Author: "Génétique des Génomes Bactériens" - Searchworks@Jio Institute Digital Library Search Results

Your search keyword '"Génétique des Génomes Bactériens"' showing total 104 results

Start Over Author "Génétique des Génomes Bactériens"

104 results on '"Génétique des Génomes Bactériens"'

1. Gene copy number and function of the APL1 immune factor changed during Anopheles evolution

Author: Abbasali Raz, Christian Mitri, Emma Brito-Fravallo, Kenneth D. Vernick, Emmanuel Bischoff, Constentin Dieme, Inge Holm, Sedigheh Zakeri, Michelle M. Riehle, Karin Eiglmeier, Mahdokht I. K. Nejad, Navid Dinparast Djadid, Génétique et Génomique des Insectes Vecteurs, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Génétique des Génomes Bactériens, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Malaria and Vector Research Group (MVRG), Institut Pasteur d'Iran, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Medical College of Wisconsin [Milwaukee] (MCW), This study received financial support to KDV from the European Commission, Horizon 2020 Infrastructures #731060 Infravec2, European Research Council, Support for frontier research, Advanced Grant #323173 AnoPath, Agence Nationale de la Recherche, #ANR-19-CE35-0004 ArboVec, and French Laboratoire d’Excellence 'Integrative Biology of Emerging Infectious Diseases' #ANR-10-LABX-62-IBEID and to MMR from National Institutes of Health, NIAID #AI121587. Funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: 731060,INFRAVEC2(2017), European Project: 323173,EC:FP7:ERC,ERC-2012-ADG_20120314,ANOPATH(2013), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Anopheles gambiae, [SDV]Life Sciences [q-bio], Gene Dosage, MESH: Gene Dosage, 0302 clinical medicine, Mosquito, MESH: Insect Proteins, MESH: Animals, Copy-number variation, MESH: Peptide Fragments, MESH: Phylogeny, Phylogeny, Gene essentiality, MESH: Evolution, Molecular, Genetics, Gene neofunctionalization, MESH: Immunologic Factors, Anopheles, 3. Good health, Infectious Diseases, MESH: Longevity, Insect immunity, Insect Proteins, 030231 tropical medicine, Longevity, MESH: Malaria, Locus (genetics), MESH: Insect Vectors, Biology, lcsh:Infectious and parasitic diseases, Evolution, Molecular, MESH: Anopheles, 03 medical and health sciences, parasitic diseases, Gene silencing, Gene family, Animals, Immunologic Factors, lcsh:RC109-216, Gene, Anopheles stephensi, [SDV.GEN]Life Sciences [q-bio]/Genetics, Research, fungi, Chaperonin 60, biology.organism_classification, Peptide Fragments, Insect Vectors, Malaria, 030104 developmental biology, MESH: Chaperonin 60, Parasitology
Abstract: Background The recent reference genome assembly and annotation of the Asian malaria vector Anopheles stephensi detected only one gene encoding the leucine-rich repeat immune factor APL1, while in the Anopheles gambiae and sibling Anopheles coluzzii, APL1 factors are encoded by a family of three paralogs. The phylogeny and biological function of the unique APL1 gene in An. stephensi have not yet been specifically examined. Methods The APL1 locus was manually annotated to confirm the computationally predicted single APL1 gene in An. stephensi. APL1 evolution within Anopheles was explored by phylogenomic analysis. The single or paralogous APL1 genes were silenced in An. stephensi and An. coluzzii, respectively, followed by mosquito survival analysis, experimental infection with Plasmodium and expression analysis. Results APL1 is present as a single ancestral gene in most Anopheles including An. stephensi but has expanded to three paralogs in an African lineage that includes only the Anopheles gambiae species complex and Anopheles christyi. Silencing of the unique APL1 copy in An. stephensi results in significant mosquito mortality. Elevated mortality of APL1-depleted An. stephensi is rescued by antibiotic treatment, suggesting that pathology due to bacteria is the cause of mortality, and indicating that the unique APL1 gene is essential for host survival. Successful Plasmodium development in An. stephensi depends upon APL1 activity for protection from high host mortality due to bacteria. In contrast, silencing of all three APL1 paralogs in An. coluzzii does not result in elevated mortality, either with or without Plasmodium infection. Expression of the single An. stephensi APL1 gene is regulated by both the Imd and Toll immune pathways, while the two signaling pathways regulate different APL1 paralogs in the expanded APL1 locus. Conclusions APL1 underwent loss and gain of functions concomitant with expansion from a single ancestral gene to three paralogs in one lineage of African Anopheles. We infer that activity of the unique APL1 gene promotes longevity in An. stephensi by conferring protection from or tolerance to an effect of bacterial pathology. The evolution of an expanded APL1 gene family could be a factor contributing to the exceptional levels of malaria transmission mediated by human-feeding members of the An. gambiae species complex in Africa.
Published: 2020
Full Text: View/download PDF

2. The CymR Regulator in Complex with the Enzyme CysK Controls Cysteine Metabolism in Bacillus subtilis

Author: Olga Soutourina, Isabelle Martin-Verstraete, Marie-Françoise Hullo, Bertrand Raynal, Philippe Noirot, Patrick England, Peggy Mervelet, Catherine Tanous, Antoine Danchin, Anne-Marie Gilles, Génétique des Génomes Bactériens, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Unité Mathématique Informatique et Génome (MIG), Institut National de la Recherche Agronomique (INRA), Biophysique des Macromolécules et de leurs Interactions, Unité de recherche Génétique Microbienne (UGM), and We are grateful to E. Courtois, E. Brito, and S. Hoos for technical assistance during this work and to P. Courtin for help with the HPLC analysis. We thank V. Fromion and A. Goelzer for helpful advice on the cysteine metabolism model and stimulating collaboration.
Subjects: [SDV]Life Sciences [q-bio], Regulator, Bacillus subtilis, Biology, MESH: Multienzyme Complexes, Models, Biological, Biochemistry, chemistry.chemical_compound, Bacterial Proteins, Multienzyme Complexes, Cysteine, MESH: Bacterial Proteins, Molecular Biology, Cysteine metabolism, chemistry.chemical_classification, Cysteine Synthase, Effector, MESH: Models, Biological, Cell Biology, MESH: Bacillus subtilis, MESH: Cysteine, Surface Plasmon Resonance, biology.organism_classification, MESH: Surface Plasmon Resonance, MESH: Cysteine Synthase, Enzyme, chemistry, Cysteine synthase complex, Signal transduction
Abstract: International audience; Several enzymes have evolved as sensors in signal transduction pathways to control gene expression, thereby allowing bacteria to adapt efficiently to environmental changes. We recently identified the master regulator of cysteine metabolism in Bacillus subtilis, CymR, which belongs to the poorly characterized Rrf2 family of regulators. We now report that the signal transduction mechanism controlling CymR activity in response to cysteine availability involves the formation of a stable complex with CysK, a key enzyme for cysteine biosynthesis. We carried out a comprehensive quantitative characterization of this regulator-enzyme interaction by surface plasmon resonance and analytical ultracentrifugation. We also showed that O-acetylserine plays a dual role as a substrate of CysK and as an effector modulating the CymR-CysK complex formation. The ability of B. subtilis CysK to bind to CymR appears to be correlated to the loss of its capacity to form a cysteine synthase complex with CysE. We propose an original model, supported by the determination of the intracellular concentrations of the different partners, by which CysK positively regulates CymR in sensing the bacterial cysteine pool.
Published: 2008
Full Text: View/download PDF

3. Integrative Conjugative Elements and Related Elements Are Major Contributors to the Genome Diversity of Streptococcus agalactiae

Author: Gérard Guédon, Elisabeth Couvé, Sophie Payot, Mathieu Brochet, Philippe Glaser, Génétique des Génomes Bactériens, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Laboratoire de génétique et microbiologie (LGM), Institut National de la Recherche Agronomique (INRA)-Université Henri Poincaré - Nancy 1 (UHP), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: DNA, Bacterial, MESH: Interspersed Repetitive Sequences, MESH: Chromosomes, Bacterial, Genomics and Proteomics, SEQUENCE GENIQUE, Biology, MESH: Genome, Bacterial, medicine.disease_cause, Synteny, Microbiology, Genome, MESH: Gene Order, BACTERIE PATHOGENE, STREPTOCOCCUS AGALACTIAE, 03 medical and health sciences, Gene Order, MESH: Polymorphism, Genetic, medicine, Molecular Biology, 030304 developmental biology, Genetics, 0303 health sciences, Polymorphism, Genetic, 030306 microbiology, MESH: Synteny, Interspersed Repetitive Sequences, Chromosomes, Bacterial, Microarray Analysis, MESH: DNA, Bacterial, MESH: Streptococcus agalactiae, MESH: Microarray Analysis, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Streptococcus agalactiae, Genome, Bacterial
Abstract: Thirty-five putative integrative conjugative elements and related elements were identified at 15 locations in the eight sequenced genomes of Streptococcus agalactiae . Twelve are composite, likely resulting from site-specific accretions. Circular forms were detected for five elements. Macroarray analysis confirmed their high plasticity and wide distribution in S. agalactiae .
Published: 2008
Full Text: View/download PDF

4. Cinnamic Acid, an Autoinducer of Its Own Biosynthesis, Is Processed via Hca Enzymes in Photorhabdus luminescens

Author: Antoine Danchin, Christelle Ganneau, Jean-François Charles, Emma Brito-Fravallo, Sylvie Bay, Sabina Chalabaev, Evelyne Turlin, Francis Biville, Génétique des Génomes Bactériens, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Chimie Organique, Membranes bactériennes, and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH: Signal Transduction, MESH: Molecular Structure, Phenylalanine ammonia-lyase, Models, Biological, Applied Microbiology and Biotechnology, Cinnamic acid, Microbiology, MESH: Phenylalanine Ammonia-Lyase, 03 medical and health sciences, chemistry.chemical_compound, Bacterial Proteins, Biosynthesis, Dioxygenase, MESH: Reverse Transcriptase Polymerase Chain Reaction, Photorhabdus luminescens, Invertebrate Microbiology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Models, Genetic, MESH: Chromatography, High Pressure Liquid, MESH: Bacterial Proteins, Chromatography, High Pressure Liquid, Phenylalanine Ammonia-Lyase, MESH: Phenylpropionates, 030304 developmental biology, chemistry.chemical_classification, MESH: Gene Expression Regulation, Bacterial, 0303 health sciences, Models, Genetic, Molecular Structure, Phenylpropionates, Ecology, biology, Reverse Transcriptase Polymerase Chain Reaction, 030306 microbiology, MESH: Models, Biological, MESH: Photorhabdus, Gene Expression Regulation, Bacterial, biology.organism_classification, MESH: Cinnamates, Enzyme, Biochemistry, chemistry, Cinnamates, Autoinducer, Photorhabdus, Signal Transduction, Food Science, Biotechnology
Abstract: Photorhabdus luminescens , an entomopathogenic bacterium and nematode symbiont, has homologues of the Hca and Mhp enzymes. In Escherichia coli , these enzymes catalyze the degradation of the aromatic compounds 3-phenylpropionate (3PP) and cinnamic acid (CA) and allow the use of 3PP as sole carbon source. P. luminescens is not able to use 3PP and CA as sole carbon sources but can degrade them. Hca dioxygenase is involved in this degradation pathway. P. luminescens synthesizes CA from phenylalanine via a phenylalanine ammonia-lyase (PAL) and degrades it via the not-yet-characterized biosynthetic pathway of 3,5-dihydroxy-4-isopropylstilbene (ST) antibiotic. CA induces its own synthesis by enhancing the expression of the stlA gene that codes for PAL. P. luminescens bacteria release endogenous CA into the medium at the end of exponential growth and then consume it. Hca dioxygenase is involved in the consumption of endogenous CA but is not required for ST production. This suggests that CA is consumed via at least two separate pathways in P. luminescens : the biosynthesis of ST and a pathway involving the Hca and Mhp enzymes.
Published: 2008
Full Text: View/download PDF

