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Accueil > Départements > Biologie des Génomes > Stéphane CHEDIN & Laurent KURAS : Physiologie et Pathogénicité des Stress

Publications

2017


  • A. F. Amorim, D. Pinto, L. Kuras, et L. Fernandes, « Absence of Gim proteins, but not GimC complex, alter stress-induced transcription », Biochimica Et Biophysica Acta, 2017.
    Résumé : Saccharomyces cerevisiae GimC (mammalian Prefoldin) is a hexameric (Gim1-6) cytoplasmic complex involved in the folding pathway of actin/tubulin. In contrast to a shared role in GimC complex, we show that absence of individual Gim proteins results in distinct stress responses. No concomitant alteration in F-actin integrity was observed. Transcription of stress responsive genes is altered in gim2Δ, gim3Δ and gim6Δ mutants: TRX2 gene is induced in these mutants but with a profile diverging from type cells, whereas CTT1 and HSP26 fail to be induced. Remaining gimΔ mutants display stress transcript abundance comparable to wild type cells. No alteration in the nuclear localization of the transcriptional activators for TRX2 (Yap1) and CTT1/HSP26 (Msn2) was observed in gim2Δ. In accordance with TRX2 induction, RNA polymerase II occupancy at TRX2 discriminates the wild type from gim2Δ and gim6Δ. In contrast, RNA polymerase II occupancy at CTT1 is similar in wild type and gim2Δ, but higher in gim6Δ. The absence of active RNA polymerase II at CTT1 in gim2Δ, but not in wild type and gim1Δ, explains the respective CTT1 transcript outputs. Altogether our results put forward the need of Gim2, Gim3 and Gim6 in oxidative and osmotic stress activated transcription; others Gim proteins are dispensable. Consequently, the participation of Gim proteins in activated-transcription is independent from the GimC complex.
    Mots-clés : DBG, Gim proteins, PEPS, stress, Transcription regulation.


  • C. Voisset, M. Blondel, G. W. Jones, G. Friocourt, G. Stahl, S. Chédin, V. Beringue, et R. Gillet, « The double life of the ribosome: when its protein folding activity supports prion propagation », Prion, p. 00-00, mars 2017.

2016



  • S. Bakari, M. Lembrouk, L. Sourd, F. Ousalem, F. André, S. Orlowski, M. Delaforge, et A. Frelet-Barrand, « Lactococcus lactis is an Efficient Expression System for Mammalian Membrane Proteins Involved in Liver Detoxification, CYP3A4, and MGST1 », Molecular Biotechnology, vol. 58, nᵒ 4, p. 299-310, 2016.
    Mots-clés : B3S, DBG, LSOD, PEPS.

  • M. Blondel, F. Soubigou, J. Evrard, P. H. Nguyen, N. Hasin, S. Chédin, R. Gillet, M. - A. Contesse, G. Friocourt, G. Stahl, G. W. Jones, et C. Voisset, « Protein Folding Activity of the Ribosome is involved in Yeast Prion Propagation », Scientific Reports, vol. 6, p. 32117, 2016.
    Résumé : 6AP and GA are potent inhibitors of yeast and mammalian prions and also specific inhibitors of PFAR, the protein-folding activity borne by domain V of the large rRNA of the large subunit of the ribosome. We therefore explored the link between PFAR and yeast prion [PSI(+)] using both PFAR-enriched mutants and site-directed methylation. We demonstrate that PFAR is involved in propagation and de novo formation of [PSI(+)]. PFAR and the yeast heat-shock protein Hsp104 partially compensate each other for [PSI(+)] propagation. Our data also provide insight into new functions for the ribosome in basal thermotolerance and heat-shocked protein refolding. PFAR is thus an evolutionarily conserved cell component implicated in the prion life cycle, and we propose that it could be a potential therapeutic target for human protein misfolding diseases.
    Mots-clés : DBG, PEPS.

