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6 results on '"MESH : Protein Subunits"'

1. Binding interface between the Salmonella σ(S)/RpoS subunit of RNA polymerase and Crl: hints from bacterial species lacking crl

Author

Christina Sizun, Jacques Bellalou, Claudine Mayer, Véronique Monteil, Mireille Nowakowski, Fabienne Levi-Acobas, Françoise Norel, François Bontems, Paola Cavaliere, Systèmes macromoléculaires et Signalisation, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Production de Protéines Recombinantes (Plate-Forme) (PRPF), Université Paris Diderot - Paris 7 (UPD7), Microbiologie structurale - Structural Microbiology (Microb. Struc. (UMR_3528 / U-Pasteur_5)), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), This work was supported by the French National Research Agency [grant ANR- 11-BSV3-009], the IR-RMN-THC (CNRS FR3050) for access to the 950 MHz spectrometer at Gif-sur-Yvette for preliminary experiments and by grants from the Institut Pasteur and the Centre National de la Recherche Scientifique. The WeNMR project (European FP7 e-Infrastructure grant, contract no. 261572, www.wenmr.eu), supported by the European Grid Initiative (EGI) through the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, South Africa, Malaysia, Taiwan, the Latin America GRID infrastructure via the Gisela project and the US Open Science Grid (OSG) are acknowledged for the use of web portals, computing and storage facilities., ANR-11-BSV3-0009,SIGMADAPT,Rôle de SigmaS dans la compétitivité et l'adaptation des bactéries à l'environnement(2011), European Project: 261572,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2010-2,WENMR(2010), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Institut de Chimie des Substances Naturelles ( ICSN ), Centre National de la Recherche Scientifique ( CNRS ), Production de Protéines Recombinantes (Plate-Forme) ( PRPF ), Université Paris Diderot - Paris 7 ( UPD7 ), Microbiologie structurale, ANR-11-BSV3-0009,SIGMADAPT,Rôle de SigmaS dans la compétitivité et l'adaptation des bactéries à l'environnement ( 2011 ), European Project : 261572,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2010-2,WENMR ( 2010 ), Institut Pasteur [Paris] - Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), ANR-11-BSV3-0009, SIGMADAPT, Rôle de SigmaS dans la compétitivité et l'adaptation des bactéries à l'environnement(2011), and European Project : 261572, EC:FP7:INFRA, FP7-INFRASTRUCTURES-2010-2, WENMR(2010)

Subjects
MESH : Models, Chemical, MESH: Pseudomonas aeruginosa/metabolism, MESH : Molecular Sequence Data, Protein Conformation, MESH : Protein Subunits, Plasma protein binding, MESH: Amino Acid Sequence, MESH: DNA-Directed RNA Polymerases/chemistry, chemistry.chemical_compound, Protein structure, MESH: Protein Conformation, MESH: Structure-Activity Relationship, MESH : Sigma Factor/ultrastructure, MESH: Bacterial Proteins/ultrastructure, Salmonella, Sigma factor, [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology, RNA polymerase, MESH: Sigma Factor/metabolism, MESH: DNA-Directed RNA Polymerases/metabolism, MESH : Structure-Activity Relationship, MESH : Protein Conformation, Genetics, Multidisciplinary, MESH : Amino Acid Sequence, MESH: Models, Chemical, food and beverages, MESH : Protein Binding, DNA-Directed RNA Polymerases, MESH: Protein Subunits, MESH : Bacterial Proteins/ultrastructure, MESH: Amino Acid Substitution, Molecular Docking Simulation, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Biochemistry, Pseudomonas aeruginosa, MESH : Molecular Docking Simulation, MESH: Bacterial Proteins/metabolism, Protein Binding, MESH: Bacterial Proteins/chemistry, MESH : Salmonella/metabolism, MESH : Pseudomonas aeruginosa/metabolism, MESH : Sigma Factor/chemistry, Protein subunit, Molecular Sequence Data, MESH : DNA-Directed RNA Polymerases/chemistry, Sigma Factor, Biology, Article, Structure-Activity Relationship, MESH: DNA-Directed RNA Polymerases/ultrastructure, MESH : DNA-Directed RNA Polymerases/ultrastructure, MESH : Amino Acid Substitution, Bacterial Proteins, Species Specificity, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Molecular Docking Simulation, MESH: Sigma Factor/chemistry, MESH : Species Specificity, MESH : Bacterial Proteins/chemistry, MESH: Protein Binding, MESH: Species Specificity, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, MESH : DNA-Directed RNA Polymerases/metabolism, Binding site, Gene, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Binding Sites, MESH: Molecular Sequence Data, fungi, MESH : Sigma Factor/metabolism, Protein Subunits, Amino Acid Substitution, Models, Chemical, chemistry, MESH: Binding Sites, MESH : Bacterial Proteins/metabolism, MESH: Salmonella/metabolism, rpoS, MESH : Binding Sites, MESH: Sigma Factor/ultrastructure
Abstract

