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Accueil > Départements > Biologie Cellulaire > Nathalie BONNEFOY : Biogenèse et fonctionnement des complexes OXPHOS mitochondriaux

Publications de l’équipe

2017


  • A. Glatigny, P. Gambette, A. Bourand-Plantefol, G. Dujardin, et M. - H. Mucchielli-Giorgi, « Development of an in silico method for the identification of subcomplexes involved in the biogenesis of multiprotein complexes in Saccharomyces cerevisiae », BMC systems biology, vol. 11, nᵒ 1, p. 67, 2017.
    Résumé : BACKGROUND: Large sets of protein-protein interaction data coming either from biological experiments or predictive methods are available and can be combined to construct networks from which information about various cell processes can be extracted. We have developed an in silico approach based on these information to model the biogenesis of multiprotein complexes in the yeast Saccharomyces cerevisiae. RESULTS: Firstly, we have built three protein interaction networks by collecting the protein-protein interactions, which involved the subunits of three complexes, from different databases. The protein-protein interactions come from different kinds of biological experiments or are predicted. We have chosen the elongator and the mediator head complexes that are soluble and exhibit an architecture with subcomplexes that could be functional modules, and the mitochondrial bc 1 complex, which is an integral membrane complex and for which a late assembly subcomplex has been described. Secondly, by applying a clustering strategy to these networks, we were able to identify subcomplexes involved in the biogenesis of the complexes as well as the proteins interacting with each subcomplex. Thirdly, in order to validate our in silico results for the cytochrome bc1 complex we have analysed the physical interactions existing between three subunits by performing immunoprecipitation experiments in several genetic context. CONCLUSIONS: For the two soluble complexes (the elongator and mediator head), our model shows a strong clustering of subunits that belong to a known subcomplex or module. For the membrane bc 1 complex, our approach has suggested new interactions between subunits in the early steps of the assembly pathway that were experimentally confirmed. Scripts can be downloaded from the site: http://bim.igmors.u-psud.fr/isips .
    Mots-clés : BIM, BIOCELL, BIOMIT, Complex assembly, DBG, Graph clustering, PPI network, Protein complex, Protein-protein interactions, Subcomplex.

  • C. H. He, D. S. Black, C. M. Allan, B. Meunier, S. Rahman, et C. F. Clarke, « Human COQ9 Rescues a coq9 Yeast Mutant by Enhancing Coenzyme Q Biosynthesis from 4-Hydroxybenzoic Acid and Stabilizing the CoQ-Synthome », Frontiers in Physiology, vol. 8, p. 463, 2017.
    Résumé : Coq9 is required for the stability of a mitochondrial multi-subunit complex, termed the CoQ-synthome, and the deamination step of Q intermediates that derive from para-aminobenzoic acid (pABA) in yeast. In human, mutations in the COQ9 gene cause neonatal-onset primary Q10 deficiency. In this study, we determined whether expression of human COQ9 could complement yeast coq9 point or null mutants. We found that expression of human COQ9 rescues the growth of the temperature-sensitive yeast mutant, coq9-ts19, on a non-fermentable carbon source and increases the content of Q6, by enhancing Q biosynthesis from 4-hydroxybenzoic acid (4HB). To study the mechanism for the rescue by human COQ9, we determined the steady-state levels of yeast Coq polypeptides in the mitochondria of the temperature-sensitive yeast coq9 mutant expressing human COQ9. We show that the expression of human COQ9 significantly increased steady-state levels of yeast Coq4, Coq6, Coq7, and Coq9 at permissive temperature. Human COQ9 polypeptide levels persisted at non-permissive temperature. A small amount of the human COQ9 co-purified with tagged Coq6, Coq6-CNAP, indicating that human COQ9 interacts with the yeast Q-biosynthetic complex. These findings suggest that human COQ9 rescues the yeast coq9 temperature-sensitive mutant by stabilizing the CoQ-synthome and increasing Q biosynthesis from 4HB. This finding provides a powerful approach to studying the function of human COQ9 using yeast as a model.
    Mots-clés : BIOCELL, BIOMIT, coenzyme Q, human homolog, Immunoprecipitation, mitochondrial metabolism, Saccharomyces cerevisiae, temperature-sensitive mutant.

  • O. Khalimonchuk, M. Bestwick, B. Meunier, T. C. Watts, et D. R. Winge, « Correction for Khalimonchuk et al., "Formation of the Redox Cofactor Centers during Cox1 Maturation in Yeast Cytochrome Oxidase" », Molecular and Cellular Biology, vol. 37, nᵒ 11, 2017.