  • T. Eychenne, E. Novikova, M. - B. Barrault, O. Alibert, C. Boschiero, N. Peixeiro, D. Cornu, V. Redeker, L. Kuras, P. Nicolas, M. Werner, et J. Soutourina, « Functional interplay between Mediator and TFIIB in preinitiation complex assembly in relation to promoter architecture », Genes & Development, vol. 30, nᵒ 18, p. 2119-2132, 2016.
    Résumé : Mediator is a large coregulator complex conserved from yeast to humans and involved in many human diseases, including cancers. Together with general transcription factors, it stimulates preinitiation complex (PIC) formation and activates RNA polymerase II (Pol II) transcription. In this study, we analyzed how Mediator acts in PIC assembly using in vivo, in vitro, and in silico approaches. We revealed an essential function of the Mediator middle module exerted through its Med10 subunit, implicating a key interaction between Mediator and TFIIB. We showed that this Mediator-TFIIB link has a global role on PIC assembly genome-wide. Moreover, the amplitude of Mediator's effect on PIC formation is gene-dependent and is related to the promoter architecture in terms of TATA elements, nucleosome occupancy, and dynamics. This study thus provides mechanistic insights into the coordinated function of Mediator and TFIIB in PIC assembly in different chromatin contexts.
    Mots-clés : DBG, GTR, Mediator, PEPS, PF, preinitiation complex, promoter architecture, RNA polymerase II transcription, Saccharomyces cerevisiae, SICAPS, TFIIB.

  • G. Klein, S. Devineau, J. C. Aude, Y. Boulard, H. Pasquier, J. Labarre, S. Pin, et J. P. Renault, « Interferences of Silica Nanoparticles in Green Fluorescent Protein Folding Processes », Langmuir: the ACS journal of surfaces and colloids, vol. 32, nᵒ 1, p. 195-202, 2016.
    Résumé : We investigated the relationship between unfolded proteins, silica nanoparticles and chaperonin to determine whether unfolded proteins could stick to silica surfaces and how this process could impair heat shock protein activity. The HSP60 catalyzed green fluorescent protein (GFP) folding was used as a model system. The adsorption isotherms and adsorption kinetics of denatured GFP were measured, showing that denaturation increases GFP affinity for silica surfaces. This affinity is maintained even if the surfaces are covered by a protein corona and allows silica NPs to interfere directly with GFP folding by trapping it in its unstructured state. We determined also the adsorption isotherms of HSP60 and its chaperonin activity once adsorbed, showing that SiO2 NP can interfere also indirectly with protein folding through chaperonin trapping and inhibition. This inhibition is specifically efficient when NPs are covered first with a layer of unfolded proteins. These results highlight for the first time the antichaperonin activity of silica NPs and ask new questions about the toxicity of such misfolded proteins/nanoparticles assembly toward cells.
    Mots-clés : B3S, DBG, Green Fluorescent Proteins, IMAPP, Nanoparticles, PEPS, Protein Folding, Silicon Dioxide.

  • G. Klein, C. Mathé, M. Biola-Clier, S. Devineau, E. Drouineau, E. Hatem, L. Marichal, B. Alonso, J. - C. Gaillard, G. Lagniel, J. Armengaud, M. Carrière, S. Chédin, Y. Boulard, S. Pin, J. - P. Renault, J. - C. Aude, et J. Labarre, « RNA-binding proteins are a major target of silica nanoparticles in cell extracts », Nanotoxicology, vol. 10, nᵒ 10, p. 1555-1564, 2016.
    Résumé : Upon contact with biological fluids, nanoparticles (NPs) are readily coated by cellular compounds, particularly proteins, which are determining factors for the localization and toxicity of NPs in the organism. Here, we improved a methodological approach to identify proteins that adsorb on silica NPs with high affinity. Using large-scale proteomics and mixtures of soluble proteins prepared either from yeast cells or from alveolar human cells, we observed that proteins with large unstructured region(s) are more prone to bind on silica NPs. These disordered regions provide flexibility to proteins, a property that promotes their adsorption. The statistical analyses also pointed to a marked overrepresentation of RNA-binding proteins (RBPs) and of translation initiation factors among the adsorbed proteins. We propose that silica surfaces, which are mainly composed of Si-O(-) and Si-OH groups, mimic ribose-phosphate molecules (rich in -O(-) and -OH) and trap the proteins able to interact with ribose-phosphate containing molecules. Finally, using an in vitro assay, we showed that the sequestration of translation initiation factors by silica NPs results in an inhibition of the in vitro translational activity. This result demonstrates that characterizing the protein corona of various NPs would be a relevant approach to predict their potential toxicological effects.
    Mots-clés : B3S, BIM, DBG, IMAPP, intrinsically disordered protein, PEPS, Protein corona, proteomics, RNA binding protein, silica nanoparticles.

