Descriptor: "MESH: Proteome" / Publisher: hal ccsd - Searchworks@Jio Institute Digital Library Search Results

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78 results on '"MESH: Proteome"'

1. Quantitative Proteomics in Yeast: From bSLIM and Proteome Discoverer Outputs to Graphical Assessment of the Significance of Protein Quantification Scores

Author: Nicolas Sénécaut, Pierre Poulain, Laurent Lignières, Samuel Terrier, Véronique Legros, Guillaume Chevreux, Gaëlle Lelandais, Jean-Michel Camadro, Institut Jacques Monod (IJM (UMR_7592)), Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), 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), ANR-18-CE44-0014,SLIM-labeling,Protéomique haute performance par réduction de la complexité isotopique in vivo(2018), and Frédéric Devaux
Subjects: Proteomics, Minora, MESH: Isotope Labeling, Mass spectrometry, MESH: Peptides, MESH: Proteomics, [SDV]Life Sciences [q-bio], KNIME, Proteome Discoverer, bSLIM, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: Saccharomyces cerevisiae, Yeast, Isotopic labeling, MESH: Proteome, Metabolism, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Quantification, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology
Abstract: Simple light isotope metabolic labeling (bSLIM) is an innovative method to accurately quantify differences in protein abundance at the proteome level in standard bottom-up experiments. The quantification process requires computation of the ratio of intensity of several isotopologs in the isotopic cluster of every identified peptide. Thus, appropriate bioinformatic workflows are required to extract the signals from the instrument files and calculate the required ratio to infer peptide/protein abundance. In a previous study (Sénécaut et al., J Proteome Res 20:1476–1487, 2021), we developed original open-source workflows based on OpenMS nodes implemented in a KNIME working environment. Here, we extend the use of the bSLIM labeling strategy in quantitative proteomics by presenting an alternative procedure to extract isotopolog intensities and process them by taking advantage of new functionalities integrated into the Minora node of Proteome Discoverer 2.4 software. We also present a graphical strategy to evaluate the statistical robustness of protein quantification scores and calculate the associated false discovery rates (FDR). We validated these approaches in a case study in which we compared the differences between the proteomes of two closely related yeast strains.
Published: 2022

2. A new molecular classification to drive precision treatment strategies in primary Sjögren’s syndrome

Author: Soret, Perrine, Le Dantec, Christelle, Desvaux, Emiko, Foulquier, Nathan, Chassagnol, Bastien, Hubert, Sandra, Christophe, Jamin, Barturen, Guillermo, Desachy, Guillaume, Devauchelle-Pensec, Valérie, Boudjeniba, Cheïma, Cornec, Divi, Saraux, Alain, Jousse-Joulin, Sandrine, Barbarroja, Nuria, Rodríguez-Pintó, Ignasi, de Langhe, Ellen, Beretta, Lorenzo, Chizzolini, Carlo, Kovács, László, Witte, Torsten, Bettacchioli, Eléonore, Buttgereit, Anne, Makowska, Zuzanna, Lesche, Ralf, Borghi, Maria Orietta, Martin, Javier, Courtade-Gaiani, Sophie, Xuereb, Laura, Guedj, Mickaël, Moingeon, Philippe, Alarcón-Riquelme, Marta, Laigle, Laurence, Pers, Jacques-Olivier, Vigone, Barbara, Lauwerys, Bernard, Maudoux, Anne-Lise, Vasconcelos, Carlos, Tavares, Ana, Faria, Raquel, Brandão, Mariana, Campar, Ana, Marinho, António, Farinha, Fátima, Almeida, Isabel, Gonzalez-Gay Mantecón, Miguel Angel, Blanco Alonso, Ricardo, Corrales Martínez, Alfonso, Cervera, Ricard, Espinosa, Gerard, Lories, Rik, Hunzelmann, Nicolas, Belz, Doreen, Baerlecken, Niklas, Stummvoll, Georg, Zauner, Michael, Lehner, Michaela, Collantes, Eduardo, Ortega-Castro, Rafaela, Aguirre-Zamorano, Ma Angeles, Escudero-Contreras, Alejandro, Castro-Villegas, Ma Carmen, Jiménez Gómez, Yolanda, Ortego, Norberto, Fernández Roldán, María Concepción, Raya, Enrique, Jiménez Moleón, Inmaculada, de Ramon, Enrique, Díaz Quintero, Isabel, Meroni, Pier Luigi, Gerosa, Maria, Schioppo, Tommaso, Artusi, Carolina, Zuber, Aleksandra, Wynar, Donatienne, Balog, Attila, Deák, Magdolna, Bocskai, Márta, Dulic, Sonja, Kádár, Gabriella, Hiepe, Falk, Thiel, Silvia, Rodriguez Maresca, Manuel, López-Berrio, Antonio, Aguilar-Quesada, Rocío, Navarro-Linares, Héctor, Ioannou, Yiannis, Chamberlain, Chris, Marovac, Jacqueline, Alarcón Riquelme, Marta, Gomes Anjos, Tania, Marañón, Concepción, Le Lann, Lucas, Simon, Quentin, Rouvière, Bénédicte, Varela, Nieves, Muchmore, Brian, Dufour, Aleksandra, Alvarez, Montserrat, Cremer, Jonathan, Lopez-Pedrera, Chary, Gerl, Velia, Khodadadi, Laleh, Cheng, Qingyu, de Groof, Aurélie, Ducreux, Julie, Trombetta, Elena, Li, Tianlu, Alvarez-Errico, Damiana, Kniesch, Katja, Azevedo, Nancy, Neves, Esmeralda, Rao, Sambasiva, Jouve, Pierre-Emmanuel, Institut de Recherches Internationales Servier [Suresnes] (IRIS), Lymphocytes B, Autoimmunité et Immunothérapies (LBAI), Université de Brest (UBO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-LabEX IGO Immunothérapie Grand Ouest, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Institut Brestois Santé Agro Matière (IBSAM), Université de Brest (UBO), Centre for Genomics and Oncological Reearch (GENYO), CHRU Brest - Service de Rhumatologie (CHU - BREST - Rhumato), Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Instituto Maimonides de Investigación Biomédica de Cordoba (IMIBIC), Universidad de Córdoba = University of Córdoba [Córdoba]-Hospital Universitario Reina Sofía, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Maggiore Hospital, IRCCS Foundation, Milano, Department of Pathology and Immunology [Geneva, Switzerland], Université de Genève = University of Geneva (UNIGE), University of Szeged [Szeged], Clinic for Immunology and Rhematology, Hannover Medical School, Hanover, Germany, Hôpital Morvan - CHRU de Brest (CHU - BREST ), Pharmaceuticals Division Bayer Pharma Aktiengesellschaft, Università degli Studi di Milano = University of Milan (UNIMI), Instituto de Parasitología y Biomedicina 'López-Neyra' (IPBLN), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Granada = University of Granada (UGR), and Michel, Geneviève
Subjects: MESH: Databases, Protein, MESH: Inflammation, [SDV.IMM] Life Sciences [q-bio]/Immunology, MESH: Flow Cytometry, MESH: Cross-Sectional Studies, MESH: DNA Methylation, MESH: Computer Simulation, cell cycle, chronic lymphocytic leukemia, liquid chromatography-tandem mass spectrometry, splicing, MESH: Autoantibodies, MESH: Interferons, MESH: RNA-Seq, MESH: Cohort Studies, MESH: Databases, Genetic, MESH: Cytokines, MESH: Humans, MESH: Middle Aged, MESH: Polymorphism, Single Nucleotide, MESH: Transcriptome, MESH: Adult, MESH: Chemokines, MESH: Male, MESH: Proteome, MESH: Sjogren's Syndrome, MESH: Genome-Wide Association Study, MESH: Biomarkers, MESH: Multigene Family, [SDV.IMM]Life Sciences [q-bio]/Immunology, MESH: Female, MESH: Computational Biology
Abstract: International audience; Abstract There is currently no approved treatment for primary Sjögren’s syndrome, a disease that primarily affects adult women. The difficulty in developing effective therapies is -in part- because of the heterogeneity in the clinical manifestation and pathophysiology of the disease. Finding common molecular signatures among patient subgroups could improve our understanding of disease etiology, and facilitate the development of targeted therapeutics. Here, we report, in a cross-sectional cohort, a molecular classification scheme for Sjögren’s syndrome patients based on the multi-omic profiling of whole blood samples from a European cohort of over 300 patients, and a similar number of age and gender-matched healthy volunteers. Using transcriptomic, genomic, epigenetic, cytokine expression and flow cytometry data, combined with clinical parameters, we identify four groups of patients with distinct patterns of immune dysregulation. The biomarkers we identify can be used by machine learning classifiers to sort future patients into subgroups, allowing the re-evaluation of response to treatments in clinical trials.
Published: 2021

3. Evaluating microbiome-directed fibre snacks in gnotobiotic mice and humans

Author: Sophie Vinoy, Carlito B. Lebrilla, Jeffrey I. Gordon, Kyleigh Kirbach, Andrew C. Heath, Bernard Henrissat, Chandani Desai, Juan Jose Castillo, Ruteja A. Barve, Omar Delannoy-Bruno, Arjun S. Raman, Robert Y. Chen, David K. Hayashi, Andrei L. Osterman, Semen A. Leyn, Nathan D. Han, Jiye Cheng, Matthew C. Hibberd, Dmitry A. Rodionov, Alexandra Meynier, Garret Couture, Vincent Lombard, Tara Wilmot, Samuel Klein, Michael J. Barratt, Architecture et fonction des macromolécules biologiques (AFMB), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0301 basic medicine, Dietary Fiber, Male, Proteome, [SDV]Life Sciences [q-bio], Disease, Overweight, MESH: Bacteroides, Inbred C57BL, Cardiovascular, Oral and gastrointestinal, Feces, Mice, 0302 clinical medicine, MESH: Blood Proteins, Bacteroides, MESH: Obesity, MESH: Animals, Food science, Cancer, 2. Zero hunger, Multidisciplinary, MESH: Middle Aged, Human studies, digestive, oral, and skin physiology, MESH: Feces, Blood Proteins, Middle Aged, 3. Good health, Stroke, MESH: Proteome, MESH: Young Adult, Female, Zero Hunger, medicine.symptom, MESH: Snacks, Adult, Adolescent, General Science & Technology, Biology, MESH: Gastrointestinal Microbiome, 03 medical and health sciences, Young Adult, MESH: Mice, Inbred C57BL, Controlled diets, MESH: Germ-Free Life, medicine, Animals, Humans, Germ-Free Life, Microbiome, Obesity, MESH: Overweight, MESH: Mice, Metabolic and endocrine, Nutrition, MESH: Adolescent, MESH: Humans, Prevention, Dietary fibre, MESH: Adult, medicine.disease, MESH: Male, Gastrointestinal Microbiome, 030104 developmental biology, MESH: Dietary Fiber, Snacks, MESH: Female, 030217 neurology & neurosurgery
Abstract: Changing food preferences brought about by westernization that have deleterious health effects1,2—combined with myriad forces that are contributing to increased food insecurity—are catalysing efforts to identify more nutritious and affordable foods3. Consumption of dietary fibre can help to prevent cardiovascular disease, type 2 diabetes and obesity4–6. A substantial number of reports have explored the effects of dietary fibre on the gut microbial community7–9. However, the microbiome is complex, dynamic and exhibits considerable intra- and interpersonal variation in its composition and functions. The large number of potential interactions between the components of the microbiome makes it challenging to define the mechanisms by which food ingredients affect community properties. Here we address the question of how foods containing different fibre preparations can be designed to alter functions associated with specific components of the microbiome. Because a marked increase in snack consumption is associated with westernization, we formulated snack prototypes using plant fibres from different sustainable sources that targeted distinct features of the gut microbiomes of individuals with obesity when transplanted into gnotobiotic mice. We used these snacks to supplement controlled diets that were consumed by adult individuals with obesity or who were overweight. Fibre-specific changes in their microbiomes were linked to changes in their plasma proteomes indicative of an altered physiological state. Fibre snacks that target distinct features of the microbiomes of donors with obesity transplanted into gnotobiotic mice also lead to fibre-specific changes in the microbiome and physiology when used in controlled-diet human studies.
Published: 2021

4. A Tandem Mass Tags (TMTs) labeling approach highlights differences between the shoot proteome of two Arabidopsis thaliana ecotypes, Col‐0 and Ws

Author: Maïté Leschevin, Karine Pageau, Paulo Marcelo, Hélène San-Clemente, Marwa Ismael, Elisabeth Jamet, Catherine Rayon, Transfrontalière BioEcoAgro (Transfrontalière BioEcoAgro), Université d'Artois (UA)-Université de Liège-Université de Picardie Jules Verne (UPJV)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biologie des Plantes et Innovation - UR UPJV 3900 (BIOPI), Université de Picardie Jules Verne (UPJV), Plateforme d’Ingénierie Cellulaire et Analyses des Protéines (ICAP) (ICAP), Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Dynamique et Evolution des Parois cellulaires végétales, Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Transfrontalière BioEcoAgro - UMR 1158 (BioEcoAgro), Université d'Artois (UA)-Université de Liège-Université de Picardie Jules Verne (UPJV)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), Université de Picardie Jules Verne (UPJV)-Transfrontalière BioEcoAgro - UMR 1158 (BioEcoAgro), Université catholique de Lille (UCL)-Université catholique de Lille (UCL)-Université d'Artois (UA)-Université de Liège-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), and Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3)
Subjects: Proteomics, quantitative proteomics, Proteome, Arabidopsis thaliana, shoot, Quantitative proteomics, Arabidopsis, Tandem mass tag, Biochemistry, MESH: Ecotype, 03 medical and health sciences, MESH: Arabidopsis* / genetics, Transcription (biology), Plant defense against herbivory, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Molecular Biology, 030304 developmental biology, Genetics, Ecotype, 0303 health sciences, biology, MESH: Proteomics, 030302 biochemistry & molecular biology, Wassilewskija ecotype, 15. Life on land, biology.organism_classification, Columbia Col-0 ecotype, TMT labeling, MESH: Proteome
Abstract: Arabidopsis has become a powerful model to study morphogenesis, plant growth, development but also plant response to environmental conditions. Over 1000 Arabidopsis genomes are available and show natural genetic variations. Among them, the main reference accessions Wassilewskija (Ws) and Columbia (Col-0), originally growing at contrasted altitudes and temperatures, are widely studied, but data contributing to their molecular phenotyping are still scarce. A global quantitative proteomics approach using isobaric stable isotope labeling (Tandem Mass Tags, TMT) was performed on Ws and Col-0. Plants have been hydroponically grown at 16 h/8 h (light/dark cycle) at 23°C day/19°C night for three weeks. A TMT labeling of the proteins extracted from their shoots has been performed and showed a differential pattern of protein abundance between them. These results have allowed identifying several proteins families possibly involved in the differential responses observed for Ws and Col-0 during plant development and upon environmental changes. In particular, Ws and Col-0 mainly differ in photosynthesis, cell wall-related proteins, plant defense/stress, ROS scavenging enzymes/redox homeostasis and DNA/RNA binding/transcription/translation/protein folding. This article is protected by copyright. All rights reserved.
Published: 2021

5. Novel Insights into Quantitative Proteomics from an Innovative Bottom-Up Simple Light Isotope Metabolic (bSLIM) Labeling Data Processing Strategy

Author: Jean-Michel Camadro, Samuel Terrier, Pierre Poulain, Lilian Yang-Crosson, Nicolas Sénécaut, Gelio Alves, Hendrik Weisser, Laurent Lignières, Gaëlle Lelandais, Yi-Kuo Yu, Institut Jacques Monod (IJM (UMR_7592)), Université de Paris (UP)-Centre National de la Recherche Scientifique (CNRS), National Center for Biotechnology Information, NLM, NIH, Bethesda, Maryland 20894, United States., STORM Therapeutics Limited, Cambridge CB22 3AT, U.K., 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), ANR-18-CE44-0014,SLIM-labeling,Protéomique haute performance par réduction de la complexité isotopique in vivo(2018), and Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)
Subjects: 0301 basic medicine, Proteomics, quantitative proteomics, MESH: Isotope Labeling, Proteome, Computer science, workflow, [SDV]Life Sciences [q-bio], Quantitative proteomics, Saccharomyces cerevisiae, KNIME, MESH: Amino Acid Sequence, Computational biology, yeast, Mass spectrometry, Biochemistry, Mass Spectrometry, Article, 03 medical and health sciences, Protein sequencing, data processing workflow, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Amino Acid Sequence, MESH: Mass Spectrometry, Data processing, light carbon isotope, In vivo metabolic labeling, 030102 biochemistry & molecular biology, biology, 12 C, MESH: Proteomics, OpenMS, Experimental data, General Chemistry, Metrics & More Article Recommendations In vivo metabolic labeling, biology.organism_classification, MESH: Proteome, 030104 developmental biology, Isotope Labeling, 12C, data processing
Abstract: International audience; Simple light isotope metabolic labeling (SLIM labeling) is an innovative method to quantify variations in the proteome based on an original in vivo labeling strategy. Heterotrophic cells grown in U-[ 12 C] as the sole source of carbon synthesize U-[ 12 C]-amino acids, which are incorporated into proteins, giving rise to U-[ 12 C]-proteins. This results in a large increase in the intensity of the monoisotope ion of peptides and proteins, thus allowing higher identification scores and protein sequence coverage in mass spectrometry experiments. This method, initially developed for signal processing and quantification of the incorporation rate of 12 C into peptides, was based on a multistep process that was difficult to implement for many laboratories. To overcome these limitations, we developed a new theoretical background to analyze bottom-up proteomics data using SLIM-labeling (bSLIM) and established simple procedures based on open-source software, using dedicated OpenMS modules, and embedded R scripts to process the bSLIM experimental data. These new tools allow computation of both the 12 C abundance in peptides to follow the kinetics of protein labeling and the molar fraction of unlabeled and 12 C-labeled peptides in multiplexing experiments to determine the relative abundance of proteins extracted under different biological conditions. They also make it possible to consider incomplete 12 C labeling, such as that observed in cells with nutritional requirements for nonlabeled amino acids. These tools were validated on an experimental dataset produced using various yeast strains of Saccharomyces cerevisiae and growth conditions. The workflows are built on the implementation of appropriate calculation modules in a KNIME working environment. These new integrated tools provide a convenient framework for the wider use of the SLIM-labeling strategy.
Published: 2021

6. Proteomic Analysis of KCNK3 Loss of Expression Identified Dysregulated Pathways in Pulmonary Vascular Cells

Author: Le Ribeuz, Hélène, Dumont, Florent, Ruellou, Guillaume, Lambert, Mélanie, Balliau, Thierry, Quatredeniers, Marceau, Girerd, Barbara, Cohen-Kaminsky, Sylvia, Mercier, Olaf, Yen-Nicolaÿ, Stéphanie, Humbert, Marc, Montani, David, Capuano, Véronique, Antigny, Fabrice, Faculté de Médecine Paris-Saclay, AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre)-Université Paris-Saclay, Hypertension pulmonaire : physiopathologie et innovation thérapeutique (HPPIT), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), Ingénierie et Plateformes au Service de l'Innovation Thérapeutique (IPSIT), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Santé et de la Recherche Médicale (INSERM), INSERM, Université Paris-Saclay, Marie Lannelongue Hospital, Therapeutic Innovation Doctoral School (ED569), Région Ile de France (convention n◦ EX024607), ANR-18-CE14-0023,KAPAH,KCNK3 une nouvelle cible thérapeutique dans l'hypertension artérielle pulmonaire(2018), Adhésion et Inflammation (LAI), Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre Chirurgical Marie Lannelongue (CCML), Hôpital Bicêtre, Plateforme d'Analyse Protéomique de Paris Sud Ouest (PAPPSO), AgroParisTech, and Antigny, Fabrice
Subjects: Proteomics, MESH: Signal Transduction, Proteome, [SDV]Life Sciences [q-bio], Myocytes, Smooth Muscle, MESH: Pulmonary Artery, Nerve Tissue Proteins, MESH: Molecular Sequence Annotation, Pulmonary Artery, Article, lcsh:Chemistry, Potassium Channels, Tandem Pore Domain, Humans, MESH: Endothelial Cells, MESH: Nerve Tissue Proteins, lcsh:QH301-705.5, Cells, Cultured, proteomic, MESH: Humans, MESH: Proteomics, Computational Biology, Endothelial Cells, MESH: Potassium Channels, Tandem Pore Domain, Molecular Sequence Annotation, MESH: Myocytes, Smooth Muscle, PAH, MESH: Gene Knockdown Techniques, MESH: Gene Expression Regulation, [SDV] Life Sciences [q-bio], MESH: Proteome, Gene Expression Regulation, lcsh:Biology (General), lcsh:QD1-999, Gene Knockdown Techniques, MESH: Biomarkers, Biomarkers, Signal Transduction, MESH: Cells, Cultured, MESH: Computational Biology, potassium channel
Abstract: International audience; The physiopathology of pulmonary arterial hypertension (PAH) is characterized by pulmonary artery smooth muscle cell (PASMC) and endothelial cell (PAEC) dysfunction, contributing to pulmonary arterial obstruction and PAH progression. KCNK3 loss of function mutations are responsible for the first channelopathy identified in PAH. Loss of KCNK3 function/expression is a hallmark of PAH. However, the molecular mechanisms involved in KCNK3 dysfunction are mostly unknown. To identify the pathological molecular mechanisms downstream of KCNK3 in human PASMCs (hPASMCs) and human PAECs (hPAECs), we used a Liquid Chromatography-Tandem Mass Spectrometry-based proteomic approach to identify the molecular pathways regulated by KCNK3. KCNK3 loss of expression was induced in control hPASMCs or hPAECs by specific siRNA targeting KCNK3. We found that the loss of KCNK3 expression in hPAECs and hPASMCs leads to 326 and 222 proteins differentially expressed, respectively. Among them, 53 proteins were common to hPAECs and hPASMCs. The specific proteome remodeling in hPAECs in absence of KCNK3 was mostly related to the activation of glycolysis, the superpathway of methionine degradation, and the mTOR signaling pathways, and to a reduction in EIF2 signaling pathways. In hPASMCs, we found an activation of the PI3K/AKT signaling pathways and a reduction in EIF2 signaling and the Purine Nucleotides De Novo Biosynthesis II and IL-8 signaling pathways. Common to hPAECs and hPASMCs, we found that the loss of KCNK3 expression leads to the activation of the NRF2-mediated oxidative stress response and a reduction in the interferon pathway. In the hPAECs and hPASMCs, we found an increased expression of HO-1 (heme oxygenase-1) and a decreased IFIT3 (interferon-induced proteins with tetratricopeptide repeats 3) (confirmed by Western blotting), allowing us to identify these axes to understand the consequences of KCNK3 dysfunction. Our experiments, based on the loss of KCNK3 expression by a specific siRNA strategy in control hPAECs and hPASMCs, allow us to identify differences in the activation of several signaling pathways, indicating the key role played by KCNK3 dysfunction in the development of PAH. Altogether, these results allow us to better understand the consequences of KCNK3 dysfunction and suggest that KCNK3 loss of expression acts in favor of the proliferation and migration of hPASMCs and promotes the metabolic shift and apoptosis resistance of hPAECs.
Published: 2020