5. Global Control of Cysteine Metabolism by CymR in Bacillus subtilis

Author: Isabelle Martin-Verstraete, Pierre Burguière, Olga Soutourina, Antoine Danchin, Sandrine Auger, Sergine Even, Génétique des Génomes Bactériens, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: DNA, Bacterial, [SDV]Life Sciences [q-bio], Mutant, DNA Footprinting, Repressor, Electrophoretic Mobility Shift Assay, Bacillus subtilis, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Bacterial Proteins, Consensus sequence, Point Mutation, Gene Regulation, Electrophoretic mobility shift assay, Cysteine, Promoter Regions, Genetic, Molecular Biology, Cysteine metabolism, Sequence Deletion, 030304 developmental biology, Regulation of gene expression, 0303 health sciences, Binding Sites, biology, Sulfates, 030306 microbiology, Gene Expression Profiling, Promoter, Gene Expression Regulation, Bacterial, biology.organism_classification, Culture Media, DNA-Binding Proteins, Repressor Proteins, Biochemistry, chemistry, Genes, Bacterial, Gene Deletion, Protein Binding
Abstract: YrzC has previously been identified as a repressor controlling ytmI expression via its regulation of YtlI activator synthesis in Bacillus subtilis. We identified YrzC as a master regulator of sulfur metabolism. Gene expression profiles of B. subtilis Δ yrzC mutant and wild-type strains grown in minimal medium with sulfate as the sole sulfur source were compared. In the mutant, increased expression was observed for 24 genes previously identified as repressed in the presence of sulfate. Since several genes involved in the pathways leading to cysteine formation were found, we propose to rename YrzC CymR, for “cysteine metabolism repressor.” A CymR-dependent binding to the promoter region of the ytlI , ssuB , tcyP , yrrT , yxeK , cysK , or ydbM gene was demonstrated using gel shift experiments. A potential CymR target site, TAAWNCN 2 ANTWNAN 3 ATMGGAATTW, was found in the promoter region of these genes. In a DNase footprint experiment, the protected region in the ytlI promoter region contained this consensus sequence. Partial deletion or introduction of point mutations in this sequence confirmed its involvement in ytlI , yrrT , and yxeK regulation. The addition of O -acetylserine in gel shift experiments prevented CymR-dependent binding to DNA for all of the targets characterized. Transcriptome analysis of a Δ cymR mutant and the wild-type strain also brought out significant changes in the expression level of a large set of genes related to stress response or to transition toward anaerobiosis.
Published: 2006
Full Text: View/download PDF

6. Universal biases in protein composition of model prokaryotes

Author: Antoine Danchin, Géraldine Pascal, Claudine Médigue, 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), Génétique des Génomes Bactériens, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris], and Centre National de la Recherche Scientifique (CNRS)
Subjects: Methanococcus, Proteome, medicine.disease_cause, Models, Biological, Biochemistry, Genome, Evolution, Molecular, Amino Acids, Aromatic, 03 medical and health sciences, chemistry.chemical_compound, Bacterial Proteins, Structural Biology, Aromatic amino acids, medicine, Inner membrane, Amino Acids, Molecular Biology, Escherichia coli, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, chemistry.chemical_classification, Base Composition, 0303 health sciences, Escherichia coli K12, biology, 030306 microbiology, Computational Biology, biology.organism_classification, Amino acid, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Prokaryotic Cells, chemistry, Hydrophobic and Hydrophilic Interactions, Genome, Bacterial, GC-content, Bacillus subtilis
Abstract: International audience; The levels of cellular organization in living organisms are the results of a variety of selection pressures. We have investigated here the final outcome of this integrated selective process in proteins of the best known microbial models Escherichia coli, Bacillus subtilis, and Methanococcus jannaschii, supposed to have undergone separate evolution for more than 1 billion years. Using multivariate analysis methods, including correspondence analysis, we studied the overall amino acid composition of all proteins making a proteome. Starting from and further developing previous results that had pointed out some general forces driving the amino acid composition of the proteomes of these model bacteria, we explored the correlations existing between the structure and functions of the proteins forming a proteome and their amino acid composition. The electric charge of amino acids measured against hydrophobicity creates a highly homogeneous cluster, made exclusively of proteins that are core components of the cytoplasmic membrane of the cell (integral inner membrane proteins). A second bias is imposed by the G+C content of the genome, indicating that protein functions are so robust with respect to amino acid changes that they can accommodate a large shift in the nucleotide content of the genome. A remarkable role of aromatic amino acids was uncovered. Expressed orphan proteins are enriched in these residues, suggesting that they might participate in a process of gain of function during evolution.
Published: 2005
Full Text: View/download PDF

7. Essential Bacillus subtilis genes

Author: Kobayashi, K., Ehrlich, S.D., Albertini, A., Amati, G., Andersen, K.K., Arnaud, M., Asai, K., Ashikaga, S., Aymerich, S., Bessieres, P., Boland, F., Brignell, S.C., Bron, S, Bunai, K., Chapuis, J, Christiansen, L.C., Danchin, A., Debarbouille, M., Dervyn, E., Deuerling, E., Devine, K., Devine, S.K., Dreesen, O., Errington, J., Fillinger, S., Foster, S.J., Fujita, Y., Galizzi, A., Gardan, R., Eschevins, C., Fukushima, T., Haga, K., Harwood, C.R, Hecker, M., Hosoya, D., Hullo, M.F., Kakeshita, H., Karamata, D., Kasahara, Y., Kawamura, F., Koga, K., Koski, P., Kuwana, R., Imamura, D., Ishimaru, M., Ishikawa, S., Ishio, I., Le Coq, D., Masson, A., Mauel, C., Meima, Roelf, Mellado, R.P., Moir, A., Moriya, S., Nagakawa, E., Nanamiya, H., Nakai, S., Nygaard, P., Ogura, M., Ohanan, T., O'Reilly, M., O'Rourke, M., Pragai, Z., Pooley, H.M., Rapoport, G., Rawlins, J.P., Rivas, L.A., Rivolta, C., Sadaie, A., Sadaie, Y., Sarvas, M, Sato, T., Saxild, H.H., Scanlan, E., Schumann, W, Seegers, J.F. M. L., Sekiguchi, J., Sekowska, A., Seror, S.J., Simon, M., Stragier, P., Studer, R., Takamatsu, H., Tanaka, T., Takeuchi, M., Thomaides, H.B., Vagner, V., van Dijl, J.M., Watabe, K., Wipat, A, Yamamoto, H., Yamamoto, M., Yamamoto, Y., Yamane, K., Yata, K., Yoshida, K., Yoshikawa, H., Zuber, U., Ogasawara, N., Ishio, [No Value], Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology, Translational Immunology Groningen (TRIGR), Graduate School of Information Science, Nara Institute of Science and Technology, Unité de recherche Génétique Microbienne (UGM), Institut National de la Recherche Agronomique (INRA), Università degli Studi di Pavia = University of Pavia (UNIPV), Trinity College Dublin, Biochimie Microbienne, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Saitama University, Rikkyo University [Tokyo], Génétique Moléculaire et Cellulaire (UGMC), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), Unité Mathématique Informatique et Génome (MIG), University of Sheffield, Newcastle University [Newcastle], University of Groningen, Université de Tsukuba = University of Tsukuba, Institute of Molecular Biology, Génétique des Génomes Bactériens, University of Bayreuth, University of Oxford, Fukuyama University, Partenaires INRAE, Shinshu University, Department of Bioscience, Tokyo University of Agriculture and Technology (TUAT), Institut für Mikrobiologie - Institute for Microbiology, Universität Greifswald - University of Greifswald, Institut de Génétique et de Biologie Microbiennes (IGBM), Université de Lausanne = University of Lausanne (UNIL), National Public Health Institute, Setsunan University, Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Tokai University School of Medicine, Institut de Biologie Physico-Chimique, Radioisotope Center, The University of Tokyo (UTokyo), University of Pavia, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], University of Oxford [Oxford], and Université de Lausanne (UNIL)
Subjects: Cell division, PROTEINS, [SDV]Life Sciences [q-bio], Coenzymes, Bacillus subtilis, medicine.disease_cause, Genome, SEQUENCE, 03 medical and health sciences, medicine, Gene, Phylogeny, Organism, 030304 developmental biology, Genetics, 0303 health sciences, Mutation, Multidisciplinary, biology, IDENTIFICATION, Nucleotides, 030306 microbiology, Cell Membrane, Biological Sciences, biology.organism_classification, GENOME, Genes, Bacterial, SURVIVAL, GROWTH, RNA, Minimal genome, Energy Metabolism, SET, Cell Division, Genome, Bacterial, Archaea
Abstract: To estimate the minimal gene set required to sustain bacterial life in nutritious conditions, we carried out a systematic inactivation of Bacillus subtilis genes. Among approximate to4,100 genes of the organism, only 192 were shown to be indispensable by this or previous work. Another 79 genes were predicted to be essential. The vast majority of essential genes were categorized in relatively few domains of cell metabolism, with about half involved in information processing, one-fifth involved in the synthesis of cell envelope and the determination of cell shape and division, and one-tenth related to cell energetics. Only 4% of essential genes encode unknown functions. Most essential genes are present throughout a wide range of Bacteria, and almost 70% can also be found in Archaea and Eucarya. However, essential genes related to cell envelope, shape, division, and respiration tend to be lost from bacteria with small genomes. Unexpectedly, most genes involved in the Embden-Meyerhof-Parnas pathway are essential. Identification of unknown and unexpected essential genes opens research avenues to better understanding of processes that sustain bacterial life, To estimate the minimal gene set required to sustain bacterial life in nutritious conditions, we carried out a systematic inactivation of Bacillus subtilis genes. Among ≈4,100 genes of the organism, only 192 were shown to be indispensable by this or previous work. Another 79 genes were predicted to be essential. The vast majority of essential genes were categorized in relatively few domains of cell metabolism, with about half involved in information processing, one-fifth involved in the synthesis of cell envelope and the determination of cell shape and division, and one-tenth related to cell energetics. Only 4% of essential genes encode unknown functions. Most essential genes are present throughout a wide range of Bacteria, and almost 70% can also be found in Archaea and Eucarya. However, essential genes related to cell envelope, shape, division, and respiration tend to be lost from bacteria with small genomes. Unexpectedly, most genes involved in the Embden–Meyerhof–Parnas pathway are essential. Identification of unknown and unexpected essential genes opens research avenues to better understanding of processes that sustain bacterial life.
Published: 2003
Full Text: View/download PDF

