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1. Ortho-proteogenomics: Multiple proteomes investigation through orthology and a new MS-based protocol

Author

Christine Carapito, Christine Schaeffer, Jean-Marc Reyrat, Alain Van Dorsselaer, Emmanuel Perrodou, Caroline Deshayes, Sebastien Gallien, Odile Lecompte, Olivier Poch, Institut Pluridisciplinaire Hubert Curien (IPHC), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Louis Pasteur - Strasbourg I, Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-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), Pathogénie des infections systémiques (UMR_S 570), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Peney, Maité, Institut Pluridisciplinaire Hubert Curien ( IPHC ), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique ( CNRS ), Institut de génétique et biologie moléculaire et cellulaire ( IGBMC ), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Spectrométrie de masse Bio-organique, UMR CNRS-ULP, Pathogénie des infections systémiques ( UMR_S 570 ), and Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS )

Subjects
Proteomics, Proteome, In silico, Mycobacterium smegmatis, Codon, Initiator, Genomics, Computational biology, Genome, Mass Spectrometry, Mycobacterium, 03 medical and health sciences, Bacterial Proteins, Species Specificity, Methods, Genetics, Genetics (clinical), 030304 developmental biology, Comparative genomics, 0303 health sciences, biology, 030302 biochemistry & molecular biology, [SDV.ETH] Life Sciences [q-bio]/Ethics, biology.organism_classification, Proteogenomics, Peptide Fragments, [SDV.ETH]Life Sciences [q-bio]/Ethics, RNA, Bacterial, [ SDV.ETH ] Life Sciences [q-bio]/Ethics, Sequence Alignment, Genome, Bacterial
Abstract

The progress in sequencing technologies irrigates biology with an ever-increasing number of genome sequences. In most cases, the gene repertoire is predicted in silico and conceptually translated into proteins. As recently highlighted, the predicted genes exhibit frequent errors, particularly in start codons, with a serious impact on subsequent biological studies. A new “ortho-proteogenomic” approach is presented here for the annotation refinement of multiple genomes at once. It combines comparative genomics with an original proteomic protocol that allows the characterization of both N-terminal and internal peptides in a single experiment. This strategy was applied to the Mycobacterium genus with Mycobacterium smegmatis as the reference, and identified 946 distinct proteins, including 443 characterized N termini. These experimental data allowed the correction of 19% of the characterized start codons, the identification of 29 proteins missed during the annotation process, and the curation, thanks to comparative genomics, of 4328 sequences of 16 other Mycobacterium proteomes.

Published
2008
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2. Proteome analysis of the culture environment supporting undifferentiated mouse embryonic stem and germ cell growth

Author

Christine Carapito, Nicolas Buhr, Agnès Hovasse, Stéphane Viville, Alain Van Dorsselaer, Christine Schaeffer, Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de masse Bio-organique, UMR CNRS-ULP, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Louis Pasteur - Strasbourg I, 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), and 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)

Subjects
Proteomics, Clinical Biochemistry, Cell, Bioinformatics, Biochemistry, Analytical Chemistry, Mice, 0302 clinical medicine, MESH: Animals, Electrophoresis, Gel, Two-Dimensional, MESH: Embryonic Stem Cells, Cells, Cultured, reproductive and urinary physiology, 0303 health sciences, Ethical issues, Culture environment, MESH: Proteomics, Reference Standards, Cell biology, medicine.anatomical_structure, embryonic structures, Proteome, MESH: Pluripotent Stem Cells, MESH: Reference Standards, MESH: Gelatin, biological phenomena, cell phenomena, and immunity, Germ cell, MESH: Cells, Cultured, Pluripotent Stem Cells, Biology, Mouse embryonic fibroblast, MESH: Coculture Techniques, 03 medical and health sciences, MESH: Cell Proliferation, medicine, Animals, Fibroblast, MESH: Mice, Embryonic Stem Cells, Cell Proliferation, 030304 developmental biology, urogenital system, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Fibroblasts, MESH: Electrophoresis, Gel, Two-Dimensional, Embryonic stem cell, Coculture Techniques, Culture Media, MESH: Germ Cells, Germ Cells, MESH: Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, MESH: Fibroblasts, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, MESH: Culture Media, Gelatin, 030217 neurology & neurosurgery
Abstract