7. ProForma: A Standard Proteoform Notation

Author: Yury O. Tsybin, Emanuele Alpi, Julia Chamot-Rooke, Ljiljana Paša-Tolić, Anthony J. Cesnik, Ying Ge, Michael R. Shortreed, Maria Jesus Martin, Lloyd M. Smith, Richard D. LeDuc, Jeffrey N. Agar, Neil L. Kelleher, Juan Antonio Vizcaíno, Joseph A. Loo, Jared B. Shaw, Veit Schwämmle, Paul O. Danis, Stefan K. Solntsev, Northwestern University [Evanston], University of Southern Denmark (SDU), University of Wisconsin-Madison, Pacific Northwest National Laboratory (PNNL), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Consortium for Top-Down Proteomics, Northeastern University [Boston], Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology (UTechS MSBio), Institut Pasteur [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), University of California [Los Angeles] (UCLA), University of California, Spectroswiss, A.J.C was supported by the Computation and Informatics in Biology and Medicine Training Program, T15LM007359. R.D.L. was supported in part by National Institute for General Medical Sciences under award P41 GM108569. V.S. acknowledges support from the EuBIC initiative, ELIXIR Denmark and the Danish Research Council. M.R.S., A.J.C., S.K.S., and L.M.S. acknowledge support of the National Institute of General Medical Sciences grant R01GM114292. J.A.V. acknowledges funding from ELIXIR and from EMBL core funds., Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and University of California (UC)
Subjects: 0301 basic medicine, Proteomics, Proteome, Computer science, International Cooperation, human readable, MESH: Amino Acid Sequence, MESH: Information Dissemination, computer.software_genre, Notation, Biochemistry, Tandem Mass Spectrometry, Research community, Use case, Databases, Protein, Parsing, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Programming language, MESH: Proteomics, standard, Biological Sciences, MESH: Proteome, MESH: Reproducibility of Results, Molecular Sequence Annotation, MESH: Computational Biology, MESH: Databases, Protein, Biochemistry & Molecular Biology, MESH: Molecular Sequence Annotation, Article, Databases, 03 medical and health sciences, MESH: Software, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Humans, Amino Acid Sequence, Protein Processing, MESH: Humans, 030102 biochemistry & molecular biology, Information Dissemination, Protein, Post-Translational, Computational Biology, Reproducibility of Results, MESH: Tandem Mass Spectrometry, General Chemistry, proteoform, MESH: International Cooperation, 030104 developmental biology, ComputingMethodologies_PATTERNRECOGNITION, MESH: Protein Processing, Post-Translational, Chemical Sciences, computer, Protein Processing, Post-Translational, Software, machine readable
Abstract: International audience; The Consortium for Top-Down Proteomics (CTDP) proposes a standardized notation, ProForma, for writing the sequence of fully characterized proteoforms. ProForma provides a means to communicate any proteoform by writing the amino acid sequence using standard one-letter notation and specifying modifications or unidentified mass shifts within brackets following certain amino acids. The notation is unambiguous, human-readable, and can easily be parsed and written by bioinformatic tools. This system uses seven rules and supports a wide range of possible use cases, ensuring compatibility and reproducibility of proteoform annotations. Standardizing proteoform sequences will simplify storage, comparison, and reanalysis of proteomic studies, and the Consortium welcomes input and contributions from the research community on the continued design and maintenance of this standard.
Published: 2018

8. Identification of novel substrates of Shigella T3SA through analysis of its virulence plasmid-encoded secretome

Author: Laurie Pinaud, Philippe J. Sansonetti, Mariana L. Ferrari, Armelle Phalipon, Robin C. Friedman, Martin von Bergen, François-Xavier Campbell-Valois, Nico Jehmlich, Pathogénie microbienne moléculaire, Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris], Biologie systémique - Systems Biology, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), Universität Leipzig [Leipzig], Chaire Microbiologie et Maladies infectieuses, Collège de France (CdF (institution)), University of Ottawa [Ottawa], Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Universität Leipzig, and Collège de France - Chaire Microbiologie et Maladies infectieuses
Subjects: 0301 basic medicine, Bacterial Diseases, Proteome, MESH: Shigella flexneri, Physiology, lcsh:Medicine, MESH: beta-Lactamases, MESH: Virulence, medicine.disease_cause, Pathology and Laboratory Medicine, Toxicology, Biochemistry, Mass Spectrometry, Shigella flexneri, Jurkat Cells, Plasmid, Medicine and Health Sciences, MESH: Jurkat Cells, Shigella, lcsh:Science, Yersinia enterocolitica, MESH: Bacterial Proteins, Multidisciplinary, biology, Bacterial Gastroenteritis, Virulence, Effector, 3. Good health, Bacterial Pathogens, Gastroenteritis, MESH: Proteome, Protein Transport, Infectious Diseases, Salmonella enterica, Medical Microbiology, Cell Processes, Shigellosis, Pathogens, Research Article, Neglected Tropical Diseases, Plasmids, 030106 microbiology, Immunoblotting, Molecular Probe Techniques, Gastroenterology and Hepatology, Research and Analysis Methods, Microbiology, beta-Lactamases, 03 medical and health sciences, Bacterial Proteins, MESH: Plasmids, Virology, medicine, Humans, Secretion, Molecular Biology Techniques, Microbial Pathogens, Molecular Biology, MESH: Mass Spectrometry, MESH: Humans, Bacteria, lcsh:R, Host Cells, Organisms, Biology and Life Sciences, Protein Secretion, Proteins, Cell Biology, biology.organism_classification, Tropical Diseases, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, MESH: HeLa Cells, lcsh:Q, Antitoxins, Physiological Processes, Viral Transmission and Infection, HeLa Cells
Abstract: International audience; Many human Gram-negative bacterial pathogens express a Type Three Secretion Apparatus (T3SA), including among the most notorious Shigella spp., Salmonella enterica, Yersinia enterocolitica and enteropathogenic Escherichia coli (EPEC). These bacteria express on their surface multiple copies of the T3SA that mediate the delivery into host cells of specific protein substrates critical to pathogenesis. Shigella spp. are Gram-negative bacterial pathogens responsible for human bacillary dysentery. The effector function of several Shigella T3SA substrates has largely been studied but their potential cellular targets are far from having been comprehensively delineated. In addition, it is likely that some T3SA substrates have escaped scrutiny as yet. Indeed, sequencing of the virulence plasmid of Shigella flexneri has revealed numerous open reading frames with unknown functions that could encode additional T3SA substrates. Taking advantage of label-free mass spectrometry detection of proteins secreted by a constitutively secreting strain of S. flexneri, we identified five novel substrates of the T3SA. We further confirmed their secretion through the T3SA and translocation into host cells using β-lactamase assays. The coding sequences of two of these novel T3SA substrates (Orf13 and Orf131a) have a guanine-cytosine content comparable to those of T3SA components and effectors. The three other T3SA substrates identified (Orf48, Orf86 and Orf176) have significant homology with antitoxin moieties of type II Toxin-Antitoxin systems usually implicated in the maintenance of low copy plasmids. While Orf13 and Orf131a might constitute new virulence effectors contributing to S. flexneri pathogenicity, potential roles for the translocation into host cells of antitoxins or antitoxin-like proteins during Shigella infection are discussed.
Published: 2017

9. Tyrosine-Nitrated Proteins: Proteomic and Bioanalytical Aspects

Author: BatthyányCarlos, DemicheliVerónica, RadiRafael, MastrogiovanniMauricio, LimaAnalía, BartesaghiSilvina, Institut Pasteur de Montevideo, Réseau International des Instituts Pasteur (RIIP), Center for Free Radical and Biomedical Research, Universidad de la República [Montevideo] (UCUR), Departamento de Bioquímica, Facultad de Medicina, and This work was supported by grants of Agencia Nacional de Investigacion e Innovacion (FCE_2014_104233), Universidad de la Republica (CSIC), and the National Institutes of Health (RO1 AI095173) to R.R. and Universidad de la Republica (CSIC) and Institut Pasteur de Montevideo to CB. Additional support to the investigators was obtained from Programa de Desarrollo de Ciencias Basicas (PEDECIBA), Universidad de la Republica (CEINBIO, Espacio Interdisciplinario), Centro de Biologıa Estructural del Mercosur (CeBEM), and Ridaline and Tecniplast through Fundacio Manuel Perez.
Subjects: 0301 basic medicine, Proteome, Physiology, [SDV]Life Sciences [q-bio], Clinical Biochemistry, medicine.disease_cause, Proteomics, Protein oxidation, Biochemistry, Mass Spectrometry, MESH: Tyrosine, chemistry.chemical_compound, MESH: Animals, MESH: Proteins, Tyrosine, General Environmental Science, Chemistry, MESH: Proteomics, Forum Review Articles, nitration, MESH: Proteome, MESH: Nitrates, Phosphorylation, Nitrosation, MESH: Nitrosation, free radicals, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Sensitivity and Specificity, peroxynitrite, 03 medical and health sciences, proteomics, Nitration, medicine, Animals, Humans, protein oxidation, Molecular Biology, MESH: Mass Spectrometry, Nitrates, MESH: Humans, Proteins, Cell Biology, MESH: Sensitivity and Specificity, 030104 developmental biology, Acetylation, MESH: Protein Processing, Post-Translational, General Earth and Planetary Sciences, Protein Processing, Post-Translational, Oxidative stress
Abstract: "Nitroproteomic" is under active development, as 3-nitrotyrosine in proteins constitutes a footprint left by the reactions of nitric oxide-derived oxidants that are usually associated to oxidative stress conditions. Moreover, protein tyrosine nitration can cause structural and functional changes, which may be of pathophysiological relevance for human disease conditions. Biological protein tyrosine nitration is a free radical process involving the intermediacy of tyrosyl radicals; in spite of being a nonenzymatic process, nitration is selectively directed toward a limited subset of tyrosine residues. Precise identification and quantitation of 3-nitrotyrosine in proteins has represented a "tour de force" for researchers. Recent Advances: A small number of proteins are preferential targets of nitration (usually less than 100 proteins per proteome), contrasting with the large number of proteins modified by other post-translational modifications such as phosphorylation, acetylation, and, notably, S-nitrosation. Proteomic approaches have revealed key features of tyrosine nitration both in vivo and in vitro, including selectivity, site specificity, and effects in protein structure and function.Identification of 3-nitrotyrosine-containing proteins and mapping nitrated residues is challenging, due to low abundance of this oxidative modification in biological samples and its unfriendly behavior in mass spectrometry (MS)-based technologies, that is, MALDI, electrospray ionization, and collision-induced dissociation.The use of (i) classical two-dimensional electrophoresis with immunochemical detection of nitrated proteins followed by protein ID by regular MS/MS in combination with (ii) immuno-enrichment of tyrosine-nitrated peptides and (iii) identification of nitrated peptides by a MIDAS™ experiment is arising as a potent methodology to unambiguously map and quantitate tyrosine-nitrated proteins in vivo. Antioxid. Redox Signal. 26, 313-328.
Published: 2017

10. Whole genome analysis of a schistosomiasis-transmitting freshwater snail

Author: Gerald M. Mkoji, Ittiprasert Wannaporn, Xiao-Jun Wu, Julia B. Carleton, Gloria I. Giraldo-Calderón, Matty Knight, Catherine S. Jones, Anthony T. Papenfuss, Elio Hideo Baba, Brian J. Raney, Richard M. Cripps, Christine Coustau, Martin T. Swain, René Feyereisen, Judith E. Humphries, Nithya Raghavan, Kathryn M. Ryan, Céline Cosseau, Karl F. Hoffmann, Michael S. Blouin, Edwin J. Routledge, TyAnna L. Lovato, Min Zhao, Olga Baron, Fabiano Sviatopolk-Mirsky Pais, Mikkel Christensens, Sandra W. Clifton, Leonid L. Moroz, Maria G. Castillo, Damian L. Trujillo, Donald P. McManus, Emanuela V. Volpi, Liana K. Jannotti-Passos, Scott P Lawton, Joanna M. Bridger, Yesid Cuesta-Astroz, Eric S. Loker, David Duval, Fernanda Ludolf, Bronwyn Rotgans, Mónica Medina, Di Liang, Benjamin Gourbal, Izinara C Rosse, Catrina Fronick, Sarah K. Buddenborg, Roberta Lima Caldeira, Umar Niazi, Aurélie Kapusta, Christoph Grunau, Scott F. Cummins, Katherine M. Buckley, Milind Misra, Matheus de Souza Gomes, LaDeana W. Hillier, Iain W. Chalmers, Guillaume Mitta, Scott J. Emrich, Kathrin K. Geyer, Wander de Jesus Jeremias, Larissa L. S. Scholte, Laurence Rodrigues do Amaral, Juliana G Assis, Jacob A. Tennessen, Emmanuel A. Pila, Patrick C. Hanington, Andrew M. Shedlock, Wesley C. Warren, Chris Botka, Sandra Grossi Gava, Coen M. Adema, Janeth J. Pena, Satwant Kaur, Chad Tomlinson, Richard Galinier, Michelle A. Gordy, Bishoy Kamel, Guilherme Oliveira, Anne E. Lockyer, Jonathan P. Rast, Andrea B. Kohn, Daniel Lawson, Richard K. Wilson, Patrick Minx, Bryony C. Bonning, Peter C. FitzGerald, Christopher J. Bayne, Omar dos Santos Carvalho, Monica Munoz-Torres, Tianfang Wang, David Rollinson, Vince Magrini, Kyle K. Biggar, Titouan Quelais, Leslie R. Noble, Utibe Bickham-Wright, Francislon Silva de Oliveira, Cédric Feschotte, Daniel J. Jackson, Joris M. Koene, Michael J. Montague, Anthony J. Walker, Lucinda Fulton, Daniel S.T. Hughes, Susan Jobling, Rob Peace, Halime D. Arican-Goktas, Nathalie Dinguirard, Timothy P. Yoshino, Mohammed Yusuf, Cesar E. Montelongo, Michael E. Geusz, Sijun Liu, Si-Ming Zhang, Kenneth B. Storey, Leon di Stephano, Yanin Limpanont, Center for Evolutionary and theoretical Immunology, Biology, The University of New Mexico [Albuquerque], The McDonnell Genome Institute (MGI), Washington University in St Louis, INSTITUTE OF BIOLOGICAL AND ENVIRONMENTAL SCIENCES, University of Aberdeen, Department of Microbiology, Immunology & Tropical Medicine and Research Center for Neglected Diseases of Poverty, George Washington University (GW), Division of Science & Mathematics, University of the District of Columbia, Fiocruz Minas - René Rachou Research Center / Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), sans affiliation, Biology Department, Medical University of South Carolina [Charleston] (MUSC), Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlândia [Uberlândia] (UFU), Department of Life Sciences, College of Health and Life Sciences, Brunel University London [Uxbridge], Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Department of Integrative Biology, Oregon State University (OSU), Department of Pathobiological Sciences, University of Wisconsin-Madison, Institute of Biochemisty and Department of Biology, Carleton University, Iowa State University (ISU), Department of Information Technology, Harvard Medical School, Harvard Medical School [Boston] (HMS), Sunnybrook Health Sciences Centre, Department of Immunology, University of Toronto, Department of Human Genetics [Salt Lake City], University of Utah, Biology, New Mexico State University, New Mexico State University, Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, EMBL-EBI, Wellcome Genome Campus, Interactions Hôtes-Pathogènes-Environnements (IHPE), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Faculty of Science, Health and Education, University of the Sunshine Coast, The Walter and Eliza Hall Institute for Medical Research (WEHI), Genomics and Bioinformatics Core Facility, University of Notre Dame [Indiana] (UND), Department of Plant and Environmental Sciences [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Genome Analysis Unit, National Cancer Institute, National Institutes of Health [Bethesda] (NIH), Biological Sciences, Bowling Green State University, Bowling Green State University, IBERS, Institute of Biological, Environmental and Rural Sciences, Biotechnology and Biological Sciences Research Council, Department of Public Health Sciences, University of Alberta, University of Alberta, Department of Biology, Lawrence University, Lawrence University, Courant Research Centre Geobiology, Georg-August University of Göttingen, Georg-August-University [Göttingen], Institute of Environment, Health & Societies, Environment and Health Theme, Brunel University London, Brunel University London, Department of Biology, Pennsylvania State University (Penn State), Penn State System-Penn State System, Faculteit der Aard- en Levenswetenschappen, Vrije Universiteit, Vrije Universiteit Amsterdam [Amsterdam] (VU), The Whitney Laboratory for Marine Bioscience, University of Florida, University of Florida [Gainesville], Molecular Parasitology Laboratory, Kingston University, Kingston University, Faculty of Science, Health, Education and Engineering (USC), Molecular Parasitology Unit, Queensland Institute of Medical Research, Penn State System, Kenya Medical Research Institute (KEMRI), Department of Neuroscience (DEPARTMENT OF NEUROSCIENCE), University of Pennsylvania [Philadelphia], Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Bioinformatics and Cancer Genomics lab Lorenzo and Pamela Galli, Melanoma Research Fellow Peter MacCallum Cancer Centre, Institute for Genomics and Bioinformatics [Irvine], University of California [Irvine] (UCI), University of California-University of California, Parasites and Vectors Division, London Centre for Neglected Tropical Disease Research, Natural History Museum, Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster [London] (UOW), Molecular Parasitology Laboratory, School of Life Sciences Pharmacy and Chemistry, Sequence characterization of the Biomphalaria glabrata genome was funded by NIH-NHGRI grant HG003079 to R.K.W., McDonnell Genome Institute, Washington University School of Medicine. Biomphalaria glabrata and Schistosoma mansoni were provided to some participating labs by the NIAID Schistosomiasis Resource Center (Biomedical Research Institute, Rockville, MD) through NIH-NIAID Contract HHSN272201000005I for distribution through BEI Resources. C.M.A. and E.S.L. acknowledge NIH grant P30GM110907 from the National Institute of General Medical Sciences (NIGMS). Publication costs were contributed equally by McDonnell Genome Institute, Washington University School of Medicine and the COBRE Center for Evolutionary and Theoretical Immunology (CETI) which is supported by NIH grant P30GM110907 from the National Institute of General Medical Sciences (NIGMS). E.S.L. acknowledges NIH/NIAID ROI AI101438. J.M.B., H.D.A.-G and M.K. acknowledge NIH-NIAID R01-AI0634808. M.Y. acknowledges UK BBSRC (BB/H022597/1). G.O. acknowledges support from FAPEMIG (RED-00014-14, PPM-00189-13) and CNPq (304138/2014-2, 309312/2012-4). R.L.C. acknowledges CNPq (503275/2011-5). T.P.Y. acknowledges NIH/NIAID RO1AI015503. K.F.H. and M.T.S. acknowledge BBSRC (BB/K005448/1). B.G. acknowledges ANR JCJC INVIMORY (ANR-13-JSV7-0009). S.E. acknowledges NIAID contract HHSN272201400029C. J.M.K. acknowledges the Research Council for Earth and Life Sciences (A.L.W., 819.01.007) and the Netherlands Organization for Scientific Research (NWO). R.M.C. acknowledges NIH GM061738 and support from the American Heart Association, Southwest Affiliate (14GRNT20490250). D.T. acknowledges NIH R25 GM075149. C.F. acknowledges NIH R01-GM077582. D.J.J. acknowledges D.F.G. JA2108/1-2. M.de S.G. acknowledges CNPq 479890/2013-7. K.M.B. and J.P.R. acknowledge NSERC 312221 and CIHR MOP74667. C.S.J., L.R.N., S.J., E.J.R., S.K. and A.E.L. acknowledge NC3R GO900802/1. K.K.B. and K.B.S. acknowledge NSERC 315051 and 6793, respectively. M.B. and C.J.B. acknowledge NIH RO1-AI109134. C.J.B. acknowledges NIH AI016137 and AI111201. B.R. acknowledges NHGRI 4U41HG002371. P.C.H., M.A.G. and E.A.P. acknowledge NSERC 418540. O.L.B. and Ch.C. acknowledge ANR-12-EMMA-0007-01. S.F.C. acknowledges Australian Research Council FT110100990., We thank S. Newfeld for discussion of actin evolution, N. El Sayed and H. Tettelin for discussion of HSP annotation and expression. We acknowledge access to the Metafer microscopy system at the I. Robinson Research Complex, Harwell, Rutherford Appleton Laboratory, Oxon, UK (BBSRC Professorial Fellowship, grant number BB/H022597/1)., Washington University in Saint Louis (WUSTL), The George Washington University (GW), Fiocruz Minas - René Rachou Research Center / Instituto René Rachou [Belo Horizonte, Brésil], Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Perpignan Via Domitia (UPVD), The Walter and Eliza Hall Institute of Medical Research (WEHI), University of Florida [Gainesville] (UF), Animal Ecology, and Adema, Coen M.
Subjects: 0301 basic medicine, MESH: Sequence Analysis, DNA, Proteome, INTERMEDIATE HOST, MESH: Schistosoma mansoni, General Physics and Astronomy, Biomphalaria, Fresh Water, Snail, Genome informatics, Genome, Freshwater snail, Pheromones, MESH: Biomphalaria/parasitology, 0302 clinical medicine, Global health, ACTIN GENES, MESH: Animals, DNA sequencing, MESH: Stress, Physiological, MESH: Evolution, Molecular, MESH: Pheromones, Multidisciplinary, biology, INVERTEBRATE, schistosomiase, Schistosoma mansoni, Corrigenda, MESH: Gene Expression Regulation, 6. Clean water, Multidisciplinary Sciences, MESH: Proteome, MESH: DNA Transposable Elements, MESH: Fresh Water, Science & Technology - Other Topics, MESH: Animal Communication, Science, 030231 tropical medicine, MANSONI, Zoology, Schistosomiasis, MESH: Host-Parasite Interactions, General Biochemistry, Genetics and Molecular Biology, Article, Host-Parasite Interactions, Evolution, Molecular, 03 medical and health sciences, Stress, Physiological, biology.animal, MESH: Schistosomiasis mansoni/transmission, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MD Multidisciplinary, parasitic diseases, medicine, Journal Article, Biomphalaria glabrata, Animals, MESH: Biomphalaria/genetics, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, BIOMPHALARIA-GLABRATA, Science & Technology, COMPLEXITY, escargot aquatique, MESH: Genome, fungi, RECOGNITION, General Chemistry, Sequence Analysis, DNA, biology.organism_classification, medicine.disease, bacterial infections and mycoses, EVOLUTION, Schistosomiasis mansoni, Animal Communication, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, 030104 developmental biology, Gene Expression Regulation, MESH: Biomphalaria/immunology, INNATE IMMUNITY, DNA Transposable Elements, VERTEBRATE, biological
Abstract: Biomphalaria snails are instrumental in transmission of the human blood fluke Schistosoma mansoni. With the World Health Organization's goal to eliminate schistosomiasis as a global health problem by 2025, there is now renewed emphasis on snail control. Here, we characterize the genome of Biomphalaria glabrata, a lophotrochozoan protostome, and provide timely and important information on snail biology. We describe aspects of phero-perception, stress responses, immune function and regulation of gene expression that support the persistence of B. glabrata in the field and may define this species as a suitable snail host for S. mansoni. We identify several potential targets for developing novel control measures aimed at reducing snail-mediated transmission of schistosomiasis., Biomphalaria glabrata is a fresh water snail that acts as a host for trematode Schistosoma mansoni that causes intestinal infection in human. This work describes the genome and transcriptome analyses from 12 different tissues of B glabrata, and identify genes for snail behavior and evolution.
Published: 2017

