetically approachable systems such as the yeast Saccharomyces cerevisiae, we can begin to understand these molecular machines and their associated defects at the molecular level. In this review, we describe what is known about the clinical syndromes induced by 58 different mutations found in the mitochondrial genes encoding membrane subunits 8 and a of ATP synthase, and evaluate their functional consequences with respect to recently described cryo-EM structures.
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Affiliation(s)
- Alain Dautant
- Institut de Biochimie et Génétique Cellulaires, Centre National de la Recherche Scientifique UMR 5095, Université de Bordeaux, Bordeaux, France
| | - Thomas Meier
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Alexander Hahn
- Department of Structural Biology, Max-Planck-Institute of Biophysics, Frankfurt, Germany
| | - Déborah Tribouillard-Tanvier
- Institut de Biochimie et Génétique Cellulaires, Centre National de la Recherche Scientifique UMR 5095, Université de Bordeaux, Bordeaux, France
| | - Jean-Paul di Rago
- Institut de Biochimie et Génétique Cellulaires, Centre National de la Recherche Scientifique UMR 5095, Université de Bordeaux, Bordeaux, France
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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13
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Niedzwiecka K, Tisi R, Penna S, Lichocka M, Plochocka D, Kucharczyk R. Two mutations in mitochondrial ATP6 gene of ATP synthase, related to human cancer, affect ROS, calcium homeostasis and mitochondrial permeability transition in yeast. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1865:117-131. [PMID: 28986220 DOI: 10.1016/j.bbamcr.2017.10.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 09/15/2017] [Accepted: 10/02/2017] [Indexed: 02/06/2023]
Abstract
The relevance of mitochondrial DNA (mtDNA) mutations in cancer process is still unknown. Since the mutagenesis of mitochondrial genome in mammals is not possible yet, we have exploited budding yeast S. cerevisiae as a model to study the effects of tumor-associated mutations in the mitochondrial MTATP6 gene, encoding subunit 6 of ATP synthase, on the energy metabolism. We previously reported that four mutations in this gene have a limited impact on the production of cellular energy. Here we show that two mutations, Atp6-P163S and Atp6-K90E (human MTATP6-P136S and MTATP6-K64E, found in prostate and thyroid cancer samples, respectively), increase sensitivity of yeast cells both to compounds inducing oxidative stress and to high concentrations of calcium ions in the medium, when Om45p, the component of porin complex in outer mitochondrial membrane (OM), was fused to GFP. In OM45-GFP background, these mutations affect the activation of yeast permeability transition pore (yPTP, also called YMUC, yeast mitochondrial unspecific channel) upon calcium induction. Moreover, we show that calcium addition to isolated mitochondria heavily induced the formation of ATP synthase dimers and oligomers, recently proposed to form the core of PTP, which was slower in the mutants. We show the genetic evidence for involvement of mitochondrial ATP synthase in calcium homeostasis and permeability transition in yeast. This paper is a first to show, although in yeast model organism, that mitochondrial ATP synthase mutations, which accumulate during carcinogenesis process, may be significant for cancer cell escape from apoptosis.