International audience; In many Gram-negative bacteria, including Salmonella enterica serovar Typhimurium (S. Typhimurium), the sigma factor RpoS/σ S accumulates during stationary phase of growth, and associates with the core RNA polymerase enzyme (E) to promote transcription initiation of genes involved in general stress resistance and starvation survival. Whereas σ factors are usually inactivated upon interaction with anti-σ proteins, σ S binding to the Crl protein increases σ S activity by favouring its association to E. Taking advantage of evolution of the σ S sequence in bacterial species that do not contain a crl gene, like Pseudomonas aeruginosa, we identified and assigned a critical arginine residue in σ S to the S. Typhimurium σ S-Crl binding interface. We solved the solution structure of S. Typhimurium Crl by NMR and used it for NMR binding assays with σ S and to generate in silico models of the σ S-Crl complex constrained by mutational analysis. The σ S-Crl models suggest that the identified arginine in σ S interacts with an aspartate of Crl that is required for σ S binding and is located inside a cavity enclosed by flexible loops, which also contribute to the interface. This study provides the basis for further structural investigation of the σ S-Crl complex. In bacteria, a primary housekeeping sigma factor and one or more alternative σ factors associate with the catalytically active RNA polymerase (RNAP) core enzyme (α 2β β 'ω , E), to form the holoenzyme Eσ , and direct transcription initiation of specific subsets of genes 1,2. In many Gram-negative bacteria, σ S /RpoS is produced during late exponential phase, or in response to stress, to modify global gene transcription and to allow stationary phase survival and general stress resistance 3–5. In the wide host-range pathogen S. Typhimurium, σ S is not only required for general stress resistance, but also for virulence, biofilm formation and development of the red dry and rough (rdar) morphotype, a colony morphology caused by the production of amyloid fibers (curli) and cellulose 6–8. The efficiency of formation of the housekeeping and alternative Eσ can be modulated by regulatory factors that bind E and/or σ 5,9. So far, Crl is the only known σ S-dedicated regulatory factor that enhances σ S activity through a direct interaction, favouring Eσ S formation 7,10–15. Analyses of sequenced bacterial genomes revealed that crl is less widespread and less conserved at the sequence level than

Published
2015
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2. FISH-quant: automatic counting of transcripts in 3D FISH images

Author

Xavier Darzacq, Adrien Senecal, Edouard Bertrand, Nathalie Ly, Christophe Zimmer, Florian Mueller, Olivier Collin, Eugenia Basyuk, Hervé Marie-Nelly, Katjana Tantale, Imagerie et Modélisation, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-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), Institut de Génomique Fonctionnelle (IGF), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), This research was supported by the Agence Nationale de la Recherche (ANR-10-BLAN-1222, ANR-09-PIRI-0024, ANR-10-INTB-1401), Sidaction, the Région Ile-de-France under C'Nano IdF (the Center of Competences in NanoSciences for the Paris region), the Fondation pour la Recherche Médicale en France (FRM) and the Institut Pasteur, We thank J. McNally for editing the manuscript., ANR-09-PIRI-0024,Chromodyn(2009), ANR-10-BLAN-1222,IMAGenEx,Imagerie de l'expression génétique dans la cellule(2010), ANR-10-INTB-1401,RNAtrans,Visualisation de molécules uniques d'ARNm et de leur topologie afin d'étudier la traduction locale dans les neurones(2010), Mueller, Florian, Programme interdisciplinaire sur les systèmes biologiques et d'innovation biomédicale - - Chromodyn2009 - ANR-09-PIRI-0024 - PIRI - VALID, BLANC - Imagerie de l'expression génétique dans la cellule - - IMAGenEx2010 - ANR-10-BLAN-1222 - BLANC - VALID, Programme Blanc International édition 2010 - Visualisation de molécules uniques d'ARNm et de leur topologie afin d'étudier la traduction locale dans les neurones - - RNAtrans2010 - ANR-10-INTB-1401 - Blanc international 2010 - VALID, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Institut de biologie de l'ENS Paris (UMR 8197/1024) ( IBENS ), École normale supérieure - Paris ( ENS Paris ) -École normale supérieure - Paris ( ENS Paris ) -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 ), Institut de Génomique Fonctionnelle ( IGF ), Centre National de la Recherche Scientifique ( CNRS ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université Montpellier 1 ( UM1 ) -Université de Montpellier ( UM ), ANR-09-PIRI-0024,Chromodyn,Mapping and modelling of chromosome dynamics ( 2009 ), ANR-10-BLAN-1222,IMAGenEx,Imagerie de l'expression génétique dans la cellule ( 2010 ), ANR-10-INTB-1401,RNAtrans,Visualisation de molécules uniques d'ARNm et de leur topologie afin d'étudier la traduction locale dans les neurones ( 2010 ), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-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)-Université de Montpellier (UM), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), and Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS)