11. The aliphatic amidase AmiE is involved in regulation of Pseudomonas aeruginosa virulence

Author: Pascal Cosette, Alain Dufour, Alexandre Crépin, Sylvie Chevalier, Pierre Cornelis, Julie Hardouin, Thibaut Rosay, Julien Vieillard, Perrine Bortolotti, Thomas Clamens, Joerg Overhage, Benoit Guery, Fergal O'Gara, Takfarinas Kentache, Anke Neidig, Teddy Grandjean, Marc G. J. Feuilloley, Marlies J. Mooij, Emeline Bouffartigues, Mélanie Hillion, Olivier Lesouhaitier, Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Laboratoire de Biotechnologie et Chimie Marines (LBCM), Université de Brest (UBO)-Université de Bretagne Sud (UBS)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Recherche translationelle relations hôte-pathogènes, Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Polymères Biopolymères Surfaces (PBS), Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut de Chimie du CNRS (INC)-Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Université Lille 2 - Faculté de Médecine, Karlsruhe Institute of Technology (KIT), University College Cork (UCC), Chimie Organique et Bioorganique : Réactivité et Analyse (COBRA), Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Normandie Université (NU)-Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie Organique Fine (IRCOF), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Plate-forme de Protéomique PISSARO, Institute for Research and Innovation in Biomedicine (IRIB), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Biologie et physiologie des états septiques, IFR114-Université de Lille, Droit et Santé, This work was supported by grants from the Communauté d’Agglomération d’Evreux, the Conseil Général de l′Eure, European Union (FEDER), the French Association 'Vaincre la Mucoviscidose' and the Partenariats Hubert Curien (PHC Ulysses). Financial support by the BioInterfaces (BIF) Program of the Karlsruhe Institute of Technology (KIT) in the Helmholtz Association is gratefully acknowledged., We wish to thank Magalie Barreau and Olivier Maillot for technical assistance. T. Clamens and T. Rosay are recipients of a doctoral fellowship from the French Ministry of Research (MRE)., Vriendenkring VUB, Microbiology, Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Faculté de Médecine Henri Warembourg - Université de Lille, Institut de Chimie Organique Fine (IRCOF), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université de Rouen Normandie (UNIROUEN), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-High-tech Research Infrastructures for Life Sciences (HeRacLeS), Normandie Université (NU)-Normandie Université (NU)-Institute for Research and Innovation in Biomedicine (IRIB), Normandie Université (NU)-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)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Bazire, Alexis
Subjects: Male, 0301 basic medicine, Virulence regulation, MESH: Pseudomonas Infections/microbiology, Proteome, health care facilities, manpower, and services, MESH: Dictyostelium/microbiology, MESH: Virulence, medicine.disease_cause, MESH: Quorum Sensing, Pilus, chemistry.chemical_compound, MESH: Caenorhabditis elegans/microbiology, MESH: Amidohydrolases/metabolism, AmiE overproduction, Dictyostelium, MESH: Animals, Lung, health care economics and organizations, MESH: Pseudomonas aeruginosa/enzymology, Multidisciplinary, Virulence, Quorum Sensing, MESH: Proteome, Pseudomonas aeruginosa, Female, Life sciences, biology, MESH: Virulence Factors, Virulence Factors, 030106 microbiology, Homoserine, MESH: Biofilms, Biology, Microbiology, Article, Amidohydrolases, Amidase, 03 medical and health sciences, Pyocyanin, MESH: Mice, Inbred C57BL, ddc:570, Journal Article, medicine, Animals, Pseudomonas Infections, cardiovascular diseases, Caenorhabditis elegans, MESH: Lung/microbiology, MESH: Pseudomonas aeruginosa/pathogenicity, Biofilm, Bacteriology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Male, MESH: Pseudomonas Infections/enzymology, Mice, Inbred C57BL, Quorum sensing, chemistry, Biofilms, FOS: Biological sciences, Pseudomonas aeruginosa virulence, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Female
Abstract: We have previously shown that the eukaryotic C-type natriuretic peptide hormone (CNP) regulates Pseudomonas aeruginosa virulence and biofilm formation after binding on the AmiC sensor, triggering the amiE transcription. Herein, the involvement of the aliphatic amidase AmiE in P. aeruginosa virulence regulation has been investigated. The proteome analysis of an AmiE over-producing strain (AmiE+) revealed an expression change for 138 proteins, including some that are involved in motility, synthesis of quorum sensing compounds and virulence regulation. We observed that the AmiE+ strain produced less biofilm compared to the wild type, and over-produced rhamnolipids. In the same line, AmiE is involved in P. aeruginosa motilities (swarming and twitching) and production of the quorum sensing molecules N-acyl homoserine lactones and Pseudomonas Quinolone Signal (PQS). We observed that AmiE overproduction reduced levels of HCN and pyocyanin causing a decreased virulence in different hosts (i.e. Dictyostelium discoideum and Caenorhabditis elegans). This phenotype was further confirmed in a mouse model of acute lung infection, in which AmiE overproduction resulted in an almost fully virulence decrease. Taken together, our data suggest that, in addition to its role in bacterial secondary metabolism, AmiE is involved in P. aeruginosa virulence regulation by modulating pilus synthesis and cell-to-cell communication.
Published: 2017

12. A Surface Biotinylation Strategy for Reproducible Plasma Membrane Protein Purification and Tracking of Genetic and Drug-Induced Alterations

Author: Katrin Hörmann, Jacques Colinge, Leonhard X. Heinz, Keiryn L. Bennett, André C. Müller, Giulio Superti-Furga, Alexey Stukalov, Institut de Recherche en Cancérologie de Montpellier (IRCM - U1194 Inserm - UM), and CRLCC Val d'Aurelle - Paul Lamarque-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)
Subjects: 0301 basic medicine, Proteomics, Proteome, plasma membrane, Biochemistry, Mass Spectrometry, Liquid chromatography–mass spectrometry, biotin, PIGS, silica beads, chemistry.chemical_classification, MESH: Proteomics, aminooxy-biotin, Anti-Bacterial Agents, MESH: Reproducibility of Results, MESH: Proteome, cell surface, shotgun proteomics, Biotinylation, MESH: Membrane Proteins, comparative analysis, MESH: Cell Line, Tumor, [SDV.CAN]Life Sciences [q-bio]/Cancer, Biology, 03 medical and health sciences, Cell Line, Tumor, MESH: Anti-Bacterial Agents, Humans, MESH: Biotinylation, Shotgun proteomics, MESH: Tunicamycin, MESH: Mass Spectrometry, Chromatography, MESH: Humans, 030102 biochemistry & molecular biology, Elution, Proteomic Profiling, Cell Membrane, Membrane Proteins, Reproducibility of Results, General Chemistry, tunicamycin, Surface coating, 030104 developmental biology, chemistry, Glycoprotein, MESH: Chromatography, Liquid, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Chromatography, Liquid, MESH: Cell Membrane
Abstract: International audience; Plasma membrane (PM) proteins contribute to the identity of a cell, mediate contact and communication, and account for more than two-thirds of known drug targets.1-8 In the past years, several protocols for the proteomic profiling of PM proteins have been described. Nevertheless, comparative analyses have mainly focused on different variations of one approach.9-11 We compared sulfo-NHS-SS-biotinylation, aminooxy-biotinylation, and surface coating with silica beads to isolate PM proteins for subsequent analysis by one-dimensional gel-free liquid chromatography mass spectrometry. Absolute and relative numbers of PM proteins and reproducibility parameters on a qualitative and quantitative level were assessed. Sulfo-NHS-SS-biotinylation outperformed aminooxy-biotinylation and surface coating using silica beads for most of the monitored criteria. We further simplified this procedure by a competitive biotin elution strategy achieving an average PM annotated protein fraction of 54% (347 proteins). Computational analysis using additional databases and prediction tools revealed that in total over 90% of the purified proteins were associated with the PM, mostly as interactors. The modified sulfo-NHS-SS-biotinylation protocol was validated by tracking changes in the plasma membrane proteome composition induced by genetic alteration and drug treatment. Glycosylphosphatidylinositol (GPI)-anchored proteins were depleted in PM purifications from cells deficient in the GPI transamidase component PIGS, and treatment of cells with tunicamycin significantly reduced the abundance of N-glycoproteins in surface purifications.
Published: 2016

13. A combined proteomic and targeted analysis unravels new toxic mechanisms for zinc oxide nanoparticles in macrophages

Author: Jean-Luc Ravanat, Thierry Rabilloud, Bastien Dalzon, Jean Marc Strub, Véronique Collin-Faure, Hélène Diemer, Marie Carrière, Alain Van Dorsselaer, Catherine Aude-Garcia, Sarah Cianférani, Protéomique, Métaux et Différenciation (ProMD ), Laboratoire de Chimie et Biologie des Métaux (LCBM - UMR 5249), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-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)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-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]), Laboratoire Lésions des Acides Nucléiques (LAN), Service de Chimie Inorganique et Biologique (SCIB - UMR E3), Institut Nanosciences et Cryogénie (INAC), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut Nanosciences et Cryogénie (INAC), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), 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), 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), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-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])-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 Nanosciences et Cryogénie (INAC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-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), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), and Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Proteomics, Cell signaling, Proteome, DNA damage, Zirconium dioxide, Biophysics, 02 engineering and technology, MESH: Zinc Oxide, Mitochondrion, Biochemistry, Cell Line, Mice, 03 medical and health sciences, chemistry.chemical_compound, Phagocytosis, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Zinc oxide, Animals, MESH: Animals, MESH: Mice, Glutathione biosynthesis, biology, Macrophages, MESH: Proteomics, Methylglyoxal, MESH: Macrophages, 021001 nanoscience & nanotechnology, Aryl hydrocarbon receptor, Methyglyoxal, Mitochondria, MESH: Cell Line, Heme oxygenase, MESH: Proteome, 030104 developmental biology, chemistry, Cell culture, Cancer cell, biology.protein, Nanoparticles, 0210 nano-technology, MESH: Nanoparticles
Abstract: The cellular responses of the J774 macrophage cell line to zinc oxide and zirconium oxide nanoparticles have been studied by a comparative quantitative, protein level based proteomic approach. The most prominent results have been validated by targeted approaches. These approaches have been carried out under culture conditions that stimulate mildly the aryl hydrocarbon receptor, thereby mimicking conditions that can be encountered in vivo in complex environments. The comparative approach with two nanoparticles allows to separate the common responses, which can be attributed to the phagocytosis event per se, from the response specific to each type of nanoparticles. The zinc-specific responses are the most prominent ones and include mitochondrial proteins too, but also signaling molecules such as MyD88, proteins associated with methylglyoxal detoxification (glyoxalase 2, aldose reductase) and deoxyribonucleotide hydrolases. The in cellulo inhibition of GAPDH by zinc was also documented, representing a possible source of methylglyoxal in the cells, leading to an increase in methylglyoxal-modified DNA bases. These observations may be mechanistically associated with the genotoxic effect of zinc and its selective effects on cancer cells.The responses of the murine J774 macrophage cell lines to two types of metallic oxide nanoparticles (zinc oxide and zirconium dioxide) were studied by a comparative 2D gel based approach. This allows sorting of shared responses from nanoparticle-specific responses. Zinc oxide nanoparticles induced specifically a strong decrease in the mitochondrial function, in phagocytosis and also an increase in the methylglyoxal-associated DNA damage, which may explain the well known genotoxicity of zinc. In conclusion, this study allows highlighting of pathways that may play an important role in the toxicity of the zinc oxide nanoparticles.
Published: 2016

14. Changes in markers associated with dendritic cells driving the differentiation of either TH2 cells or regulatory T cells correlate with clinical benefit during allergen immunotherapy

Author: Magalie Duchateau, Emmanuel Nony, Vincent Lombardi, Philippe Moingeon, Julia Chamot-Rooke, Laurent Mascarell, Hélène Moussu, Marc Pallardy, Julien Bouley, Véronique Baron-Bodo, Claire Gueguen, Sonia Luce, Stallergenes SA (Stallergenes), Stallergenes, Spectrométrie de Masse structurale et protéomique, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Faculté de Pharmacie [Châtenay-Malabry], Université Paris-Sud - Paris 11 - Faculté de médecine (UP11 UFR Médecine), Université Paris-Sud - Paris 11 (UP11)-Université Paris-Sud - Paris 11 (UP11)-Université Paris-Saclay, Supported by Stallergenes. C.G. was supported by a CIFRE fellowship from ANRT (Association Nationale de la Recherche et de la Technologie, grant no. 1470/2011). C.G., J.B., H.M., E.N., V.B.-B., L.M., and P.M. are employees at Stallergenes SA., and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Male, Proteome, Cellular differentiation, [SDV]Life Sciences [q-bio], Epitopes, T-Lymphocyte, T-Lymphocytes, Regulatory, 0302 clinical medicine, Immunophenotyping, Immunology and Allergy, Cluster Analysis, MESH: Desensitization, Immunologic, MESH: Immunoglobulin G, education.field_of_study, MESH: Cytokines, MESH: Dendritic Cells, Allergen, GATA3, Cell Differentiation, MESH: Gene Expression Regulation, 3. Good health, MESH: Proteome, medicine.anatomical_structure, Antigens, Surface, monocyte, Cytokines, Pollen, biomarker, Female, MESH: Cell Differentiation, MESH: Allergens, MESH: Immunophenotyping, dendritic cell, MESH: Antigens, Surface, MESH: Hypersensitivity, Immunology, Biology, Peripheral blood mononuclear cell, sublingual immunotherapy, MESH: Epitopes, T-Lymphocyte, 03 medical and health sciences, MESH: Gene Expression Profiling, Th2 Cells, MESH: Th2 Cells, medicine, Hypersensitivity, Humans, education, MESH: Humans, Monocyte, Gene Expression Profiling, MESH: T-Lymphocytes, Regulatory, Rhinitis, Allergic, Seasonal, MESH: Rhinitis, Allergic, Seasonal, Dendritic cell, Dendritic Cells, Allergens, MESH: ROC Curve, MESH: Cluster Analysis, MESH: Male, OX40 ligand, Ferritin light chain, 030104 developmental biology, Gene Expression Regulation, ROC Curve, Desensitization, Immunologic, Immunoglobulin G, MESH: Pollen, MESH: Biomarkers, MESH: Female, Biomarkers, 030215 immunology
Abstract: International audience; Background: Regulatory dendritic cell (DC) markers, such as C1Q, are upregulated in PBMCs of patients with grass pollen allergy exhibiting clinical benefit during allergen immunotherapy (AIT).Objectives: We sought to define markers differentially expressed in human monocyte-derived DCs differentiated toward a proallergic (DCs driving the differentiation of TH2 cells [DC2s]) phenotype and investigate whether changes in such markers in the blood correlate with AIT efficacy.Methods: Transcriptomes and proteomes of monocyte-derived DCs polarized toward DCs driving the differentiation of TH1 cells (DC1s), DC2s, or DCs driving the differentiation of regulatory T cells (DCreg cells) profiles were compared by using genome-wide cDNA microarrays and label-free quantitative proteomics, respectively. Markers differentially regulated in DC2s and DCreg cells were assessed by means of quantitative PCR in PBMCs from 80 patients with grass pollen allergy before and after 2 or 4 months of sublingual AIT in parallel with rhinoconjunctivitis symptom scores.Results: We identified 20 and 26 new genes/proteins overexpressed in DC2s and DCreg cells, respectively. At an individual patient level, DC2-associated markers, such as CD141, GATA3, OX40 ligand, and receptor-interacting serine/threonine-protein kinase 4 (RIPK4), were downregulated after a 4-month sublingual AIT course concomitantly with an upregulation of DCreg cell-associated markers, including complement C1q subcomponent subunit A (C1QA), FcγRIIIA, ferritin light chain (FTL), and solute carrier organic anion transporter family member 2B1 (SLCO2B1), in the blood of clinical responders as opposed to nonresponders. Changes in such markers were better correlated with clinical benefit than alterations of allergen-specific CD4(+) T-cell or IgG responses.Conclusions: A combination of 5 markers predominantly expressed by blood DCs (ie, C1Q and CD141) or shared with lymphoid cells (ie, FcγRIIIA, GATA3, and RIPK4) reflecting changes in the balance of regulatory/proallergic responses in peripheral blood can be used as early as after 2 months to monitor the early onset of AIT efficacy.
Published: 2016

15. Cell wall proteome of sugarcane stems: comparison of a destructive and a non-destructive extraction method showed differences in glycoside hydrolases and peroxidases

Author: Thais Regiani Cataldi, Carlos Alberto Labate, Elisabeth Jamet, Maria Juliana Calderan-Rodrigues, Maria Beatriz Calderan Rodrigues Bonassi, Rafael Pont-Lezica, Juliana Guimarães Fonseca, Hélène San Clemente, Thibaut Douché, Universidade de São Paulo (USP), Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), Dynamique et Evolution des Parois cellulaires végétales, Laboratoire de Recherche en Sciences Végétales (LRSV), 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), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Signal peptide, Proteomics, Glycoside Hydrolases, Proteome, Plant Science, Biology, Stem, 01 natural sciences, MESH: Saccharum, Cell wall, Second generation ethanol, MESH: Peroxidases, 03 medical and health sciences, Saccharum sp, MESH: Cell Wall, Cell Wall, MESH: Glycoside Hydrolases, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Glycoside hydrolase, Ethanol fuel, Plant Proteins, 2. Zero hunger, MESH: Plant Stems, Plant Stems, MESH: Plant Proteins, Cell wall protein, Saccharum, MESH: Proteome, 030104 developmental biology, Peroxidases, Biochemistry, Bagasse, Intracellular, Research Article, 010606 plant biology & botany
Abstract: Background Sugarcane has been used as the main crop for ethanol production for more than 40 years in Brazil. Recently, the production of bioethanol from bagasse and straw, also called second generation (2G) ethanol, became a reality with the first commercial plants started in the USA and Brazil. However, the industrial processes still need to be improved to generate a low cost fuel. One possibility is the remodeling of cell walls, by means of genetic improvement or transgenesis, in order to make the bagasse more accessible to hydrolytic enzymes. We aimed at characterizing the cell wall proteome of young sugarcane culms, to identify proteins involved in cell wall biogenesis. Proteins were extracted from the cell walls of 2-month-old culms using two protocols, non-destructive by vacuum infiltration vs destructive. The proteins were identified by mass spectrometry and bioinformatics. Results A predicted signal peptide was found in 84 different proteins, called cell wall proteins (CWPs). As expected, the non-destructive method showed a lower percentage of proteins predicted to be intracellular than the destructive one (33 % vs 44 %). About 19 % of CWPs were identified with both methods, whilst the infiltration protocol could lead to the identification of 75 % more CWPs. In both cases, the most populated protein functional classes were those of proteins related to lipid metabolism and oxido-reductases. Curiously, a single glycoside hydrolase (GH) was identified using the non-destructive method whereas 10 GHs were found with the destructive one. Quantitative data analysis allowed the identification of the most abundant proteins. Conclusions The results highlighted the importance of using different protocols to extract proteins from cell walls to expand the coverage of the cell wall proteome. Ten GHs were indicated as possible targets for further studies in order to obtain cell walls less recalcitrant to deconstruction. Therefore, this work contributed to two goals: enlarge the coverage of the sugarcane cell wall proteome, and provide target proteins that could be used in future research to facilitate 2G ethanol production. Electronic supplementary material The online version of this article (doi:10.1186/s12870-015-0677-0) contains supplementary material, which is available to authorized users.
Published: 2016