8. Characterization of NrnA homologs from Mycobacterium tuberculosis and Mycoplasma pneumoniae

Author: Undine Mechold, Guillaume Postic, Antoine Danchin, Génétique des Génomes Bactériens, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), AMAbiotics SAS, Biochimie des Interactions Macromoléculaires / Biochemistry of Macromolecular Interactions, Part of this work was supported by MICROME, a Collaborative Project funded by the European Commission within its FP7 Program, under thethematic area ‘‘BIO-INFORMATICS-Microbial genomics and bio-informatics,’’ contract no. 222886-2., European Project: 222886,EC:FP7:KBBE,FP7-KBBE-2007-2A,MICROME(2009), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH: Mutation, MESH: Mycobacterium tuberculosis, [SDV]Life Sciences [q-bio], Mutant, Bacillus subtilis, medicine.disease_cause, Article, MESH: Recombinant Proteins, Streptococcus mutans, 03 medical and health sciences, medicine, Escherichia coli, Nucleotide, Molecular Biology, 030304 developmental biology, chemistry.chemical_classification, MESH: Genetic Complementation Test, 0303 health sciences, Mutation, biology, MESH: Escherichia coli, 030306 microbiology, Oligonucleotide, Genetic Complementation Test, RNA, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Mycobacterium tuberculosis, biology.organism_classification, MESH: Streptococcus mutans, Phosphoric Monoester Hydrolases, Recombinant Proteins, 3. Good health, Mycoplasma pneumoniae, MicroRNAs, Enzyme, chemistry, Biochemistry, MESH: Exoribonucleases, Exoribonucleases, MESH: Phosphoric Monoester Hydrolases, MESH: Mycoplasma pneumoniae, MESH: MicroRNAs
Abstract: Processive RNases are unable to degrade efficiently very short oligonucleotides, and they are complemented by specific enzymes, nanoRNases, that assist in this process. We previously identified NrnA (YtqI) from Bacillus subtilis as a bifunctional protein with the ability to degrade nanoRNA (RNA oligos ≤5 nucleotides) and to dephosphorylate 3′-phosphoadenosine 5′-phosphate (pAp) to AMP. While the former activity is analogous to that of oligoribonuclease (Orn) from Escherichia coli, the latter corresponds to CysQ. NrnA homologs are widely present in bacterial and archaeal genomes. They are found preferably in genomes that lack Orn or CysQ homologs. Here, we characterize NrnA homologs from important human pathogens, Mpn140 from Mycoplasma pneumoniae, and Rv2837c from Mycobacterium tuberculosis. Like NrnA, these enzymes degrade nanoRNA and dephosphorylate pAp in vitro. However, they show dissimilar preferences for specific nanoRNA substrate lengths. Whereas NrnA prefers RNA 3-mers with a 10-fold higher specific activity compared to 5-mers, Rv2837c shows a preference for nanoRNA of a different length, namely, 2-mers. Mpn140 degrades Cy5-labeled nanoRNA substrates in vitro with activities varying within one order of magnitude as follows: 5-mer>4-mer>3-mer>2-mer. In agreement with these in vitro activities, both Rv2837c and Mpn140 can complement the lack of their functional counterparts in E. coli: CysQ and Orn. The NrnA homolog from Streptococcus mutans, SMU.1297, was previously shown to hydrolyze pAp and to complement an E. coli cysQ mutant. Here, we show that SMU.1297 can complement an E. coli orn− mutant, suggesting that having both pAp-phosphatase and nanoRNase activity is a common feature of NrnA homologs.
Published: 2012
Full Text: View/download PDF

9. Complex phenotypes of a mutant inactivated for CymR, the global regulator of cysteine metabolism in Bacillus subtilis

Author: Hullo, Marie-Françoise, Martin-Verstraete, Isabelle, Soutourina, Olga, Génétique des Génomes Bactériens, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Bactéries anaérobies et Toxines, Institut Pasteur [Paris], Research was supported by grants from the Centre National de la Recherche Scientifique (CNRS URA 2171), the Institut Pasteur (PTR N°256) and the Agence Nationale de la Recherche (EcoMet program, ANR-06-PNRA-014), We are grateful to A. Danchin for helpful discussions. We thank P. Courtin for metabolite analysis. I.M.-V. and O.S. are full and assistant professors at the Université Paris 7, respectively, ANR-06-PNRA-0014,ECOMET,ECOMET : Ecosysteme Fromager: Etude fonctionnelle de métabolisme du soufre(2006), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)
Subjects: [SDV]Life Sciences [q-bio], disulfide stress, Gene Expression Regulation, Bacterial, Phenotype, Bacterial Proteins, Genes, Regulator, Mutation, oxidative stress, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Gene Silencing, tellurite, cysteine metabolism regulator, cysteine, Bacillus subtilis
Abstract: International audience; We characterized various phenotypes of a mutant inactivated for CymR, the master regulator of cysteine metabolism in Bacillus subtilis. The deletion of cymR resulted in impaired growth in the presence of cystine and increased sensitivity to hydrogen peroxide-, disulfide-, paraquat-and tellurite-induced stresses. Estimation of metabolite pools suggested that these phenotypes could be the result of profound metabolic changes in the DcymR mutant including an increase of the intracellular cysteine pool and hydrogen sulfide formation, as well as a depletion of branched-chain amino acids.
Published: 2010
Full Text: View/download PDF

10. Global regulation of gene expression in response to cysteine availability in Clostridium perfringens

Author: Tohru Shimizu, Kaori Ohtani, Bruno Dupuy, Gaelle André, Marc Monot, Elise Haudecoeur, Isabelle Martin-Verstraete, Génétique des Génomes Bactériens, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Bactéries anaérobies et Toxines, Institut Pasteur [Paris] (IP), Pathogénèse des Bactéries Anaérobies / Pathogenesis of Bacterial Anaerobes (PBA (U-Pasteur_6)), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7), Université Paris Diderot - Paris 7 (UPD7), Department of Bacteriology, Kanazawa University (KU), CNRS URA 2171 and the Institut Pasteur (PTR N°256). G. A was the recipient of a grant from the Ministère de l'enseignement supérieur et de la recherche and from the Pasteur-Weizmann foundation., Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris], Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7), and Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]
Subjects: Microbiology (medical), Clostridium perfringens, Operon, Molecular Sequence Data, lcsh:QR1-502, Sulfur metabolism, MESH: Sequence Alignment, MESH: Amino Acid Sequence, medicine.disease_cause, Microbiology, lcsh:Microbiology, Clostridia, 03 medical and health sciences, chemistry.chemical_compound, Bacterial Proteins, medicine, Amino Acid Sequence, Cysteine, MESH: Bacterial Proteins, 030304 developmental biology, Regulation of gene expression, MESH: Clostridium perfringens, 0303 health sciences, MESH: Gene Expression Regulation, Bacterial, Methionine, MESH: Molecular Sequence Data, biology, 030306 microbiology, Gene Expression Regulation, Bacterial, MESH: Cysteine, biology.organism_classification, MESH: Sulfur, Regulon, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, Biochemistry, Sequence Alignment, Sulfur, Research Article
Abstract: Background Cysteine has a crucial role in cellular physiology and its synthesis is tightly controlled due to its reactivity. However, little is known about the sulfur metabolism and its regulation in clostridia compared with other firmicutes. In Clostridium perfringens, the two-component system, VirR/VirS, controls the expression of the ubiG operon involved in methionine to cysteine conversion in addition to the expression of several toxin genes. The existence of links between the C. perfringens virulence regulon and sulfur metabolism prompted us to analyze this metabolism in more detail. Results We first performed a tentative reconstruction of sulfur metabolism in C. perfringens and correlated these data with the growth of strain 13 in the presence of various sulfur sources. Surprisingly, C. perfringens can convert cysteine to methionine by an atypical still uncharacterized pathway. We further compared the expression profiles of strain 13 after growth in the presence of cystine or homocysteine that corresponds to conditions of cysteine depletion. Among the 177 genes differentially expressed, we found genes involved in sulfur metabolism and controlled by premature termination of transcription via a cysteine specific T-box system (cysK-cysE, cysP1 and cysP2) or an S-box riboswitch (metK and metT). We also showed that the ubiG operon was submitted to a triple regulation by cysteine availability via a T-box system, by the VirR/VirS system via the VR-RNA and by the VirX regulatory RNA. In addition, we found that expression of pfoA (theta-toxin), nagL (one of the five genes encoding hyaluronidases) and genes involved in the maintenance of cell redox status was differentially expressed in response to cysteine availability. Finally, we showed that the expression of genes involved in [Fe-S] clusters biogenesis and of the ldh gene encoding the lactate dehydrogenase was induced during cysteine limitation. Conclusion Several key functions for the cellular physiology of this anaerobic bacterium were controlled in response to cysteine availability. While most of the genes involved in sulfur metabolism are regulated by premature termination of transcription, other still uncharacterized mechanisms of regulation participated in the induction of gene expression during cysteine starvation.
Published: 2010
Full Text: View/download PDF

