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11 results on '"MESH : Saccharomyces cerevisiae Proteins"'

1. High phosphatidylinositol 4-phosphate (PI4P)-dependent ATPase activity for the Drs2p-Cdc50p flippase after removal of its N- and C-terminal extensions

Author

Philippe Champeil, Pierre Le Maréchal, Joseph A. Lyons, Poul Nissen, José Luis Vázquez-Ibar, Cédric Montigny, Aurore Jacquot, Thibaud Dieudonné, Jakob Ulstrup, Miriam-Rose Ash, Guillaume Lenoir, Hassina Azouaoui, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut des Neurosciences Paris-Saclay (NeuroPSI), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Nordic-EMBL Partnership for Molecular Medicine, and PUMPkin (DANDRITE), Centre for Membrane Pumps in Cells and Disease (PUMPKIN), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Institut des Neurosciences de Paris-Saclay ( Neuro-PSI ), Université Paris-Sud - Paris 11 ( UP11 ) -Centre National de la Recherche Scientifique ( CNRS ), Nordic-EMBL Partnership for Molecular Medicine, and PUMPkin ( DANDRITE ), and Centre for Membrane Pumps in Cells and Disease ( PUMPKIN )

Subjects
0301 basic medicine, Phosphatidylinositol 4-phosphate, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, MESH : Saccharomyces cerevisiae, Plasma protein binding, Biochemistry, MESH: Thrombin, chemistry.chemical_compound, MESH : Phosphorylation, [ SDV.NEU.SC ] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Cognitive Sciences, 0302 clinical medicine, Adenosine Triphosphate, MESH: Saccharomyces cerevisiae Proteins, Phosphatidylinositol Phosphates, ATP hydrolysis, MESH : Arginine, lipid-protein interaction, MESH: Adenosine Triphosphate, MESH : Adenosine Triphosphate, Phospholipid Transfer Proteins, Phosphorylation, Phospholipids, MESH : Phospholipid Transfer Proteins, medicine.diagnostic_test, [SDV.NEU.PC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Psychology and behavior, Hydrolysis, Autophosphorylation, MESH: Phospholipid Transfer Proteins, Thrombin, MESH: Arginine, [SDV.NEU.SC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Cognitive Sciences, MESH : Protein Binding, Phosphatidylserine, MESH: Phosphatidylinositol Phosphates, MESH: Saccharomyces cerevisiae, phosphoinositide, [ SDV.NEU.NB ] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, inhibition mechanism, MESH: Protein Domains, autophosphorylation, MESH : Mutation, MESH: Hydrolysis, Protein Binding, CDC50 protein, phosphatidylserine, Saccharomyces cerevisiae Proteins, MESH : Proteolysis, MESH: Mutation, Proteolysis, MESH : Calcium-Transporting ATPases, MESH: Proteolysis, Calcium-Transporting ATPases, Saccharomyces cerevisiae, Biology, Arginine, MESH : Phospholipids, MESH: Calcium-Transporting ATPases, MESH : Saccharomyces cerevisiae Proteins, [ SDV.NEU.PC ] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Psychology and behavior, 03 medical and health sciences, Protein Domains, MESH : Hydrolysis, Membrane Biology, medicine, Journal Article, MESH : Phosphatidylinositol Phosphates, MESH: Protein Binding, Phosphatidylinositol, Molecular Biology, MESH: Phospholipids, MESH: Phosphorylation, MESH : Protein Domains, MESH : Thrombin, Cell Biology, Flippase, flippase, 030104 developmental biology, chemistry, Mutation, 030217 neurology & neurosurgery, limited proteolysis
Abstract

International audience; P4-ATPases, also known as phospholipid flippases, are responsible for creating and maintaining transbilayer lipid asymmetry in eukaryotic cell membranes. Here, we use limited proteolysis to investigate the role of the N and C termini in ATP hydrolysis and auto-inhibition of the yeast flippase Drs2p-Cdc50p. We show that limited proteolysis of the detergent-solubilized and purified yeast flippase may result in more than 1 order of magnitude increase of its ATPase activity, which remains dependent on phosphatidylinositol 4-phosphate (PI4P), a regulator of this lipid flippase, and specific to a phosphatidylserine substrate. Using thrombin as the protease, Cdc50p remains intact and in complex with Drs2p, which is cleaved at two positions, namely after Arg104 and after Arg 1290, resulting in a homogeneous sample lacking 104 and 65 residues from its N and C termini, respectively. Removal of the 1291-1302-amino acid region of the C-terminal extension is critical for relieving the auto-inhibition of full-length Drs2p, whereas the 1-104 N-terminal residues have an additional but more modest significance for activity. The present results therefore reveal that trimming off appropriate regions of the terminal extensions of Drs2p can greatly increase its ATPase activity in the presence of PI4P and demonstrate that relief of such auto-inhibition remains compatible with subsequent regulation by PI4P. These experiments suggest that activation of the Drs2p-Cdc50p flippase follows a multistep mechanism, with preliminary release of a number of constraints, possibly through the binding of regulatory proteins in the trans-Golgi network, followed by full activation by PI4P.