Subjects
MESH : RNA, Messenger, Transcription, Genetic, [SDV]Life Sciences [q-bio], MESH : Protein Subunits, MESH : Actins, MESH : Models, Biological, Biochemistry, 0302 clinical medicine, Image Processing, Computer-Assisted, MESH: In Situ Hybridization, Fluorescence, In Situ Hybridization, Fluorescence, Genetics, 0303 health sciences, medicine.diagnostic_test, Fluorescence in situ hybridization, MESH: Protein Subunits, MESH: Image Processing, Computer-Assisted, MESH : In Situ Hybridization, Fluorescence, [SDV] Life Sciences [q-bio], MESH: Reproducibility of Results, MESH : Computer Simulation, MESH : Imaging, Three-Dimensional, MESH : RNA Polymerase II, RNA Polymerase II, MESH : Image Processing, Computer-Assisted, Biotechnology, Computational biology, MESH: Imaging, Three-Dimensional, Biology, MESH: Actins, Models, Biological, 03 medical and health sciences, Imaging, Three-Dimensional, MESH: Computer Simulation, medicine, Computer Simulation, RNA, Messenger, Molecular Biology, Gene, 030304 developmental biology, MESH: RNA, Messenger, Messenger RNA, [ SDV ] Life Sciences [q-bio], MESH : Reproducibility of Results, MESH: Transcription, Genetic, MESH: Models, Biological, RNA, MESH : Transcription, Genetic, Reproducibility of Results, Cell Biology, Actins, Computational biology and bioinformatics, MESH: RNA Polymerase II, Protein Subunits, 030217 neurology & neurosurgery
Abstract

International audience; Transcription is inherently stochastic even in clonal cell populations 1. Studies at single-cell-single-molecule level enable a quantitative understanding of the underlying regulatory mechanisms 2,3. A widely used technique is single-molecule RNA fluorescence in-situ hybridization (FISH), in which fluorescent probes target the mRNA of interest and individual molecules appear as bright diffraction-limited spots (Fig. 1a,b) 3. Recent experimental progress makes FISH easy to use 4 , but a dedicated image analysis tool is currently missing. Available methods allow counting of isolated mature mRNAs but cannot reliably quantify the dense mRNA aggregates at transcription sites (TS) in three dimensions (3D), particularly of highly transcribing genes 4. We developed FISH-QUANT to close this gap (Supplementary Note 1)

Published
2013
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3. AMP-activated protein kinase in the regulation of hepatic energy metabolism: from physiology to therapeutic perspectives.: AMPK in the liver