The therapeutical interest of pluripotent cells and ethical issues related to the establishment of human embryonic stem cell (ESC) or embryonic germ cell (EGC) lines raise the understanding of the mechanism underlying pluripotency to a fundamental issue. Establishing a protein pluripotency signature for these cells can be complicated by the presence of unrelated proteins produced by the culture environment. Here, we have analyzed the environment supporting ESC and EGC growth, and established 2-D reference maps for each constituent present in this culture environment: mouse embryonic fibroblast feeder cells, culture medium (CM) and gelatin. The establishment of these reference maps is essential prior to the study of ESC and EGC specific proteomes. Indeed, these maps can be subtracted from ESC or EGC maps to allow focusing on spots specific for ESCs or EGCs. Our study led to the identification of 110 unique proteins from fibroblast feeder cells and 23 unique proteins from the CM, which represent major contaminants of ESC and EGC proteomes. For gelatin, no collagen-specific proteins were identified, most likely due to difficulties in resolution and low quantities. Furthermore, no differences were observed between naive and conditioned CM. Finally, we compared these reference maps to ESC 2-D gels and isolated 17 ESC specific spots. Among these spots, proteins that had already been identified in previous human and mouse ESC proteomes were identified but no apparent ESC-specific pluripotency marker could be identified. This work represents an essential step in furthering the knowledge of environmental factors supporting ESC and EGC growth.

Published
2007
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3. Self-Assembly of a Diferrous Triple-Stranded Helicate with Bis(2,2‘-Bipyridine) Ligands: Thermodynamic and Kinetic Intermediates

Author

Fatin-Rouge , N., Blanc , Sylvie, Leize , E., Van Dorsselaer , A., Baret , P., Pierre , J.-L., Albrecht-Gary , A.-M., Meyer , Michel, Institut UTINAM (Univers, transport, interfaces, nanostructures, atmosphère et environnement, molécules) (Besançon), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux ( IPREM ), Université de Pau et des Pays de l'Adour ( UPPA ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de spectrométrie de masse des interactions et des systèmes, Chimie de la matière complexe ( CMC ), Université de Strasbourg ( UNISTRA ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Strasbourg ( UNISTRA ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Spectrométrie de masse Bio-organique, UMR CNRS-ULP, Laboratoire de Chimie Biomimétique , LEDSS, Université Joseph Fourier - Grenoble 1 ( UJF ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de Chimie Moléculaire de l'Université de Bourgogne [Dijon] ( ICMUB ), Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Univers, Transport, Interfaces, Nanostructures, Atmosphère et environnement, Molécules (UMR 6213) (UTINAM), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Chimie de la matière complexe (CMC), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-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), Laboratoire d'études dynamiques et structurales de la sélectivité (LEDSS), Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Institut de Chimie Moléculaire de l'Université de Bourgogne [Dijon] (ICMUB), and Université de Bourgogne (UB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Models, Molecular, Magnetic Resonance Spectroscopy, Spin states, Stereochemistry, Molecular Conformation, Protonation, Ligands, 010402 general chemistry, [ CHIM ] Chemical Sciences, 01 natural sciences, 2,2'-Bipyridine, Dissociation (chemistry), Ferrous, Inorganic Chemistry, chemistry.chemical_compound, 2,2'-Dipyridyl, [CHIM]Chemical Sciences, Physical and Theoretical Chemistry, nuclear magnetic resonance spectroscopy, mass spectrometry, allosterism, Molecular Structure, 010405 organic chemistry, Chemistry, Ligand, Nucleic Acid Hybridization, Nuclear magnetic resonance spectroscopy, 0104 chemical sciences, Kinetics, Crystallography, iron complex, Spectrophotometry, Potentiometry, Proton NMR, Thermodynamics, 2 2' bipyridine derivative
Abstract

cited By 40; International audience; The protonation and iron(II) coordination properties of a bis(2,2′-bipyridine) ligand L were investigated in methanol. The protonated forms showed allosteric effects due to the flexibility of the strand. Speciation studies of the corresponding ferrous complexes were carried out as a function of pH and iron(II) concentrations. A combination of electrospray mass spectroscopy, potentiometry, and spectrophotometry allowed the determination in solution of three ferrous complexes, one mononuclear (L2Fe2+) and two dinuclear (L2Fe24+ and L3Fe24+) species. Their structure was deduced from the metal spin state and confirmed by 1H NMR measurements and molecular modeling. The dissociation process of the triple-stranded diferrous helicate L3Fe24+ by OH- revealed two rate-limiting steps. The former leads to the formation of a monoferrous triple-stranded compound via a classical mechanism, which involves hydroxy-ferrous complexes. A similar process was observed in the latter step for the release of the ferrous cation from the mononuclear intermediate. Taking into account the structural, thermodynamic, and kinetic features provided by the present study, we could propose a self-assembling mechanism of the triple-stranded diferrous helicate.