2015



  • A. Kaya, M. V. Gerashchenko, I. Seim, J. Labarre, M. B. Toledano, et V. N. Gladyshev, « Adaptive aneuploidy protects against thiol peroxidase deficiency by increasing respiration via key mitochondrial proteins », Proceedings of the National Academy of Sciences, vol. 112, nᵒ 34, p. 10685-10690, août 2015.
    Mots-clés : Adaptation, Physiological, Aneuploidy, Antimycin A, BIOCELL, Chromosome Deletion, Chromosomes, Fungal, Cytochrome-c Peroxidase, DBG, Electron Transport, Gene Deletion, Gene Dosage, Genes, Fungal, Heat-Shock Proteins, Hydrogen Peroxide, Membrane Proteins, Mitochondrial Proteins, Oligomycins, oxidative stress, Oxidoreductases Acting on Sulfur Group Donors, PEPS, Peroxidases, Reactive Oxygen Species, respiration, Rotenone, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, SOC, thiol peroxidase.
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Publications des membres de l’équipe avant 2015

-  Hatem E, Berthonaud V, Dardalhon M, et al. Glutathione is essential to preserve nuclear function and cell survival under oxidative stress. Free Radic Biol Med. 2014 ;67:103–14. doi:10.1016/j.freeradbiomed.2013.10.807.

- Devineau S, Boulard Y, Labarre J. Protéines et nanoparticules, ça colle... ou pas. Biofutur. 2013 ;347:34–38.

-  Lacombe T, Poh SL, Barbey R, Kuras L. Mediator is an intrinsic component of the basal RNA polymerase II machinery in vivo. Nucleic Acids Res. 2013 ;41(21):9651–62. doi:10.1093/nar/gkt701.

-  Mathé C, Devineau S, Aude J-C, et al. Structural determinants for protein adsorption/non-adsorption to silica surface. PLoS One. 2013 ;8(11):e81346. doi:10.1371/journal.pone.0081346.

-  Zhou L, Le Roux G, Ducrot C, et al. Repression of class I transcription by cadmium is mediated by the protein phosphatase 2A. Nucleic Acids Res. 2013 ;41(12):6087–97. doi:10.1093/nar/gkt335.

-  Baudouin-Cornu P, Lagniel G, Kumar C, Huang M-E, Labarre J. Glutathione degradation is a key determinant of glutathione homeostasis. J Biol Chem. 2012 ;287(7):4552–61. doi:10.1074/jbc.M111.315705.

-  Peric D, Labarre J, Chevalier F, Rousselet G. Impairing the microRNA biogenesis pathway induces proteome modifications characterized by size bias and enrichment in antioxidant proteins. Proteomics. 2012 ;12(14):2295–302. doi:10.1002/pmic.201100461.

-  Molin M, Yang J, Hanzén S, Toledano MB, Labarre J, Nyström T. Life span extension and H(2)O(2) resistance elicited by caloric restriction require the peroxiredoxin Tsa1 in Saccharomyces cerevisiae. Mol Cell. 2011 ;43(5):823–33. doi:10.1016/j.molcel.2011.07.027.

-  Cormier L, Barbey R, Kuras L. Transcriptional plasticity through differential assembly of a multiprotein activation complex. Nucleic Acids Res. 2010 ;38(15):4998–5014. doi:10.1093/nar/gkq257.

-  Delalande O, Desvaux H, Godat E, et al. Cadmium-glutathione solution structures provide new insights into heavy metal detoxification. FEBS J. 2010 ;277(24):5086–96. doi:10.1111/j.1742-4658.2010.07913.x.

-  Gardarin A, Chédin S, Lagniel G, et al. Endoplasmic reticulum is a major target of cadmium toxicity in yeast. Mol Microbiol. 2010 ;76(4):1034–48. doi:10.1111/j.1365-2958.2010.07166.x.

-  Godat E, Madalinski G, Muller L, Heilier J-F, Labarre J, Junot C. Mass spectrometry-based methods for the determination of sulfur and related metabolite concentrations in cell extracts. Methods Enzymol. 2010 ;473:41–76. doi:10.1016/S0076-6879(10)73002-0.

-  Baudouin-Cornu P, Lagniel G, Chédin S, Labarre J. Development of a new method for absolute protein quantification on 2-D gels. Proteomics. 2009 ;9(20):4606–15. doi:10.1002/pmic.200800975.