Published
2017

2. Trm112p Is a 15-kDa Zinc Finger Protein Essential for the Activity of Two tRNA and One Protein Methyltransferases in Yeast

Author

Léon Dirick, Bruno Lapeyre, Glenn R. Björk, Marie-Hélène Mazauric, Suresh K. Purushothaman, Centre de recherches de biochimie macromoléculaire ( CRBM ), Université Montpellier 1 ( UM1 ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ) -IFR122-Centre National de la Recherche Scientifique ( CNRS ), Institut de Génétique Moléculaire de Montpellier ( IGMM ), Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Centre de recherche en Biologie Cellulaire (CRBM), Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Institut de Génétique Moléculaire de Montpellier (IGMM), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)

Subjects
Proteomics, MESH : DNA, MESH: tRNA Methyltransferases, MESH : Saccharomyces cerevisiae, MESH : Models, Genetic, Biochemistry, MESH: Recombinant Proteins, MESH : Proteomics, MESH: Saccharomyces cerevisiae Proteins, MESH : Anticodon, RNA, Transfer, MESH : Catalysis, MESH: Models, Genetic, Zinc finger, tRNA Methyltransferases, MESH : Cell Nucleus, 0303 health sciences, MESH : Chromatin, MESH: Proteomics, 030302 biochemistry & molecular biology, MESH: DNA, Zinc Fingers, MESH : Protein Binding, Translation (biology), MESH: Saccharomyces cerevisiae, MESH : Mitosis, Chromatin, Recombinant Proteins, MESH : tRNA Methyltransferases, Transfer RNA, T arm, MESH : Mutation, Protein Binding, MESH: Cell Nucleus, TRNA modification, Saccharomyces cerevisiae Proteins, MESH: Mutation, MESH : Recombinant Proteins, Saccharomyces cerevisiae, Mitosis, MESH : RNA, Transfer, Biology, Catalysis, Chromatin remodeling, MESH: Chromatin, MESH : Saccharomyces cerevisiae Proteins, 03 medical and health sciences, Anticodon, MESH: Anticodon, MESH: Zinc Fingers, MESH: Protein Binding, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH : Zinc Fingers, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, 030304 developmental biology, Cell Nucleus, Models, Genetic, TRNA Methyltransferase, DNA, Cell Biology, MESH: Mitosis, MESH: Catalysis, MESH: RNA, Transfer, biology.organism_classification, Mutation, RNA
Abstract

International audience; The degenerate base at position 34 of the tRNA anticodon is the target of numerous modification enzymes. In Saccharomyces cerevisiae, five tRNAs exhibit a complex modification of uridine 34 (mcm(5)U(34) and mcm(5)s(2)U(34)), the formation of which requires at least 25 different proteins. The addition of the last methyl group is catalyzed by the methyltransferase Trm9p. Trm9p interacts with Trm112p, a 15-kDa protein with a zinc finger domain. Trm112p is essential for the activity of Trm11p, another tRNA methyltransferase, and for Mtq2p, an enzyme that methylates the translation termination factor eRF1/Sup45. Here, we report that Trm112p is required in vivo for the formation of mcm(5)U(34) and mcm(5)s(2)U(34). When produced in Escherichia coli, Trm112p forms a complex with Trm9p, which renders the latter soluble. This recombinant complex catalyzes the formation of mcm(5)U(34) on tRNA in vitro but not mcm(5)s(2)U(34). An mtq2-0 trm9-0 strain exhibits a synthetic growth defect, thus revealing the existence of an unexpected link between tRNA anticodon modification and termination of translation. Trm112p is associated with other partners involved in ribosome biogenesis and chromatin remodeling, suggesting that it has additional roles in the cell.

Published
2010

3. TheYTA7gene is involved in the regulation of the isoprenoid pathway in the yeastSaccharomyces cerevisiae

Author

Véronique Anton Leberre, Klaudia Kuranda, Serguei Sokol, Thierry Bergès, Francis Karst, Grazyna Palamarczyk, Kariona A. Grabińska, Jean Marie François, Institute of Biochemistry and Biophysics, Polska Akademia Nauk ( PAN ), PhyMoTS, Physiologie Moléculaire du Transport du Sucre chez les Végétaux ( PhyMoTS ), Université de Poitiers-Centre National de la Recherche Scientifique ( CNRS ) -Université de Poitiers-Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés ( LISBP ), Institut National de la Recherche Agronomique ( INRA ) -Institut National des Sciences Appliquées - Toulouse ( INSA Toulouse ), Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Centre National de la Recherche Scientifique ( CNRS ), Centre de recherche en myologie, Université Pierre et Marie Curie - Paris 6 (UPMC)-Association française contre les myopathies (AFM-Téléthon)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Polska Akademia Nauk (PAN), Transport des assimilats (TA), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), INRA - Mathématiques et Informatique Appliquées (Unité MIAJ), Institut National de la Recherche Agronomique (INRA), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Physiologie Moléculaire du Transport des Sucres chez les Végétaux (PhyMoTS), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Polska Akademia Nauk = Polish Academy of Sciences (PAN), and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Association française contre les myopathies (AFM-Téléthon)-Université Pierre et Marie Curie - Paris 6 (UPMC)

Subjects
[ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Chromosomal Proteins, Non-Histone, [SDV]Life Sciences [q-bio], Prenyltransferase, MESH : Saccharomyces cerevisiae, lovastatin, MESH : Gene Deletion, Endoplasmic Reticulum, Applied Microbiology and Biotechnology, chemistry.chemical_compound, zaragozic acid, MESH : Geranyltranstransferase, MESH : Nuclear Envelope, Gene Expression Regulation, Fungal, 0303 health sciences, MESH : Endoplasmic Reticulum, ATP synthase, biology, Geranyltranstransferase, General Medicine, Biochemistry, lipids (amino acids, peptides, and proteins), Lovastatin, MESH : Terpenes, MESH : Chromosomal Proteins, Non-Histone, medicine.drug, YTA7, Saccharomyces cerevisiae Proteins, Glycosylation, Nuclear Envelope, Coenzyme A, Saccharomyces cerevisiae, isoprenoid pathway, Microbiology, MESH : Saccharomyces cerevisiae Proteins, 03 medical and health sciences, Biosynthesis, Transferases, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH : Gene Expression Regulation, Fungal, medicine, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH : Transferases, 030304 developmental biology, Terpenes, 030306 microbiology, organic chemicals, Membrane Proteins, Zaragozic acid, biology.organism_classification, ERG20, chemistry, MESH : Membrane Proteins, biology.protein, Gene Deletion
Abstract