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Affiliation(s)
- Katarzyna Niedzwiecka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Renata Tisi
- Dept. Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy; Milan Center for Neuroscience, Milan, Italy
| | - Sara Penna
- Dept. Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Malgorzata Lichocka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Danuta Plochocka
- 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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14
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Wen S, Niedzwiecka K, Zhao W, Xu S, Liang S, Zhu X, Xie H, Tribouillard-Tanvier D, Giraud MF, Zeng C, Dautant A, Kucharczyk R, Liu Z, di Rago JP, Chen H. Identification of G8969>A in mitochondrial ATP6 gene that severely compromises ATP synthase function in a patient with IgA nephropathy. Sci Rep 2016; 6:36313. [PMID: 27812026 PMCID: PMC5095641 DOI: 10.1038/srep36313] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 10/13/2016] [Indexed: 12/04/2022] Open
Abstract
Here we elucidated the pathogenesis of a 14-year-old Chinese female who initially developed an isolated nephropathy followed by a complex clinical presentation with brain and muscle problems, which indicated that the disease process was possibly due to a mitochondrial dysfunction. Careful evaluation of renal biopsy samples revealed a decreased staining of cells induced by COX and NADH dehydrogenase activities, and a strong fragmentation of the mitochondrial network. These anomalies were due to the presence of a mutation in the mitochondrial ATP6 gene, G8969>A. This mutation leads to replacement of a highly conserved serine residue at position 148 of the a-subunit of ATP synthase. Increasing the mutation load in cybrid cell lines was paralleled by the appearance of abnormal mitochondrial morphologies, diminished respiration and enhanced production of reactive oxygen species. An equivalent of the G8969>A mutation in yeast had dramatic consequences on ATP synthase, with a block in proton translocation. The mutation was particularly abundant (89%) in the kidney compared to blood and urine, which is likely the reason why this organ was affected first. Based on these findings, we suggest that nephrologists should pay more attention to the possibility of a mitochondrial dysfunction when evaluating patients suffering from kidney problems.
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Affiliation(s)
- Shuzhen Wen
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Katarzyna Niedzwiecka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Weiwei Zhao
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Shutian Xu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Shaoshan Liang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Xiaodong Zhu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Honglang Xie
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Déborah Tribouillard-Tanvier
- CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33077 Bordeaux, France.,Université de Bordeaux, IBGC, UMR 5095, F-33077 Bordeaux, France.,INSERM, Institut de Biochimie et Génétique Cellulaires, F-33077 Bordeaux, France
| | - Marie-France Giraud
- CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33077 Bordeaux, France.,Université de Bordeaux, IBGC, UMR 5095, F-33077 Bordeaux, France
| | - Caihong Zeng
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Alain Dautant
- CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33077 Bordeaux, France.,Université de Bordeaux, IBGC, UMR 5095, F-33077 Bordeaux, France
| | - Róża Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Zhihong Liu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Jean-Paul di Rago
- CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33077 Bordeaux, France.,Université de Bordeaux, IBGC, UMR 5095, F-33077 Bordeaux, France
| | - Huimei Chen
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
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15
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Niedzwiecka K, Kabala AM, Lasserre JP, Tribouillard-Tanvier D, Golik P, Dautant A, di Rago JP, Kucharczyk R. Yeast models of mutations in the mitochondrial ATP6 gene found in human cancer cells. Mitochondrion 2016; 29:7-17. [PMID: 27083309 DOI: 10.1016/j.mito.2016.04.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 04/08/2016] [Accepted: 04/08/2016] [Indexed: 01/09/2023]
Abstract
Since the discovery of somatic mtDNA mutations in tumor cells, multiple studies have focused on establishing a causal relationship between those changes and alterations in energy metabolism, a hallmark of cancer cells. Yet the consequences of these mutations on mitochondrial function remain largely unknown. In this study, Saccharomyces cerevisiae has been used as a model to investigate the functional consequences of four cancer-associated missense mutations (8914C>A, 8932C>T, 8953A>G, 9131T>C) found in the mitochondrial MT-ATP6 gene. This gene encodes the a-subunit of F1FO-ATP synthase, which catalyzes the last steps of ATP production in mitochondria. Although the four studied mutations affected well-conserved residues of the a-subunit, only one of them (8932C>T) had a significant impact on mitochondrial function, due to a less efficient incorporation of the a-subunit into ATP synthase. Our findings indicate that these ATP6 genetic variants found in human tumors are neutral mitochondrial genome substitutions with a limited, if any, impact on the energetic function of mitochondria.