Published
2000
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4. Copurification of the FpvA ferric pyoverdin receptor of Pseudomonas aeruginosa with its iron-free ligand: implications for siderophore-mediated iron transport

Author

Schalk Ij, Prome D, Poole K, Abdallah Ma, Van Dorsselaer A, Pattus F, Pavel Kyslík, Institut Gilbert-Laustriat : Biomolécules, Biotechnologie, Innovation Thérapeutique, Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Laboratory of Enzyme Technology, Czech Academy of Sciences [Prague] (CAS), Institut de pharmacologie et de biologie structurale (IPBS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, 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), Department of Microbiology and Immunology (D MICROBIOLOGY IMMUNOLOGY), Queen's University [Kingston, Canada], Czech Academy of Sciences [Prague] (ASCR), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de masse Bio-organique, UMR CNRS-ULP, Queen's University [Kingston], 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), and 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)

Subjects
Circular dichroism, Siderophore, Siderophores, MESH: Amino Acid Sequence, Ligands, 7. Clean energy, Biochemistry, Copurification, MESH: Circular Dichroism, FepA, MESH: Ligands, MESH: Endopeptidases, MESH: Bacterial Proteins, 0303 health sciences, Chemistry, Circular Dichroism, Hydrolysis, Ligand (biochemistry), Transport protein, MESH: Oligopeptides, MESH: Pseudomonas aeruginosa, Pseudomonas aeruginosa, Bacterial outer membrane, Oligopeptides, MESH: Hydrolysis, medicine.drug, Bacterial Outer Membrane Proteins, Protein Binding, MESH: Pigments, Biological, MESH: Biological Transport, Molecular Sequence Data, Iron Chelating Agents, 03 medical and health sciences, Bacterial Proteins, Endopeptidases, medicine, MESH: Protein Binding, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, MESH: Siderophores, 030304 developmental biology, MESH: Molecular Sequence Data, 030306 microbiology, MESH: Bacterial Outer Membrane Proteins, Biological Transport, Pigments, Biological, biochemical phenomena, metabolism, and nutrition, MESH: Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, MESH: Iron Chelating Agents, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Ferric
Abstract

The Pseudomonas aeruginosa FpvA receptor is a TonB-dependent outer membrane transport protein that catalyzes uptake of ferric pyoverdin across the outer membrane. Surprisingly, FpvA expressed in P. aeruginosa grown in an iron-deficient medium copurifies with a ligand X that we have characterized by UV, fluorescence, and mass spectrometry as being iron-free pyoverdin (apo-PaA). PaA was absent from FpvA purified from a PaA-deficient P. aeruginosa strain. The properties of ligand binding in vitro revealed very similar affinities of apo-PaA and ferric-PaA to FpvA. Fluorescence resonance energy transfer was used to study in vitro the formation of the FpvA-PaA-Fe complex in the presence of PaA-Fe or citrate-Fe. The circular dichroism spectrum of FpvA indicated a 57% beta-structure content typical of porins and in agreement with the 3D structures of the siderophore receptors FhuA and FepA. In the absence of the protease's inhibitors, a truncated form of FpvA lacking 87 amino acids at its N-terminus was purified. This truncated form still bound PaA, and its beta-sheet content was conserved. This N-terminal region displays significant homology to the N-terminal periplasmic extensions of FecA from Escherichia coli and PupB from Pseudomonas putida, which were previously shown to be involved in signal transduction. This suggests a similar function for FpvA. The mechanism of iron transport in P. aeruginosa via the pyoverdin pathway is discussed in the light of all these new findings.

Published
1999
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5. Differential display of peptides induced during the immune response of Drosophila: A matrix-assisted laser desorption ionization time-of-flight mass spectrometry study

Author

Philippe BULET, Uttenweiler-Joseph, S., Moniatte, M., Dorsselaer, A., Hoffmann, J. A., Réponse immunitaire et developpement chez les insectes (RIDI - UPR 9002), Université de Strasbourg (UNISTRA)-Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de masse Bio-organique, UMR CNRS-ULP, Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-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), 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), and Uttenweiler, Sandrine

Subjects
Peptide Biosynthesis, MESH: Drosophila, MESH: Peptides, [SDV]Life Sciences [q-bio], MESH: Anti-Infective Agents, [SDV] Life Sciences [q-bio], MESH: Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Anti-Infective Agents, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Animals, MESH: Animals, MESH: Peptide Biosynthesis, Drosophila, Peptides, ComputingMilieux_MISCELLANEOUS
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