-  Boisnard S, Lagniel G, Garmendia-Torres C, et al. H2O2 activates the nuclear localization of Msn2 and Maf1 through thioredoxins in Saccharomyces cerevisiae. Eukaryot Cell. 2009 ;8(9):1429–38. doi:10.1128/EC.00106-09.

-  Labarre J, Forestier C, Bourguignon J. Mécanismes de détoxication du cadmium chez les eucaryotes. In : Ménager M-T, Garnier-Laplace J, Goyffon M, eds. Toxicologie Nucléaire Environnementale et Humaine,. Lavoisier ; 2009:213–229.

-  Baudouin-Cornu P. [Stoichiometric, my dear Watson !]. Med Sci (Paris). 2008 ;24(5):483–9.

-  Labarre J, Forestier C. Le cadmium : des mécanismes à élucider. Biofutur. 2008 ;291:30–33.

-  Madalinski G, Godat E, Alves S, et al. Direct introduction of biological samples into a LTQ-Orbitrap hybrid mass spectrometer as a tool for fast metabolome analysis. Anal Chem. 2008 ;80(9):3291–303. doi:10.1021/ac7024915.

-  Pereira Y, Lagniel G, Godat E, Baudouin-Cornu P, Junot C, Labarre J. Chromate causes sulfur starvation in yeast. Toxicol Sci. 2008 ;106(2):400–12. doi:10.1093/toxsci/kfn193.

-  Tribouillard-Tanvier D, Dos Reis S, Gug F, et al. Protein folding activity of ribosomal RNA is a selective target of two unrelated antiprion drugs. PLoS One. 2008 ;3(5):e2174. doi:10.1371/journal.pone.0002174.

-  Alic N, Ayoub N, Landrieux E, et al. Selectivity and proofreading both contribute significantly to the fidelity of RNA polymerase III transcription. Proc Natl Acad Sci U S A. 2007 ;104(25):10400–5. doi:10.1073/pnas.0704116104.

-  Baudouin-Cornu P, Thomas D. Evolutionary biology : oxygen at life’s boundaries. Nature. 2007 ;445(7123):35–6. doi:10.1038/nature05521.

-  Baudouin-Cornu P, Thomas D. [On the role played by oxygen in evolution]. Med Sci (Paris). 2007 ;23(3):255–7.

-  Chédin S, Laferté A, Hoang T, Lafontaine DLJ, Riva M, Carles C. Is ribosome synthesis controlled by pol I transcription ? Cell Cycle. 2007 ;6(1):11–5.

-  Molin M, Renault J-P, Lagniel G, Pin S, Toledano M, Labarre J. Ionizing radiation induces a Yap1-dependent peroxide stress response in yeast. Free Radic Biol Med. 2007 ;43(1):136–44. doi:10.1016/j.freeradbiomed.2007.04.007.

-  Thorsen M, Lagniel G, Kristiansson E, et al. Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiol Genomics. 2007 ;30(1):35–43. doi:10.1152/physiolgenomics.00236.2006.

-  Baudouin-Cornu P, Labarre J. Regulation of the cadmium stress response through SCF-like ubiquitin ligases : comparison between Saccharomyces cerevisiae, Schizosaccharomyces pombe and mammalian cells. Biochimie. 2006 ;88(11):1673–85. doi:10.1016/j.biochi.2006.03.001.

-  Bragg JG, Thomas D, Baudouin-Cornu P. Variation among species in proteomic sulphur content is related to environmental conditions. Proc Biol Sci. 2006 ;273(1591):1293–300. doi:10.1098/rspb.2005.3441.

-  Laferté A, Favry E, Sentenac A, Riva M, Carles C, Chédin S. The transcriptional activity of RNA polymerase I is a key determinant for the level of all ribosome components. Genes Dev. 2006 ;20(15):2030–40. doi:10.1101/gad.386106.

-  Leroy C, Cormier L, Kuras L. Independent recruitment of mediator and SAGA by the activator Met4. Mol Cell Biol. 2006 ;26(8):3149–63. doi:10.1128/MCB.26.8.3149-3163.2006.