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Affiliation(s)
- Katarzyna Niedzwiecka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Anna Magdalena Kabala
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Institut de Biochimie et Génétique Cellulaires, CNRS UMR5095, Université de Bordeaux, 1 rue Camille Saint-Saëns, 33077 Bordeaux Cedex, France
| | - Jean-Paul Lasserre
- Institut de Biochimie et Génétique Cellulaires, CNRS UMR5095, Université de Bordeaux, 1 rue Camille Saint-Saëns, 33077 Bordeaux Cedex, France
| | - Déborah Tribouillard-Tanvier
- Institut de Biochimie et Génétique Cellulaires, CNRS UMR5095, Université de Bordeaux, 1 rue Camille Saint-Saëns, 33077 Bordeaux Cedex, France
| | - Pawel Golik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Poland
| | - Alain Dautant
- Institut de Biochimie et Génétique Cellulaires, CNRS UMR5095, Université de Bordeaux, 1 rue Camille Saint-Saëns, 33077 Bordeaux Cedex, France
| | - Jean-Paul di Rago
- Institut de Biochimie et Génétique Cellulaires, CNRS UMR5095, Université de Bordeaux, 1 rue Camille Saint-Saëns, 33077 Bordeaux Cedex, France
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
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16
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Lasserre JP, Dautant A, Aiyar RS, Kucharczyk R, Glatigny A, Tribouillard-Tanvier D, Rytka J, Blondel M, Skoczen N, Reynier P, Pitayu L, Rötig A, Delahodde A, Steinmetz LM, Dujardin G, Procaccio V, di Rago JP. Yeast as a system for modeling mitochondrial disease mechanisms and discovering therapies. Dis Model Mech 2016; 8:509-26. [PMID: 26035862 PMCID: PMC4457039 DOI: 10.1242/dmm.020438] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial diseases are severe and largely untreatable. Owing to the many essential processes carried out by mitochondria and the complex cellular systems that support these processes, these diseases are diverse, pleiotropic, and challenging to study. Much of our current understanding of mitochondrial function and dysfunction comes from studies in the baker's yeast Saccharomyces cerevisiae. Because of its good fermenting capacity, S. cerevisiae can survive mutations that inactivate oxidative phosphorylation, has the ability to tolerate the complete loss of mitochondrial DNA (a property referred to as ‘petite-positivity’), and is amenable to mitochondrial and nuclear genome manipulation. These attributes make it an excellent model system for studying and resolving the molecular basis of numerous mitochondrial diseases. Here, we review the invaluable insights this model organism has yielded about diseases caused by mitochondrial dysfunction, which ranges from primary defects in oxidative phosphorylation to metabolic disorders, as well as dysfunctions in maintaining the genome or in the dynamics of mitochondria. Owing to the high level of functional conservation between yeast and human mitochondrial genes, several yeast species have been instrumental in revealing the molecular mechanisms of pathogenic human mitochondrial gene mutations. Importantly, such insights have pointed to potential therapeutic targets, as have genetic and chemical screens using yeast. Summary: In this Review, we discuss the use of budding yeast to understand mitochondrial diseases and help in the search for their treatments.
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Affiliation(s)
- Jean-Paul Lasserre
- University Bordeaux-CNRS, IBGC, UMR 5095, 1 rue Camille Saint-Saëns, Bordeaux F-33000, France
| | - Alain Dautant
- University Bordeaux-CNRS, IBGC, UMR 5095, 1 rue Camille Saint-Saëns, Bordeaux F-33000, France
| | - Raeka S Aiyar
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Roza Kucharczyk
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Annie Glatigny
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Université Paris-Sud, 1 avenue de la terrasse, Gif-sur-Yvette 91198, France
| | - Déborah Tribouillard-Tanvier
- Institut National de la Santé et de la Recherche Médicale UMR1078, Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé, Etablissement Français du Sang (EFS) Bretagne, CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest F-29200, France
| | - Joanna Rytka
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Marc Blondel
- Institut National de la Santé et de la Recherche Médicale UMR1078, Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé, Etablissement Français du Sang (EFS) Bretagne, CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest F-29200, France
| | - Natalia Skoczen
- University Bordeaux-CNRS, IBGC, UMR 5095, 1 rue Camille Saint-Saëns, Bordeaux F-33000, France Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Pascal Reynier