16. Quantifying domain-ligand affinities and specificities by high-throughput holdup assay

Author: Yves Nominé, Sebastian Charbonnier, Patricia Cassonnet, Anne Forster, Julie Abdat, Marilyne Blémont, Nicolas Wolff, Kevin Ricquier, Renaud Vincentelli, Katja Luck, Juline Poirson, Marie-Laure Straub, Jérôme Reboul, Jolanta Polanowska, Jeremy Turchetto, Gilles Travé, Francois, Jean-Paul Borg, Yves Jacob, Murielle Masson, 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), Biotechnologie et signalisation cellulaire (BSC), Université de Strasbourg (UNISTRA)-Institut de recherche de l'Ecole de biotechnologie de Strasbourg (IREBS)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université (AMU)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Résonance Magnétique Nucléaire des Biomolécules, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Equipe labellisée Ligue contre le Cancer, Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)), Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), This work was supported by institutional support from CNRS, Université de Strasbourg, Infrastructures Biologie Santé et Agronomie (Ibisa) and grants from the Association pour la Recherche contre le Cancer (ARC) (no. 3171), Agence Nationale de la Recherche (ANR-MIME-2007 EPI-HPV-3D), US National Institutes of Health (NIH grant R01CA134737), Ligue contre le Cancer and Alsace contre le Cancer. K.L. was supported by grants of Région Alsace and ARC. J. Poirson was supported by a grant of the Ligue Régionale contre le Cancer. J.-P.B. is supported in part by grants from La Ligue Contre le Cancer, Institut paoli-Calmettes, Cancéropôle PACA and SIRIC (INCa-DGOS-Inserm 6038). J.-P.B. is supported as a scholar of Institut Universitaire de France, SIRIC 6038United States Department of Health & Human Services National Institutes of Health (NIH) - USA NIH National Cancer Institute (NCI) R01CA134737, We thank the CCSB (Harvard University) for kindly providing clones of the human ORFeome, and T. Rolland, M.A. Delsuc, D. Altschuh, B. Kieffer, A. Dejaegere and all members of the 'Oncoproteins' team for helpful discussions and advice., ANR-07-MIME-0009,EPI-HPV-3D,Vers la compréhension fonctionelle et structurale de l'interactome cellulaire des protéines précoces des Papilloma Virus Humains.(2007), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Wolff, Nicolas, Microbiologie, immunologie et maladies émergentes - Vers la compréhension fonctionelle et structurale de l'interactome cellulaire des protéines précoces des Papilloma Virus Humains. - - EPI-HPV-3D2007 - ANR-07-MIME-0009 - MIME - VALID, Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche de l'Ecole de biotechnologie de Strasbourg (IREBS), and Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]
Subjects: Proteome, Protein Conformation, MESH: PDZ Domains, MESH: DNA-Binding Proteins / chemistry, [SDV]Life Sciences [q-bio], Amino Acid Motifs, PDZ Domains, Ligands, Biochemistry, MESH: Amino Acid Motifs, Protein structure, MESH: Protein Conformation, Protein Interaction Mapping, MESH: Ligands, [SDV.BBM.BC] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], ComputingMilieux_MISCELLANEOUS, MESH: Oncogene Proteins, Viral / chemistry, MESH: High-Throughput Screening Assays, 0303 health sciences, Chromatography, MESH: Kinetics, Systems Biology, 030302 biochemistry & molecular biology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV] Life Sciences [q-bio], DNA-Binding Proteins, MESH: Proteome, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], MESH: Systems Biology, MESH: Proteins / chemistry, Biotechnology, MESH: Protein Interaction Mapping / methods, High-throughput screening, PDZ domain, Computational biology, Biology, MESH: Chromatography, DNA-binding protein, Article, Protein–protein interaction, 03 medical and health sciences, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Humans, Short linear motif, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], MESH: Repressor Proteins / chemistry, Molecular Biology, 030304 developmental biology, MESH: Humans, Proteins, Cell Biology, Oncogene Proteins, Viral, Affinities, Molecular biology, High-Throughput Screening Assays, Repressor Proteins, Kinetics
Abstract: Many protein interactions are mediated by small linear motifs interacting specifically with defined families of globular domains. Quantifying the specificity of a motif requires measuring and comparing its binding affinities to all its putative target domains. To this aim, we developed the high-throughput holdup assay, a chromatographic approach that can measure up to a thousand domain-motif equilibrium binding affinities per day. Extracts of overexpressed domains are incubated with peptide-coated resins and subjected to filtration. Binding affinities are deduced from microfluidic capillary electrophoresis of flow-throughs. After benchmarking the approach on 210 PDZ-peptide pairs with known affinities, we determined the affinities of two viral PDZ-binding motifs derived from Human Papillomavirus E6 oncoproteins for 209 PDZ domains covering 79% of the human PDZome. We obtained exquisite sequence-dependent binding profiles, describing quantitatively the PDZome recognition specificity of each motif. This approach, applicable to many categories of domain-ligand interactions, has a wide potential for quantifying the specificities of interactomes.
Published: 2015

17. Global human tissue profiling and protein network analysis reveals distinct levels of transcriptional germline-specificity and identifies target genes for male infertility

Author: Romain Mathieu, Aurélie Lardenois, Bertrand Evrard, Wolfgang Schulze, Alexandre Gattiker, Philippe Demougin, Bernard Jégou, Frédéric Chalmel, Michael Primig, Caroline Feig, Christiane Kirchhoff, Transcriptional networks in gametogenesis and cancer, Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), École des Hautes Études en Santé Publique [EHESP] (EHESP), Department of Andrology, Universitaetsklinikum Hamburg-Eppendorf = University Medical Center Hamburg-Eppendorf [Hamburg] (UKE), Biozentrum [Basel, Suisse], University of Basel (Unibas), School of Life Sciences [Lausanne], Ecole Polytechnique Fédérale de Lausanne (EPFL), Environnement viral et chimique & reproduction, Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Santé et de la Recherche Médicale (INSERM)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université d'Angers (UA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Santé et de la Recherche Médicale (INSERM)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université d'Angers (UA)
Subjects: Male, Target, Proteome, Somatic cell, Amino Acid Motifs, interactome, Network, Gene, Germline, Male infertility, Transcriptome, MESH: Amino Acid Motifs, 0302 clinical medicine, regulatory motifs, MESH: Child, Cryptorchidism, Testis, MESH: Animals, Child, Promoter Regions, Genetic, MESH: Organ Specificity, Oligonucleotide Array Sequence Analysis, Genetics, Regulation of gene expression, 0303 health sciences, 030219 obstetrics & reproductive medicine, MESH: Testis, Rehabilitation, Obstetrics and Gynecology, Phenotype, MESH: Gene Expression Regulation, DNA-Binding Proteins, MESH: Proteome, Organ Specificity, Mammalia, Specificity, MESH: Spermatogenesis, Human, Adult, MESH: Rats, Biology, MESH: Infertility, Male, 03 medical and health sciences, MESH: Gene Expression Profiling, Species Specificity, MESH: Cryptorchidism, Male sterility, MESH: Promoter Regions, Genetic, medicine, Animals, Humans, MESH: Species Specificity, RNA, Messenger, Spermatogenesis, Infertility, Male, 030304 developmental biology, MESH: RNA, Messenger, Vertebrata, Tissue, MESH: Humans, Male genital diseases, Gene Expression Profiling, Protein, MESH: Adult, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, medicine.disease, MESH: Male, Rats, Gene expression profiling, Reproductive Medicine, Gene Expression Regulation, MESH: Oligonucleotide Array Sequence Analysis, transcriptome, MESH: DNA-Binding Proteins
Abstract: International audience; BACKGROUND: Mammalian spermatogenesis is a process that involves a complex expression program in both somatic and germ cells present in the male gonad. A number of studies have attempted to define the transcriptome of male meiosis and gametogenesis in rodents and primates. Few human transcripts, however, have been associated with testicular somatic cells and germ cells at different post-natal developmental stages and little is known about their level of germline-specificity compared with non-testicular tissues. METHODS: We quantified human transcripts using GeneChips and a total of 47 biopsies from prepubertal children diagnosed with undescended testis, infertile adult patients whose spermatogenesis is arrested at consecutive stages and fertile control individuals. These results were integrated with data from enriched normal germ cells, non-testicular expression data, phenotype information, predicted regulatory DNA-binding motifs and interactome data. RESULTS: Among 3580 genes for which we found differential transcript concentrations in somatic and germ cells present in human testis, 933 were undetectable in 45 embryonic and adult non-testicular tissues, including many that were corroborated at protein level by published gene annotation data and histological high-throughput protein immunodetection assays. Using motif enrichment analyses, we identified regulatory promoter elements likely involved in germline development. Finally, we constructed a regulatory disease network for human fertility by integrating expression signals, interactome information, phenotypes and functional annotation data. CONCLUSIONS: Our results provide broad insight into the post-natal human testicular transcriptome at the level of cell populations and in a global somatic tissular context. Furthermore, they yield clues for genetic causes of male infertility and will facilitate the identification of novel cancer/testis genes as targets for cancer immunotherapies.
Published: 2012

18. Hereditary systemic amyloidosis due to Asp76Asn variant β2-microglobulin

Author: Jean-Michel Goujon, Mathieu Boimard, Corinne Lacombe, Violaine Planté-Bordeneuve, Philip N. Hawkins, Monica Stoppini, Julie A. Vrana, Mark B. Pepys, Guy Touchard, Vittorio Bellotti, Riccardo Porcari, Thierry Maisonobe, Franck Bridoux, Sophie Valleix, Julian D. Gillmore, Ahmet Dogan, Martino Bolognesi, Jason D. Theis, Pierre Lozeron, Sofia Giorgetti, Marc Delpech, Catherine Lacroix, Stefano Ricagno, David H. Adams, Brigitte Nedelec, Palma Mangione, Laboratoire de Biochimie et Génétique Moléculaire, Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Université Paris Descartes - Paris 5 (UPD5), Contrôle de la Réponse Immune B et des Lymphoproliférations (CRIBL), Centre National de la Recherche Scientifique (CNRS)-Université de Limoges (UNILIM)-Génomique, Environnement, Immunité, Santé, Thérapeutique (GEIST FR CNRS 3503), Service de néphrologie - hémodialyse et transplantation rénale, Centre hospitalier universitaire de Poitiers (CHU Poitiers), Laboratoire d'anatomopathologie, Université de Limoges (UNILIM)-Génomique, Environnement, Immunité, Santé, Thérapeutique (GEIST FR CNRS 3503)-Centre National de la Recherche Scientifique (CNRS), Assistance publique - Hôpitaux de Paris (AP-HP)-Université Paris Descartes - Paris 5 ( UPD5 ), Contrôle de la Réponse Immune B et des Lymphoproliférations ( CRIBL ), Centre National de la Recherche Scientifique ( CNRS ) -Université de Limoges ( UNILIM ) -Génomique, Environnement, Immunité, Santé, Thérapeutique ( GEIST FR CNRS 3503 ), Université de Poitiers-Centre hospitalier universitaire de Poitiers ( CHU Poitiers ), Ischémie - Reperfusion en transplatation rénale, Université de Poitiers-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Centre hospitalier universitaire de Poitiers ( CHU Poitiers ), and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Descartes - Paris 5 (UPD5)
Subjects: Male, MESH: Hydrogen-Ion Concentration, Proteome, MESH: Protein Structure, Quaternary, MESH : beta 2-Microglobulin, MESH : Diarrhea, MESH: Monitoring, Physiologic, 0302 clinical medicine, [ SDV.IMM ] Life Sciences [q-bio]/Immunology, MESH : Female, Genes, Dominant, 0303 health sciences, MESH: Middle Aged, biology, Amyloidosis, MESH: Infant, Newborn, Fibrillogenesis, MESH : Genes, Dominant, General Medicine, Middle Aged, MESH : Amyloidosis, Familial, Pedigree, MESH: Glass, MESH: Proteome, MESH: Diarrhea, Sjogren's Syndrome, MESH : Glass, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, Protein folding, MESH: beta 2-Microglobulin, MESH : Scalp, Amyloidosis, Familial, Diarrhea, medicine.medical_specialty, Amyloid, MESH: Pedigree, MESH : Male, MESH : Proteome, MESH : Infant, Newborn, Fibril, MESH: Scalp, 03 medical and health sciences, MESH : Hydrogen-Ion Concentration, MESH : Protein Structure, Quaternary, Internal medicine, medicine, Humans, MESH : Middle Aged, MESH: Fetal Blood, Protein Structure, Quaternary, 030304 developmental biology, MESH : Fetal Blood, MESH: Humans, Beta-2 microglobulin, business.industry, MESH : Humans, MESH : Monitoring, Physiologic, MESH: Electrodes, medicine.disease, MESH: Amyloidosis, Familial, In vitro, MESH: Male, Transthyretin, Endocrinology, MESH: Sjogren's Syndrome, MESH : Pedigree, biology.protein, MESH : Sjogren's Syndrome, beta 2-Microglobulin, business, MESH: Genes, Dominant, MESH: Female, 030217 neurology & neurosurgery, MESH : Electrodes
Abstract: International audience; We describe a kindred with slowly progressive gastrointestinal symptoms and autonomic neuropathy caused by autosomal dominant, hereditary systemic amyloidosis. The amyloid consists of Asp76Asn variant β(2)-microglobulin. Unlike patients with dialysis-related amyloidosis caused by sustained high plasma concentrations of wild-type β(2)-microglobulin, the affected members of this kindred had normal renal function and normal circulating β(2)-microglobulin values. The Asp76Asn β(2)-microglobulin variant was thermodynamically unstable and remarkably fibrillogenic in vitro under physiological conditions. Previous studies of β(2)-microglobulin aggregation have not shown such amyloidogenicity for single-residue substitutions. Comprehensive biophysical characterization of the β(2)-microglobulin variant, including its 1.40-Å, three-dimensional structure, should allow further elucidation of fibrillogenesis and protein misfolding.
Published: 2012

19. Plasmodium falciparum infection-induced changes in erythrocyte membrane proteins

Author: Samuel Granjeaud, Thierry Fusai, Lionel Almeras, Christophe Rogier, Maya Belghazi, Stéphanie Bourdon, Marylin Torrentino-Madamet, Albin Fontaine, Mathieu Pophillat, Patrick Fourquet, Unité de Recherche en Biologie et Epidémiologie Parasitaires, Institut de Médecine Tropicale du Service de Santé des Armées-Centre National de la Recherche Scientifique (CNRS), Centre de recherche en neurobiologie - neurophysiologie de Marseille (CRN2M), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre d'Immunologie de Marseille - Luminy (CIML), Technologies avancées pour le génôme et la clinique (TAGC), Epidémiologie, Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), This study was supported by Délégation Générale pour l'Armement (DGA, SalivaPuls Project grant nos. 07CO406 and 03CO008-05, ArthroSer Project grant no. 10Ca401)., Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)
Subjects: Erythrocytes, Proteome, Difference gel electrophoresis, [SDV]Life Sciences [q-bio], Plasmodium falciparum, 030231 tropical medicine, MESH: Erythrocyte Membrane, Mass Spectrometry, Microbiology, 03 medical and health sciences, 0302 clinical medicine, parasitic diseases, medicine, Humans, Parasite hosting, Electrophoresis, Gel, Two-Dimensional, MESH: Plasmodium falciparum, 030304 developmental biology, MESH: Mass Spectrometry, 0303 health sciences, Pregnancy-associated malaria, MESH: Humans, General Veterinary, biology, MESH: Erythrocytes, Erythrocyte Membrane, MESH: Host-Pathogen Interactions, Membrane Proteins, General Medicine, biology.organism_classification, MESH: Electrophoresis, Gel, Two-Dimensional, Molecular biology, Fold change, 3. Good health, MESH: Proteome, Red blood cell, Infectious Diseases, medicine.anatomical_structure, Membrane protein, Insect Science, Host-Pathogen Interactions, Parasitology, MESH: Membrane Proteins
Abstract: International audience; Over the past decade, advances in proteomic and mass spectrometry techniques and the sequencing of the Plasmodium falciparum genome have led to an increasing number of studies regarding the parasite proteome. However, these studies have focused principally on parasite protein expression, neglecting parasite-induced variations in the host proteome. Here, we investigated P. falciparum-induced modifications of the infected red blood cell (iRBC) membrane proteome, taking into account both host and parasite proteome alterations. Furthermore, we also determined if some protein changes were associated with genotypically distinct P. falciparum strains. Comparison of host membrane proteomes between iRBCs and uninfected red blood cells using fluorescence-based proteomic approaches, such as 2D difference gel electrophoresis revealed that more than 100 protein spots were highly up-represented (fold change increase greater than five) following P. falciparum infection for both strains (i.e. RP8 and Institut Pasteur Pregnancy Associated Malaria). The majority of spots identified by mass spectrometry corresponded to Homo sapiens proteins. However, infection-induced changes in host proteins did not appear to affect molecules located at the outer surface of the plasma membrane. The under-representation of parasite proteins could not be attributed to deficient parasite protein expression. Thus, this study describes for the first time that considerable host protein modifications were detected following P. falciparum infection at the erythrocyte membrane level. Further analysis of infection-induced host protein modifications will improve our knowledge of malaria pathogenesis.
Published: 2012

20. Lipoproteins of Enterococcus faecalis: bioinformatic identification, expression analysis and relation to virulence

Author: Charlène Leneveu, Yanick Auffray, Alain Rincé, Sylvie Chevalier, Fany Reffuveille, Laboratoire de Microbiologie de l’Environnement (LME), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Recherche Agronomique (INRA), Laboratoire de Microbiologie du Froid – Signaux et Micro-Environnement (LMDF-SME), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Institut National de la Recherche Agronomique (INRA)-Université de Caen Normandie (UNICAEN), Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM), and Unité de Recherche Risques Microbiens (U2RM)
Subjects: MESH: Enterococcus faecalis, Proteome, Lipoproteins, [SDV]Life Sciences [q-bio], Virulence, MESH: Virulence, MESH: Genome, Bacterial, Microbiology, Genome, Enterococcus faecalis, 03 medical and health sciences, Bacterial Proteins, Gene, MESH: Bacterial Proteins, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Oligonucleotide Array Sequence Analysis, 0303 health sciences, MESH: Gene Expression Regulation, Bacterial, biology, 030306 microbiology, Microarray analysis techniques, Computational Biology, Membrane Proteins, Gene Expression Regulation, Bacterial, biology.organism_classification, MESH: Lipoproteins, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Proteome, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Membrane protein, MESH: Oligonucleotide Array Sequence Analysis, MESH: Membrane Proteins, Bacteria, Genome, Bacterial, MESH: Computational Biology
Abstract: Enterococcus faecalisis a ubiquitous bacterium that is capable of surviving in a broad range of natural environments, including the human host, as either a natural commensal or an opportunistic pathogen involved in severe hospital-acquired infections. How such opportunistic pathogens cause fatal infections is largely unknown but it is likely that they are equipped with sophisticated systems to perceive external signals and interact with eukaryotic cells. Accordingly, being partially exposed at the cell exterior, some surface-associated proteins are involved in several steps of the infection process. Among them are lipoproteins, representing about 25 % of the surface-associated proteins, which could play a major role in bacterial virulence processes. This review focuses on the identification of 90 lipoprotein-encoding genes in the genome of theE. faecalisV583 clinical strain and their putative roles, and provides a transcriptional comparison of microarray data performed in environmental conditions including blood and urine. Taken together, these data suggest a potential involvement of lipoproteins inE. faecalisvirulence, making them serious candidates for vaccine production.
Published: 2011

21. Toward characterizing seed vigor in alfalfa through proteomic analysis of germination and priming

Author: Dominique Job, Claudette Job, Rafika Yacoubi, Maya Belghazi, Wided Chaïbi, Physiologie des plantes et des champignons lors de l'infection, Bayer Cropscience-Centre National de la Recherche Scientifique (CNRS), Centre de recherche en neurobiologie - neurophysiologie de Marseille (CRN2M), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Unité de Recherche de Biologie et Physiologie Cellulaires Végétales, and Université de Tunis El Manar (UTM)
Subjects: 0106 biological sciences, Proteomics, MESH: Sodium Chloride, Proteome, Protein metabolism, Germination, Priming (agriculture), MESH: Germination, Sodium Chloride, 01 natural sciences, Biochemistry, Salinity stress, Polyethylene Glycols, 03 medical and health sciences, chemistry.chemical_compound, Stress, Physiological, Electrophoresis, Gel, Two-Dimensional, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], MESH: Stress, Physiological, 030304 developmental biology, Plant Proteins, MESH: Medicago sativa, 2. Zero hunger, 0303 health sciences, biology, MESH: Plant Proteins, MESH: Proteomics, food and beverages, General Chemistry, Metabolism, 15. Life on land, biology.organism_classification, MESH: Electrophoresis, Gel, Two-Dimensional, MESH: Proteome, Agronomy, chemistry, MESH: Polyethylene Glycols, MESH: Seeds, Seedling, Seedlings, Seeds, Stress conditions, MESH: Seedling, 010606 plant biology & botany, Medicago sativa
Abstract: International audience; Alfalfa, the most widely grown leguminous crop in the world, is generally exposed to severe salinity stress in Tunisia, notably affecting its germination performance. Toward a better understanding of alfalfa seed vigor, we have used proteomics to characterize protein changes occurring during germination and osmopriming, a pretreatment that accelerates germination and improves seedling uniformity particularly under stress conditions. The data revealed that germination was accompanied by dynamic changes of 79 proteins, which are mainly involved in protein metabolism, cell structure, metabolism, and defense. Comparative proteomic analysis also revealed 63 proteins specific to osmopriming, 65 proteins preferentially varying during germination, and 14 proteins common to both conditions. Thus, the present study unveiled the unexpected finding that osmopriming cannot simply be considered as an advance of germination-related processes but involves other mechanisms improving germination such as the mounting of defense mechanisms enabling osmoprimed seeds to surmount environmental stresses potentially occurring during germination. The present results therefore provide novel avenues toward understanding the mechanisms of invigoration of low vigor seeds by priming treatments that are widely used both in commercial applications and in developing countries (on farm seed priming) to better control crop yields.
Published: 2011