11. The Trw Type IV Secretion System of Bartonella Mediates Host-Specific Adhesion to Erythrocytes

Author: Antoine Danchin, Christoph Dehio, Huanming Yang, Francis Biville, Henri L Saenz, Geneviève Marignac, Philipp Engel, Muriel Vayssier-Taussat, Lionel Arnaud, Sandra Cescau, Hong Kuan Deng, Henri Jean Boulouis, Maria Mavris, Evelyne Lenaour, Jing Wang, Maxime Québatte, Danielle Le Rhun, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Focal area infection biology, Biozentrum, Université de Bâle, Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire d'Alfort (ENVA)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Génétique des Génomes Bactériens, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Beijing Genomics Institute, This work was supported by grant Hem-Bart06-08 from Agence Nationale de la Recherche (to M.V.-T.), grant 31003A-109925 from the Swiss National Science Foundation (to C.D.), grant 55005501 from the Howard Hughes Medical Institute (to C.D.), and grant 51RT-0_126008 (InfectX) in the frame of the SystemsX.ch Swiss Initiative for Systems Biology (to C.D.), University of Zurich, Vayssier-Taussat, Muriel, École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Beijing Genomics Institute [Shenzhen] (BGI), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: green fluorescent protein, Bartonella tribocorum, Erythrocytes, [SDV]Life Sciences [q-bio], 2405 Parasitology, Bacteremia, Computational Biology/Comparative Sequence Analysis, Virulence factor, Infectious Diseases/Bacterial Infections, Mice, sécrétion, SX00 SystemsX.ch, sp. nov, Biology (General), SX06 InfectX, bactérie, 0303 health sciences, Mice, Inbred BALB C, Microbiology/Microbial Evolution and Genomics, biology, listeria-monocytogenes, experimental-infection, phylogenetic analysis, pathogen bartonella, maximum-likelihood, henselae, quintana, 2404 Microbiology, caractère génétique, invasion, Genetics and Genomics/Gene Function, Evolutionary Biology/Microbial Evolution and Genomics, protéine, Bartonella quintana, Female, Bartonella, Microbiology/Cellular Microbiology and Pathogenesis, bactérie pathogène, Bartonella Infection, Research Article, Bartonella birtlesii, Virulence Factors, QH301-705.5, SX20 Research, Technology and Development Projects, Immunology, Microbiology, 03 medical and health sciences, Bacterial Proteins, 1311 Genetics, Virology, Bartonella Infections, Genetics, Cell Adhesion, 1312 Molecular Biology, Animals, Humans, Molecular Biology, 030304 developmental biology, 2403 Immunology, Bartonella henselae, 030306 microbiology, RC581-607, biology.organism_classification, bacterial infections and mycoses, infection, Rats, Cell Biology/Cell Adhesion, Cats, 2406 Virology, 570 Life sciences, Parasitology, Bartonella bacilliformis, Immunologic diseases. Allergy
Abstract: Bacterial pathogens typically infect only a limited range of hosts; however, the genetic mechanisms governing host-specificity are poorly understood. The α-proteobacterial genus Bartonella comprises 21 species that cause host-specific intraerythrocytic bacteremia as hallmark of infection in their respective mammalian reservoirs, including the human-specific pathogens Bartonella quintana and Bartonella bacilliformis that cause trench fever and Oroya fever, respectively. Here, we have identified bacterial factors that mediate host-specific erythrocyte colonization in the mammalian reservoirs. Using mouse-specific Bartonella birtlesii, human-specific Bartonella quintana, cat-specific Bartonella henselae and rat-specific Bartonella tribocorum, we established in vitro adhesion and invasion assays with isolated erythrocytes that fully reproduce the host-specificity of erythrocyte infection as observed in vivo. By signature-tagged mutagenesis of B. birtlesii and mutant selection in a mouse infection model we identified mutants impaired in establishing intraerythrocytic bacteremia. Among 45 abacteremic mutants, five failed to adhere to and invade mouse erythrocytes in vitro. The corresponding genes encode components of the type IV secretion system (T4SS) Trw, demonstrating that this virulence factor laterally acquired by the Bartonella lineage is directly involved in adherence to erythrocytes. Strikingly, ectopic expression of Trw of rat-specific B. tribocorum in cat-specific B. henselae or human-specific B. quintana expanded their host range for erythrocyte infection to rat, demonstrating that Trw mediates host-specific erythrocyte infection. A molecular evolutionary analysis of the trw locus further indicated that the variable, surface-located TrwL and TrwJ might represent the T4SS components that determine host-specificity of erythrocyte parasitism. In conclusion, we show that the laterally acquired Trw T4SS diversified in the Bartonella lineage to facilitate host-restricted adhesion to erythrocytes in a wide range of mammals., Author Summary Pathogens are—as the result of adaptive evolution in their principal host(s)—typically limited in the range of hosts that they can infect successfully. However, infrequently such host-restricted pathogens may undergo a spontaneous host switch, which can lead to the evolution of pathogens with altered host specificity. Most human pathogens evolved this way, and animal-specific pathogens have thus to be considered as an important reservoir for the emergence of novel human pathogens. Despite host-specificity representing a common feature of pathogens, the underlying molecular mechanisms are largely unknown. In this study we have used bacterial pathogens of the genus Bartonella to identify bacterial factors involved in the determination of host specificity. The bartonellae represent an excellent model to study host-specificity as each species is adapted to cause an intracellular infection of erythrocytes exclusively in its respective reservoir host(s). Using a genetic approach in combination with erythrocyte infection models in vitro and in vivo we demonstrate that a surface-located bacterial nanomachine—a so-called type IV secretion system—determines host specificity of erythrocyte infection. Our work sheds light on the molecular basis of host specificity and establishes an experimental model for studying the evolutionary processes facilitating spontaneous host shifts.
Published: 2010
Full Text: View/download PDF

12. Identification of brevibacteriaceae by multilocus sequence typing and comparative genomic hybridization analyses

Author: Isabelle Martin-Verstraete, Valentin Loux, Sophie Landaud, Jérôme Mounier, Jean-Yves Coppée, Caroline Proux, Hugo Duvergey, Jean-François Gibrat, Tatiana Vallaeys, Marie-Pierre Forquin, Pascal Bonnarme, Génie et Microbiologie des Procédés Alimentaires (GMPA), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génétique des Génomes Bactériens, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Unité Mathématique Informatique et Génome (MIG), Institut National de la Recherche Agronomique (INRA), Puces à ADN (Plate-Forme 2) (PF2), Institut Pasteur [Paris], Ecosystèmes lagunaires : organisation biologique et fonctionnement (ECOLAG), Université Montpellier 2 - Sciences et Techniques (UM2)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP), and Vallaeys, Tatiana
Subjects: phylogénétique, SÉQUENCE D'ACIDE AMINÉ, MESH: Sequence Analysis, DNA, MESH: Base Sequence, brevibacteriaceae, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Applied Microbiology and Biotechnology, MESH: Genotype, STRAIN TYPING, COMPARATIVE GENOMIC, HYBRIDIZATION, GENOMIQUE, MESH: Brevibacterium, Methods, MESH: DNA Fingerprinting, Brevibacterium, Cluster Analysis, MESH: Genetic Variation, MESH: Phylogeny, Phylogeny, Oligonucleotide Array Sequence Analysis, bactérie, Genetics, 0303 health sciences, Comparative Genomic Hybridization, Ecology, Strain (biology), Bacterial Typing Techniques, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, DNA profiling, Biotechnology, Brevibacteriaceae, Genotype, Sequence analysis, Molecular Sequence Data, MESH: Sequence Alignment, Sequence alignment, Biology, MESH: Bacterial Typing Techniques, 03 medical and health sciences, Genetic variation, 030304 developmental biology, MESH: Molecular Sequence Data, Base Sequence, 030306 microbiology, génome, gène, Genetic Variation, Sequence Analysis, DNA, DNA Fingerprinting, MESH: Cluster Analysis, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Comparative Genomic Hybridization, MESH: Oligonucleotide Array Sequence Analysis, Multilocus sequence typing, Sequence Alignment, Food Science, Comparative genomic hybridization
Abstract: Multilocus sequence typing with nine selected genes is shown to be a promising new tool for accurate identifications of Brevibacteriaceae at the species level. A developed microarray also allows intraspecific diversity investigations of Brevibacterium aurantiacum showing that 13% to 15% of the genes of strain ATCC 9174 were absent or divergent in strain BL2 or ATCC 9175.
Published: 2009
Full Text: View/download PDF

13. CymR, the master regulator of cysteine metabolism in Staphylococcus aureus , controls host sulphur source utilization and plays a role in biofilm formation

Author: Olivier Poupel, Jean-Yves Coppée, Tarek Msadek, Isabelle Martin-Verstraete, Olga Soutourina, Antoine Danchin, Génétique des Génomes Bactériens, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Biologie des Bactéries Pathogènes à Gram-positif, Puces à ADN (Plate-Forme 2) (PF2), Institut Pasteur [Paris], Research was supported by grants from the Centre National de la Recherche Scientifique (CNRS URA 2171 and 2172), from the Institut Pasteur (Grand Programme Horizontal N°9 and PTR N°256) and from the European Commission (Grants BACELL Health, LSHG‐CT‐2004‐503468, StaphDynamics, LHSM‐CT‐2006‐019064 and BaSysBio, LSHG‐CT‐2006‐037469)., We are grateful to S. Foster for providing us with S. aureus strains and enriching discussions. We thank E. Krin for helpful discussions on transcriptome analysis, S. Dubrac for invaluable assistance with the macroarray design and quality control, helpful discussion and critical reading of the manuscript, and J. Fert for technical assistance at the beginning of this work. We are thankful to C. Beloin for help and enriching discussions on biofilm formation assays. We thank O. Sismeiro and C. Lacroix for macroarray preparation and S. Rousseau and P. Vantadour for loading transcriptome data on GenoScript database. I.M.‐V. and O.S. are full and assistant professors at the Université Paris 7 respectively., European Project: 26873,BACELL HEALTH, European Project: 35105,STAPHDYNAMICS, European Project: 38901,BASYSBIO, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)
Subjects: Staphylococcus aureus, [SDV]Life Sciences [q-bio], Mutant, Sulfur metabolism, MESH: Biofilms, Biology, Microbiology, Transcriptome, 03 medical and health sciences, chemistry.chemical_compound, MESH: Gene Expression Profiling, Bacterial Proteins, Transcription (biology), MESH: Staphylococcus aureus, Molecular Biology, Gene, MESH: Bacterial Proteins, Cysteine metabolism, 030304 developmental biology, 0303 health sciences, MESH: Gene Expression Regulation, Bacterial, 030306 microbiology, Gene Expression Profiling, Biofilm, MESH: Cystine, Gene Expression Regulation, Bacterial, Repressor Proteins, MESH: Sulfur, RNA, Bacterial, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Biochemistry, chemistry, Genes, Bacterial, MESH: Repressor Proteins, Biofilms, Cystine, MESH: Genes, Bacterial, MESH: RNA, Bacterial, Sulfur, Cysteine
Abstract: International audience; We have characterized the master regulator of cysteine metabolism, CymR, in Staphylococcus aureus. CymR repressed the transcription of genes involved in pathways leading to cysteine formation. Eight direct DNA targets were identified using gel-shift or footprinting experiments. Comparative transcriptome analysis and in vitro studies indicated that CysM, the OAS-thiol-lyase, was also implicated in this regulatory system. OAS, the direct precursor of cysteine, prevents CymR-dependent binding to DNA. This study has allowed us to predict sulphur metabolism functions for previously uncharacterized S. aureus genes. We show that S. aureus is able to grow on homocysteine as the sole sulphur source suggesting efficient MccA and MccB-dependent conversion of this compound into cysteine. We propose that SA1850 is a new thiosulphate transporter and that TcyP and TcyABC are l-cystine transporters. CymR directly controls the use of sulphur sources of human origin such as taurine and homocysteine. The cymR mutant also displayed a reduced capacity to form biofilms, indicating that CymR is involved in controlling this process in S. aureus via an ica-independent mechanism. These data indicate that fine-tuning of sulphur metabolism plays an important part in the physiology of this major pathogen and its adaptation to environmental conditions and survival in the host.
Published: 2009
Full Text: View/download PDF

14. Population structure of human isolates of Streptococcus agalactiae from Dakar and Bangui

Author: Raymond Bercion, Mathieu Brochet, Elisabeth Couvé, Philippe Glaser, Jean-Marie Sire, Génétique des Génomes Bactériens, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur de Bangui, Réseau International des Instituts Pasteur (RIIP), Institut Pasteur de Dakar, and Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]
Subjects: Serotype, MESH: Sequence Analysis, DNA, Epidemiology, Population structure, Sequence Homology, medicine.disease_cause, MESH: Genotype, MESH: Streptococcal Infections, Genotype, MESH: DNA Fingerprinting, Cluster Analysis, MESH: Sequence Homology, 0303 health sciences, Molecular Epidemiology, Senegal, 3. Good health, Bacterial Typing Techniques, DNA profiling, Female, Microbiology (medical), DNA, Bacterial, Biology, MESH: Bacterial Typing Techniques, Microbiology, Streptococcus agalactiae, 03 medical and health sciences, MESH: Senegal, Streptococcal Infections, medicine, Humans, MESH: Molecular Epidemiology, Serotyping, 030304 developmental biology, MESH: Humans, Molecular epidemiology, 030306 microbiology, MESH: Serotyping, Sequence Analysis, DNA, Sequence types, Streptococcaceae, biology.organism_classification, Virology, DNA Fingerprinting, MESH: Cluster Analysis, MESH: Streptococcus agalactiae, MESH: DNA, Bacterial, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Female
Abstract: Multilocus sequence types of 163 human Streptococcus agalactiae strains isolated in Bangui and Dakar were analyzed. We identified local specificities in the distribution of sequence types and capsular serotypes. However, the overall population structure is similar to that in the United States and Europe, suggesting that few specific clones colonize humans.
Published: 2009
Full Text: View/download PDF