International audience; The isoprenoid pathway in yeasts is important not only for sterol biosynthesis but also for the production of nonsterol molecules, deriving from farnesyl diphosphate (FPP), implicated in N-glycosylation and biosynthesis of heme and ubiquinones. FPP formed from mevalonate in a reaction catalyzed by FPP synthase (Erg20p). In order to investigate the regulation of Erg20p in Saccharomyces cerevisiae, we searched for its protein partners using a two-hybrid screen, and identified five interacting proteins, among them Yta7p. Subsequently, we showed that Yta7p was a membrane-associated protein localized both to the nucleus and to the endoplasmic reticulum. Deletion of YTA7 affected the enzymatic activity of cis-prenyltransferase (the enzyme that utilizes FPP for dolichol biosynthesis) and the cellular levels of isoprenoid compounds. Additionally, it rendered cells hypersensitive to lovastatin, an inhibitor of 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) that acts upstream of FPP synthase in the isoprenoid pathway. While HMGR is encoded by two genes, HMG1 and HMG2, only HMG2 overexpression was able to restore growth of the yta7Delta cells in the presence of lovastatin. Moreover, the expression level of the S. cerevisiae YTA7 gene was altered upon impairment of the isoprenoid pathway not only by lovastatin but also by zaragozic acid, an inhibitor of squalene synthase. Altogether, these results provide substantial evidence of Yta7p involvement in the regulation of isoprenoid biosynthesis.

Published
2009

4. Adaptive aneuploidy protects against thiol peroxidase deficiency by increasing respiration via key mitochondrial proteins

Author

Vadim N. Gladyshev, Maxim V. Gerashchenko, Michel B. Toledano, Inge Seim, Jean Labarre, Alaattin Kaya, Division of Genetics, Department of Medicine, Brigham & Women's Hospital, Harvard Medical School, Physiologie et Pathogénicité des Stress (PEPS), Département Biologie des Génomes (DBG), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie et de Technologies de Saclay (IBITECS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Stress Oxydatif et Cancer (SOC), Département Biologie Cellulaire (BioCell), Physiologie et Pathogénicité des Stress ( PEPS ), Département Biologie des Génomes ( DBG ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Institut de Biologie et de Technologies de Saclay ( IBITECS ), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Laboratoire Stress Oxydants et Cancer ( LSOC ), and Département Biologie Cellulaire ( BioCell )

Subjects
MESH : Chromosomes, Fungal, [SDV]Life Sciences [q-bio], MESH : Peroxidases, MESH : Saccharomyces cerevisiae, Gene Dosage, MESH : Reactive Oxygen Species, Antimycin A, MESH : Gene Deletion, MESH: Oligomycins, Mitochondrion, MESH: Heat-Shock Proteins, medicine.disease_cause, MESH : Aneuploidy, MESH : Antimycin A, MESH: Gene Dosage, MESH : Rotenone, MESH: Peroxidases, thiol peroxidase, 0302 clinical medicine, MESH: Saccharomyces cerevisiae Proteins, oxidative stress, MESH : Gene Dosage, Oxidoreductases Acting on Sulfur Group Donors, MESH : Oligomycins, MESH : Adaptation, Physiological, Heat-Shock Proteins, MESH : Electron Transport, 2. Zero hunger, chemistry.chemical_classification, 0303 health sciences, Multidisciplinary, Dosage compensation, biology, Cytochrome c peroxidase, MESH: Mitochondrial Proteins, MESH: Reactive Oxygen Species, Biological Sciences, MESH: Saccharomyces cerevisiae, MESH: Chromosomes, Fungal, Adaptation, Physiological, Biochemistry, Peroxidases, MESH: Hydrogen Peroxide, MESH: Membrane Proteins, MESH: Oxidoreductases Acting on Sulfur Group Donors, Chromosome Deletion, Chromosomes, Fungal, Peroxidase, Saccharomyces cerevisiae Proteins, Cellular respiration, MESH: Chromosome Deletion, Saccharomyces cerevisiae, Genes, Fungal, MESH : Saccharomyces cerevisiae Proteins, Electron Transport, Mitochondrial Proteins, 03 medical and health sciences, Rotenone, medicine, MESH: Aneuploidy, MESH : Cytochrome-c Peroxidase, MESH: Cytochrome-c Peroxidase, MESH: Electron Transport, MESH : Mitochondrial Proteins, 030304 developmental biology, Reactive oxygen species, [ SDV ] Life Sciences [q-bio], Membrane Proteins, Hydrogen Peroxide, MESH : Heat-Shock Proteins, Cytochrome-c Peroxidase, biology.organism_classification, MESH : Chromosome Deletion, Aneuploidy, MESH: Adaptation, Physiological, MESH : Oxidoreductases Acting on Sulfur Group Donors, chemistry, MESH : Membrane Proteins, MESH: Gene Deletion, biology.protein, Oligomycins, MESH : Genes, Fungal, MESH : Hydrogen Peroxide, MESH: Rotenone, MESH: Antimycin A, MESH: Genes, Fungal, Reactive Oxygen Species, 030217 neurology & neurosurgery, Oxidative stress, respiration, Gene Deletion
Abstract