- UMR CNRS 6214-INSERM U1083, Angers 49933, Cedex 9, France Département de Biochimie et Génétique, Centre Hospitalier Universitaire d'Angers, Angers 49933, Cedex 9, France
| | - Laras Pitayu
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Université Paris-Sud, rue Gregor Mendel, Orsay 91405, France
| | - Agnès Rötig
- Inserm U1163, Hôpital Necker-Enfants-Malades, Institut Imagine, Université Paris Descartes-Sorbonne Paris Cité, 149 rue de Sèvres, Paris 75015, France
| | - Agnès Delahodde
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Université Paris-Sud, rue Gregor Mendel, Orsay 91405, France
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, CA 94304, USA Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5301, USA
| | - Geneviève Dujardin
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Université Paris-Sud, 1 avenue de la terrasse, Gif-sur-Yvette 91198, France
| | - Vincent Procaccio
- UMR CNRS 6214-INSERM U1083, Angers 49933, Cedex 9, France Département de Biochimie et Génétique, Centre Hospitalier Universitaire d'Angers, Angers 49933, Cedex 9, France
| | - Jean-Paul di Rago
- University Bordeaux-CNRS, IBGC, UMR 5095, 1 rue Camille Saint-Saëns, Bordeaux F-33000, France
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Biolistic Transformation for Delivering DNA into the Mitochondria. Fungal Biol 2015. [DOI: 10.1007/978-3-319-10142-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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18
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Pathological Mutations of the Mitochondrial Human Genome: the Instrumental Role of the Yeast S. cerevisiae. Diseases 2014. [DOI: 10.3390/diseases2010024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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19
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Kredics L, Szekeres A, Czifra D, Vágvölgyi C, Leitgeb B. Recent results in alamethicin research. Chem Biodivers 2013; 10:744-71. [PMID: 23681724 DOI: 10.1002/cbdv.201200390] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Indexed: 12/20/2022]
Affiliation(s)
- László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged.
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Kabala AM, Lasserre JP, Ackerman SH, di Rago JP, Kucharczyk R. Defining the impact on yeast ATP synthase of two pathogenic human mitochondrial DNA mutations, T9185C and T9191C. Biochimie 2013; 100:200-6. [PMID: 24316278 DOI: 10.1016/j.biochi.2013.11.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 11/25/2013] [Indexed: 12/18/2022]
Abstract
Mutations in the human mitochondrial ATP6 gene encoding ATP synthase subunit a/6 (referred to as Atp6p in yeast) are at the base of neurodegenerative disorders like Neurogenic Ataxia and Retinitis Pigmentosa (NARP), Leigh syndrome (LS), Charcot-Marie-Tooth (CMT), and ataxia telangiectasia. In previous studies, using the yeast Saccharomyces cerevisiae as a model we were able to better define how several of these mutations impact the ATP synthase. Here we report the construction of yeast models of two other ATP6 pathogenic mutations, T9185C and T9191C. The first one was reported as conferring a mild, sometimes reversible, CMT clinical phenotype; the second one has been described in a patient presenting with severe LS. We found that an equivalent of the T9185C mutation partially impaired the functioning of yeast ATP synthase, with only a 30% deficit in mitochondrial ATP production. An equivalent of the mutation T9191C had much more severe effects, with a nearly complete block in yeast Atp6p assembly and an >95% drop in the rate of ATP synthesis. These findings provide a molecular basis for the relative severities of the diseases induced by T9185C and T9191C.
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Affiliation(s)
- Anna Magdalena Kabala
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Institut de Biochimie et Génétique Cellulaires, CNRS UMR5095, Université Bordeaux Segalen, 1 Rue Camille Saint-Saëns, Bordeaux 33077 cedex, France
| | - Jean-Paul Lasserre
- Institut de Biochimie et Génétique Cellulaires, CNRS UMR5095, Université Bordeaux Segalen, 1 Rue Camille Saint-Saëns, Bordeaux 33077 cedex, France
| | - Sharon H Ackerman
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Jean-Paul di Rago
- Institut de Biochimie et Génétique Cellulaires, CNRS UMR5095, Université Bordeaux Segalen, 1 Rue Camille Saint-Saëns, Bordeaux 33077 cedex, France
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
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