15. Enhanced structural and functional genome elucidation of the arsenite-oxidizing strain Herminiimonas arsenicoxydans by proteomics data

Author: Christine Carapito, Michaël Heymann, Sandrine Koechler, Philippe N. Bertin, Evelyne Turlin, Claudine Médigue, Alain Van Dorsselaer, Valérie Kugler, Florence Arsène-Ploetze, Stéphanie Weiss, Stéphane Cruveiller, Magalie Stauffert, Jessica Cleiss, Jean-Yves Coppée, Génétique moléculaire, génomique, microbiologie (GMGM), Université Louis Pasteur - Strasbourg I-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)-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), 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), Génétique des Génomes Bactériens, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Puces à ADN (Plate-Forme 2) (PF2), Institut Pasteur [Paris] (IP), Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut Gilbert-Laustriat : Biomolécules, Biotechnologie, Innovation Thérapeutique, 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), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Compartimentation et dynamique cellulaires (CDC), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Curie [Paris]-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)-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), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Institut Pasteur [Paris], 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 Paris-Saclay, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC), Laboratoire de Spectrométrie de masse Bio-organique, UMR CNRS-ULP, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), and Centre National de la Recherche Scientifique (CNRS)-Institut Curie-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: Proteomics, Proteome, Arsenites, Biology, Tandem mass spectrometry, Models, Biological, Biochemistry, Transcriptome, 03 medical and health sciences, chemistry.chemical_compound, Oxalobacteraceae, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Herminiimonas arsenicoxydans, 030304 developmental biology, Arsenite, Genetics, Gel electrophoresis, 0303 health sciences, 030306 microbiology, General Medicine, Genome project, biology.organism_classification, chemistry, Oxidation-Reduction, Genome, Bacterial
Abstract: International audience; The arsenite-oxidizing strain Herminiimonas arsenicoxydans proteome was investigated with gel electrophoresis and tandem mass spectrometry analyses. The comparison of experimental and theoretical M(r) and pI, as well as that of peptide sequences identified by MS and predicted protein sequences, allowed the correction of five protein annotations. More importantly, the functional analysis of SDS- and 2D-PAGE proteome maps obtained in the presence of arsenic, combined with partial transcriptomic results indicate that H. arsenicoxydans expressed genes and proteins required not only for arsenic detoxification or stress response but also involved in motility, exopolysaccharide synthesis, phosphate import or energetic metabolism. This study provides therefore new insights into the adaptation processes of H. arsenicoxydans in response to arsenic.
Published: 2009
Full Text: View/download PDF

16. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths

Author: Edouard Bingen, Olivier Clermont, Chantal Le Bouguénec, Zoé Rouy, Sophie Oztas, James R. Johnson, Anne-Marie Gilles, Erick Denamur, Marie Touchon, Olivier Tenaillon, David Vallenet, Valérie Barbe, Marie-Agnès Petit, Meriem El Karoui, Stéphane Bonacorsi, Dominique Schneider, Louis Garry, Eduardo P. C. Rocha, Alexandra Calteau, Antoine Danchin, Xavier Nassif, Ivan Matic, Vanessa Martinez-Jéhanne, Jérôme Tourret, Sophie Mangenot, Christophe Pichon, Jean Marc Ghigo, Claude Saint Ruf, Philippe Bidet, Claire Hoede, Eric Frapy, Christiane Bouchier, Simon Baeriswyl, Benoit Vacherie, Stéphane Cruveiller, Mathilde Lescat, Odile Bouvet, Carole Dossat, Claudine Médigue, Médéric Diard, Hélène Chiapello, Atelier de BioInformatique (ABI), Université Pierre et Marie Curie - Paris 6 (UPMC), Génomique évolutive des microbes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Ecologie et Evolution des Microorganismes (EEM), Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), 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), Génétique moléculaire, évolutive et médicale, IFR65-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris 7, Hôpital Robert Debré-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Génomique (Plate-Forme) - Genomics Platform, Institut Pasteur [Paris] (IP), 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), Mathématique, Informatique, et Génomique, Institut National de la Recherche Agronomique (INRA), Génétique des Génomes Bactériens, 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), Génétique des Biofilms, Veterans Affairs Medical Center, Department of Medecine, University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, Pathogénie Bactérienne des Muqueuses, Unité des Bactéries Lactiques et Pathogènes Opportunistes, Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble] (LAPM), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Gagnon, Jean, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot - Paris 7 (UPD7)-Université Paris 13 (UP13)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Génomique (Plate-Forme), Institut Pasteur [Paris], University of Minnesota [Twin Cities], IFR65-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Atelier de BioInformatique ( ABI ), Université Pierre et Marie Curie - Paris 6 ( UPMC ), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Ecologie et Evolution des Microorganismes ( EEM ), Université Paris 13 ( UP13 ) -Université Paris Diderot - Paris 7 ( UPD7 ) -Université Sorbonne Paris Cité ( USPC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), IFR65-Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Hôpital Robert Debré-Université Paris Diderot - Paris 7 ( UPD7 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Institut National de la Recherche Agronomique ( INRA ), 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 ), University of Minnesota [Minneapolis], Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble] ( LAPM ), and Université Joseph Fourier - Grenoble 1 ( UJF ) -Centre National de la Recherche Scientifique ( CNRS )
Subjects: MESH : Escherichia coli, Cancer Research, MESH : Polymorphism, Genetic, MESH : Recombination, Genetic, MESH : Models, Genetic, MESH : Models, Biological, MESH: Genome, Bacterial, Genome, MESH: Genetics, Gene flow, MESH : Genetics, MESH: Models, Genetic, MESH: Phylogeny, bioinformatique, Phylogeny, Genetics (clinical), MESH: Evolution, Molecular, Recombination, Genetic, bactérie, 2. Zero hunger, Genetics, Likelihood Functions, 0303 health sciences, Phylogenetic tree, MESH: Escherichia coli, MESH: Genomics, Genomics, Genome project, Evolutionary Biology/Microbial Evolution and Genomics, MESH: DNA Transposable Elements, MESH : DNA Transposable Elements, MESH: Recombination, Genetic, escherichia coli, MESH : Likelihood Functions, Research Article, lcsh:QH426-470, MESH : Genome, Bacterial, Biology, Models, Biological, Evolution, Molecular, 03 medical and health sciences, Phylogenetics, MESH: Polymorphism, Genetic, Escherichia coli, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Genome, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH : Evolution, Molecular, Gene conversion, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Comparative genomics, Polymorphism, Genetic, Evolutionary Biology/Evolutionary and Comparative Genetics, Models, Genetic, 030306 microbiology, génome, MESH : Genomics, MESH: Models, Biological, MESH : Phylogeny, Microbiology/Medical Microbiology, lcsh:Genetics, DNA Transposable Elements, MESH: Likelihood Functions, MESH : Genome, Genome, Bacterial
Abstract: The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We uniformly (re-) annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Within the ∼18,000 families of orthologous genes, we found ∼2,000 common to all strains. Although recombination rates are much higher than mutation rates, we show, both theoretically and using phylogenetic inference, that this does not obscure the phylogenetic signal, which places the B2 phylogenetic group and one group D strain at the basal position. Based on this phylogeny, we inferred past evolutionary events of gain and loss of genes, identifying functional classes under opposite selection pressures. We found an important adaptive role for metabolism diversification within group B2 and Shigella strains, but identified few or no extraintestinal virulence-specific genes, which could render difficult the development of a vaccine against extraintestinal infections. Genome flux in E. coli is confined to a small number of conserved positions in the chromosome, which most often are not associated with integrases or tRNA genes. Core genes flanking some of these regions show higher rates of recombination, suggesting that a gene, once acquired by a strain, spreads within the species by homologous recombination at the flanking genes. Finally, the genome's long-scale structure of recombination indicates lower recombination rates, but not higher mutation rates, at the terminus of replication. The ensuing effect of background selection and biased gene conversion may thus explain why this region is A+T-rich and shows high sequence divergence but low sequence polymorphism. Overall, despite a very high gene flow, genes co-exist in an organised genome., Author Summary Although abundant knowledge has been accumulated regarding the E. coli laboratory strain K-12, little is known about the evolutionary trajectories that have driven the high diversity observed among natural isolates of the species, which encompass both commensal and highly virulent intestinal and extraintestinal pathogenic strains. We have annotated or re-annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Although recombination rates are much higher than mutation rates, we were able to reconstruct a robust phylogeny based on the ∼2,000 genes common to all strains. Based on this phylogeny, we established the evolutionary scenario of gains and losses of thousands of specific genes, identifying functional classes under opposite selection pressures. This genome flux is confined to very few positions in the chromosome, which are the same for every genome. Notably, we identified few or no extraintestinal virulence-specific genes. We also defined a long-scale structure of recombination in the genome with lower recombination rates at the terminus of replication. These findings demonstrate that, despite a very high gene flow, genes can co-exist in an organised genome.
Published: 2009
Full Text: View/download PDF

17. Identification of mechanisms involved in iron and haem uptake in Bartonella birtlesii : in silico and in vivo approaches

Author: Muriel Vayssier-Taussat, Sandra Cescau, Jing Wang, E. Nijssen, Francis Biville, Génétique et biochimie des microorganismes (GBM), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris], Evolution et Génomique Bactériennes, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Unité mixte de recherche biologie moléculaire et immunologie parasitaires et fongiques, Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire d'Alfort (ENVA)-Agence Française de Sécurité Sanitaire des Aliments (AFSSA)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Beijing Genomics Institute [Shenzhen] (BGI), Membranes bactériennes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Génétique des Génomes Bactériens, Agence Française de Sécurité Sanitaire des Aliments (AFSSA)-École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), and Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire - Alfort (ENVA)-Agence Française de Sécurité Sanitaire des Aliments (AFSSA)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)
Subjects: Microbiology (medical), Bartonella birtlesii, BARTONELLA BIRTLESII, Iron, In silico, [SDV]Life Sciences [q-bio], Mutant, Heme, Biology, Models, Biological, Mice, 03 medical and health sciences, 0302 clinical medicine, Plasmid, Bacterial Proteins, Bartonella Infections, hemic and lymphatic diseases, polycyclic compounds, Animals, Inner membrane, Gene, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, digestive, oral, and skin physiology, Structural gene, Computational Biology, Membrane Transport Proteins, General Medicine, bacterial infections and mycoses, Infectious Diseases, Biochemistry, bacteria, Bartonella, Bacterial outer membrane, 030217 neurology & neurosurgery
Abstract: Beijing Genome Institute, Beijing,ChinaINTRODUCTIONBartonella birtlesii (B. birtlesii), like other Bartonellaspecies, has to face various conditions with regardto the presence of haem in its environments(arthropods, mammals, intra- or extracellular).B. birtlesiihas an intraerythrocytic lifestyle in itsnatural host, the mouse. Inside mice, the extra-cellular free haem concentration is low. In con-trast, when invading and multiplying inside theerythrocyte, B. birtlesii has to challenge toxic highhaem concentrations. Similar to other Bartonellaspecies [1], the B. birtlesii genome does not encodefor the haem biosynthesis pathway. The presenceof a haem uptake system is thus important forBartonellae. Here we investigated the function oftwo components of a putative haem uptakesystem encoded in B. birtlesii, and other Bartonellaegenomes.RESULTS AND DISCUSSIONIn silico identiﬁcation of B. birtlesii genespotentially involved in iron and⁄or haem uptakeAnalysis of the B. birtlesii genome reveals that,similar to other Bartonella species, this a-proteo-bacterium contains only inner membrane ironABC transporters. Genes encoding for an outermembrane iron transporter or a complete sidero-phore biosynthesis pathway are missing in theB. birtlesii genome. Also, the B. birtlesii genomedoes not encode for iron storage proteins (Ftn,Bfn, Dps). In contrast, Bartonellae genomesencode for a complete putative haem transportsystem (Fig. 1). Similar to other bacteria likeNeisseria meningitidis, Bartonellae could use haemas an iron source after its transport and itsdegradation into the cytoplasm. Regulation of theiron-related processes in could simi-larly to other a-proteobacteria involve Mur⁄Fur,RirA and Irr regulators encoded in its genome.Irr was shown to be involved in the regulation ofan outer membrane haem transporter in Brady-rhizobium japonicum. The modulation of the leveland the activity of the components of the haemuptake machinery might be important for theBartonellae lifestyle. Characterisation of Bartonellatribocorum hutA, tonB and exbB mutants as abac-teriaemic strains also underlines the importanceof the haem uptake process in Bartonellae [2].We undertook a functional characterisation ofB. birtlesii HutA [3] and TonB [4], two compo-nents required for the transport of haem throughthe outer membrane. HutA, already characterisedin Vibrio cholerae, transports haem through theouter membrane and requires energy transmittedby the TonB protein [3].Expression and activity of TonB from B. birtlesiiexpressed in Escherichia coliThe tonB structural gene from B. birtlesii wasampliﬁed and cloned in vector pBAD24 givingpBAD24::tonBB.bir. To test activity of TonB fromB. birtlesii, we introduced plasmid pBAD24::ton-BB.bir in strain C600tonB. The strain C600tonBpBAD24::tonBB.bir was tested for growth on LBplates in the presence of the strong Fe
Published: 2009
Full Text: View/download PDF