International audience; Aerobic respiration is a fundamental energy-generating process; however, there is cost associated with living in an oxygen-rich environment, because partially reduced oxygen species can damage cellular components. Organisms evolved enzymes that alleviate this damage and protect the intracellular milieu, most notably thiol peroxidases, which are abundant and conserved enzymes that mediate hydrogen peroxide signaling and act as the first line of defense against oxidants in nearly all living organisms. Deletion of all eight thiol peroxidase genes in yeast (∆8 strain) is not lethal, but results in slow growth and a high mutation rate. Here we characterized mechanisms that allow yeast cells to survive under conditions of thiol peroxidase deficiency. Two independent ∆8 strains increased mitochondrial content, altered mitochondrial distribution, and became dependent on respiration for growth but they were not hypersensitive to H2O2. In addition, both strains independently acquired a second copy of chromosome XI and increased expression of genes encoded by it. Survival of ∆8 cells was dependent on mitochondrial cytochrome-c peroxidase (CCP1) and UTH1, present on chromosome XI. Coexpression of these genes in ∆8 cells led to the elimination of the extra copy of chromosome XI and improved cell growth, whereas deletion of either gene was lethal. Thus, thiol peroxidase deficiency requires dosage compensation of CCP1 and UTH1 via chromosome XI aneuploidy, wherein these proteins support hydroperoxide removal with the reducing equivalents generated by the electron transport chain. To our knowledge, this is the first evidence of adaptive aneuploidy counteracting oxidative stress.

Published
2015

5. Identification of relations between risk factors and their pathologies or health conditions by mining scientific literature

Author

Hamon, Thierry, Graña, Martin, Raggio, Víctor, Grabar, Natalia, Naya, Hugo, Laboratoire d'Informatique Médicale et de BIOinformatique (LIM&BIO), Université Paris 13 (UP13), Institut Pasteur de Montevideo, Réseau International des Instituts Pasteur (RIIP), Centre de Recherche des Cordeliers (CRC (UMR_S 872)), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Laboratoire d'Informatique Médicale et de BIOinformatique ( LIM&BIO ), Université Paris 13 ( UP13 ), Réseau International des Instituts Pasteur ( RIIP ) -Institut Pasteur de Montevideo, Centre de Recherche des Cordeliers ( CRC (UMR_S 872) ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), and Hôpital Européen Georges Pompidou [APHP] ( HEGP )

Subjects
MESH : Quantitative Trait Loci, MESH: Abstracting and Indexing as Topic, MESH : Saccharomyces cerevisiae, MESH : Microsatellite Repeats, MESH: Semantics, MESH: Natural Language Processing, Medical Subject Headings, MESH: Saccharomyces cerevisiae Proteins, Risk Factors, MESH: Risk Factors, MESH: Disease, Data Mining, Disease, MESH : Semantics, MESH : Mycological Typing Techniques, [ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: Phylogeny, MESH : Minisatellite Repeats, MESH : Trans-Activators, MESH: Polymorphism, Single Nucleotide, MESH : Polymorphism, Single Nucleotide, MESH : Natural Language Processing, MESH : Databases, Bibliographic, MESH : Risk Factors, MESH: Saccharomyces cerevisiae, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Semantics, MESH : Disease, MESH : Abstracting and Indexing as Topic, MESH : United States, Abstracting and Indexing, MESH: Trans-Activators, MESH : Medical Subject Headings, MESH: Medical Subject Headings, MESH : Saccharomyces cerevisiae Proteins, [ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM], MESH: Mycological Typing Techniques, MESH: United States, Natural Language Processing, MESH : Data Mining, MESH: Data Mining, MESH : Nuclear Proteins, MESH : Phylogeny, Databases, Bibliographic, United States, MESH: Quantitative Trait Loci, MESH: Databases, Bibliographic, MESH: Minisatellite Repeats, MESH: Microsatellite Repeats, MESH : Databases as Topic, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], MESH: Databases as Topic, MESH: Nuclear Proteins
Abstract

International audience; Risk factors discovery and prevention is an active research field within the biomedical domain. Despite abundant existing information on risk factors, as found in bibliographical databases or on several websites, accessing this information may be difficult. Methods from Natural Language Processing and Information Extraction can be helpful to access it more easily. Specifically, we show a procedure for analyzing massive amounts of scientific literature and for detecting linguistically marked associations between pathologies and risk factors. This approach allowed us to extract over 22,000 risk factors and associated pathologies. The performed evaluations pointed out that (1) over 88% of risk factors for coronary heart disease are correct, (2) associated pathologies, when they could be compared to MeSH indexing, are correct in about 70%, and (3) in existing terminologies links between risk factors and their pathologies are seldom recorded.