Author

Benoit Viollet, Marc Foretz, Sophie Hébrard, Fabrizio Andreelli, Bruno Guigas, Rémi Mounier, Jocelyne Leclerc, Louise Lantier, Institut Cochin (UMR_S567 / UMR 8104), Université Paris Descartes - Paris 5 (UPD5) - Institut National de la Santé et de la Recherche Médicale (INSERM) - Centre National de la Recherche Scientifique (CNRS), Division of cardiology, Université Catholique de Louvain (UCL), Department of Molecular Cell Biology, Leiden University Medical Center (LUMC), Déterminants génétiques du diabète de type 2 et de ses complications vasculaires, Université Paris Diderot - Paris 7 (UPD7) - Institut National de la Santé et de la Recherche Médicale (INSERM), Service de Diabétologie-Endocrinologie-Nutrition, Assistance publique - Hôpitaux de Paris (AP-HP) - AP-HP - Hôpital Bichat - Claude Bernard [Paris] - Université Paris Diderot - Paris 7 (UPD7), FP6 EXGENESIS Integrated Project (LSHM-CT- 2004-005272), PNRD, ALFEDIAM, Institut Benjamin Delessert., Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Catholique de Louvain = Catholic University of Louvain (UCL), Déterminants génétiques du diabète de type 2 et de ses complications vasculaires ((U 695)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Diderot - Paris 7 (UPD7), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Diderot - Paris 7 (UPD7), Université Paris Diderot - Paris 7 (UPD7)-AP-HP - Hôpital Bichat - Claude Bernard [Paris], and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)

Subjects
Liver Cirrhosis, MESH : Ribonucleotides, MESH : Fatty Liver, Physiology, Protein Conformation, MESH : Protein Subunits, MESH : Dyslipidemias, AMP-Activated Protein Kinases, 0302 clinical medicine, MESH: Protein Conformation, AMP-activated protein kinase, MESH : Lipid Metabolism, energy metabolism, Glucose homeostasis, Homeostasis, MESH: Animals, MESH: AMP-Activated Protein Kinases, Beta oxidation, MESH: Fatty Liver, MESH : Protein Conformation, MESH: Lipid Metabolism, [SDV.MHEP.EM] Life Sciences [q-bio]/Human health and pathology/Endocrinology and metabolism, 0303 health sciences, biology, MESH: Energy Metabolism, MESH: Gluconeogenesis, hepatic glucose production, MESH : AMP-Activated Protein Kinases, [SDV.MHEP.EM]Life Sciences [q-bio]/Human health and pathology/Endocrinology and metabolism, MESH: Protein Subunits, Mitochondria, MESH: Glucose, MP-activated protein kinase, MESH: Homeostasis, 030220 oncology & carcinogenesis, MESH : Homeostasis, Lipogenesis, MESH : Aminoimidazole Carboxamide, type 2 diabetes, MESH : Mitochondria, MESH: Liver Cirrhosis, medicine.medical_specialty, MESH: Mitochondria, MESH : Gluconeogenesis, Carbohydrate metabolism, MESH: Aminoimidazole Carboxamide, liver, Article, 03 medical and health sciences, Internal medicine, MESH: Hypoglycemic Agents, medicine, Animals, Humans, Hypoglycemic Agents, MESH : Liver Cirrhosis, 030304 developmental biology, Dyslipidemias, fatty liver, MESH: Humans, MESH : Glucose, MESH: Dyslipidemias, MESH : Humans, Gluconeogenesis, AMPK, MESH : Liver, Lipid metabolism, Ribonucleotides, Aminoimidazole Carboxamide, Lipid Metabolism, MESH : Hypoglycemic Agents, MESH : Energy Metabolism, Protein Subunits, therapeutic, Endocrinology, Glucose, MESH: Ribonucleotides, Mitochondrial biogenesis, biology.protein, MESH : Animals, MESH: Liver
Abstract

International audience; As the liver is central in the maintenance of glucose homeostasis and energy storage, knowledge of the physiology as well as physiopathology of hepatic energy metabolism is a prerequisite to our understanding of whole-body metabolism. Hepatic fuel metabolism changes considerably depending on physiological circumstances (fed vs. fasted state). In consequence, hepatic carbohydrate, lipid and protein synthesis/utilization are tightly regulated according to needs. Fatty liver and hepatic insulin resistance (both frequently associated with the metabolic syndrome) or increased hepatic glucose production (as observed in type 2 diabetes) resulted from alterations in substrates oxidation/storage balance in the liver. Because AMP-activated protein kinase (AMPK) is considered as a cellular energy sensor, it is important to gain understanding of the mechanism by which hepatic AMPK coordinates hepatic energy metabolism. AMPK has been implicated as a key regulator of physiological energy dynamics by limiting anabolic pathways (to prevent further ATP consumption) and by facilitating catabolic pathways (to increase ATP generation). Activation of hepatic AMPK leads to increased fatty acid oxidation and simultaneously inhibition of hepatic lipogenesis, cholesterol synthesis and glucose production. In addition to a short-term effect on specific enzymes, AMPK also modulates the transcription of genes involved in lipogenesis and mitochondrial biogenesis. The identification of AMPK targets in hepatic metabolism should be useful in developing treatments to reverse metabolic abnormalities of type 2 diabetes and the metabolic syndrome.