22. Species specific amino acid sequence-protein local structure relationships: An analysis in the light of a structural alphabet

Author: De Brevern, Alexandre, Joseph, Agnel Praveen, Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), and French Ministry of Research University Paris Diderot the Institute of Blood Transfusion (INTS) the Institute for Health and Medical Research(INSERM).
Subjects: MESH: Databases, Protein, amino acids, MESH: Amino Acids, MESH: Molecular Sequence Data, malaria, MESH: Protein Structure, Secondary, secondary structure, MESH: Amino Acid Sequence, MESH: Saccharomyces cerevisiae, MESH: Cluster Analysis, MESH: Proteome, MESH: Structure-Activity Relationship, Protein Blocks, MESH: Species Specificity, structural alphabet, MESH: Arabidopsis, MESH: Proteins, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, protein folds, MESH: Plasmodium falciparum
Abstract: International audience; Protein structure analysis and prediction methods are based on non-redundant data extracted from the available protein structures, regardless of the species from which the protein originates. Hence, these datasets represent the global knowledge on protein folds, which constitutes a generic distribution of amino acid sequence-protein structure (AAS-PS) relationships. In this study, we try to elucidate whether the AAS-PS relationship could possess specificities depending on the specie. For this purpose, we have chosen three different species: Saccharomyces cerevisiae, Plasmodium falciparum and Arabidopsis thaliana. We analyzed the AAS-PS behaviors of the proteins from these three species and compared it to the "expected" distribution of a classical non-redundant databank. With the classical secondary structure description, only slight differences in amino acid preferences could be observed. With a more precise description of local protein structures (Protein Blocks), significant changes could be highlighted. S. cerevisiae's AAS-PS relationship is close to the general distribution, while striking differences are observed in the case of A. thaliana. P. falciparum is the most distant one. This study presents some interesting view-points on AAS-PS relationship. Certain species exhibit unique preferences for amino acids to be associated with protein local structural elements. Thus, AAS-PS relationships are species dependent. These results can give useful insights for improving prediction methodologies which take the species specific information into account.
Published: 2011

23. Purification and identification of sperm surface proteins and changes during epididymal maturation

Author: Jean Luc Gatti, Françoise Dacheux, Jean-Louis Dacheux, Ana-Paula Teixeira-Gomes, Valérie Labas, Clémence Belleannée, Maya Belghazi, Centre de recherche en neurobiologie - neurophysiologie de Marseille (CRN2M), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), and Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS)
Subjects: Male, Proteome, Swine, Proteomics, Biochemistry, 0302 clinical medicine, protein purification, Protein purification, Electrophoresis, Gel, Two-Dimensional, MESH: Animals, Polyacrylamide gel electrophoresis, Integral membrane protein, membrane, MESH: Swine, Gel electrophoresis, 0303 health sciences, 030219 obstetrics & reproductive medicine, Spermatozoon, animal proteomic, MESH: Spermatozoa, Epididymis, Spermatozoa, Cell biology, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], MESH: Proteome, medicine.anatomical_structure, Electrophoresis, Polyacrylamide Gel, MESH: Membrane Proteins, Acrosome, epididymis, MESH: Sperm Maturation, MESH: Epididymis, Biotin, Biology, MESH: Acrosome, 03 medical and health sciences, MESH: Biotin, medicine, Animals, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Molecular Biology, 030304 developmental biology, urogenital system, maturation, Membrane Proteins, MESH: Electrophoresis, Gel, Two-Dimensional, Sperm, MESH: Male, Sperm Maturation, MESH: Electrophoresis, Polyacrylamide Gel
Abstract: Adresses actuelles : Dr Maya Belghazi, IFR Jean Roche, Faculté de Médecine, 13344 Marseille Dr Jean-Luc Gatti, UMR IBSV, INRA-CNRS-Université de Nice, 06903 Sophia Antipolis; International audience; Surface membrane proteins have a key role in the sequential interactions between spermatozoa and oocytes. The aim of this study was to characterize protein changes occurring during post-testicular differentiation using a new overall approach to study surface membrane proteins of spermatozoa. A dedicated protocol based on specific purification of surface membrane proteins labeled with sulfo-NHS-SS-biotin was developed for this purpose. Appropriate gel electrophoresis separation and purification methods combined with standard proteomic methods were then used to identify and quantify surface membrane proteins from immature and mature spermatozoa. Membrane-associated proteins were discriminated from integral membrane proteins by differential solubilization. Protein regionalization on the spermatozoon surface was achieved by comparative analysis of the surface protein extracts from the entire spermatozoa and from periacrosomal sperm plasma membranes. Identification of several known proteins and of new proteins related to the process of epididymal maturation showed the reliability of this protocol for specific purification of a subproteome and identification of new sperm membrane proteins. This approach opens up a new area in the search for male fertility markers.
Published: 2011

24. Differential liver proteome mapping of control and cadmium-fed rats

Author: Pierre-Marie Badot, C. Schaeffer, F. Hispard, Hélène Martin, A. de Vaufleury, Renaud Scheifler, Lysiane Richert, Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biophotonique et Pharmacologie - UMR 7213 (LBP), Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA)), Conseil Regional of Franche-Comte, ADEME (Agence De l'Environnement et de la Maitrise de l'Energie) [0572 C0058], ANR (Agence Nationale de la Recherche) [ANR-05-ECC0-004], Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Laboratoire de spectrométrie de masse bioorganique, institut pluridisciplinaire hubert curien ( UMRCNRS-ULP7178 ), Laboratoire de Biophotonique et Pharmacologie - UMR 7213 ( LBP ), Centre National de la Recherche Scientifique ( CNRS ) -Réseau nanophotonique et optique, Université de Strasbourg ( UNISTRA ) -Université de Haute-Alsace (UHA) Mulhouse - Colmar ( Université de Haute-Alsace (UHA) ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Strasbourg ( UNISTRA ) -Université de Haute-Alsace (UHA) Mulhouse - Colmar ( Université de Haute-Alsace (UHA) ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Magmas et Volcans ( LMV ), and Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Université Jean Monnet [Saint-Étienne] ( UJM ) -Centre National de la Recherche Scientifique ( CNRS )
Subjects: Proteome, Health, Toxicology and Mutagenesis, [ SDV.TOX.ECO ] Life Sciences [q-bio]/Toxicology/Ecotoxicology, Phosphatidylethanolamine Binding Protein, GUIDELINES, 01 natural sciences, TOXICITY, MESH : Protein Interaction Mapping, Protein Interaction Mapping, PF-2D, Metallothionein, MESH: Thiobarbituric Acid Reactive Substances, Electrophoresis, Gel, Two-Dimensional, MESH : Female, MESH: Animals, MESH : Cadmium, MESH : Environmental Pollutants, MESH: Superoxide Dismutase, 0303 health sciences, Cadmium, GEL, MESH : Rats, General Medicine, Repeatability, Pollution, 3. Good health, TIME, MESH: Proteome, Biochemistry, Liver, MESH: Environmental Pollutants, Toxicity, Environmental Pollutants, Female, [SDV.TOX.ECO]Life Sciences [q-bio]/Toxicology/Ecotoxicology, LIQUID-CHROMATOGRAPHY, Rat liver, TISSUES, MESH: Rats, MESH: Cadmium, chemistry.chemical_element, MESH : Proteome, MESH : Thiobarbituric Acid Reactive Substances, Biology, BINDING PROTEIN, MESH : Rats, Wistar, Thiobarbituric Acid Reactive Substances, 03 medical and health sciences, Digestive exposure, Ecotoxicology, Animals, MESH : Superoxide Dismutase, Rats, Wistar, 030304 developmental biology, FLIGHT-MASS-SPECTROMETRY, IDENTIFICATION, Superoxide Dismutase, METALLOTHIONEIN, Binding protein, 010401 analytical chemistry, MESH: Protein Interaction Mapping, Public Health, Environmental and Occupational Health, MESH : Liver, MESH : Electrophoresis, Gel, Two-Dimensional, MESH: Rats, Wistar, MESH: Electrophoresis, Gel, Two-Dimensional, 0104 chemical sciences, Rats, MESH: Phosphatidylethanolamine Binding Protein, chemistry, MESH : Phosphatidylethanolamine Binding Protein, MESH : Animals, MESH: Female, MESH: Liver
Abstract: International audience; A comparative study of proteome maps from control and Cd-exposed rat liver was performed using a new technology of two-dimensional liquid chromatography separation method (PF-2D system, Beckman Coulter). Rats were fed for one month 0 or 100 μg Cd g(-1). The between-replicate and between-sample variations showed good repeatability and suitable reproducibility for the two dimensions of separation of proteins. In this complex mixture, PF-2D led to the separation of two major peaks which differed between control and Cd-exposed rat livers, one being identified by mass spectrometry as Cu/Zn superoxide dismutase (SOD), a well-known biomarker of Cd exposure, the other as phosphatidylethanolamine binding protein (PEBP). SOD content was decreased in Cd-exposed rat liver, compared to the control group which was corroborated by a significant decrease of SOD activity. PEBP content also tended to be decreased after Cd exposure. Present results demonstrate interest but also limitations of proteomic approach using PF-2D system to analyze effects of chemicals on organisms.
Published: 2011

25. Loss of Dicer in Sertoli cells has a major impact on the testicular proteome of mice

Author: Charles E. Vejnar, Marguerite Neerman-Arbez, Charles Pineau, Antoine Rolland, Olivier Schaad, Serge Nef, Marilena D. Papaioannou, Florian Guillou, Alexandre Fort, Mélanie Lagarrigue, Patrick Descombes, Evgeny M. Zdobnov, Florence Aubry, Françoise Kühne, Department of Genetic Medicine and Development [Geneva], Université de Genève (UNIGE), Virus, Environnement et Reproduction, Groupe d'Etude de la Reproduction Chez l'Homme et les Mammiferes (GERHM), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-IFR140-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-IFR140-Institut National de la Santé et de la Recherche Médicale (INSERM)-Swiss Institute of Bioinformatics (SIB), Swiss Institute of Bioinformatics-Swiss Institute of Bioinformatics, Swiss Institute of Bioinformatics (SIB), Swiss Institute of Bioinformatics, Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-IFR140-Institut National de la Santé et de la Recherche Médicale (INSERM)-Station commune de Recherches en Ichtyophysiologie, Biodiversité et Environnement (SCRIBE), Institut National de la Recherche Agronomique (INRA)-IFR140-Institut National de la Recherche Agronomique (INRA), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-IFR140-Institut National de la Santé et de la Recherche Médicale (INSERM), Genomics Platform, University of Geneva [Switzerland]-National Center of Competence in Research ‘Frontiers in Genetics', Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL)-Université de Lausanne (UNIL), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Station commune de Recherches en Ichtyophysiologie, Biodiversité et Environnement (SCRIBE), Institut National de la Recherche Agronomique (INRA)-Institut National de la Recherche Agronomique (INRA), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Station commune de Recherches en Ichtyophysiologie, Biodiversité et Environnement (SCRIBE), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), Université de Genève = University of Geneva (UNIGE), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL)-Université de Lausanne = University of Lausanne (UNIL), Université de Lausanne = University of Lausanne (UNIL), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Station commune de Recherches en Ichtyophysiologie, Biodiversité et Environnement (SCRIBE), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Genève = University of Geneva (UNIGE)-National Center of Competence in Research ‘Frontiers in Genetics', Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), and Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Superoxide Dismutase/genetics/metabolism, Enzymologic, Ribonuclease III, Male, Transcription, Genetic, Proteome, Ribonuclease III/deficiency/genetics, Proteome/metabolism, Inbred C57BL, Biochemistry, Transgenic, Analytical Chemistry, Mice, Superoxide Dismutase-1, MESH: Ribonuclease III, Genes, Reporter, Luciferases, Firefly, RNA interference, Tandem Mass Spectrometry, Testis, MESH: Up-Regulation, ddc:576.5, MESH: Animals, Promoter Regions, Genetic, Luciferases, Luciferases, Firefly/biosynthesis/genetics, 3' Untranslated Regions, MESH: Superoxide Dismutase, Sequence Deletion, Regulation of gene expression, 0303 health sciences, MESH: Testis, MESH: Gene Expression Regulation, Enzymologic, Testis/metabolism/pathology, 030302 biochemistry & molecular biology, MESH: 3' Untranslated Regions, MESH: Sequence Deletion, Sertoli cell, Up-Regulation, MESH: Proteome, medicine.anatomical_structure, RNA Interference, Transcription, Germ cell, MESH: Mice, Transgenic, MESH: RNA Interference, Mice, Transgenic, Biology, Gene Expression Regulation, Enzymologic, Promoter Regions, MicroRNAs/genetics/metabolism, 03 medical and health sciences, MESH: Gene Expression Profiling, Genetic, MESH: Sertoli Cells, MESH: Mice, Inbred C57BL, microRNA, MESH: Promoter Regions, Genetic, medicine, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Firefly, Reporter, MESH: Mice, 030304 developmental biology, Sertoli Cells, MESH: Luciferases, Firefly, Superoxide Dismutase, Research, Gene Expression Profiling, MESH: Transcription, Genetic, MESH: Genes, Reporter, MESH: Tandem Mass Spectrometry, Molecular biology, MESH: Male, Mice, Inbred C57BL, MicroRNAs, Gene Expression Regulation, Genes, biology.protein, Sertoli Cells/metabolism, Spermatogenesis, MESH: MicroRNAs, Dicer
Abstract: International audience; Sertoli cells (SCs) are the central, essential coordinators of spermatogenesis, without which germ cell development cannot occur. We previously showed that Dicer, an RNaseIII endonuclease required for microRNA (miRNA) biogenesis, is absolutely essential for Sertoli cells to mature, survive, and ultimately sustain germ cell development. Here, using isotope-coded protein labeling, a technique for protein relative quantification by mass spectrometry, we investigated the impact of Sertoli cell-Dicer and subsequent miRNA loss on the testicular proteome. We found that, a large proportion of proteins (50 out of 130) are up-regulated by more that 1.3-fold in testes lacking Sertoli cell-Dicer, yet that this protein up-regulation is mild, never exceeding a 2-fold change, and is not preceeded by alterations of the corresponding mRNAs. Of note, the expression levels of six proteins of interest were further validated using the Absolute Quantification (AQUA) peptide technology. Furthermore, through 3'UTR luciferase assays we identified one up-regulated protein, SOD-1, a Cu/Zn superoxide dismutase whose overexpression has been linked to enhanced cell death through apoptosis, as a likely direct target of three Sertoli cell-expressed miRNAs, miR-125a-3p, miR-872 and miR-24. Altogether, our study, which is one of the few in vivo analyses of miRNA effects on protein output, suggests that, at least in our system, miRNAs play a significant role in translation control.
Published: 2011

26. Species specific amino acid sequence-protein local structure relationships: An analysis in the light of a structural alphabet.: species‟ sequence - structure relationship

Author: Alexandre G. de Brevern, Agnel Praveen Joseph, Université Paris Diderot - Paris 7 (UPD7), Institut National de la Transfusion Sanguine [Paris] (INTS), Institut de Biosciences et de Biotechnologies de Grenoble (ex-IRTSV) (BIG), Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes (UGA), Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), French Ministry of Research University Paris Diderot the Institute of Blood Transfusion (INTS) the Institute for Health and Medical Research(INSERM)., and Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])
Subjects: MESH: Amino Acids, Proteome, Structural alphabet, [SDV]Life Sciences [q-bio], Arabidopsis, MESH: Protein Structure, Secondary, MESH: Amino Acid Sequence, Protein Structure, Secondary, Protein structure, MESH: Structure-Activity Relationship, Cluster Analysis, Arabidopsis thaliana, MESH: Arabidopsis, MESH: Proteins, Databases, Protein, Peptide sequence, Protein secondary structure, MESH: Plasmodium falciparum, chemistry.chemical_classification, 0303 health sciences, Applied Mathematics, 030302 biochemistry & molecular biology, General Medicine, MESH: Saccharomyces cerevisiae, Amino acid, MESH: Proteome, Biochemistry, Modeling and Simulation, Protein Blocks, Amino acids, General Agricultural and Biological Sciences, Statistics and Probability, MESH: Databases, Protein, Molecular Sequence Data, Plasmodium falciparum, Saccharomyces cerevisiae, Computational biology, Biology, Local structure, General Biochemistry, Genetics and Molecular Biology, Structure-Activity Relationship, 03 medical and health sciences, Species Specificity, Secondary structure, MESH: Species Specificity, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, Protein folds, 030304 developmental biology, MESH: Molecular Sequence Data, General Immunology and Microbiology, Proteins, biology.organism_classification, MESH: Cluster Analysis, Malaria, chemistry
Abstract: International audience; Protein structure analysis and prediction methods are based on non-redundant data extracted from the available protein structures, regardless of the species from which the protein originates. Hence, these datasets represent the global knowledge on protein folds, which constitutes a generic distribution of amino acid sequence-protein structure (AAS-PS) relationships. In this study, we try to elucidate whether the AAS-PS relationship could possess specificities depending on the specie. For this purpose, we have chosen three different species: Saccharomyces cerevisiae, Plasmodium falciparum and Arabidopsis thaliana. We analyzed the AAS-PS behaviors of the proteins from these three species and compared it to the "expected" distribution of a classical non-redundant databank. With the classical secondary structure description, only slight differences in amino acid preferences could be observed. With a more precise description of local protein structures (Protein Blocks), significant changes could be highlighted. S. cerevisiae's AAS-PS relationship is close to the general distribution, while striking differences are observed in the case of A. thaliana. P. falciparum is the most distant one. This study presents some interesting view-points on AAS-PS relationship. Certain species exhibit unique preferences for amino acids to be associated with protein local structural elements. Thus, AAS-PS relationships are species dependent. These results can give useful insights for improving prediction methodologies which take the species specific information into account.
Published: 2011

27. Species specific amino acid sequence-protein local structure relationships: An analysis in the light of a structural alphabet

Author: de Brevern, Alexandre, Joseph, Agnel Praveen, de Brevern, Alexandre G., Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), and French Ministry of Research University Paris Diderot the Institute of Blood Transfusion (INTS) the Institute for Health and Medical Research(INSERM).
Subjects: MESH: Databases, Protein, amino acids, MESH: Amino Acids, MESH: Molecular Sequence Data, malaria, MESH: Protein Structure, Secondary, secondary structure, MESH: Amino Acid Sequence, MESH: Saccharomyces cerevisiae, MESH: Cluster Analysis, MESH: Proteome, MESH: Structure-Activity Relationship, Protein Blocks, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Species Specificity, structural alphabet, MESH: Arabidopsis, MESH: Proteins, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, protein folds, MESH: Plasmodium falciparum
Abstract: International audience; Protein structure analysis and prediction methods are based on non-redundant data extracted from the available protein structures, regardless of the species from which the protein originates. Hence, these datasets represent the global knowledge on protein folds, which constitutes a generic distribution of amino acid sequence-protein structure (AAS-PS) relationships. In this study, we try to elucidate whether the AAS-PS relationship could possess specificities depending on the specie. For this purpose, we have chosen three different species: Saccharomyces cerevisiae, Plasmodium falciparum and Arabidopsis thaliana. We analyzed the AAS-PS behaviors of the proteins from these three species and compared it to the "expected" distribution of a classical non-redundant databank. With the classical secondary structure description, only slight differences in amino acid preferences could be observed. With a more precise description of local protein structures (Protein Blocks), significant changes could be highlighted. S. cerevisiae's AAS-PS relationship is close to the general distribution, while striking differences are observed in the case of A. thaliana. P. falciparum is the most distant one. This study presents some interesting view-points on AAS-PS relationship. Certain species exhibit unique preferences for amino acids to be associated with protein local structural elements. Thus, AAS-PS relationships are species dependent. These results can give useful insights for improving prediction methodologies which take the species specific information into account.
Published: 2011

28. Altered regulation of the OmpF porin by Fis in Escherichia coli during an evolution experiment and between B and K-12 strains