Published
2010

6. Two RNA polymerase I subunits control the binding and release of Rrn3 during transcription

Author

Beckouet, Frédéric, Labarre-Mariotte, Sylvie, Albert, Benjamin, Imazawa, Yukiko, Werner, Michel, Gadal, Olivier, Nogi, Yasuhisa, Kwapisz, Marta, BECKOUET, Frederic, Thuriaux, Pierre, Service de Biologie Intégrative et Génétique Moléculaire (SBIGeM), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire de biologie moléculaire eucaryote (LBME), Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Service de Biologie Intégrative et Génétique Moléculaire ( SBIGeM ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de biologie moléculaire eucaryote du CNRS ( LBME ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Models, Molecular, MESH : Molecular Sequence Data, MESH : Transcription Factors, Transcription, Genetic, MESH: RNA Polymerase I, MESH: Sequence Homology, Amino Acid, [SDV]Life Sciences [q-bio], MESH : Protein Subunits, MESH : Saccharomyces cerevisiae, RNA polymerase II, MESH: Amino Acid Sequence, chemistry.chemical_compound, MESH : Mycophenolic Acid, 0302 clinical medicine, MESH: Saccharomyces cerevisiae Proteins, Sigma factor, RNA Polymerase I, RNA polymerase, Enzyme Inhibitors, ComputingMilieux_MISCELLANEOUS, Polymerase, MESH: Chromatin Immunoprecipitation, 0303 health sciences, biology, MESH : RNA Polymerase I, MESH : Amino Acid Sequence, MESH : Protein Binding, Articles, MESH: Transcription Factors, MESH : Schizosaccharomyces pombe Proteins, MESH: Protein Subunits, MESH: Saccharomyces cerevisiae, MESH : Sequence Homology, Amino Acid, MESH: Schizosaccharomyces, MESH : Dimerization, MESH: Enzyme Inhibitors, Transcription factor II D, MESH : Mutation, Dimerization, Pol1 Transcription Initiation Complex Proteins, MESH: Models, Molecular, Plasmids, Protein Binding, MESH : Pol1 Transcription Initiation Complex Proteins, Chromatin Immunoprecipitation, Saccharomyces cerevisiae Proteins, MESH: Mutation, MESH : Models, Molecular, Termination factor, Molecular Sequence Data, RNA-dependent RNA polymerase, Saccharomyces cerevisiae, MESH: Two-Hybrid System Techniques, MESH : Saccharomyces cerevisiae Proteins, 03 medical and health sciences, MESH : Chromatin Immunoprecipitation, MESH: Plasmids, Two-Hybrid System Techniques, Schizosaccharomyces, RNA polymerase I, MESH: Protein Binding, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, MESH: Pol1 Transcription Initiation Complex Proteins, Molecular Biology, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, 030304 developmental biology, MESH: Mycophenolic Acid, MESH : Enzyme Inhibitors, MESH: Molecular Sequence Data, Sequence Homology, Amino Acid, MESH: Transcription, Genetic, MESH : Transcription, Genetic, MESH: Schizosaccharomyces pombe Proteins, Cell Biology, Mycophenolic Acid, Molecular biology, Protein Subunits, chemistry, MESH : Schizosaccharomyces, MESH : Two-Hybrid System Techniques, MESH: Dimerization, MESH : Plasmids, Mutation, biology.protein, Schizosaccharomyces pombe Proteins, 030217 neurology & neurosurgery, Transcription Factors
Abstract

International audience; Rpa34 and Rpa49 are nonessential subunits of RNA polymerase I, conserved in species from Saccharomyces cerevisiae and Schizosaccharomyces pombe to humans. Rpa34 bound an N-terminal region of Rpa49 in a two-hybrid assay and was lost from RNA polymerase in an rpa49 mutant lacking this Rpa34-binding domain, whereas rpa34Delta weakened the binding of Rpa49 to RNA polymerase. rpa34Delta mutants were caffeine sensitive, and the rpa34Delta mutation was lethal in a top1Delta mutant and in rpa14Delta, rpa135(L656P), and rpa135(D395N) RNA polymerase mutants. These defects were shared by rpa49Delta mutants, were suppressed by the overexpression of Rpa49, and thus, were presumably mediated by Rpa49 itself. rpa49 mutants lacking the Rpa34-binding domain behaved essentially like rpa34Delta mutants, but strains carrying rpa49Delta and rpa49-338::HIS3 (encoding a form of Rpa49 lacking the conserved C terminus) had reduced polymerase occupancy at 30 degrees C, failed to grow at 25 degrees C, and were sensitive to 6-azauracil and mycophenolate. Mycophenolate almost fully dissociated the mutant polymerase from its ribosomal DNA (rDNA) template. The rpa49Delta and rpa49-338::HIS3 mutations had a dual effect on the transcription initiation factor Rrn3 (TIF-IA). They partially impaired its recruitment to the rDNA promoter, an effect that was bypassed by an N-terminal deletion of the Rpa43 subunit encoded by rpa43-35,326, and they strongly reduced the release of the Rrn3 initiation factor during elongation. These data suggest a dual role of the Rpa49-Rpa34 dimer during the recruitment of Rrn3 and its subsequent dissociation from the elongating polymerase.

Published
2008

7. The Hsp90 chaperone controls the biogenesis of L7Ae RNPs through conserved machinery

Author

Nathalie Marmier-Gourrier, Tamás Kiss, Edouard Bertrand, Beáta E. Jády, Bruno Charpentier, Christina Pescia, Séverine Boulon, Céline Verheggen, Bérengère Pradet-Balade, Alain Krol, Benjamin Rothé, Barbara Bardoni, Laurence Wurth, Christine Allmang, Christiane Branlant, Marie-Cécile Robert, Institut de Génétique Moléculaire de Montpellier (IGMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Maturation des ARN et enzymologie moléculaire (MAEM), Cancéropôle du Grand Est-Université Henri Poincaré - Nancy 1 (UHP)-IFR111-Centre National de la Recherche Scientifique (CNRS), Architecture et réactivité de l'ARN (ARN), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Laboratoire de biologie moléculaire eucaryote (LBME), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique Moléculaire de Montpellier ( IGMM ), Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Maturation des ARN et enzymologie moléculaire ( MAEM ), Cancéropôle du Grand Est-Université Henri Poincaré - Nancy 1 ( UHP ) -IFR111-Centre National de la Recherche Scientifique ( CNRS ), Architecture et réactivité de l'ARN ( ARN ), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de biologie moléculaire eucaryote du CNRS ( LBME ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de génétique et biologie moléculaire et cellulaire ( IGBMC ), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3)