-  Menant A, Baudouin-Cornu P, Peyraud C, Tyers M, Thomas D. Determinants of the ubiquitin-mediated degradation of the Met4 transcription factor. J Biol Chem. 2006 ;281(17):11744–54. doi:10.1074/jbc.M600037200.

-  Tamás MJ, Labarre J, Toledano MB, Wysocki R. Mechanisms of toxic metal tolerance in yeast. In : ; 2006:395–454. doi:10.1007/4735_105.

-  Barbey R, Baudouin-Cornu P, Lee TA, et al. Inducible dissociation of SCF(Met30) ubiquitin ligase mediates a rapid transcriptional response to cadmium. EMBO J. 2005 ;24(3):521–32. doi:10.1038/sj.emboj.7600556.

-  ELafaye A, Junot C, Pereira Y, et al. Combined proteome and metabolite-profiling analyses reveal surprising insights into yeast sulfur metabolism. J Biol Chem. 2005 ;280(26):24723–30. doi:10.1074/jbc.M502285200.

-  Baudouin-Cornu P, Schuerer K, Marlière P, Thomas D. Intimate evolution of proteins. Proteome atomic content correlates with genome base composition. J Biol Chem. 2004 ;279(7):5421–8. doi:10.1074/jbc.M306415200.

-  Bourbon H-M, Aguilera A, Ansari AZ, et al. A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II. Mol Cell. 2004 ;14(5):553–7. doi:10.1016/j.molcel.2004.05.011.

-  Fiévet J, Dillmann C, Lagniel G, et al. Assessing factors for reliable quantitative proteomics based on two-dimensional gel electrophoresis. Proteomics. 2004 ;4(7):1939–49. doi:10.1002/pmic.200300731.

-  Kuras L. Characterization of protein-DNA association in vivo by chromatin immunoprecipitation. Methods Mol Biol. 2004 ;284:147–62. doi:10.1385/1-59259-816-1:147.

-  Biteau B, Labarre J, Toledano MB. ATP-dependent reduction of cysteine-sulphinic acid by S. cerevisiae sulphiredoxin. Nature. 2003 ;425(6961):980–4. doi:10.1038/nature02075.

-  Kuras L, Borggrefe T, Kornberg RD. Association of the Mediator complex with enhancers of active genes. Proc Natl Acad Sci U S A. 2003 ;100(24):13887–91. doi:10.1073/pnas.2036346100.

-  Fauchon M, Lagniel G, Aude J-C, et al. Sulfur Sparing in the Yeast Proteome in Response to Sulfur Demand. Mol Cell. 2002 ;9(4):713–723. doi:10.1016/S1097-2765(02)00500-2.

-  Geisberg J V., Moqtaderi Z, Kuras L, Struhl K. Mot1 Associates with Transcriptionally Active Promoters and Inhibits Association of NC2 in Saccharomyces cerevisiae. Mol Cell Biol. 2002 ;22(23):8122–8134. doi:10.1128/MCB.22.23.8122-8134.2002.

-  Kuras L, Rouillon A, Lee T a, Barbey R, Tyers M, Thomas D. Dual regulation of the met4 transcription factor by ubiquitin-dependent degradation and inhibition of promoter recruitment. Mol Cell. 2002 ;10(1):69–80.

-  Mencía M, Moqtaderi Z, Geisberg J V, Kuras L, Struhl K. Activator-specific recruitment of TFIID and regulation of ribosomal protein genes in yeast. Mol Cell. 2002 ;9(4):823–33.

-  Baudouin-Cornu P, Surdin-Kerjan Y, Marlière P, Thomas D. Molecular evolution of protein atomic composition. Science. 2001 ;293(5528):297–300. doi:10.1126/science.1061052.

-  Vido K, Spector D, Lagniel G, Lopez S, Toledano MB, Labarre J. A proteome analysis of the cadmium response in Saccharomyces cerevisiae. J Biol Chem. 2001 ;276(11):8469–74. doi:10.1074/jbc.M008708200.

-  Spector D, Labarre J, Toledano MB. A genetic investigation of the essential role of glutathione : mutations in the proline biosynthesis pathway are the only suppressors of glutathione auxotrophy in yeast. J Biol Chem. 2001 ;276(10):7011–6. doi:10.1074/jbc.M009814200.

-  Kuras L, Kosa P, Mencia M, Struhl K. TAF-Containing and TAF-independent forms of transcriptionally active TBP in vivo. Science. 2000

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