Published
2009
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4. Transforming growth factor beta controls the directional migration of hepatocyte cohorts by modulating their adhesion to fibronectin

Author

Urszula Hibner, Fabien Binamé, Patrice Lassus, Institut de Génétique Moléculaire de Montpellier ( IGMM ), Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de Génétique Moléculaire de Montpellier (IGMM), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)

Subjects
rac1 GTP-Binding Protein, MESH : Cell Line, MESH : Protein Subunits, Apoptosis, Cell Communication, Integrin alpha5, MESH : Hepatocytes, Epithelium, Mesoderm, MESH: Hepatocytes, Mice, 0302 clinical medicine, Cell Movement, Transforming Growth Factor beta, MESH: Fibronectins, MESH : Cell Movement, MESH : Fibronectins, MESH: Animals, MESH: Cell Movement, MESH: Mesoderm, 0303 health sciences, MESH : Gene Expression Regulation, MESH: Cell Surface Extensions, MESH : Mesoderm, Articles, Adhesion, MESH: Protein Subunits, MESH: Gene Expression Regulation, Cell biology, medicine.anatomical_structure, 030220 oncology & carcinogenesis, Hepatocyte, MESH: Integrin alpha5, MESH : Cell Communication, MESH : Cell Membrane, MESH : Cell Surface Extensions, Biology, Cell Line, MESH: Cell Adhesion, MESH: Gene Expression Profiling, 03 medical and health sciences, MESH : rac1 GTP-Binding Protein, MESH : Integrin alpha5, MESH: Cell Communication, MESH : Mice, Cell Adhesion, medicine, Animals, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Mice, Molecular Biology, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Transforming Growth Factor beta, 030304 developmental biology, MESH: Humans, MESH: rac1 GTP-Binding Protein, Gene Expression Profiling, MESH: Apoptosis, MESH : Gene Expression Profiling, Cell Membrane, MESH : Humans, Cell Biology, MESH : Epithelium, Fibronectins, MESH: Cell Line, Fibronectin, Protein Subunits, MESH: Epithelium, MESH : Cell Adhesion, MESH : Transforming Growth Factor beta, Gene Expression Regulation, Hepatocytes, biology.protein, Cell Surface Extensions, MESH : Animals, MESH : Apoptosis, MESH: Cell Membrane, Transforming growth factor
Abstract

International audience; Transforming growth factor beta (TGF-beta) has a strong impact on liver development and physiopathology, exercised through its pleiotropic effects on growth, differentiation, survival, and migration. When exposed to TGF-beta, the mhAT3F cells, immortalized, highly differentiated hepatocytes, maintained their epithelial morphology and underwent dramatic alterations of adhesion, leading to partial or complete detachment from a culture plate, followed by readhesion and spreading. These alterations of adhesive behavior were caused by sequential changes in expression of the alpha5beta1 integrin and of its ligand, the fibronectin. The altered specificity of anchorage to the extracellular matrix gave rise to changes in cells' collective motility: cohorts adhering to fibronectin maintained a persistent, directional motility, with ezrin-rich pathfinder cells protruding from the tips of the cohorts. The absence of adhesion to fibronectin prevented the appearance of polarized pathfinders and lead to random, oscillatory motility. Our data suggest a novel role for TGF-beta in the control of collective migration of epithelial cohorts.

Published
2008
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5. 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
Full Text
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6. Catalase activity and expression in developing sunflower seeds as related to drying