Subjects
MESH: Signal Transduction, Protein Folding, MESH : Saccharomyces cerevisiae, MESH: DNA Helicases, Cell Cycle Proteins, MESH : Cell Cycle Proteins, MESH: Saccharomyces cerevisiae Proteins, Heterogeneous-Nuclear Ribonucleoprotein L, MESH : DNA Helicases, RUVBL2, MESH : Cell Proliferation, Conserved Sequence, Research Articles, MESH: Evolution, Molecular, Ribonucleoprotein, Adenosine Triphosphatases, 0303 health sciences, MESH: Conserved Sequence, biology, 030302 biochemistry & molecular biology, Nuclear Proteins, RNA-Binding Proteins, MESH : Protein Binding, MESH : HSP90 Heat-Shock Proteins, Hsp90, MESH: Saccharomyces cerevisiae, Cell biology, DNA-Binding Proteins, MESH : Heterogeneous-Nuclear Ribonucleoprotein L, MESH : DNA-Binding Proteins, MESH: Molecular Chaperones, Protein Binding, Signal Transduction, MESH : Protein Folding, Ribosomal Proteins, Saccharomyces cerevisiae Proteins, animal structures, MESH: Protein Folding, MESH : RNA-Binding Proteins, Saccharomyces cerevisiae, Article, Evolution, Molecular, MESH : Saccharomyces cerevisiae Proteins, 03 medical and health sciences, MESH: Cell Cycle Proteins, MESH : Conserved Sequence, MESH: Cell Proliferation, MESH: Adenosine Triphosphatases, MESH: HSP90 Heat-Shock Proteins, MESH: Heterogeneous-Nuclear Ribonucleoprotein L, MESH: Protein Binding, snRNP, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, HSP90 Heat-Shock Proteins, MESH : Evolution, Molecular, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, 030304 developmental biology, R2TP complex, Cell Proliferation, MESH : Signal Transduction, MESH : Adenosine Triphosphatases, DNA Helicases, MESH : Molecular Chaperones, RNA, MESH : Nuclear Proteins, Cell Biology, MESH: RNA-Binding Proteins, Chaperone (protein), biology.protein, MESH: Nuclear Proteins, Biogenesis, MESH: DNA-Binding Proteins, Molecular Chaperones, Transcription Factors
Abstract

International audience; RNA-binding proteins of the L7Ae family are at the heart of many essential ribonucleoproteins (RNPs), including box C/D and H/ACA small nucleolar RNPs, U4 small nuclear RNP, telomerase, and messenger RNPs coding for selenoproteins. In this study, we show that Nufip and its yeast homologue Rsa1 are key components of the machinery that assembles these RNPs. We observed that Rsa1 and Nufip bind several L7Ae proteins and tether them to other core proteins in the immature particles. Surprisingly, Rsa1 and Nufip also link assembling RNPs with the AAA + adenosine triphosphatases hRvb1 and hRvb2 and with the Hsp90 chaperone through two conserved adaptors, Tah1/hSpagh and Pih1. Inhibition of Hsp90 in human cells prevents the accumulation of U3, U4, and telomerase RNAs and decreases the levels of newly synthesized hNop58, hNHP2, 15.5K, and SBP2. Thus, Hsp90 may control the folding of these proteins during the formation of new RNPs. This suggests that Hsp90 functions as a master regulator of cell proliferation by allowing simultaneous control of cell signaling and cell growth.

Published
2008

8. Model peptides based on the binding loop of the copper metallochaperone Atx1: selectivity of the consensus sequence MxCxxC for metal ions Hg(II), Cu(I), Cd(II), Pb(II) and Zn(II)

Author

Didier Boturyn, Michel Ferrand, Pierre Rousselot-Pailley, Olivier Sénèque, Pascal Dumy, Colette Lebrun, Serge Crouzy, Pascale Delangle, Laboratoire de Chimie et Biologie des Métaux (LCBM - UMR 5249), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences Moléculaires de Marseille (ISM2), Centre National de la Recherche Scientifique (CNRS)-École Centrale de Marseille (ECM)-Aix Marseille Université (AMU), Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques (LCBPT - UMR 8601), Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), Reconnaissance Ionique et Chimie de Coordination (RICC), SYstèmes Moléculaires et nanoMatériaux pour l’Energie et la Santé (SYMMES), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS), Laboratoire de biophysique moléculaire et cellulaire (LBMC), Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF), Département de Chimie Moléculaire (DCM), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'études dynamiques et structurales de la sélectivité (LEDSS), Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Université Joseph Fourier - Grenoble 1 (UJF)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie et Biologie des Métaux ( LCBM - UMR 5249 ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ), Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques ( LCBPT - UMR 8601 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Centre National de la Recherche Scientifique ( CNRS ), Reconnaissance Ionique et Chimie de Coordination ( RICC ), SYstèmes Moléculaires et nanoMatériaux pour l’Energie et la Santé ( SYMMES ), Centre National de la Recherche Scientifique ( CNRS ) -Institut Nanosciences et Cryogénie ( INAC ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Grenoble Alpes ( UGA ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Grenoble Alpes ( UGA ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut Nanosciences et Cryogénie ( INAC ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Grenoble Alpes ( UGA ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Grenoble Alpes ( UGA ), Département de Chimie Moléculaire ( DCM ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Institut de Chimie du CNRS (INC)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5), Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 ( UGSF ), Institut National de la Recherche Agronomique ( INRA ) -Université de Lille-Centre National de la Recherche Scientifique ( CNRS ), Institut des Sciences Moléculaires de Marseille ( ISM2 ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Centrale de Marseille ( ECM ) -Aix Marseille Université ( AMU ), Laboratoire de biophysique moléculaire et cellulaire ( LBMC ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'études dynamiques et structurales de la sélectivité ( LEDSS ), and Université Joseph Fourier - Grenoble 1 ( UJF ) -Centre National de la Recherche Scientifique ( CNRS )