18. Degradation of nanoRNA is performed by multiple redundant RNases in Bacillus subtilis

Author: Ciarán Condon, Undine Mechold, Antoine Danchin, Vasily Ogryzko, Ming Fang, Wencke-Maria Zeisberg, Génétique des Génomes Bactériens, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie physico-chimique (IBPC (FR_550)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Interactions moléculaires et cancer (IMC (UMR 8126)), Signalisation, noyaux et innovations en cancérologie (UMR8126), Université Paris-Sud - Paris 11 (UP11)-Institut Gustave Roussy (IGR)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Institut Gustave Roussy (IGR)-Centre National de la Recherche Scientifique (CNRS), European Union Network of Excellence BioSapiens[LSHG CT-2003-503265 to A.D.], the French ResearchAgency (Agence nationale de la recherche) [BLAN06-3_135068 toC.C.], La Ligue Contre le Cancer[9ADO1217/1B1-BIOCE to V.O.], Institut national duCancer [247343/1B1-BIOCE to V.O.]. Funding for openaccess charge: Institut Pasteur., Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], and Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH: Ribonucleases, MESH: Mutation, RNase P, Mutant, Bacillus subtilis, Biology, medicine.disease_cause, 03 medical and health sciences, Ribonucleases, MESH: RNA, Genetics, medicine, Genomic library, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Phylogeny, Escherichia coli, Phylogeny, 030304 developmental biology, 0303 health sciences, MESH: Genetic Complementation Test, Oligoribonucleotides, Nucleic Acid Enzymes, 030306 microbiology, Genetic Complementation Test, fungi, MESH: DNA, RNA, DNA, respiratory system, MESH: Bacillus subtilis, biology.organism_classification, Molecular biology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Complementation, Biochemistry, Mutation, MESH: Oligoribonucleotides, sense organs, Exoribonuclease activity
Abstract: International audience; Escherichia coli possesses only one essential oligoribonuclease (Orn), an enzyme that can degrade oligoribonucleotides of five residues and shorter in length (nanoRNA). Firmicutes including Bacillus subtilis do not have an Orn homolog. We had previously identified YtqI (NrnA) as functional analog of Orn in B. subtilis. Screening a genomic library from B. subtilis for genes that can complement a conditional orn mutant, we identify here YngD (NrnB) as a second nanoRNase in B. subtilis. Like NrnA, NrnB is a member of the DHH/DHHA1 protein family of phosphoesterases. NrnB degrades nanoRNA 5-mers in vitro similarily to Orn. Low expression levels of NrnB are sufficient for orn complementation. YhaM, a known RNase present in B. subtilis, degrades nanoRNA efficiently in vitro but requires high levels of expression for only partial complementation of the orn(-) strain. A triple mutant (nrnA(-), nrnB(-), yhaM(-)) in B. subtilis is viable and shows almost no impairment in growth. Lastly, RNase J1 seems also to have some 5'-to-3' exoribonuclease activity on nanoRNA and thus can potentially finish degradation of RNA. We conclude that, unlike in E. coli, degradation of nanoRNA is performed in a redundant fashion in B. subtilis.
Published: 2009
Full Text: View/download PDF

19. Tissue Compartment Analysis for Biomarker Discovery by Gene Expression Profiling

Author: Antoine Disset, Jacques Tostain, Christian Genin, Alexandre Loupy, Olga Soutourina, Rabary Rajerison, Jean-Paul Duong Van Huyen, Alain Doucet, Lydie Cheval, Guorong Li, Laboratoire de physiologie génomique et de physiopathologie rénale (CNRS ERL 7226), Centre National de la Recherche Scientifique (CNRS)-Centre de Recherche des Cordeliers, Génomique, physiologie et physiopathologie rénales, Université Pierre et Marie Curie - Paris 6 (UPMC)-UMRS 872, Génétique des Génomes Bactériens, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Service d'urologie-andrologie, CHU Saint-Etienne-Université Jean Monnet [Saint-Étienne] (UJM)-Hôpital nord, Laboratoire d'immunologie, CHU Saint-Etienne, This work was supported in part by grants from the Ligue Nationale contre le cancer, Comité de Paris (grants R05/75-43 and RS07/75-62)., Laboratoire de physiologie, physiopathologie et génomique rénales, Centre National de la Recherche Scientifique (CNRS)-Centre de Recherche des Cordeliers (CRC (UMR_S_1138 / U1138)), École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris Cité (UPCité)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris Cité (UPCité), Centre de Recherche des Cordeliers (CRC (UMR_S 872)), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Service d'Urologie - Andrologie [CHU Saint-Etienne], Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E)-Université Jean Monnet - Saint-Étienne (UJM), and Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E)
Subjects: Proteomics, Biopsy, 030232 urology & nephrology, lcsh:Medicine, Bioinformatics, Kidney, MESH: Biopsy, 0302 clinical medicine, MESH: Reverse Transcriptase Polymerase Chain Reaction, Gene expression, Serial analysis of gene expression, Biomarker discovery, lcsh:Science, 0303 health sciences, Multidisciplinary, medicine.diagnostic_test, Reverse Transcriptase Polymerase Chain Reaction, MESH: Genomics, MESH: Proteomics, Genetics and Genomics/Gene Expression, Genomics, MESH: Reproducibility of Results, Nephrology, RNA extraction, Research Article, MESH: Computational Biology, DNA, Complementary, Computational biology, Biology, 03 medical and health sciences, MESH: Gene Expression Profiling, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], medicine, Humans, RNA, Messenger, Cell Biology/Gene Expression, 030304 developmental biology, MESH: RNA, Messenger, Models, Statistical, MESH: Humans, Gene Expression Profiling, lcsh:R, Computational Biology, Reproducibility of Results, MESH: DNA, Complementary, MESH: Kidney, Gene expression profiling, MESH: Biomarkers, lcsh:Q, Biomarkers, MESH: Models, Statistical
Abstract: International audience; Background: Although high throughput technologies for gene profiling are reliable tools, sample/tissue heterogeneity limits their outcomes when applied to identify molecular markers. Indeed, inter-sample differences in cell composition contribute to scatter the data, preventing detection of small but relevant changes in gene expression level. To date, attempts to circumvent this difficulty were based on isolation of the different cell structures constituting biological samples. As an alternate approach, we developed a tissue compartment analysis (TCA) method to assess the cell composition of tissue samples, and applied it to standardize data and to identify biomarkers.Methodology/principal findings: TCA is based on the comparison of mRNA expression levels of specific markers of the different constitutive structures in pure isolated structures, on the one hand, and in the whole sample on the other. TCA method was here developed with human kidney samples, as an example of highly heterogeneous organ. It was validated by comparison of the data with those obtained by histo-morphometry. TCA demonstrated the extreme variety of composition of kidney samples, with abundance of specific structures varying from 5 to 95% of the whole sample. TCA permitted to accurately standardize gene expression level amongst >100 kidney biopsies, and to identify otherwise imperceptible molecular disease markers.Conclusions/significance: Because TCA does not require specific preparation of sample, it can be applied to all existing tissue or cDNA libraries or to published data sets, inasmuch specific operational compartments markers are available. In human, where the small size of tissue samples collected in clinical practice accounts for high structural diversity, TCA is well suited for the identification of molecular markers of diseases, and the follow up of identified markers in single patients for diagnosis/prognosis and evaluation of therapy efficiency. In laboratory animals, TCA will interestingly be applied to central nervous system where tissue heterogeneity is a limiting factor.
Published: 2009
Full Text: View/download PDF

20. Shaping a bacterial genome by large chromosomal replacements, the evolutionary history of Streptococcus agalactiae

Author: Elisabeth Couvé, Philippe Glaser, Patrick Trieu-Cuot, Frank Kunst, Claire Poyart, Shaynoor Dramsi, Mathieu Brochet, Christophe Rusniok, Génétique des Génomes Bactériens, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Biologie des bactéries intracellulaires, Biologie des Bactéries Pathogènes à Gram-positif, Institut Cochin (UMR_S567 / UMR 8104), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-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 Paris Descartes - Paris 5 (UPD5), Institut Pasteur [Paris] - Centre National de la Recherche Scientifique (CNRS), 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: MESH: Chromosomes, Bacterial, MESH: Biological Evolution, Bacterial genome size, Biology, medicine.disease_cause, MESH: Genome, Bacterial, Streptococcus agalactiae, Population genomics, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetic variation, MESH: Polymorphism, Genetic, medicine, Humans, MESH: Genetic Variation, MESH: Models, Genetic, 030304 developmental biology, Genetics, 0303 health sciences, Genetic diversity, Multidisciplinary, MESH: Humans, Polymorphism, Genetic, Models, Genetic, 030306 microbiology, Chromosome, Genetic Variation, MESH: Conjugation, Genetic, Chromosomes, Bacterial, Biological Sciences, MESH: Streptococcus agalactiae, Biological Evolution, Conjugation, Genetic, Horizontal gene transfer, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Homologous recombination, Genome, Bacterial
Abstract: Bacterial populations are subject to complex processes of diversification that involve mutation and horizontal DNA transfer mediated by transformation, transduction, or conjugation. Tracing the evolutionary events leading to genetic changes allows us to infer the history of a microbe. Here, we combine experimental and in silico approaches to explore the forces that drive the genome dynamics of Streptococcus agalactiae , the leading cause of neonatal infections. We demonstrate that large DNA segments of up to 334 kb of the chromosome of S. agalactiae can be transferred through conjugation from multiple initiation sites. Consistently, a genome-wide map analysis of nucleotide polymorphisms among eight human isolates demonstrated that each chromosome is a mosaic of large chromosomal fragments from different ancestors suggesting that large DNA exchanges have contributed to the genome dynamics in the natural population. The analysis of the resulting genetic flux led us to propose a model for the evolutionary history of this species in which clonal complexes of clinical importance derived from a single clone that evolved by exchanging large chromosomal regions with more distantly related strains. The emergence of this clone could be linked to selective sweeps associated with the reduction of genetic diversity in three regions within a large panel of human isolates. Up to now sex in bacteria has been assumed to involve mainly small regions; our results define S. agalactiae as an alternative paradigm in the study of bacterial evolution.
Published: 2008
Full Text: View/download PDF