Author: Thomas Hindré, Dominique Schneider, Richard E. Lenski, Jérôme Garin, Lauriane Kuhn, Estelle Crozat, Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble] (LAPM), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Institut de Biosciences et de Biotechnologies de Grenoble (ex-IRTSV) (BIG), Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Etude de la dynamique des protéomes (EDyP ), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), 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)-Institut National de la Santé et de la Recherche Médicale (INSERM)-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)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Laboratoire d'étude de la dynamique des protéomes (LEDyP), Université Joseph Fourier - Grenoble 1 (UJF)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])
Subjects: MESH: Mutation, Proteome, Molecular Sequence Data, Porins, MESH: Escherichia coli Proteins, Biology, MESH: Base Sequence, medicine.disease_cause, Microbiology, MESH: Factor For Inversion Stimulation Protein, 03 medical and health sciences, Factor For Inversion Stimulation Protein, medicine, Escherichia coli, Gene Regulation, Electrophoresis, Gel, Two-Dimensional, Allele, Molecular Biology, Gene, 030304 developmental biology, Regulation of gene expression, Genetics, 0303 health sciences, Experimental evolution, Mutation, MESH: Molecular Sequence Data, MESH: Porins, Strain (chemistry), Base Sequence, 030306 microbiology, MESH: Escherichia coli, Escherichia coli Proteins, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], MESH: Electrophoresis, Gel, Two-Dimensional, MESH: Gene Expression Regulation, MESH: Proteome, Gene Expression Regulation, MESH: Gene Deletion, Porin, Gene Deletion
Abstract: The phenotypic plasticity of global regulatory networks provides bacteria with rapid acclimation to a wide range of environmental conditions, while genetic changes in those networks provide additional flexibility as bacteria evolve across long time scales. We previously identified mutations in the global regulator-encoding gene fis that enhanced organismal fitness during a long-term evolution experiment with Escherichia coli . To gain insight into the effects of these mutations, we produced two-dimensional protein gels with strains carrying different fis alleles, including a beneficial evolved allele and one with an in-frame deletion. We found that Fis controls the expression of the major porin-encoding gene ompF in the E. coli B-derived ancestral strain used in the evolution experiment, a relationship that has not been described before. We further showed that this regulatory connection evolved over two different time scales, perhaps explaining why it was not observed before. On the longer time scale, we showed that this regulation of ompF by Fis is absent from the more widely studied K-12 strain and thus is specific to the B strain. On a shorter time scale, this regulatory linkage was lost during 20,000 generations of experimental evolution of the B strain. Finally, we mapped the Fis binding sites in the ompF regulatory region, and we present a hypothetical model of ompF expression that includes its other known regulators.
Published: 2011

29. Proteomic analysis of the spermatogonial stem cell compartment in dogfish Scyliorhinus canicula L

Author: Pierrick Auvray, Régis Lavigne, Geraldine Loppion, Pascal Sourdaine, Charles Pineau, Physiologie et Ecophysiologie des Mollusques Marins (PE2M), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), Groupe d'Etude de la Reproduction Chez l'Homme et les Mammiferes (GERHM), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM), Plate-forme protéomique [Rennes], Plateforme Génomique Santé Biogenouest®, CIFRE (ANRT and C.RIS Pharma), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)
Subjects: Male, endocrine system, Proteome, Physiology, MESH: Spermatogonia, Protein subunit, Blotting, Western, MESH: Stem Cells, Biology, Proteomics, Biochemistry, Mass Spectrometry, 03 medical and health sciences, 0302 clinical medicine, Testis, Genetics, medicine, Animals, MESH: Blotting, Western, MESH: Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Spermatogenesis, Molecular Biology, 030304 developmental biology, MESH: Mass Spectrometry, 0303 health sciences, 030219 obstetrics & reproductive medicine, MESH: Testis, Stem Cells, Scyliorhinus canicula, MESH: Immunohistochemistry, biology.organism_classification, Sertoli cell, Shark, Immunohistochemistry, Molecular biology, Spermatogonia, MESH: Male, MESH: Proteome, medicine.anatomical_structure, MESH: Dogfish, Dogfish, Stem cell, MESH: Spermatogenesis
Abstract: International audience; In the dogfish (Scyliorhinus canicula L.) the testicular germinative zone (GZ), composed of large isolated spermatogonia surrounded by elongating pre-Sertoli cells, is located between the albuginea and the ventrolateral intratesticular vessel. During the spermatogenic wave, cysts radiate in maturational order forming distinct testicular zones. In this study, soluble proteins of the GZ and of the zone containing cysts with spermatocytes were separated by two-dimensional electrophoresis. Gel images were matched and then evaluated for GZ-specific proteins. From the1400 protein spots identified, 680 were found to be apparently specific to this zone. Using MALDI-TOF/TOF mass spectrometry, de novo sequences were obtained for 33 proteins out of the 169 selected for identification by mass spectrometry, but only 16 of these 169 proteins were identified. One of them, proteasome subunit alpha-6, was analyzed further by immunohistochemistry. This study demonstrates the utility of the dogfish as a model for proteome analysis of the spermatogonial stem cell niche, even if it remains restricted by the lack of genomic data available on Elasmobranchs.
Published: 2010

30. USP9x-mediated deubiquitination of EFA6 regulates de novo tight junction assembly

Author: Hiroyuki Sakagami, Delphine Theard, Frédéric Luton, Michel Franco, Edward A. Fon, Julie Milanini, Mariagrazia Partisani, Stephen A. Wood, Florian Labarrade, Institut de pharmacologie moléculaire et cellulaire (IPMC), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Department of Anatomy, Kitasato University School of Medicine, Montreal Neurological Institute and Hospital, McGill University = Université McGill [Montréal, Canada], National Centre for Adult Stem Cell Research, and Griffith University [Brisbane]
Subjects: Proteome, Cellular differentiation, tight junction, Nerve Tissue Proteins, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, EFA6, Article, General Biochemistry, Genetics and Molecular Biology, MESH: Tight Junctions, Cell Line, Tight Junctions, Deubiquitinating enzyme, MESH: Dogs, 03 medical and health sciences, Dogs, 0302 clinical medicine, Ubiquitin, Cell polarity, Animals, MESH: Animals, MESH: Nerve Tissue Proteins, Molecular Biology, 030304 developmental biology, 0303 health sciences, General Immunology and Microbiology, biology, Tight junction, General Neuroscience, Ubiquitination, Epithelial Cells, USP9x, MESH: Ubiquitin Thiolesterase, MESH: Gene Expression Regulation, MESH: Gene Knockdown Techniques, Cell biology, MESH: Cell Line, MESH: Proteome, proteasome, Gene Expression Regulation, Proteasome, MESH: Epithelial Cells, Gene Knockdown Techniques, biology.protein, MESH: Ubiquitination, Ubiquitin Thiolesterase, 030217 neurology & neurosurgery, Biogenesis, Deubiquitination
Abstract: International audience; In epithelial cells, the tight junction (TJ) functions as a permeability barrier and is involved in cellular differentiation and proliferation. Although many TJ proteins have been characterized, little is known about the sequence of events and temporal regulation of TJ assembly in response to adhesion cues. We report here that the deubiquitinating enzyme USP9x has a critical function in TJ biogenesis by controlling the levels of the exchange factor for Arf6 (EFA6), a protein shown to facilitate TJ formation, during a narrow temporal window preceding the establishment of cell polarity. At steady state, EFA6 is constitutively ubiquitinated and turned over by the proteasome. However, at newly forming contacts, USP9x-mediated deubiquitination protects EFA6 from proteasomal degradation, leading to a transient increase in EFA6 levels. Consistent with this model, USP9x and EFA6 transiently co-localize at primordial epithelial junctions. Furthermore, knockdown of either EFA6 or USP9x impairs TJ biogenesis and EFA6 overexpression rescues TJ biogenesis in USP9x-knockdown cells. As the loss of cell polarity is a critical event in the metastatic spread of cancer, these findings may help to understand the pathology of human carcinomas.
Published: 2010

31. Distinct proteomic features of two fibrogenic liver cell populations: hepatic stellate cells and portal myofibroblasts

Author: Michel Vaubourdolle, Thorsten Burmester, Joëlle Vinh, Paulo Marcelo, Nelly Bosselut, Axelle Cadoret, Bruno Baudin, Chantal Housset, Colette Rey, Spectrométrie de Masse Biologique et Protéomique (USR3149 / FRE2032) (SMBP), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de mécanique des sols, structures et matériaux (MSSMat), CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), CHU Saint-Antoine [AP-HP], and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)
Subjects: Liver Cirrhosis, Proteomics, MESH: Portal System, Proteome, Clinical Biochemistry, MESH: Amino Acid Sequence, MESH: Rats, Sprague-Dawley, Biochemistry, Rats, Sprague-Dawley, Extracellular matrix, 0302 clinical medicine, Fibrosis, Electrophoresis, Gel, Two-Dimensional, MESH: Animals, Cells, Cultured, 0303 health sciences, MESH: Peptides, Liver cell, MESH: Proteomics, Cytoglobin, 030302 biochemistry & molecular biology, Globins, 3. Good health, MESH: Proteome, Portal System, Actin Depolymerizing Factors, 030211 gastroenterology & hepatology, MESH: Liver Cirrhosis, MESH: Cells, Cultured, Cell type, MESH: Rats, Molecular Sequence Data, Biology, 03 medical and health sciences, MESH: Gene Expression Profiling, MESH: Hepatic Stellate Cells, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH: Actin Depolymerizing Factors, Hepatic Stellate Cells, medicine, MESH: Globins, Animals, Amino Acid Sequence, Molecular Biology, 030304 developmental biology, MESH: Molecular Sequence Data, Gene Expression Profiling, Mesenchymal stem cell, Fibroblasts, medicine.disease, MESH: Electrophoresis, Gel, Two-Dimensional, Molecular biology, Rats, MESH: Fibroblasts, Immunology, Hepatic stellate cell, Peptides, Wound healing
Abstract: International audience; In chronic liver diseases, the accumulation of extracellular matrix leading to fibrosis is caused by myofibroblasts, the origins of which are debatable. We performed a comparative proteomic study to identify markers and gain insight into distinct functions of myofibroblasts derived either from hepatic stellate cells (HSCs) or from portal mesenchymal cells. After isolation from normal liver and culture in similar conditions, myofibroblastic HSCs (MF-HSCs) presented enlarged cytoplasms whereas portal myofibroblasts (PMFs) were more proliferative, and formed more stress fibers. The two cell types were subjected to comparative analyses by 2-D MS/MS. Six proteins were overexpressed in PMFs, with myofibroblast-related typical functions. Among them, cofilin-1 showed the greatest difference in expression and a lower pI than expected. Immunoblot demonstrated higher levels of phosphorylation, a modification of the protein implicated in stress fiber formation. Eleven proteins, mostly involved in stress response, were overexpressed in MF-HSCs. Cytoglobin had the highest level of overexpression, as confirmed by reverse transcription quantitative real-time PCR, immunoblot and immunocytochemical analyses. These results identify cytoglobin as the best marker for distinguishing MF-HSCs from PMFs and suggest different functions for the two cell populations in the liver wound healing response, with a prominent role for PMFs in scar formation.
Published: 2010

32. Reconstruction of metabolic pathways, protein expression, and homeostasis machineries across maize bundle sheath and mesophyll chloroplasts: large-scale quantitative proteomics using the first maize genome assembly

Author: Giulia Friso, Qi Sun, Wojciech Majeran, Klaas J. van Wijk, Mingshu Huang, Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Life Sciences Core Laboratories Center, Cornell University [New York], and Department of plant Biology
Subjects: 0106 biological sciences, Proteomics, MESH: Genome, Plant, Chloroplasts, Protein family, Proteome, Physiology, MESH: Zea mays, Quantitative proteomics, Biochemical Processes and Macromolecular Structures, Plant Science, Biology, 01 natural sciences, Genome, Zea mays, Mass Spectrometry, 03 medical and health sciences, Protein Annotation, Gene Expression Regulation, Plant, Gene Duplication, Genetics, Homeostasis, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MESH: Models, Genetic, MESH: Gene Expression Regulation, Plant, 030304 developmental biology, 2. Zero hunger, MESH: Mass Spectrometry, 0303 health sciences, MESH: Chloroplasts, Models, Genetic, MESH: Proteomics, MESH: Gene Duplication, Computational Biology, Chloroplast, MESH: Proteome, Biochemistry, MESH: Homeostasis, MESH: Metabolic Networks and Pathways, Multigene Family, MESH: Multigene Family, Chloroplast Proteins, Genome, Plant, Metabolic Networks and Pathways, 010606 plant biology & botany, MESH: Computational Biology
Abstract: Chloroplasts in differentiated bundle sheath (BS) and mesophyll (M) cells of maize (Zea mays) leaves are specialized to accommodate C4 photosynthesis. This study provides a reconstruction of how metabolic pathways, protein expression, and homeostasis functions are quantitatively distributed across BS and M chloroplasts. This yielded new insights into cellular specialization. The experimental analysis was based on high-accuracy mass spectrometry, protein quantification by spectral counting, and the first maize genome assembly. A bioinformatics workflow was developed to deal with gene models, protein families, and gene duplications related to the polyploidy of maize; this avoided overidentification of proteins and resulted in more accurate protein quantification. A total of 1,105 proteins were assigned as potential chloroplast proteins, annotated for function, and quantified. Nearly complete coverage of primary carbon, starch, and tetrapyrole metabolism, as well as excellent coverage for fatty acid synthesis, isoprenoid, sulfur, nitrogen, and amino acid metabolism, was obtained. This showed, for example, quantitative and qualitative cell type-specific specialization in starch biosynthesis, arginine synthesis, nitrogen assimilation, and initial steps in sulfur assimilation. An extensive overview of BS and M chloroplast protein expression and homeostasis machineries (more than 200 proteins) demonstrated qualitative and quantitative differences between M and BS chloroplasts and BS-enhanced levels of the specialized chaperones ClpB3 and HSP90 that suggest active remodeling of the BS proteome. The reconstructed pathways are presented as detailed flow diagrams including annotation, relative protein abundance, and cell-specific expression pattern. Protein annotation and identification data, and projection of matched peptides on the protein models, are available online through the Plant Proteome Database.
Published: 2010

33. Tsetse flies, trypanosomes, humans and animals: what is proteomics revealing about their crosstalks?

Author: Philippe Holzmuller, Gérard Cuny, David Biron, Pascal Grébaut, Interactions hôtes-vecteurs-parasites-environnement dans les maladies tropicales négligées dues aux trypanosomatides (UMR INTERTRYP), Université de Bordeaux (UB)-Institut de Recherche pour le Développement (IRD)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université de Bordeaux (UB), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA)
Subjects: Proteomics, Proteome, Protozoan Proteins, L73 - Maladies des animaux, Biochemistry, Basic research, MESH: Insect Proteins, Expression des gènes, MESH: Animals, MESH: Protozoan Proteins, MESH: Tsetse Flies, 0303 health sciences, biology, MESH: Proteomics, 030302 biochemistry & molecular biology, Protéine, 3. Good health, MESH: Proteome, Vecteur de maladie, Insect Proteins, %22">Glossina , L72 - Organismes nuisibles des animaux, Genre humain, MESH: Trypanosoma, Trypanosoma, Glossina, Tsetse Flies, Zoology, Computational biology, Relation hôte pathogène, MESH: Insect Vectors, MESH: Host-Parasite Interactions, Host-Parasite Interactions, 03 medical and health sciences, Animals, Humans, Molecular Biology, 030304 developmental biology, Génie génétique, MESH: Humans, Developmental cycle, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, biology.organism_classification, Insect Vectors, Treatment management, Vector (epidemiology), Mammifère, U30 - Méthodes de recherche
Abstract: International audience; Human and animal African trypanosomoses, or sleeping sickness and Nagana, are neglected vector-borne parasitic diseases caused by protozoa belonging to the Trypanosoma genus. Advances in proteomics offer new tools to better understand host-vector-parasite crosstalks occurring during the complex parasitic developmental cycle, and to determine the outcome of both transmission and infection. In this review, we summarize proteomics studies performed on African trypanosomes and on the interactions with their vector and mammalian hosts. We discuss the contributions and pitfalls of using diverse proteomics tools, and argue about the interest of pathogenoproteomics, both to generate advances in basic research on the best knowledge and understanding of host-vector-pathogen interactions, and to lead to the concrete development of new tools to improve diagnosis and treatment management of trypanosomoses in the near future.
Published: 2010

34. Disulfide bond formation and cysteine exclusion in gram-positive bacteria

Author: Fabrice Neiers, Gunnar von Heijne, Andreas Bernsel, Peter Mellroth, Birgitta Henriques-Normark, Robert Daniels, Staffan Normark, Department of Microbiology, Tumor and Cell Biology, Ajouter cet établissement, Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm University, Centre des Sciences du Goût et de l'Alimentation [Dijon] (CSGA), Centre National de la Recherche Scientifique (CNRS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), Swedish Institute for Infectious Disease Control, Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Centre des Sciences du Goût et de l'Alimentation [Dijon] ( CSGA ), and Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS )
Subjects: Proteomics, MESH: Oxidation-Reduction, Cytoplasm, Protein Folding, MESH : Oxygen, Proteome, Organic chemistry, Biochemistry, Corynebacterium glutamicum, MESH: Gram-Positive Bacteria, MESH : Protein Transport, MESH : Bacterial Proteins, Disulfides, MESH: Bacterial Proteins, SDV:BC, 0303 health sciences, MESH: Gene Expression Regulation, Bacterial, biology, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Organisms/Bacteria, Bacterial, MESH: Corynebacterium glutamicum, MESH : Corynebacterium glutamicum, Protein/Secretion, Transport protein, Actinobacteria, MESH: Proteome, Protein Transport, MESH : Gram-Positive Bacteria, Electrophoresis, Polyacrylamide Gel, Protein folding, Oxidation-Reduction, MESH: Oxygen, MESH : Protein Folding, MESH : Gene Expression Regulation, Bacterial, MESH: Actinobacteria, Electrophoresis, MESH : Cytoplasm, MESH: Protein Transport, Firmicutes, Gram-positive bacteria, MESH: Protein Folding, Bacterial Proteins, Cysteine, Polyacrylamide Gel, Gene Expression Regulation, Gram-Positive Bacteria, Oxygen, MESH : Actinobacteria, MESH : Proteome, Protein/Export, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, MESH : Electrophoresis, Polyacrylamide Gel, 03 medical and health sciences, [ CHIM.ORGA ] Chemical Sciences/Organic chemistry, MESH: Disulfides, Genomics, Proteomics, and Bioinformatics, Protein/Disulfide, Molecular Biology, 030304 developmental biology, MESH : Oxidation-Reduction, MESH : Cysteine, [ SDV.BC ] Life Sciences [q-bio]/Cellular Biology, 030306 microbiology, MESH: Cytoplasm, Protein/Folding, Gene Expression Regulation, Bacterial, Cell Biology, MESH: Cysteine, biology.organism_classification, Enzymes/Oxidation-Reduction, Sulfhydryls/Disulfide, Chimie organique, 13. Climate action, MESH : Disulfides, Bacteria, MESH: Electrophoresis, Polyacrylamide Gel
Abstract: International audience; Most secretion pathways in bacteria and eukaryotic cells are challenged by the requirement for their substrate proteins to mature after they traverse a membrane barrier and enter a reactive oxidizing environment. For Gram-positive bacteria, the mechanisms that protect their exported proteins from misoxidation during their post-translocation maturation are poorly understood. To address this, we separated numerous bacterial species according to their tolerance for oxygen and divided their proteomes based on the predicted subcellular localization of their proteins. We then applied a previously established computational approach that utilizes cysteine incorporation patterns in proteins as an indicator of enzymatic systems that may exist in each species. The Sec-dependent exported proteins from aerobic Gram-positive Actinobacteria were found to encode cysteines in an even-biased pattern indicative of a functional disulfide bond formation system. In contrast, aerobic Gram-positive Firmicutes favor the exclusion of cysteines from both their cytoplasmic proteins and their substantially longer exported proteins. Supporting these findings, we show that Firmicutes, but not Actinobacteria, tolerate growth in reductant. We further demonstrate that the actinobacterium Corynebacterium glutamicum possesses disulfide-bonded proteins and two dimeric Dsb-like enzymes that can efficiently catalyze the formation of disulfide bonds. Our results suggest that cysteine exclusion is an important adaptive strategy against the challenges presented by oxidative environments.
Published: 2010

35. Proteome screens for Cys residues oxidation: the redoxome

Author: Chiappetta, G., Ndiaye, S., Aeid Igbaria, Kumar, C., Vinh, J., Toledano, M. B., Spectrométrie de Masse Biologique et Protéomique (USR3149 / FRE2032) (SMBP), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Proteomics, MESH: Oxidation-Reduction, MESH: Humans, Proteome, MESH: Proteomics, MESH: Models, Biological, Proteins, MESH: Cysteine, Models, Biological, MESH: Proteome, MESH: Protein Processing, Post-Translational, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Animals, Humans, MESH: Animals, MESH: Proteins, Cysteine, Oxidation-Reduction, Protein Processing, Post-Translational
Abstract: International audience; The oxidation of the cysteine (Cys) residue to sulfenic (-S-OH), disulfide (-S-S-), or S-nitroso (S-NO) forms are thought to be a posttranslational modifications that regulate protein function. However, despite a few solid examples of its occurrence, thiol-redox regulation of protein function is still debated and often seen as an exotic phenomenon. A systematic and exhaustive characterization of all oxidized Cys residues, an experimental approach called redox proteomics or redoxome analysis, should help establish the physiological scope of Cys residue oxidation and give clues to its mechanisms. Redox proteomics still remains a technical challenge, mainly because of the labile nature of thiol-redox reactions and the lack of tools to directly detect the modified residues. Here we consider recent technical advances in redox proteomics, focusing on a gel-based fluorescent method and on the shotgun OxICAT technique.
Published: 2010