Subjects
Models, Molecular, MESH: Metalloproteins, Amino Acid Motifs, Peptide, 01 natural sciences, MESH : Spectrophotometry, Ultraviolet, MESH: Amino Acid Motifs, MESH : Metalloproteins, MESH: Saccharomyces cerevisiae Proteins, MESH : Peptides, Cyclic, MESH: Spectrophotometry, Ultraviolet, MESH: Nuclear Magnetic Resonance, Biomolecular, Metalloprotein, [ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Peptide sequence, Conserved Sequence, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, Cyclic compound, MESH: Conserved Sequence, [ CHIM.COOR ] Chemical Sciences/Coordination chemistry, MESH: Chromatography, Gel, MESH : Spectrometry, Mass, Electrospray Ionization, MESH: Metals, Heavy, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Cyclic peptide, MESH : Metals, Heavy, Chromatography, Gel, MESH : Carrier Proteins, Selectivity, MESH: Models, Molecular, Spectrometry, Mass, Electrospray Ionization, MESH : Amino Acid Motifs, Saccharomyces cerevisiae Proteins, Stereochemistry, MESH : Models, Molecular, Metal ions in aqueous solution, chemistry.chemical_element, MESH: Carrier Proteins, MESH : Nuclear Magnetic Resonance, Biomolecular, 010402 general chemistry, MESH: Spectrometry, Mass, Electrospray Ionization, Peptides, Cyclic, Inorganic Chemistry, MESH : Saccharomyces cerevisiae Proteins, MESH : Conserved Sequence, Metals, Heavy, Metalloproteins, MESH : Chromatography, Gel, [CHIM.COOR]Chemical Sciences/Coordination chemistry, Physical and Theoretical Chemistry, Nuclear Magnetic Resonance, Biomolecular, MESH: Peptides, Cyclic, 010405 organic chemistry, Copper, 0104 chemical sciences, chemistry, Spectrophotometry, Ultraviolet, Carrier Proteins
Abstract

International audience; The amino acid sequence MxCxxC is conserved in many soft-metal transporters that are involved in the control of the intracellular concentration of ions such as Cu(I), Hg(II), Zn(II), Cd(II), and Pb(II). A relevant task is thus the selectivity of the motif MxCxxC for these different metal ions. To analyze the coordination properties and the selectivity of this consensus sequence, we have designed two model peptides that mimic the binding loop of the copper chaperone Atx1: the cyclic peptide P(C) c(GMTCSGCSRP) and its linear analogue P(L) (Ac-MTCSGCSRPG-NH2). By using complementary analytical and spectroscopic methods, we have demonstrated that 1:1 complexes are obtained with Cu(I) and Hg(II), whereas 1:1 and 1:2 (M:P) species are successively formed with Zn(II), Cd(II), and Pb(II). The complexation properties of the cyclic and linear peptides are very close, but the cyclic compound provides systematically higher affinity constants than its unstructured analogue. The introduction of a xPGx motif that forms a type II beta turn in P(C) induces a preorganization of the binding loop of the peptide that enhances the stabilities of the complexes (up to 2 orders of magnitude difference for the Hg complexes). The affinity constants were measured in the absence of any reducing agent that would compete with the peptides and range in the order Hg(II) > Cu(I) >> Cd(II) > Pb(II) > Zn(II). This sequence is thus highly selective for Cu(I) compared to the essential ion Zn(II) that could compete in vivo or compared to the toxic ions Cd(II) and Pb(II). Only Hg(II) may be an efficient competitor of Cu(I) for binding to the MxCxxC motif in metalloproteins.

Published
2006

9. Cytochrome c and SDS: a molten globule protein with altered axial ligation

Author

Arnaud Bondon, Paul R. Vasos, Paola Turano, Gérard Simonneaux, Ivano Bertini, Soizic Chevance, Dept Chem Ugo Schiff, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Magnet Resonance Ctr CERM, Magnet Resonance Center (CERM), Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques (LCBPT - UMR 8601), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences Chimiques de Rennes (ISCR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Firenze = University of Florence (UniFI), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), University of Florence (UNIFI), Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Rennes-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES), University of Florence, Magnet Resonance Center ( CERM ), Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques ( LCBPT - UMR 8601 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Centre National de la Recherche Scientifique ( CNRS ), Institut des Sciences Chimiques de Rennes ( ISCR ), Université de Rennes 1 ( UR1 ), and Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Ecole Nationale Supérieure de Chimie de Rennes-Institut National des Sciences Appliquées ( INSA ) -Centre National de la Recherche Scientifique ( CNRS )

Subjects
Magnetic Resonance Spectroscopy, Time Factors, Cytochrome, MESH : Cytochromes c, Protein Conformation, MESH : Saccharomyces cerevisiae, MESH : Rotation, 01 natural sciences, Protein structure, MESH: Protein Conformation, MESH: Rotation, MESH: Saccharomyces cerevisiae Proteins, Structural Biology, MESH : Myocardium, MESH: Animals, MESH : Protein Conformation, MESH : Viscosity, 0303 health sciences, biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Chemistry, Viscosity, Cytochrome c, Cytochromes c, Sodium Dodecyl Sulfate, Nuclear magnetic resonance spectroscopy, MESH: Cytochromes c, Ligand (biochemistry), MESH: Saccharomyces cerevisiae, Molten globule, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Protons, MESH : Time Factors, MESH: Sodium Dodecyl Sulfate, Saccharomyces cerevisiae Proteins, MESH: Myocardium, Rotation, MESH: Viscosity, Saccharomyces cerevisiae, 010402 general chemistry, MESH : Saccharomyces cerevisiae Proteins, 03 medical and health sciences, MESH : Protons, Animals, Horses, MESH: Horses, Molecular Biology, Rotational correlation time, MESH : Sodium Dodecyl Sulfate, 030304 developmental biology, MESH: Magnetic Resonance Spectroscopy, Myocardium, MESH: Time Factors, Random coil, 0104 chemical sciences, Crystallography, biology.protein, MESH : Horses, MESH : Magnetic Resonance Spectroscopy, MESH : Animals, MESH: Protons, [ SDV.BBM.BS ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM]
Abstract