Author

Françoise Corbineau, Juliette Leymarie, Arnaud Lehner, Daniel Côme, Sandra Rousseau, Christophe Bailly, Laboratoire de Biologie du Développement (LBD), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-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), Biologie des Semences = Seed biology (LBD-E01), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-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)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Laboratoire de Biologie du Développement ( LBD ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Biologie des Semences = Seed biology ( LBD-E01 ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale ( Glyco-MEV ), Université de Rouen Normandie ( UNIROUEN ), Normandie Université ( NU ) -Normandie Université ( NU ), VIBS ( GIPSA-VIBS ), Département Images et Signal ( GIPSA-DIS ), Grenoble Images Parole Signal Automatique ( GIPSA-lab ), Université Pierre Mendès France - Grenoble 2 ( UPMF ) -Université Stendhal - Grenoble 3-Université Joseph Fourier - Grenoble 1 ( UJF ) -Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ) -Université Pierre Mendès France - Grenoble 2 ( UPMF ) -Université Stendhal - Grenoble 3-Université Joseph Fourier - Grenoble 1 ( UJF ) -Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ) -Grenoble Images Parole Signal Automatique ( GIPSA-lab ), Université Pierre Mendès France - Grenoble 2 ( UPMF ) -Université Stendhal - Grenoble 3-Université Joseph Fourier - Grenoble 1 ( UJF ) -Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ) -Université Pierre Mendès France - Grenoble 2 ( UPMF ) -Université Stendhal - Grenoble 3-Université Joseph Fourier - Grenoble 1 ( UJF ) -Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-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), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-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)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS)

Subjects
0106 biological sciences, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Physiology, MESH : Protein Subunits, Plant Science, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], 01 natural sciences, Lipid peroxidation, chemistry.chemical_compound, [ SDV.BBM.BC ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Gene Expression Regulation, Plant, Malondialdehyde, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], [SDV.BDD.GAM]Life Sciences [q-bio]/Development Biology/Gametogenesis, 2. Zero hunger, MESH : Isoenzymes, 0303 health sciences, MESH: Helianthus, [ SDV.BV.PEP ] Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, food and beverages, Helianthus annuus, [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], Catalase, MESH: Protein Subunits, Sunflower, Isoenzymes, Horticulture, [ SDV.BV.AP ] Life Sciences [q-bio]/Vegetal Biology/Plant breeding, seed drying, Germination, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Seeds, MESH: Isoenzymes, Helianthus, MESH: Hydrogen Peroxide, seed development, Peroxidase, MESH: Malondialdehyde, hydrogen peroxide, [ SDV.BBM.BM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Flowers, Biology, [ SDV.BC.IC ] Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], 03 medical and health sciences, [ SDV.BBM.MN ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], [ SDV.BDD.GAM ] Life Sciences [q-bio]/Development Biology/Gametogenesis, MESH : Catalase, MESH: Catalase, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Botany, MESH : Helianthus, MESH: Gene Expression Regulation, Plant, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], 030304 developmental biology, MESH : Malondialdehyde, MESH : Flowers, [ SDV.BC.BC ] Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], [ SDV.BIO ] Life Sciences [q-bio]/Biotechnology, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, MESH: Flowers, MESH : Seeds, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, [ CHIM.POLY ] Chemical Sciences/Polymers, Protein Subunits, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, [CHIM.POLY]Chemical Sciences/Polymers, chemistry, MESH: Seeds, biology.protein, Dormancy, MESH : Hydrogen Peroxide, Desiccation, MESH : Gene Expression Regulation, Plant, 010606 plant biology & botany
Abstract

International audience; Changes in catalase (CAT) activity and in CAT isoform pattern and expression were investigated in developing sunflower (Helianthus annuus L.) seeds during desiccation on the mother plant and after artificial drying on the flowerheads. Seeds regularly desiccated during their development on the mother plant and reached mass maturity at c. 42 d after flowering (DAF). Freshly harvested seeds did not germinate at any stage of development because they were dormant, but their dormancy was broken after 5-6 months of dry storage. Immature seeds were desiccation-tolerant at 24 DAF since they were able to germinate fully after artificial drying on the flowerheads followed by dry storage. CAT activity increased in non-dehydrated seeds during their development, reaching a maximum a little after seed mass maturity and after artificial drying in immature seeds. This stimulation of CAT activity by natural and artificial drying was related to changes in CAT isoform pattern. Of the four constitutive CAT subunits, that of 59 kDa was always present, but dehydration induced the synthesis of a 55 kDa subunit. This synthesis of the CAT 55 kDa subunit resulted from an activation of the CATA1 gene, suggesting that the regulation of catalase activity and synthesis by drying occurred at the transcriptional level. The increase in CAT activity induced by seed drying was associated with a decrease in hydrogen peroxide level and in lipid peroxidation. These results suggest that CAT plays a role during seed desiccation by preventing dehydration-related oxidative damage and that H(2)O(2) may play a role in the regulation of CAT gene expression and the transduction pathway of the dehydration signal.

Published
2004
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