36. A genome-wide study of PDZ-domain interactions in C. elegans reveals a high frequency of non-canonical binding

Author: Jean-Paul Borg, Nicolas Lenfant, Jérôme Reboul, Shizue Omi, Jolanta Polanowska, Sophie Bamps, Centre de Recherche en Cancérologie de Marseille (CRCM / U891 Inserm), Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre d'Immunologie de Marseille - Luminy (CIML), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institute of Integrative and Comparative Biology, University of Leeds, This work was supported by an institutional grant from INSERM, the INSERM-AVENIR program and Association pour la Recherche sur le Cancer. N.L. was funded by INSERM-Region PACA and Association pour la Recherche sur le Cancer PhD fellowship. S.B. was a recipient of INSERM Poste Vert fellowship., and BMC, Ed.
Subjects: lcsh:QH426-470, Proteome, Immunoprecipitation, lcsh:Biotechnology, PDZ domain, PDZ Domains, Computational biology, Plasma protein binding, Biology, Proteomics, MESH: Two-Hybrid System Techniques, Interactome, Protein–protein interaction, 03 medical and health sciences, lcsh:TP248.13-248.65, Two-Hybrid System Techniques, MESH: Caenorhabditis elegans, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Consensus Sequence, Genetics, MESH: PDZ Domains, Animals, MESH: Protein Binding, MESH: Animals, MESH: Genome, MESH: Consensus Sequence, Caenorhabditis elegans, Caenorhabditis elegans Proteins, 030304 developmental biology, 0303 health sciences, Genome, MESH: Immunoprecipitation, 030302 biochemistry & molecular biology, Reproducibility of Results, MESH: Caenorhabditis elegans Proteins, biology.organism_classification, MESH: Reproducibility of Results, MESH: Proteome, lcsh:Genetics, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Protein Binding, Research Article, Biotechnology
Abstract: BackgroundProteins may evolve through the recruitment and modification of discrete domains, and in many cases, protein action can be dissected at the domain level. PDZ domains are found in many important structural and signaling complexes, and are generally thought to interact with their protein partners through a C-terminal consensus sequence. We undertook a comprehensive search for protein partners of all individual PDZ domains inC. elegansto characterize their function and mode of interaction.ResultsCoupling high-throughput yeast two-hybrid screens with extensive validation by co-affinity purification, we defined a domain-orientated interactome map. This integrates PDZ domain proteins in numerous cell-signaling pathways and shows that PDZ domain proteins are implicated in an unexpectedly wide range of cellular processes. Importantly, we uncovered a high frequency of non-canonical interactions, not involving the C-terminus of the protein partner, which were directly confirmed in most cases. We completed our study with the generation of a yeast array representing the entire set of PDZ domains fromC. elegansand provide a proof-of-principle for its application to the discovery of PDZ domain targets for any protein or peptide of interest.ConclusionsWe provide an extensive domain-centered dataset, together with a clone resource, that will help future functional study of PDZ domains. Through this unbiased approach, we revealed frequent non-canonical interactions between PDZ domains and their protein partners that will require a re-evaluation of this domain's molecular function.[The protein interactions from this publication have been submitted to the IMEx (http://www.imexconsortium.org) consortium through IntAct (PMID: 19850723) and assigned the identifier IM-14654]
Published: 2010

37. An integrative genomics approach for deciphering the complex interactions between ascorbate metabolism and fruit growth and composition in tomato

Author: Catherine Deborde, Moftah Alhagdow, Marc Lahaye, Hélène Gautier, David Page, Johann Petit, Martine Lemaire-Chamley, Virginie Garcia, Annick Moing, Mireille Faurobert, Laurent Gil, Pierre Baldet, Barbara Gouble, Noé Gest, Capucine Massot, Jean-Luc Poëssel, Bjoern Usadel, Jean-Paul Bouchet, Daniel J. Jacob, Antoine de Daruvar, Christophe Rothan, Louise Gilbert, Jean-Luc Giraudel, Mickaël Maucourt, Mathilde Causse, Dominique Rolin, Rebecca Stevens, Département d'ergonomie, ENSC/IPB, Université de Bordeaux (UB), Biologie végétale intégrative (BVI), Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, Centre de Bioinformatique de Bordeaux (CBIB), CGFB, Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), Institut National de la Recherche Agronomique (INRA), Unité de recherche PSH, Laboratoire Bordelais de Recherche en Informatique (LaBRI), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Unité de recherche Génétique et amélioration des fruits et légumes (GALF), Biologie du Fruit, Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1, Laboratoire de Physico -& Toxico Chimie des systèmes naturels (LPTC), Université Sciences et Technologies - Bordeaux 1-Centre National de la Recherche Scientifique (CNRS), Sécurité et Qualité des Produits d'Origine Végétale (SQPOV), Institut National de la Recherche Agronomique (INRA)-Avignon Université (AU), Max-Planck-Institut, and Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA)
Subjects: 0106 biological sciences, Complex systems, VTC: Vitamin C, Proteome, [SDV]Life Sciences [q-bio], Mutant, MESH: Ascorbate Oxidase, Ascorbic Acid, AsA: Ascorbic acid, 01 natural sciences, Biologie intégrative, Transcriptome, MDHAR, Solanum lycopersicum, MESH: Lycopersicon esculentum, BIOLOGIE CELLULAIRE, AO: Ascorbate oxidase, MESH: Ascorbic Acid, NADH, NADPH Oxidoreductases, CELL WALL, ASCORBIQUE ACID, Plant Proteins, 2. Zero hunger, 0303 health sciences, MESH: NADH, NADPH Oxidoreductases, Monodehydroascorbate reductase Ascorbic acid, MESH: Plant Proteins, MESH: Genomics, food and beverages, General Medicine, Genomics, MESH: Carbohydrate Epimerases, Plants, Genetically Modified, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: Proteome, Paroi, Phenotype, Biochemistry, GME: GDP-d-mannose-3, Gene Knockdown Techniques, SYSTEMS BIOLOGY, Metabolome, MESH: Oxidoreductases Acting on CH-CH Group Donors, General Agricultural and Biological Sciences, MESH: Fruit, Metabolic Networks and Pathways, MESH: Metabolome, GalLDH: L-Galactono-1, Oxidoreductases Acting on CH-CH Group Donors, Systems biology, Biology, MESH: Phenotype, General Biochemistry, Genetics and Molecular Biology, Systèmes complexes, 03 medical and health sciences, MESH: Gene Expression Profiling, Tomate, MESH: Analysis of Variance, 030304 developmental biology, 4-Lactone Dehydrogenase, Systems biology Ascorbate, Analysis of Variance, General Immunology and Microbiology, Gene Expression Profiling, Ascorbic acid, MESH: Gene Knockdown Techniques, Systems Integration, 5 -epimerase, Metabolic pathway, MESH: Plants, Genetically Modified, MESH: Metabolic Networks and Pathways, Fruit, Ascorbate Oxidase, TOMATO, MESH: Systems Integration, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Carbohydrate Epimerases, 010606 plant biology & botany
Abstract: International audience; Very few reports have studied the interactions between ascorbate and fruit metabolism. In order to get insights into the complex relationships between ascorbate biosynthesis/recycling and other metabolic pathways in the fruit, we undertook a fruit systems biology approach. To this end, we have produced tomato transgenic lines altered in ascorbate content and redox ratio by RNAi-targeting several key enzymes involved in ascorbate biosynthesis (2 enzymes) and recycling (2 enzymes). In the VTC (ViTamin C) Fruit project, we then generated phenotypic and genomic (transcriptome, proteome, metabolome) data from wild type and mutant tomato fruit at two stages of fruit development, and developed or implemented statistical and bioinformatic tools as a web application (named VTC Tool box) necessary to store, analyse and integrate experimental data in tomato. By using Kohonen's self-organizing maps (SOMs) to cluster the biological data, pair-wise Pearson correlation analyses and simultaneous visualization of transcript/protein and metabolites (MapMan), this approach allowed us to uncover major relationships between ascorbate and other metabolic pathways.
Published: 2009

38. Power and limitations of electrophoretic separations in proteomics strategies

Author: Rabilloud, Thierry, Vaezzadeh, Ali R, Potier, Noelle, Lelong, Cécile, Leize-Wagner, Emmanuelle, Chevallet, Mireille, Biochimie et biophysique des systèmes intégrés (BBSI), Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF), Laboratoire de Protéomique Clinique, Service de Médecine de Laboratoire, HCUG, Hôpital Universitaire de Genève, Institut de Chimie de Strasbourg, Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier - Grenoble 1 (UJF)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), and Hôpital Universitaire de Genève = University Hospitals of Geneva (HUG)
Subjects: Genomics (q-bio.GN), Electrophoresis, Proteomics, MESH: Mass Spectrometry, MESH: Humans, Proteome, MESH: Peptides, MESH: Proteomics, MESH: Research Design, Proteins, MESH: Electrophoresis, Mass Spectrometry, MESH: Proteome, Research Design, FOS: Biological sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Animals, Humans, Quantitative Biology - Genomics, MESH: Animals, MESH: Proteins, Peptides
Abstract: International audience; Proteomics can be defined as the large-scale analysis of proteins. Due to the complexity of biological systems, it is required to concatenate various separation techniques prior to mass spectrometry. These techniques, dealing with proteins or peptides, can rely on chromatography or electrophoresis. In this review, the electrophoretic techniques are under scrutiny. Their principles are recalled, and their applications for peptide and protein separations are presented and critically discussed. In addition, the features that are specific to gel electrophoresis and that interplay with mass spectrometry (i.e., protein detection after electrophoresis, and the process leading from a gel piece to a solution of peptides) are also discussed.
Published: 2009

39. Chlamydomonas proteomics

Author: Norbert Rolland, Ariane Atteia, Paulette Decottignies, Jérôme Garin, Michael Hippler, Georg Kreimer, Stéphane D Lemaire, Maria Mittag, Volker Wagner, Laboratoire de physiologie cellulaire végétale (LPCV), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Institut de biochimie et biophysique moléculaire et cellulaire (IBBMC), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'étude de la dynamique des protéomes (LEDyP), Université Joseph Fourier - Grenoble 1 (UJF)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institute for Plant Biochemistry and Biotechnology, Westfälische Wilhelms-Universität Münster (WWU), Department of Biology, Friedrich Alexander University, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Institut de biotechnologie des plantes (IBP), Institut für Allgemeine Botanik und Pflanzenphysiologie, Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Friedrich Alexander University [Erlangen-Nürnberg], Friedrich-Schiller-Universität Jena, Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-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), and Westfälische Wilhelms-Universität Münster = University of Münster (WWU)
Subjects: Proteomics, 0106 biological sciences, Microbiology (medical), MESH: Chlamydomonas reinhardtii, MESH: Algal Proteins, Algae, proteome, Protozoan Proteins, review, macromolecular substances, 01 natural sciences, Microbiology, 03 medical and health sciences, Animals, MESH: Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Protozoan Proteins, 030304 developmental biology, 0303 health sciences, MESH: Proteomics, Algal Proteins, Chlamydomonas, MESH: Proteome, Infectious Diseases, protein, Chlamydomonas reinhardtii, 010606 plant biology & botany
Abstract: International audience; Chlamydomonas reinhardtii is a biflagellate and photosynthetic unicellular alga that has long fascinated scientists because it combines characteristics of both plants and animals. Chlamydomonas offers the simplicity of a unicellular organism that is amenable to genetic screening, molecular, and biochemical approaches, as well as to transformation of its nuclear, plastid, or mitochondrial genomes. Over the past decade, proteomics based studies of Chlamydomonas have provided major research contributions in the areas of photosynthesis, molecular biology, and evolution. This review refers to technical and biological aspects of proteomics studies that have been recently performed on the C. reinhardtii model organism.
Published: 2009

40. Proteomic analysis of Brucella suis under oxygen deficiency reveals flexibility in adaptive expression of various pathways

Author: Michael Kersten, Alois Harder, Séverine Loisel-Meyer, Holger C. Scholz, Sascha Al Dahouk, Stephan Köhler, Véronique Jubier-Maurin, Herbert Tomaso, Heinrich Neubauer, Centre d’études d’Agents Pathogènes et Biotechologies pour la Santé (CPBS), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), RWTH Aachen University, Bundeswehr Institute of Microbiology, Friedrich-Loeffler-Institut (FLI), Toplab GmbH, Martinsried, Germany, and Institut de Recherche en Infectiologie de Montpellier (IRIM)
Subjects: Proteomics, MESH: Combined Modality Therapy, Proteome, Brucella suis, MESH: Risk Assessment, Nitrate Reductase, Biochemistry, MESH: Proportional Hazards Models, Electrophoresis, Gel, Two-Dimensional, Glycolysis, Anaerobiosis, Promoter Regions, Genetic, MESH: Stress, Physiological, Beta oxidation, MESH: Bacterial Proteins, MESH: Cohort Studies, MESH: Brucella suis, MESH: Treatment Outcome, MESH: Aged, 0303 health sciences, MESH: Middle Aged, MESH: Proteomics, MESH: Neoplasm Staging, MESH: Confidence Intervals, MESH: Proteome, MESH: Chemotherapy, Adjuvant, MESH: Survival Analysis, MESH: Lymphoma, Primary Cutaneous Anaplastic Large Cell, MESH: Glycolysis, MESH: Disease Progression, Metabolic Networks and Pathways, MESH: Oxygen, MESH: Biopsy, Needle, MESH: Radiotherapy, Adjuvant, MESH: Probability, Brucella, Biology, MESH: Prognosis, MESH: Surgical Procedures, Operative, MESH: Multivariate Analysis, Microbiology, 03 medical and health sciences, Bacterial Proteins, MESH: Sex Factors, Stress, Physiological, MESH: Analysis of Variance, Respiration, MESH: Anaerobiosis, MESH: Promoter Regions, Genetic, Molecular Biology, 030304 developmental biology, MESH: Age Factors, MESH: Humans, 030306 microbiology, MESH: Skin Neoplasms, MESH: Retrospective Studies, MESH: Immunohistochemistry, biology.organism_classification, MESH: Electrophoresis, Gel, Two-Dimensional, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Male, Oxygen, MESH: Metabolic Networks and Pathways, Fermentation, MESH: Nitrate Reductase, MESH: Female, Bacteria
Abstract: International audience; Low oxygen tension was proposed to be one of the environmental parameters characteristic of the patho-physiological conditions of natural infections by Brucella suis. We previously showed that various respiratory pathways may be used by B. suis in response to microaerobiosis and anaerobiosis. Here, we compare the whole proteome of B. suis exposed to such low-oxygenated conditions to that obtained from bacteria grown under ambient air using 2-D DIGE. Data showed that the reduction of basal metabolism was in line with low or absence of growth of B. suis. Under both microaerobiosis and anaerobiosis, glycolysis and denitrification were favored. In addition, fatty acid oxidation and possibly citrate fermentation could also contribute to energy production sufficient for survival under anaerobiosis. When oxygen availability changed and became limiting, basic metabolic processes were still functional and variability of respiratory pathways was observed to a degree unexpected for a strictly aerobic microorganism. This highly flexible respiration probably constitutes an advantage for the survival of Brucella under the restricted oxygenation conditions encountered within host tissue.
Published: 2009

41. The use of proteome similarity for the qualitative and quantitative profiling of reperfused myocardium

Author: Renaud Tissier, Johannes P. C. Vissers, James I. Langridge, Scott J. Geromanos, Bijan Ghaleh, Anne Hulin, Alain Berdeaux, Joanne B. Connolly, Sandrine Pons, Waters Corporation, Institut Mondor de recherche biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Service de pharmacologie clinique [Mondor], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), and Guellaen, Georges
Subjects: Male, Proteome, Clinical Biochemistry, MESH: Rabbits, Peptide, MESH: Amino Acid Sequence, Proteomics, 01 natural sciences, Biochemistry, Homology (biology), Mass Spectrometry, Analytical Chemistry, label-free quantitative proteomics, Liquid chromatography–mass spectrometry, MESH: Myocardial Reperfusion, proteome similarity, MESH: Animals, MESH: Proteins, Peptide sequence, chemistry.chemical_classification, 0303 health sciences, Chemistry, General Medicine, Amino acid, MESH: Proteome, MESH: Reproducibility of Results, Rabbits, MESH: Myocardium, Molecular Sequence Data, Myocardial Reperfusion, 03 medical and health sciences, ion density, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Animals, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, Gene, 030304 developmental biology, reperfused myocardium, MESH: Mass Spectrometry, Chromatography, MESH: Humans, MESH: Molecular Sequence Data, Myocardium, 010401 analytical chemistry, Proteins, Reproducibility of Results, Cell Biology, data-independent scanning, MESH: Male, 0104 chemical sciences, LC-MS, MESH: Chromatography, Liquid, Chromatography, Liquid
Abstract: International audience; An LC-MS-based approach is presented for the identification and quantification of proteins from unsequenced organisms. The method relies on the preservation of homology across species and the similarity in detection characteristics of proteomes in general. Species related proteomes share similarity that progresses from the amino acid frequency distribution to the complete amino sequence of matured proteins. Moreover, the comparative analysis between theoretical and experimental proteome distributions can be used as a measure for the correctness of detection and identification obtained through LC-MS-based schemes. Presented are means to the identification and quantification of rabbit myocardium proteins, immediately after inducing cardiac arrest, using a data-independent LC-MS acquisition strategy. The employed method of acquisition affords accurate mass information on both the precursor and associated product ions, whilst preserving and recording the intensities of the ions. The latter facilitates label-free quantification. The experimental ion density observations obtained for the rabbit sub proteome were found to share great similarity with five other mammalian samples, including human heart, human breast tissue, human plasma, rat liver and a mouse cell line. Redundant, species-homologues peptide identifications from other mammalian organisms were used for initial protein identification, which were complemented with peptide identifications of translated gene sequences. The feasibility and accuracy of label-free quantification of the identified peptides and proteins utilizing above mentioned strategy is demonstrated for selected cardiac rabbit proteins.
Published: 2009

42. Proteomic investigation of enzymes involved in 2-ethylhexyl nitrate biodegradation in Mycobacterium austroafricanum IFP 2173

Author: Rémy Marchal, Elodie Nicolau, Lauriane Kuhn, Yves Jouanneau, Jouanneau, Yves, Laboratoire de Chimie et Biologie des Métaux (LCBM - UMR 5249), 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), 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), IFP Energies nouvelles (IFPEN), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Laboratoire Bourguignon des Matériaux et Procédés (LABOMAP), Arts et Métiers Sciences et Technologies, HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), 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]), and HESAM Université (HESAM)-HESAM Université (HESAM)
Subjects: Proteomics, Mycobacterium austroafricanum, Proteome, Molecular Sequence Data, AlkB, Aldehyde dehydrogenase, Cytochrome P450, CYP153, MESH: Base Sequence, Microbiology, Isozyme, MESH: Biodegradation, Environmental, beta-oxidation, Mycobacterium, 2-Ethylhexyl nitrate, MESH: Alkane 1-Monooxygenase, 03 medical and health sciences, Bacterial Proteins, MESH: Mycobacterium, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Molecular Biology, [SDV.BBM.BC] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], MESH: Bacterial Proteins, 030304 developmental biology, Alcohol dehydrogenase, chemistry.chemical_classification, Gel electrophoresis, 0303 health sciences, Nitrates, MESH: Molecular Sequence Data, biology, Base Sequence, 030306 microbiology, MESH: Proteomics, General Medicine, Alkane hydroxylase, biology.organism_classification, MESH: Proteome, Enzyme, Biodegradation, Environmental, chemistry, Biochemistry, MESH: Nitrates, biology.protein, Cytochrome P-450 CYP4A
Abstract: International audience; 2-Ethyhexyl nitrate (2-EHN) is a synthetic chemical used as a diesel fuel additive, which is recalcitrant to biodegradation. In this study, the enzymes involved in 2-EHN degradation were investigated in Mycobacterium austroafricanum IFP 2173. Using two-dimensional gel electrophoresis and a shotgun proteomic approach, a total of 398 proteins appeared to be more abundant in cells exposed to 2-EHN than in acetate-grown cells. This set of proteins includes multiple isoenzymes of the beta-oxidation pathway, two alcohol and one aldehyde dehydrogenase, as well as four cytochromes P450, including one CYP153 which functions as an alkane hydroxylase. Strain IFP 2173 was also found to contain two alkB-like genes encoding putative membrane-bound alkane hydroxylases. RT-PCR experiments showed that the gene encoding the CYP153 protein, as well as alkB genes, were expressed on 2-EHN. These findings are discussed in the light of a recently proposed 2-EHN degradation pathway involving an initial attack by an alkane hydroxylase and one turn of beta-oxidation, leading to the accumulation of a gamma-lactone as a dead-end product.
Published: 2009