International audience; Saccharomices cerevisiae (yeast iso-1) cytochrome c has been investigated in the presence of 100 mM SDS in order to simulate the interaction of cytochrome c with membrane. Under these circumstances, a high spin species with detached methionine axial ligand is observed through NMR, in analogy to findings on the horse heart protein. However, at variance with the latter system, for the yeast protein also a low spin species is detected, which appears to be present with a concentration of about 40% with respect to that of the high spin species. The R(1), R(2), [1H]-15N NOE of backbone amides which are not affected by paramagnetism are homogeneous and allow a simultaneous analysis of the data for the two species. The result is that the rotational correlation time is larger than in water and larger than expected on the basis of viscosity of the SDS-containing solution. This finding suggests interactions of cytochrome c with SDS. Furthermore, it appears that there is subnanosecond backbone mobility, which also accounts for the decreased intensity of NOE cross-peaks and may be associated with equilibria between helical and random coil structure. The dynamic behavior appears to be a common feature of the high spin and low spin species and is consistent with the presence of a molten globule state. The molten globule nature of the protein could account for the presence of the different axial coordination of the heme iron. Such findings are meaningful with respect to the physiology of cytochrome c as electron transfer protein and as promoter of apoptosis.

Published
2004

10. Genetic identification of neurons controlling a sexually dimorphic behaviour

Author

Gatti , S., Ferveur , J. F., Martin , J. R., Neurobiologie de l'apprentissage, de la mémoire et de la communication ( NAMC ), Université Paris-Sud - Paris 11 ( UP11 ) -Centre National de la Recherche Scientifique ( CNRS ), Développement et Communication Chimique chez les Insectes ( DCCI ), and Centre National de la Recherche Scientifique ( CNRS ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement

Subjects
MESH : Recombinant Fusion Proteins, MESH : Transcription Factors, MESH : Male, fungi, MESH : Animals, Genetically Modified, MESH : Sex Characteristics, MESH : Nuclear Proteins, MESH : Neurons, MESH : Nervous System Physiology, MESH : Saccharomyces cerevisiae Proteins, MESH : Locomotion, [ SDV.NEU ] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], MESH : Drosophila melanogaster, MESH : Fungal Proteins, MESH : Female, MESH : Animals, MESH : Sexual Behavior, Animal, MESH : Motor Activity
Abstract

In the fruit fly Drosophila melanogaster, locomotor activity is sexually dimorphic: female flies constantly modulate their activity pattern whereas males show a steadier, stereotyped walking pace [1]. Here, we mapped the area of the brain controlling this behavioural dimorphism. Adult male Drosophila expressing a dominant feminising transgene in a small cluster of neurons in the pars intercerebralis exhibited a female-like pattern of locomotor activity. Genetic ablation of these neurons prevented the feminisation of the locomotor activity of transgenic males. The results suggest that this cluster of neurons modulates sex-specific activity, but is not involved in initiating fly locomotion. Nor does it control male courtship behaviour, because feminisation of courtship was not correlated with the feminisation of locomotor activity.

Published
2000

11. A 1,3-beta-glucanosyltransferase isolated from the cell wall of Aspergillus fumigatus is a homologue of the yeast Bgl2p

Author

Mouyna , Isabelle, Hartland , Robbert P., Fontaine , Thierry, Diaquin , Michel, Simenel , Catherine, Delepierre , Murielle, Henrissat , Bernard, Latgé , Jean-Paul, Aspergillus, Institut Pasteur [Paris], Résonance Magnétique Nucléaire, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Architecture et fonction des macromolécules biologiques ( AFMB ), Centre National de la Recherche Scientifique ( CNRS ) -Aix Marseille Université ( AMU ) -Institut National de la Recherche Agronomique ( INRA ), and The authors thank J. d’Alayer for performing the amino acid sequencing and J. Lemoine for the matrix-assisted de- sorption/time-of-flight mass spectrometry analysis. I. Mouyna and R. Hartland made equal contributions to the work published.

Subjects
MESH : Chromatography, Ion Exchange, MESH : Molecular Sequence Data, MESH : Cloning, Molecular, MESH : Candida albicans, MESH : Amino Acid Sequence, MESH : Sequence Alignment, MESH : Glucan Endo-1,3-beta-D-Glucosidase, MESH : Saccharomyces cerevisiae, MESH : Sequence Homology, Amino Acid, MESH : Saccharomyces cerevisiae Proteins, MESH : Aspergillus fumigatus, MESH : Genes, Fungal, MESH : DNA, Fungal, MESH : Transformation, Genetic, skin and connective tissue diseases, [ SDV.MP.MYC ] Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, MESH : Sequence Analysis, DNA, MESH : Cell Wall
Abstract

International audience; A 1,3-beta-glucanosyltransferase which introduces intrachain 1,6-beta linkages into 1,3-beta-glucan was isolated from the cell wall of Aspergillus fumigatus. The biochemical and molecular characterization of the A. fumigatus transferase showed it was homologous to the Saccharomyces cerevisiae and Candida albicans transferase Bgl2p. A null mutant constructed in A. fumigatus by gene replacement did not show a distinct phenotype from the parental strain. The putative function of this major cell-wall-associated protein is discussed.

Published
1998

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