21. A model for thermal exchange in axons during action potential propagation

Author: Jean-Baptiste Masson, Guilhem Gallot, Laboratoire d'optique et biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Génétique in Silico, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Génétique des Génomes Bactériens, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Masson, Jean-Baptiste
Subjects: Hot Temperature, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Models, Neurological, Biophysics, Neural Conduction, Thermodynamics, Action Potentials, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, 7. Clean energy, Article, Ion, 03 medical and health sciences, 0302 clinical medicine, Thermal, Computer Simulation, Thermal analysis, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, 030304 developmental biology, Neurons, 0303 health sciences, [PHYS.PHYS.PHYS-BIO-PH] Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Internal energy, business.industry, Chemistry, General Medicine, Mechanics, Action (physics), Axons, Power (physics), Energy Transfer, Statistical physics, business, 030217 neurology & neurosurgery, Energy (signal processing), Thermal energy
Abstract: International audience; Several experiments have shown that during propagation of the action potential in axons, thermal energy is locally exchanged. In this paper, we use a simple model based on statistical physics to show that an important part of this exchange comes from the physics of the effusion. We evaluate, during the action potential propagation, the variation of internal energy and of the energy associated with the chemical potential of the effusion of water and ions to extract the thermal energy exchanged. The temperature exchanged is then evaluated on the area where the action potential is active. Results give a good correspondence between experimental work and this model, showing that an important part of the thermal energy exchange comes from the statistical cooling power of the effusion.
Published: 2008
Full Text: View/download PDF

22. Multiple displacement amplification for complex mixtures of DNA fragments

Author: Sonia Baconnais, Eric Le Cam, Muhammad Shoaib, Undine Mechold, Marc Lipinski, Vasily Ogryzko, Interactions moléculaires et cancer (IMC (UMR 8126)), Signalisation, noyaux et innovations en cancérologie (UMR8126), Centre National de la Recherche Scientifique (CNRS)-Institut Gustave Roussy (IGR)-Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)-Institut Gustave Roussy (IGR)-Université Paris-Sud - Paris 11 (UP11), Institut Gustave Roussy (IGR), Génétique des Génomes Bactériens, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Centre National de la Recherche Scientifique (CNRS)-Institut Gustave Roussy (IGR)-Université Paris-Sud - Paris 11 (UP11), Université Paris-Sud - Paris 11 (UP11)-Institut Gustave Roussy (IGR)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Institut Gustave Roussy (IGR)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Université Paris-Sud - Paris 11 (UP11)-Institut Gustave Roussy (IGR)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Chromatin Immunoprecipitation, lcsh:QH426-470, [SDV]Life Sciences [q-bio], lcsh:Biotechnology, Biology, Genetic analysis, 03 medical and health sciences, chemistry.chemical_compound, lcsh:TP248.13-248.65, Genetics, Humans, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Whole Genome Amplification, 0303 health sciences, Methodology Article, 030302 biochemistry & molecular biology, Multiple displacement amplification, Nucleic acid amplification technique, DNA, Molecular biology, Chromatin, lcsh:Genetics, chemistry, Rolling circle replication, Biophysics, DNA microarray, Nucleic Acid Amplification Techniques, Biotechnology, HeLa Cells
Abstract: Background A fundamental requirement for genomic studies is the availability of genetic material of good quality and quantity. The desired quantity and quality are often hard to obtain when target DNA is composed of complex mixtures of relatively short DNA fragments. Here, we sought to develop a method to representatively amplify such complex mixtures by converting them to long linear and circular concatamers, from minute amounts of starting material, followed by phi29-based multiple displacement amplification. Results We report here proportional amplification of DNA fragments that were first converted into concatamers starting from DNA amounts as low as 1 pg. Religations at low concentration (< 1 ng/μ L) preferentially lead to fragment self-circularization, which are then amplified independently, and result in non-uniform amplification. To circumvent this problem, an additional (stuffer) DNA was added during religation (religation concentration > 10 ng/μ L), which helped in the formation of long concatamers and hence resulted in uniform amplification. To confirm its usefulness in research, DP1 bound chromatin was isolated through ChIP and presence of DHFR promoter was detected using q-PCR and compared with an irrelevant GAPDH promoter. The results clearly indicated that when ChIP material was religated in presence of stuffer DNA (improved MDA), it allowed to recover the original pattern, while standard MDA and MDA without stuffer DNA failed to do so. Conclusion We believe that this method allows for generation of abundant amounts of good quality genetic material from a complex mixture of short DNA fragments, which can be further used in high throughput genetic analysis.
Published: 2008
Full Text: View/download PDF

23. Collective behavior during the exit of a wetting liquid through a network of channels

Author: Charles N. Baroud, Xin C. Wang, Jean-Baptiste Masson, Laboratoire d'hydrodynamique (LadHyX), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Massachusetts Institute of Technology (MIT), Laboratoire d'optique et biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Génétique in Silico, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Génétique des Génomes Bactériens, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Collective behavior, Surface Properties, Microfluidics, Thermodynamics, 01 natural sciences, Models, Biological, 010305 fluids & plasmas, Physics::Fluid Dynamics, Biomaterials, Colloid and Surface Chemistry, 0103 physical sciences, Lubrication, 010306 general physics, Microchannel, Chemistry, Drop (liquid), Water, Mechanics, Surfaces, Coatings and Films, Electronic, Optical and Magnetic Materials, Volumetric flow rate, Solutions, Limit analysis, Cascade, Wettability, Wetting, Hydrophobic and Hydrophilic Interactions
Abstract: International audience; The exit of a wetting fluid from a thin microchannel into a sudden expansion is studied experimentally. In the case of the exit from a single channel, the advancing interface converges to a parabolic shape after an initial transient, in accordance with the lubrication limit analysis of a spreading drop. The experiments are then repeated for the exit from two parallel channels. At early times, the two exiting drops behave independently and display the same evolution as a single exiting droplet, while at late times we recover a single parabolic profile. The transition between the early and late states is due to the merging of the two drops, which is associated with a sudden increase in the flow rate. This is the signature of a collective effect which acts to redistribute the fluid spatially. Finally, the experiment is generalized to the case of seven parallel channels where a cascade of two-by-two mergings is observed, indicating that local interactions dominate the dynamics which lead to the global state of the system. Cop. 2008 Elsevier Inc. All rights reserved.
Published: 2007
Full Text: View/download PDF

24. Human gene organization driven by the coordination of replication and transcription

Author: Yves d'Aubenton-Carafa, Maxime Huvet, Samuel Nicolay, Alain Arneodo, Benjamin Audit, Marie Touchon, Claude Thermes, Centre de génétique moléculaire (CGM), Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique de l'ENS Lyon (Phys-ENS), École normale supérieure - Lyon (ENS Lyon)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Laboratoire Joliot Curie, École normale supérieure - Lyon (ENS Lyon)-Centre National de la Recherche Scientifique (CNRS), Génétique des Génomes Bactériens, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: DNA Replication, Letter, Transcription, Genetic, replication origins, Eukaryotic DNA replication, Replication Origin, Computational biology, Biology, Origin of replication, Pre-replication complex, S Phase, 03 medical and health sciences, 0302 clinical medicine, Minichromosome maintenance, Control of chromosome duplication, SeqA protein domain, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Gene Duplication, Gene Order, Genetics, Humans, genome organization, Genetics (clinical), 030304 developmental biology, 0303 health sciences, Base Sequence, Models, Genetic, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Chromatin, Licensing factor, Genes, Origin recognition complex, DNA, Intergenic, replication domains, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], transcription, 030217 neurology & neurosurgery
Abstract: In this work, we investigated a large-scale organization of the human genes with respect to putative replication origins. We developed an appropriate multiscale method to analyze the nucleotide compositional skew along the genome and found that in more than one-quarter of the genome, the skew profile presents characteristic patterns consisting of successions of N-shaped structures, designated here N-domains, bordered by putative replication origins. Our analysis of recent experimental timing data confirmed that, in a number of cases, domain borders coincide with replication initiation zones active in the early S phase, whereas the central regions replicate in the late S phase. Around the putative origins, genes are abundant and broadly expressed, and their transcription is co-oriented with replication fork progression. These features weaken progressively with the distance from putative replication origins. At the center of domains, genes are rare and expressed in few tissues. We propose that this specific organization could result from the constraints of accommodating the replication and transcription initiation processes at chromatin level, and reducing head-on collisions between the two machineries. Our findings provide a new model of gene organization in the human genome, which integrates transcription, replication, and chromatin structure as coordinated determinants of genome architecture.
Published: 2007
Full Text: View/download PDF

25. Control of methionine synthesis and uptake by MetR and homocysteine in Streptococcus mutans

Author: Céline Gautier, Stephen McGovern, Isabelle Martin-Verstraete, Eric Guédon, Pierre Renault, Brice Sperandio, Dusko Ehrlich, Unité de recherche Génétique Microbienne (UGM), Institut National de la Recherche Agronomique (INRA), Génétique des Génomes Bactériens, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot - Paris 7 (UPD7), and Institut Pasteur [Paris]
Subjects: Homocysteine, Transcription, Genetic, [SDV]Life Sciences [q-bio], Mutant, Molecular Sequence Data, Electrophoretic Mobility Shift Assay, Genetics and Molecular Biology, transcription termination control, in-vivo, Microbiology, Models, Biological, escherichia-coli k-12, Streptococcus mutans, 03 medical and health sciences, chemistry.chemical_compound, Methionine, Bacterial Proteins, Transcription (biology), Sequence Homology, Nucleic Acid, lactococcus-lactis, transport, salmonella-typhimurium, bacillus-subtilis, s-mk box, activator-binding site, gram-positive bacteria, Methionine synthase, Promoter Regions, Genetic, Molecular Biology, Gene, 030304 developmental biology, Regulation of gene expression, chemistry.chemical_classification, 0303 health sciences, biology, Base Sequence, 030306 microbiology, Gene Expression Regulation, Bacterial, Amino acid, chemistry, Biochemistry, biology.protein, Trans-Activators, Protein Binding
Abstract: MetR (formerly Smu.1225), a regulator of the LysR family, controls key genes for methionine supply in Streptococcus mutans . An S. mutans metR mutant is unable to transport l -methionine and to grow in the absence of this amino acid. Accordingly, MetR activates transcription by binding to the promoter regions of two gene clusters and smu.1487, whose products are involved in methionine biosynthesis (MetEF and Smu.1487) and uptake (AtmBDE). Transcriptional activation by MetR requires the presence of a 17-bp palindromic sequence, the Met box. Base substitutions in the Met box hinder the formation of a MetR-DNA complex and abolish MetR-dependent activation, showing that Met boxes correspond to MetR recognition sites. Activation by MetR occurs in methionine-depleted medium and is rapidly triggered under nonactivating conditions by the addition of homocysteine. This intermediate of methionine biosynthesis increases the affinity of MetR for DNA in vitro and appears to be the MetR coeffector in vivo. Homocysteine plays a crucial role in methionine metabolic gene regulation by controlling MetR activity. A similar mechanism of homocysteine- and MetR-dependent control of methionine biosynthetic genes operates in S. thermophilus . These data suggest a common mechanism for the regulation of the methionine supply in streptococci. However, some streptococcal species are unable to synthesize the homocysteine coeffector. This intriguing feature is discussed in the light of comparative genomics and streptococcal ecology.
Published: 2007
Full Text: View/download PDF