43. Metalloprotease Vsm Is the Major Determinant of Toxicity for Extracellular Products of Vibrio splendidus

Author: Denis Saulnier, Didier Mazel, Hélène Munier-Lehmann, Monique Zagorec, Claude Delsert, Marie-Christine Champomier-Vergès, Frédérique Le Roux, Johan Binesse, Biologie systémique - Systems Biology, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Génétique et Pathologie des Mollusques Marins, 17390 La Tremblade, France. (LGPMM), Santé, Génétique et Microbiologie des Mollusques (IFREMER SG2M), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), 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), Unité de recherche Flore Lactique et Environnement Carné (UFLEC), Institut National de la Recherche Agronomique (INRA), Institut Pasteur [Paris], Plasticité du Génome Bactérien (PGB), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Génétique et Pathologie (LGP), Amélioration génétique, du contrôle des performances et de la santé des mollusques marins (AGSAE), Chimie Organique, This study was carried out with financial assistance from the Institut Pasteur, the Centre National de la Recherche Scientifique (CNRS-URA 2171), the Institut Françcais de Recherche pour l'Exploitation de la Mer (IFREMER), and the Institut de Génomique Marine (Ministère de la Recherche contract no. 0425). Johan Binesse acknowledges a Ph.D. scholarship from the French Ministry of Research and Technology (MRT)., and Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH: Sequence Analysis, DNA, Proteome, MESH: Sequence Homology, Amino Acid, [SDV]Life Sciences [q-bio], Mutant, species, Applied Microbiology and Biotechnology, Virulence factor, Mice, MESH: Animals, Pathogen, MESH: Bacterial Proteins, Cells, Cultured, 0303 health sciences, Metalloproteinase, Ecology, MESH: Genomics, Genomics, musculoskeletal system, MESH: Mollusca, MESH: Proteome, cardiovascular system, MESH: Metalloproteases, Biotechnology, MESH: Cells, Cultured, DNA, Bacterial, Virulence Factors, education, Molecular Sequence Data, Bacillus thuringiensis, Virulence, Biology, Microbiology, 03 medical and health sciences, MESH: Vibrio, Bacterial Proteins, Extracellular, Invertebrate Microbiology, Animals, MESH: Mice, 030304 developmental biology, MESH: Virulence Factors, Vibrio, MESH: Bacillus thuringiensis, MESH: Molecular Sequence Data, Sequence Homology, Amino Acid, 030306 microbiology, Wild type, Sequence Analysis, DNA, Fibroblasts, biology.organism_classification, Molecular biology, MESH: DNA, Bacterial, proteins, MESH: Fibroblasts, MESH: Gene Deletion, Mollusca, Metalloproteases, Genomic, Gene Deletion, Food Science
Abstract: Genomic data combined with reverse genetic approaches have contributed to the characterization of major virulence factors of Vibrio species; however, these studies have targeted primarily human pathogens. Here, we investigate virulence factors in the oyster pathogen Vibrio splendidus LGP32 and show that toxicity is correlated to the presence of a metalloprotease and its corresponding vsm gene. Comparative genomics showed that an avirulent strain closely related to LGP32 lacked the metalloprotease. The toxicity of LGP32 metalloprotease was confirmed by exposing mollusk and mouse fibroblastic cell lines to extracellular products (ECPs) of the wild type (wt) and a vsm deletion mutant (Δ vsm mutant). The ECPs of the wt induced a strong cytopathic effect whose severity was cell type dependent, while those of the Δ vsm mutant were much less toxic, and exposure to purified protein demonstrated the direct toxicity of the Vsm metalloprotease. Finally, to investigate Vsm molecular targets, a proteomic analysis of the ECPs of both LGP32 and the Δ vsm mutant was performed, revealing a number of differentially expressed and/or processed proteins. One of these, the VSA1062 metalloprotease, was found to have significant identity to the immune inhibitor A precursor, a virulence factor of Bacillus thuringiensis . Deletion mutants corresponding to several of the major proteins were constructed by allelic exchange, and the ECPs of these mutants proved to be toxic to both cell cultures and animals. Taken together, these data demonstrate that Vsm is the major toxicity factor in the ECPs of V. splendidus .
Published: 2008

44. Proteomic study of the impact of the JAK2-V617F mutation on the phenotype of essential thrombocythemia

Author: Pascal Mossuz, François Girodon, Sylvie Hermouet, A Bouamrani, François Berger, Eric Lippert, Praloran Vincent, Irène Dobo, Marie Arlotto, Jean-Yves Cahn, Laboratoire d'hématologie cellulaire et moléculaire (DBPC), CHU Grenoble, Grenoble Institut des Neurosciences (GIN), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire d'hématologie, CHU Bordeaux [Bordeaux], Laboratoire d'Hématologie, Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM), Département de cancérologie et d'hématologie, CHU Grenoble-Hôpital Michallon, and Issartel, Jean-Paul
Subjects: Male, Proteomics, Cancer Research, Apolipoprotein B, Proteome, medicine.disease_cause, MESH: Polycythemia Vera, MESH: Janus Kinase 2, 0302 clinical medicine, Polycythemia vera, hemic and lymphatic diseases, MESH: Blood Proteins, Polycythemia Vera, 0303 health sciences, Mutation, biology, MESH: Proteomics, Hematology, Blood Proteins, Phenotype, MESH: Amino Acid Substitution, MESH: Proteome, 030220 oncology & carcinogenesis, Female, JAK2 V617F, Thrombocythemia, Essential, MESH: Genetic Diseases, Inborn, Mutation, Missense, MESH: Phenotype, 03 medical and health sciences, Genetics, medicine, Humans, Allele, Molecular Biology, 030304 developmental biology, MESH: Mutation, Missense, MESH: Humans, Essential thrombocythemia, Genetic Diseases, Inborn, Cell Biology, Janus Kinase 2, medicine.disease, Molecular biology, MESH: Male, Amino Acid Substitution, Serum proteome, Immunology, biology.protein, MESH: Thrombocythemia, Essential, MESH: Female
Abstract: International audience; OBJECTIVE: Previous studies have suggested that two subtypes of essential thrombocythemia (ET) could be separated on the basis of their JAK2 status (V617F-positive or V617F-negative), with a continuum between V617F-positive ET and polycythemia vera (PV). Nevertheless, increasingly contradictory data on the impact of JAK2-V617F (presence and load) on ET phenotype highlight the need for further investigations. MATERIALS AND METHODS: We investigated the influence of JAK2-V617F on ET phenotype using mass spectrometry-based analysis of serum protein profiles of ET patients, comparatively with PV patients. RESULTS: V617F-positive ET and PV displayed significant differences in their serum protein profiles. Furthermore, JAK2-V617F presence did not impact significantly the serum proteome of ET patients: we observed very few differences in serum protein profiles of V617F-positive and -negative ET. Reciprocally, clustering of ET patients on the basis of their serum protein profiles did not correlate with JAK2-V617F presence. Finally, the JAK2-V617F load did not influence serum apolipoprotein A-1 levels in ET, a previously validated marker of JAK2-V617F allele burden in PV. CONCLUSION: Serum proteome of ET patients was not influenced by the presence of JAK2-V617F or by high V617F allelic ratio (up to 50%) suggesting that ET phenotype is, at best, only partially influenced by the JAK2-V617F mutation.
Published: 2008

45. Differential proteomic screen to evidence proteins ubiquitinated upon mitotic exit in cell-free extract of Xenopus laevis embryos

Author: Jacek Z. Kubiak, Aude Pascal, Guy G. Poirier, Jean-Philippe Gagné, Julian Vasilescu, Franck Bazile, Franck Chesnel, Daniel Figeys, Geneviève Mercier, Ken Sin Lo, Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Axe cancer, Université Laval [Québec] (ULaval)-CHUQ Research Center, Ottawa Institute of Systems Biology, University of Ottawa [Ottawa], De Villemeur, Hervé, Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Proteomics, Embryo, Nonmammalian, Proteome, Cell, Xenopus, Xenopus Proteins, Biochemistry, law.invention, MESH: Recombinant Proteins, Xenopus laevis, MESH: Histidine, Ubiquitin, law, MESH: Cell-Free System, MESH: Animals, MESH: Xenopus Proteins, 0303 health sciences, MESH: Proteomics, 030302 biochemistry & molecular biology, Cell cycle, Recombinant Proteins, MESH: Proteome, medicine.anatomical_structure, Recombinant DNA, Female, MESH: Ubiquitin, Mitosis, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, 03 medical and health sciences, Affinity chromatography, MESH: Xenopus laevis, medicine, Animals, Histidine, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, 030304 developmental biology, Cell-Free System, Ubiquitination, MESH: Embryo, Nonmammalian, General Chemistry, MESH: Mitosis, biology.organism_classification, Mitotic exit, biology.protein, MESH: Ubiquitination, MESH: Female
Abstract: International audience; Post-translational modification of proteins via ubiquitination plays a crucial role in numerous vital functions of the cell. Polyubiquitination is one of the key regulatory processes involved in regulation of mitotic progression. Here we describe a differential proteomic screen dedicated to identification of novel proteins ubiquitinated upon mitotic exit in cell-free extract of Xenopus laevis embryo. Mutated recombinant His6-tagged ubiquitin (Ubi (K48R)) was added to mitotic extract from which we purified conjugated proteins, as well as associated proteins in nondenaturing conditions by cobalt affinity chromatography. Proteins eluted from Ubi (K48R) supplemented and control extracts were compared by LC-MS/MS analysis after monodimensional SDS-PAGE. A total of 144 proteins potentially ubiquitinated or associated with them were identified. Forty-one percent of these proteins were shown to be involved in ubiquitination and/or proteasomal degradation pathway confirming the specificity of the screen. Twelve proteins, among them ubiquitin itself, were shown to carry a "GG" or "LRGG" remnant tag indicating their direct ubiquitination. Interestingly, sequence analysis of ubiquitinated substrates carrying these tags indicated that in Xenopus cell-free embryo extract supplemented with Ubi (K48R) the majority of polyubiquitination occurred through lysine-11 specific ubiquitin chain polymerization. The potential interest in this atypical form of ubiquitination as well as usefulness of our method in analyzing atypical polyubiquitin species is discussed.
Published: 2008

46. Extent of N-terminal modifications in cytosolic proteins from eukaryotes

Author: Benoît Valot, Carmela Giglione, Christelle Espagne, Myriam Ferro, Thierry Meinnel, Aude Martinez, José A. Traverso, Geneviève Ephritikhine, Michel Zivy, Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), La plante et son environnement (PSE), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Institut National Agronomique Paris-Grignon (INA P-G)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), 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)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA), Université Paris Diderot - Paris 7 (UPD7), Institut National de la Santé et de la Recherche Médicale (INSERM)-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), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])
Subjects: Proteome, Palmitic Acid, MESH: Amino Acid Sequence, Proteomics, Biochemistry, Genome, Myristic Acid, MESH: Eukaryotic Cells, chemistry.chemical_compound, Cytosol, MESH: Cytosol, MESH: Proteins, MESH: Animals, MESH: Peptide Fragments, Peptide sequence, Cells, Cultured, 0303 health sciences, biology, 030302 biochemistry & molecular biology, Acetylation, MESH: Archaeal Proteins, MESH: Predictive Value of Tests, MESH: Proteome, Eukaryotic Cells, Eukaryote, MESH: Fungal Proteins, MESH: Acetylation, MESH: Cells, Cultured, Archaeal Proteins, Molecular Sequence Data, MESH: Arabidopsis Proteins, Fungal Proteins, 03 medical and health sciences, Predictive Value of Tests, Animals, Humans, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Amino Acid Sequence, Molecular Biology, 030304 developmental biology, Methionine, MESH: Molecular Sequence Data, MESH: Humans, Arabidopsis Proteins, Robustness (evolution), Proteins, biology.organism_classification, Peptide Fragments, chemistry, MESH: Myristic Acid, MESH: Protein Processing, Post-Translational, MESH: Palmitic Acid, Protein Processing, Post-Translational
Abstract: International audience; Most proteins in all organisms undergo crucial N-terminal modifications involving N-terminal methionine excision, N-alpha-acetylation or N-myristoylation (N-Myr), or S-palmitoylation. We investigated the occurrence of these poorly annotated but essential modifications in proteomes, focusing on eukaryotes. Experimental data for the N-terminal sequences of animal, fungi, and archaeal proteins, were used to build dedicated predictive modules in a new software. In vitro N-Myr experiments were performed with both plant and animal N-myristoyltransferases, for accurate prediction of the modification. N-terminal modifications from the fully sequenced genome of Arabidopsis thaliana were determined by MS. We identified 105 new modified protein N-termini, which were used to check the accuracy of predictive data. An accuracy of more than 95% was achieved, demonstrating (i) overall conservation of the specificity of the modification machinery in higher eukaryotes and (ii) robustness of the prediction tool. Predictions were made for various proteomes. Proteins that had undergone both N-terminal methionine (Met) cleavage and N-acetylation were found to be strongly overrepresented among the most abundant proteins, in contrast to those retaining their genuine unblocked Met. Here we propose that the nature of the second residue of an ORF is a key marker of the abundance of the mature protein in eukaryotes.
Published: 2008

47. BAGET: a web server for the effortless retrieval of prokaryotic gene context and sequence

Author: Jacques Oberto, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)
Subjects: Statistics and Probability, Web server, Proteome, Information Storage and Retrieval, Context (language use), Computational biology, Biology, computer.software_genre, Biochemistry, Genome, User-Computer Interface, 03 medical and health sciences, MESH: Sequence Analysis, MESH: Software, Databases, Genetic, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Gene, MESH: Databases, Genetic, 030304 developmental biology, MESH: User-Computer Interface, Genetics, Internet, 0303 health sciences, Bacteria, 030302 biochemistry & molecular biology, Rich Text Format, Nucleic acid sequence, MESH: Information Storage and Retrieval, computer.file_format, Archaea, Computer Science Applications, MESH: Proteome, Computational Mathematics, Sequence logo, MESH: Bacteria, MESH: Internet, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Computational Theory and Mathematics, MESH: Archaea, Database Management Systems, Web service, Sequence Analysis, computer, Software, MESH: Database Management Systems
Abstract: Summary: BAGET (Bacterial and Archaeal Gene Exploration Tool) is a web service designed to facilitate extraction, by molecular geneticists and phylogeneticists, of specific gene and protein sequences from completely determined prokaryotic genomes. Upon selection of a particular prokaryotic organism and gene, two levels of visual gene context information are provided on a single dynamic page: (i) a graphical representation of a user defined portion of the chromosome centered on the gene of interest and (ii) the DNA sequence of the query gene, of the immediate neighboring genes and the intergenic regions each identified by a consistent color code. The aminoacid sequence is provided for protein-coding query genes. Query results can be exported as a rich text format (RTF) word processor file for printing, archival or further analysis. Availability: http://archaea.u-psud.fr/bin/baget.dll
Published: 2008

48. The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology

Author: Michael Primig, Frédéric Chalmel, Groupe d'Etude de la Reproduction Chez l'Homme et les Mammiferes (GERHM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Forgeron, Christine
Subjects: MESH: Signal Transduction, Proteome, Data management, Biochemistry, User-Computer Interface, 0302 clinical medicine, Structural Biology, Protein Interaction Mapping, lcsh:QH301-705.5, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], Oligonucleotide Array Sequence Analysis, 0303 health sciences, Biological data, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Systems Biology, Applied Mathematics, Chromosome Mapping, Genome project, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Computer Science Applications, MESH: Proteome, 030220 oncology & carcinogenesis, MESH: Systems Biology, lcsh:R858-859.7, User interface, DNA microarray, MESH: Computer Graphics, Algorithms, Signal Transduction, Systems biology, MESH: Algorithms, Computational biology, Biology, lcsh:Computer applications to medicine. Medical informatics, Data type, 03 medical and health sciences, Annotation, MESH: Gene Expression Profiling, MESH: Software, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Computer Graphics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, 030304 developmental biology, MESH: User-Computer Interface, Information retrieval, business.industry, Gene Expression Profiling, MESH: Molecular Biology, MESH: Protein Interaction Mapping, Systems Integration, lcsh:Biology (General), MESH: Oligonucleotide Array Sequence Analysis, MESH: Systems Integration, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, MESH: Chromosome Mapping, Software
Abstract: Background High-throughput genome biological experiments yield large and multifaceted datasets that require flexible and user-friendly analysis tools to facilitate their interpretation by life scientists. Many solutions currently exist, but they are often limited to specific steps in the complex process of data management and analysis and some require extensive informatics skills to be installed and run efficiently. Results We developed the Annotation, Mapping, Expression and Network (AMEN) software as a stand-alone, unified suite of tools that enables biological and medical researchers with basic bioinformatics training to manage and explore genome annotation, chromosomal mapping, protein-protein interaction, expression profiling and proteomics data. The current version provides modules for (i) uploading and pre-processing data from microarray expression profiling experiments, (ii) detecting groups of significantly co-expressed genes, and (iii) searching for enrichment of functional annotations within those groups. Moreover, the user interface is designed to simultaneously visualize several types of data such as protein-protein interaction networks in conjunction with expression profiles and cellular co-localization patterns. We have successfully applied the program to interpret expression profiling data from budding yeast, rodents and human. Conclusion AMEN is an innovative solution for molecular systems biological data analysis freely available under the GNU license. The program is available via a website at the Sourceforge portal which includes a user guide with concrete examples, links to external databases and helpful comments to implement additional functionalities. We emphasize that AMEN will continue to be developed and maintained by our laboratory because it has proven to be extremely useful for our genome biological research program.
Published: 2008

49. Transcriptome of Aphanomyces euteiches: new oomycete putative pathogenicity factors and metabolic pathways

Author: Christophe Jacquet, Elodie Gaulin, Arnaud Bottin, Catherine Mathe, Bernard Dumas, Patrick Wincker, Mohammed-Amine Madoui, Arnaud Couloux, Surfaces Cellulaires et Signalisation chez les Végétaux (SCSV), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-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), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Proteome, UniGene, lcsh:Medicine, MESH: Plant Roots, 01 natural sciences, Plant Roots, lcsh:Science, Genetics, Oomycete, Expressed Sequence Tags, 0303 health sciences, Expressed sequence tag, Multidisciplinary, Microbiology/Microbial Evolution and Genomics, Genetics and Genomics/Functional Genomics, food and beverages, MESH: Proteome, Oomycetes, MESH: Oomycetes, Phytophthora, Aphanomyces euteiches, MESH: Membrane Proteins, Metabolic Networks and Pathways, Research Article, Plant Biology/Plant-Biotic Interactions, MESH: Aphanomyces, Virulence Factors, Genes, Fungal, Aphanomyces, Biology, MESH: Expressed Sequence Tags, 03 medical and health sciences, MESH: Gene Expression Profiling, Botany, MESH: Gene Library, Gene family, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 030304 developmental biology, Gene Library, MESH: Virulence Factors, MESH: Phytophthora, Gene Expression Profiling, lcsh:R, fungi, Membrane Proteins, Microbiology/Plant-Biotic Interactions, Cellulose binding, biology.organism_classification, MESH: Metabolic Networks and Pathways, lcsh:Q, MESH: Genes, Fungal, 010606 plant biology & botany
Abstract: International audience; Aphanomyces euteiches is an oomycete pathogen that causes seedling blight and root rot of legumes, such as alfalfa and pea. The genus Aphanomyces is phylogenically distinct from well-studied oomycetes such as Phytophthora sp., and contains species pathogenic on plants and aquatic animals. To provide the first foray into gene diversity of A. euteiches, two cDNA libraries were constructed using mRNA extracted from mycelium grown in an artificial liquid medium or in contact to plant roots. A unigene set of 7,977 sequences was obtained from 18,864 high-quality expressed sequenced tags (ESTs) and characterized for potential functions. Comparisons with oomycete proteomes revealed major differences between the gene content of A. euteiches and those of Phytophthora species, leading to the identification of biosynthetic pathways absent in Phytophthora, of new putative pathogenicity genes and of expansion of gene families encoding extracellular proteins, notably different classes of proteases. Among the genes specific of A. euteiches are members of a new family of extracellular proteins putatively involved in adhesion, containing up to four protein domains similar to fungal cellulose binding domains. Comparison of A. euteiches sequences with proteomes of fully sequenced eukaryotic pathogens, including fungi, apicomplexa and trypanosomatids, allowed the identification of A. euteiches genes with close orthologs in these microorganisms but absent in other oomycetes sequenced so far, notably transporters and non-ribosomal peptide synthetases, and suggests the presence of a defense mechanism against oxidative stress which was initially characterized in the pathogenic trypanosomatids.
Published: 2008

50. Proteome analysis of apoptosis signaling by S-trityl-L-cysteine, a potent reversible inhibitor of human mitotic kinesin Eg5

Author: Dimitrios A. Skoufias, Hanne Kolsrud Hustoft, Yasmina Saoudi, Frank Kozielski, Bernd Thiede, Peter R. Jungblut, Rose-Laure Indorato, Margarita Strozynski, The Beatson Institute for Cancer Research, University of Glasgow, Institut de biologie structurale (IBS - UMR 5075 ), 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), Grenoble Institut des Neurosciences (GIN), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM), Groupe Physiopathologie du Cytosquelette (GPC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Biochemistry/Protein Analysis Core Facility [MPIIB Berlin], Max Planck Institute for Infection Biology (MPIIB), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Biotechnology center of Oslo, Faculty of Medicine [Oslo], University of Oslo (UiO)-University of Oslo (UiO)-Rigshospitalet [Copenhagen], Copenhagen University Hospital-Copenhagen University Hospital, NT05-3_42614, ARC contract number 3973) Agence Nationale de la Recherche NT05-3_42614, Collaboration, 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 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)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Andrieux, Annie
Subjects: MESH: Signal Transduction, Programmed cell death, Paclitaxel, Proteome, Aurora A kinase, Kinesins, Mitosis, Stathmin, Apoptosis, Biochemistry, Motor protein, 03 medical and health sciences, 0302 clinical medicine, Translationally-controlled tumor protein, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Cysteine, MESH: Paclitaxel, Molecular Biology, 030304 developmental biology, 0303 health sciences, MESH: Humans, biology, MESH: Apoptosis, MESH: Cysteine, MESH: Mitosis, 3. Good health, Cell biology, MESH: Hela Cells, MESH: Proteome, Spindle checkpoint, 030220 oncology & carcinogenesis, biology.protein, Kinesin, MESH: Kinesin, HeLa Cells, Signal Transduction
Abstract: International audience; Mitotic kinesins represent potential drug targets for anticancer chemotherapy. Inhibitors of different chemical classes have been identified that target human Eg5, a kinesin responsible for the establishment of the bipolar spindle. One potent Eg5 inhibitor is S-trityl-L-cysteine (STLC), which arrests cells in mitosis and exhibits tumor growth inhibition activity. However, the underlying mechanism of STLC action on the molecular level is unknown. Here, cells treated with STLC were blocked in mitosis through activation of the spindle assembly checkpoint as shown by the phosphorylated state of BubR1 and the accumulation of mitosis specific phosphorylation on histone H3 and aurora A kinase. Using live cell imaging, we observed prolonged mitotic arrest and subsequent cell death after incubation of GFP-alpha-tubulin HeLa cells with STLC. Activated caspase-9 occurred before cleavage of caspase-8 leading to the accumulation of the activated executioner caspase-3 suggesting that STLC induces apoptosis through the intrinsic apoptotic pathway. Proteome analysis following STLC treatment revealed 33 differentially regulated proteins of various cellular processes, 31 of which can be linked to apoptotic cell death. Interestingly, four identified proteins, chromobox protein homolog, RNA-binding Src associated in mitosis 68 kDa protein, stathmin, and translationally controlled tumor protein can be linked to mitotic and apoptotic processes.
Published: 2008

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