  • C. Panozzo, A. Laleve, D. Tribouillard-Tanvier, J. Ostojić, C. Sellem, G. Friocourt, A. Bourand-Plantefol, A. Burg, A. Delahodde, M. Blondel, et G. Dujardin, « Chemicals or mutations that target mitochondrial translation can rescue the respiratory deficiency of yeast bcs1 mutants », Biochimica Et Biophysica Acta, 2017.
    Résumé : Bcs1p is a chaperone that is required for the incorporation of the Rieske subunit within complex III of the mitochondrial respiratory chain. Mutations in the human gene BCS1L (BCS1-like) are the most frequent nuclear mutations resulting in complex III-related pathologies. In yeast, the mimicking of some pathogenic mutations causes a respiratory deficiency. We have screened chemical libraries and found that two antibiotics, pentamidine and clarithromycin, can compensate two bcs1 point mutations in yeast, one of which is the equivalent of a mutation found in a human patient. As both antibiotics target the large mtrRNA of the mitoribosome, we focused our analysis on mitochondrial translation. We found that the absence of non-essential translation factors Rrf1 or Mif3, which act at the recycling/initiation steps, also compensates for the respiratory deficiency of yeast bcs1 mutations. At compensating concentrations, both antibiotics, as well as the absence of Rrf1, cause an imbalanced synthesis of respiratory subunits which impairs the assembly of the respiratory complexes and especially that of complex IV. Finally, we show that pentamidine also decreases the assembly of complex I in nematode mitochondria. It is well known that complexes III and IV exist within the mitochondrial inner membrane as supramolecular complexes III2/IV in yeast or I/III2/IV in higher eukaryotes. Therefore, we propose that the changes in mitochondrial translation caused by the drugs or by the absence of translation factors, can compensate for bcs1 mutations by modifying the equilibrium between illegitimate, and thus inactive, and active supercomplexes.
    Mots-clés : Antibiotics, Bcs1 protein, BIOCELL, BIOMIT, FDMITO, Mitochondria, Respiratory chain, translation, Yeast.

2016



  • T. Delerue, F. Khosrobakhsh, M. Daloyau, L. J. Emorine, A. Dedieu, C. J. Herbert, N. Bonnefoy, L. Arnauné-Pelloquin, et P. Belenguer, « Loss of Msp1p in Schizosaccharomyces pombe induces a ROS-dependent nuclear mutator phenotype that affects mitochondrial fission genes », FEBS Letters, vol. 590, nᵒ 20, p. 3544-3558, 2016.
    Mots-clés : BIOCELL, BIOMIT, mitochondrial DNA, mitochondrial fission and fusion, Schizosaccharomyces pombe.


  • A. Lalève, C. Vallières, M. - P. Golinelli-Cohen, C. Bouton, Z. Song, G. Pawlik, S. M. Tindall, S. V. Avery, J. Clain, et B. Meunier, « The antimalarial drug primaquine targets Fe–S cluster proteins and yeast respiratory growth », Redox Biology, vol. 7, p. 21-29, 2016.
    Mots-clés : Aconitase, Aconitate Hydratase, Antimalarials, ATP-Binding Cassette Transporters, BIOCELL, BIOMIT, Cytochrome-B(5) Reductase, Gene Expression Regulation, Fungal, Gene Knockout Techniques, Malaria, Mitochondria, Molecular Chaperones, oxidative stress, Primaquine, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Sod2, Superoxide Dismutase, Yeast model.


  • J. Ostojić, C. Panozzo, A. Bourand-Plantefol, C. J. Herbert, G. Dujardin, et N. Bonnefoy, « Ribosome recycling defects modify the balance between the synthesis and assembly of specific subunits of the oxidative phosphorylation complexes in yeast mitochondria », Nucleic Acids Research, vol. 44, nᵒ 12, p. 5785-5797, juill. 2016.
  • Z. Song, A. Laleve, C. Vallières, J. E. McGeehan, R. E. Lloyd, et B. Meunier, « Human Mitochondrial Cytochrome b Variants Studied in Yeast: Not All Are Silent Polymorphisms », Human Mutation, vol. 37, nᵒ 9, p. 933-941, 2016.
    Résumé : Variations in mitochondrial DNA (mtDNA) cytochrome b (mt-cyb) are frequently found within the healthy population, but also occur within a spectrum of mitochondrial and common diseases. mt-cyb encodes the core subunit (MT-CYB) of complex III, a central component of the oxidative phosphorylation system that drives cellular energy production and homeostasis. Despite significant efforts, most mt-cyb variations identified are not matched with corresponding biochemical data, so their functional and pathogenic consequences in humans remain elusive. While human mtDNA is recalcitrant to genetic manipulation, it is possible to introduce human-associated point mutations into yeast mtDNA. Using this system, we reveal direct links between human mt-cyb variations in key catalytic domains of MT-CYB and significant changes to complex III activity or drug sensitivity. Strikingly, m.15257G>A (p.Asp171Asn) increased the sensitivity of yeast to the antimalarial drug atovaquone, and m.14798T>C (p.Phe18Leu) enhanced the sensitivity of yeast to the antidepressant drug clomipramine. We demonstrate that while a small number of mt-cyb variations had no functional effect, others have the capacity to alter complex III properties, suggesting they could play a wider role in human health and disease than previously thought. This compendium of new mt-cyb-biochemical relationships in yeast provides a resource for future investigations in humans.
    Mots-clés : Atovaquone, BIOCELL, BIOMIT, clomipramine, mitochondrial DNA, MT-CYB, Yeast model.

2015



  • J. - P. Lasserre, A. Dautant, R. S. Aiyar, R. Kucharczyk, A. Glatigny, D. Tribouillard-Tanvier, J. Rytka, M. Blondel, N. Skoczen, P. Reynier, L. Pitayu, A. Rotig, A. Delahodde, L. M. Steinmetz, G. Dujardin, V. Procaccio, et J. - P. di Rago, « Yeast as a system for modeling mitochondrial disease mechanisms and discovering therapies », Disease Models & Mechanisms, vol. 8, nᵒ 6, p. 509-526, juin 2015.
    Mots-clés :0Animals, BIM, BIOCELL, BIOMIT, DBG, DNA, Fungal, Drug screening, FDMITO, Genetic suppressors, Humans, Mitochondria, Mitochondrial disease, Mitochondrial Diseases, Models, Biological, OXPHOS, Saccharomyces cerevisiae, Translational Medical Research, Yeast.


  • R. E. Lloyd, K. Keatley, D. T. J. Littlewood, B. Meunier, W. V. Holt, Q. An, S. C. Higgins, S. Polyzoidis, K. F. Stephenson, K. Ashkan, H. L. Fillmore, G. J. Pilkington, et J. E. McGeehan, « Identification and functional prediction of mitochondrial complex III and IV mutations associated with glioblastoma », Neuro-Oncology, vol. 17, nᵒ 7, p. 942-952, juill. 2015.
    Mots-clés : Adolescent, Adult, Aged, BIOCELL, BIOMIT, Brain Neoplasms, DNA, Mitochondrial, Electron Transport Complex III, Electron Transport Complex IV, Female, functional prediction, glioblastoma, Humans, Male, Middle Aged, mitochondrial DNA (mtDNA) mutation, Molecular Docking Simulation, Mutation, structural analysis, subgrouping.


  • C. Nesti, M. C. Meschini, B. Meunier, M. Sacchini, S. Doccini, A. Romano, S. Petrillo, I. Pezzini, N. Seddiki, A. Rubegni, F. Piemonte, M. A. Donati, G. Brasseur, et F. M. Santorelli, « Additive effect of nuclear and mitochondrial mutations in a patient with mitochondrial encephalomyopathy », Human Molecular Genetics, vol. 24, nᵒ 11, p. 3248-3256, juin 2015.
    Mots-clés : Adenosine Triphosphate, Adult, Amino Acid Sequence, Base Sequence, BIOCELL, BIOMIT, Diagnosis, Differential, DNA Mutational Analysis, Female, Humans, Mitochondrial Encephalomyopathies, Molecular Diagnostic Techniques, Molecular Sequence Data, Mutation, Missense, Polymorphism, Restriction Fragment Length, Saccharomyces cerevisiae.


  • Z. Song, J. Clain, B. I. Iorga, C. Vallières, A. Lalève, N. Fisher, et B. Meunier, « Interplay between the hinge region of iron sulphur protein and the Qo site in the bc1 complex — Analysis of Plasmodium-like mutations in the yeast enzyme », Biochimica et Biophysica Acta (BBA) - Bioenergetics, vol. 1847, nᵒ 12, p. 1487-1494, 2015.
    Mots-clés : Amino Acid Sequence, Animals, BIOCELL, BIOMIT, Catalysis, Cytochrome b Group, Genetics, Iron-Sulfur Proteins, Malaria parasite, Models, Molecular, Molecular Sequence Data, Plasmodium falciparum, Respiratory complex III, Sequence Homology, Amino Acid, Superoxide production, Superoxides, Yeast model.

  • Z. Song, J. Clain, B. I. Iorga, Z. Yi, N. Fisher, et B. Meunier, « Saccharomyces cerevisiae-based mutational analysis of the bc1 complex Qo site residue 279 to study the trade-off between atovaquone resistance and function », Antimicrobial Agents and Chemotherapy, vol. 59, nᵒ 7, p. 4053-4058, 2015.
    Résumé : The bc1 complex is central to mitochondrial bioenergetics and the target of the antimalarial drug atovaquone that binds in the quinol oxidation (Qo) site of the complex. Structural analysis has shown that the Qo site residue Y279 (Y268 in Plasmodium falciparum) is key for atovaquone binding. Consequently, atovaquone resistance can be acquired by mutation of that residue. In addition to the probability of amino acid substitution, the level of atovaquone resistance and the loss of bc1 complex activity that are associated with the novel amino acid would restrict the nature of resistance-driven mutations occurring on atovaquone exposure in native parasite populations. Using the yeast model, we characterized the effect of all the amino acid replacements resulting from a single nucleotide substitution at codon 279: Y279C, Y279D, Y279F, Y279H, Y279N, and Y279S (Y279C, D, F, H, N, and S). Two residue changes that required a double nucleotide substitution, Y279A and W, were added to the series. We found that mutations Y279A, C, and S conferred high atovaquone resistance but decreased the catalytic activity. Y279F had wild-type enzymatic activity and sensitivity to atovaquone, while the other substitutions caused a dramatic respiratory defect. The results obtained with the yeast model were examined in regard to atomic structure and compared to the reported data on the evolution of acquired atovaquone resistance in P. falciparum.
    Mots-clés : Amino Acid Substitution, Antimalarials, Atovaquone, BIOCELL, Biological Evolution, BIOMIT, Catalysis, Codon, DNA Mutational Analysis, Drug Resistance, Electron Transport Complex III, Hydroquinones, Ligands, Models, Molecular, Mutation, Oxidation-Reduction, Plasmodium falciparum, Saccharomyces cerevisiae.
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Principales publications 2011-2014

  • Ostojić, J., Glatigny, A., Herbert, C. J., Dujardin, G. and Bonnefoy, N. (2014) Does the study of genetic interactions help predict the function of mitochondrial proteins in Saccharomyces cerevisiae ? Biochimie 100, 27–37.
  • Dujeancourt, L., Richter, R., Chrzanowska-Lightowlers, Z. M., Bonnefoy, N. and Herbert, C. J. (2013) Interactions between peptidyl tRNA hydrolase homologs and the ribosomal release factor Mrf1 in S. pombe mitochondria. Mitochondrion 13, 871–80.
  • Herbert, C. J., Golik, P. and Bonnefoy, N. (2013) Yeast PPR proteins, watchdogs of mitochondrial gene expression. RNA Biol. 10, 1477–94.
  • Ostojić, J., Panozzo, C., Lasserre, J.-P., Nouet, C., Courtin, F., Blancard, C., di Rago, J.-P. and Dujardin, G. (2013) The energetic state of mitochondria modulates complex III biogenesis through the ATP-dependent activity of Bcs1. Cell Metab. 18, 567–77.
  • Herrmann, J.M., Wöllhaf, M.W. and Bonnefoy, N. (2013) Control of protein synthesis in yeast mitochondria : The concept of translational activators. Biochim Biophys Acta, 1833, 286-294.
  • -* Vallières, C., Fisher, N. and Meunier, B. (2013). Reconstructing the Qo site of Plasmodium falciparum bc1 complex in the yeast enzyme. PLoS One. 12, e71726.
  • Kühl, I., Fox, T.D. and Bonnefoy, N. (2012) Schizosaccharomyces pombe homologs of the Saccharomyces cerevisiae mitochondrial proteins Cbp6 and Mss51 function at a post-translational step of respiratory complex biogenesis. Mitochondrion 12, 381-390.
  • Vallières, C., Fisher, N., Antoine, T., Al-Helal, M., Stocks, P., Berry, N., Lawrenson, A.S., Ward, S.A., O’ Neill, P.M., Biagini, G.A. and Meunier, B. (2012). HDQ, a potent inhibitor of Plasmodium falciparum proliferation targeting the Qi site of the bc1 complex. Antimicrob. Agents Chemother. 56, 3739-3747.
  • Vallières, C., Fisher,N., Lemoine, M., Pamlard, O., Beaupierre, S., Guillou, C. and Meunier, B. (2012). A rapid in vivo colorimetric library screen for inhibitors of microbial respiration. ACS Chem. Biol.7, 1659-65.
  • Kühl, I., Dujeancourt, L., Gaisne, M., Herbert, C. J. and Bonnefoy, N. (2011) A genome wide study in fission yeast reveals nine PPR proteins that regulate mitochondrial gene expression. Nucleic Acids Res. 39, 8029–41.
  • Vallières, C., Trouillard, M., Dujardin, G. and Meunier, B. (2011) Deleterious effect of the Qo inhibitor compound resistance-conferring mutation G143A in the intron-containing cytochrome b gene and mechanisms for bypassing it. Appl. Environ. Microbiol. 77, 2088–93.

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