26. Structural and functional consequences of single amino acid substitutions in the pyrimidine base binding pocket of Escherichia coli CMP kinase

Author: Ofiteru, Augustin, Bucurenci, Nadia, Alexov, Emil, Bertrand, Thomas, Briozzo, Pierre, Munier-Lehmann, Hélène, Gilles, Anne-Marie, Laboratory of Enzymology and Applied Microbiology, Institut Cantacuzène, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Department of Physics and Astronomy [Clemson], Clemson University, Chimie Biologique (UCB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Chimie Organique, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Génétique des Génomes Bactériens, Chimie Organique (UCO), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Models, Molecular, Aspartic Acid, Sequence Homology, Amino Acid, Molecular Sequence Data, Hydrogen Bonding, Arginine, carbohydrates (lipids), Kinetics, Adenosine Triphosphate, Methionine, Pyrimidines, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Escherichia coli, Serine, Amino Acid Sequence, Amino Acids, Nucleoside-Phosphate Kinase
Abstract: International audience; Bacterial CMP kinases are specific for CMP and dCMP, whereas the related eukaryotic NMP kinase phosphorylates CMP and UMP with similar efficiency. To explain these differences in structural terms, we investigated the contribution of four key amino acids interacting with the pyrimidine ring of CMP (Ser36, Asp132, Arg110 and Arg188) to the stability, catalysis and substrate specificity of Escherichia coli CMP kinase. In contrast to eukaryotic UMP/CMP kinases, which interact with the nucleobase via one or two water molecules, bacterial CMP kinase has a narrower NMP-binding pocket and a hydrogen-bonding network involving the pyrimidine moiety specific for the cytosine nucleobase. The side chains of Arg110 and Ser36 cannot establish hydrogen bonds with UMP, and their substitution by hydrophobic amino acids simultaneously affects the K(m) of CMP/dCMP and the k(cat) value. Substitution of Ser for Asp132 results in a moderate decrease in stability without significant changes in K(m) value for CMP and dCMP. Replacement of Arg188 with Met does not affect enzyme stability but dramatically decreases the k(cat)/K(m) ratio compared with wild-type enzyme. This effect might be explained by opening of the enzyme/nucleotide complex, so that the sugar no longer interacts with Asp185. The reaction rate for different modified CMP kinases with ATP as a variable substrate indicated that none of changes induced by these amino acid substitutions was 'propagated' to the ATP subsite. This 'modular' behavior of E. coli CMP kinase is unique in comparison with other NMP kinases.
Published: 2007
Full Text: View/download PDF

27. A tale of two oxidation states: bacterial colonization of arsenic-rich environments

Author: Caroline Dossat, Barbara Schoepp, Jean Weissenbach, Yuko Makita, Valérie Barbe, Patricia Siguier, Béatrice Segurens, Michael Chandler, Wolfgang Nitschke, Sophie Mangenot, Zoé Rouy, Stéphanie Weiss, David Vallenet, Benoit Cournoyer, Diliana D. Simeonova, Philippe Ortet, Antoine Danchin, Florence Arsène-Ploetze, Sandrine Koechler, Christine Carapito, Mohamed Barakat, Evelyne Krin, Didier Lièvremont, Daniel Muller, Emmanuelle Leize, Simon Duval, Philippe N. Bertin, Marie-Claire Lett, Nicolas Perdrial, Michaël Heymann, Stéphane Cruveiller, Aurélie Lieutaud, Violaine Bonnefoy, Evelyne Turlin, Claudine Médigue, Emmanuel Talla, Alain Van Dorsselaer, Génétique moléculaire, génomique, microbiologie (GMGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), 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), Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes (LEMIRE), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-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)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Génétique des Génomes Bactériens, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pluridisciplinaire Hubert Curien (IPHC), Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Centre de géochimie de la surface (CGS), Centre National de la Recherche Scientifique (CNRS)-Université Louis Pasteur - Strasbourg I-Institut national des sciences de l'Univers (INSU - CNRS), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), 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 Paris-Saclay, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Génétique moléculaire, génomique, microbiologie ( GMGM ), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique ( CNRS ), Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes ( LEMIRE ), Université de la Méditerranée - Aix-Marseille 2-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de chimie bactérienne ( LCB ), Aix Marseille Université ( AMU ) -Centre National de la Recherche Scientifique ( CNRS ), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Institut Pluridisciplinaire Hubert Curien ( IPHC ), Laboratoire de microbiologie et génétique moléculaires ( LMGM ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Centre de géochimie de la surface ( CGS ), Institut national des sciences de l'Univers ( INSU - CNRS ) -Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique ( CNRS ), Structure et évolution des génomes ( SEG ), and CNS-Université d'Évry-Val-d'Essonne ( UEVE ) -Centre National de la Recherche Scientifique ( CNRS )
Subjects: MESH: Oxidation-Reduction, Cancer Research, Drug Resistance, MESH : Models, Biological, QH426-470, MESH : Carbon, MESH : Drug Resistance, Bacterial, MESH: Genome, Bacterial, Arsenic, Bacteria, Biodegradation, Environmental, Carbon, Bacterial, Energy Metabolism, Genome, Metals, Models, Biological, Oxidation-Reduction, Phylogeny, MESH: Biodegradation, Environmental, 0302 clinical medicine, Herminiimonas arsenicoxydans, MESH: Phylogeny, ComputingMilieux_MISCELLANEOUS, Genetics (clinical), 0303 health sciences, Ecology, MESH: Energy Metabolism, MESH : Arsenic, 6. Clean water, Biodegradation, Environmental, Research Article, inorganic chemicals, MESH : Biodegradation, Environmental, MESH : Genome, Bacterial, Energy metabolism, chemistry.chemical_element, MESH: Carbon, Biology, Genomic databases, Microbiology, Models, Biological, 03 medical and health sciences, Bacterial colonization, Bioremediation, Drug Resistance, Bacterial, MESH: Arsenic, MESH: Drug Resistance, Bacterial, SDV:BBM, Genetics, MESH : Bacteria, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, MESH : Oxidation-Reduction, MESH: Metals, 030306 microbiology, MESH : Metals, MESH: Models, Biological, MESH : Phylogeny, Computational Biology, Oxidation reduction, Genetics and Genomics, biology.organism_classification, Archaea, MESH : Energy Metabolism, Eubacteria, MESH: Bacteria, Positive chemotaxis, chemistry, 13. Climate action, Genome, Bacterial, 030217 neurology & neurosurgery
Abstract: Microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. Finding a means of preserving natural environments—including ground and surface waters—from arsenic constitutes a major challenge facing modern society. Although this metalloid is ubiquitous on Earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. In-depth exploration of the genome of the β-proteobacterium Herminiimonas arsenicoxydans with regard to physiology, genetics, and proteomics, revealed that it possesses heretofore unsuspected mechanisms for coping with arsenic. Aside from multiple biochemical processes such as arsenic oxidation, reduction, and efflux, H. arsenicoxydans also exhibits positive chemotaxis and motility towards arsenic and metalloid scavenging by exopolysaccharides. These observations demonstrate the existence of a novel strategy to efficiently colonize arsenic-rich environments, which extends beyond oxidoreduction reactions. Such a microbial mechanism of detoxification, which is possibly exploitable for bioremediation applications of contaminated sites, may have played a crucial role in the occupation of ancient ecological niches on earth., Author Summary Microorganisms play a crucial role in nutrient biogeochemical cycles. Arsenic is found throughout the environment from both natural and anthropogenic sources. Its inorganic forms are highly toxic and impair the physiology of most higher organisms. Arsenic contamination of groundwater supplies is giving rise to increasingly severe human health problems in both developing and industrial countries. In the present work, we investigated the metabolism of this metalloid in Herminiimonas arsenicoxydans, a representative organism of a novel bacterial genus widespread in aquatic environments. Examination of the genome sequence and experimental evidence revealed that it is remarkably capable of coping with arsenic. Our observations support the existence of multiple strategies allowing arsenic-metabolizing microbes to efficiently colonize toxic environments. In particular, arsenic oxidation and scavenging may have played a crucial role in the development of early stages of life on Earth. Such mechanisms may one day be exploited as part of a potential bioremediation strategy in toxic environments.
Published: 2007
Full Text: View/download PDF

28. Persistent biases in the amino acid composition of prokaryotic proteins

Author: Antoine Danchin, Claudine Médigue, Géraldine Pascal, Institut Pasteur [Paris], Institut Pasteur [Paris] (IP), Génétique des Génomes Bactériens, and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Chemical Phenomena, Biochemical Phenomena, Lysine, Computational biology, Biology, Biochemistry, Cell Membrane Structures, Genome, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Asparagine, Amino Acids, Phylogeny, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Chemistry, Physical, 030302 biochemistry & molecular biology, Tryptophan, DNA, Genetic code, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Amino acid, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Prokaryotic Cells, chemistry, Multigene Family, Proteome, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Cysteine
Abstract: International audience; Correspondence analysis of 28 proteomes selected to span the entire realm of prokaryotes revealed universal biases in the proteins' amino acid distribution. Integral Inner Membrane Proteins always form an individual cluster, which can then be used to predict protein localisation in unknown proteomes, independently of the organism's biotope or kingdom. Orphan proteins are consistently rich in aromatic residues. Another bias is also ubiquitous: the amino acid composition is driven by the G + C content of the first codon position. An unexpected bias is driven, in many proteomes, by the AAN box of the genetic code, suggesting some functional biochemical relationship between asparagine and lysine. Less-significant biases are driven by the rare amino acids, cysteine and tryptophan. Some allow identification of species-specific functions or localisation such as surface or exported proteins. Errors in genome annotations are also revealed by correspondence analysis, making it useful for quality control and correction.
Published: 2006
Full Text: View/download PDF

29. Identification of genes and proteins involved in the pleiotropic response to arsenic stress in Caenibacter arsenoxydans, a metalloresistant beta-proteobacterium with an unsequenced genome

Author: Emmanuelle Leize-Wagner, Sandrine Koechler, Evelyne Turlin, Christine Carapito, Philippe N. Bertin, Alain Van Dorsselaer, Antoine Danchin, Marie-Claire Lett, Daniel Muller, 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), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Laboratoire de Biologie Tumorale, CRLCC Paul Strauss, XLIM (XLIM), Université de Limoges (UNILIM)-Centre National de la Recherche Scientifique (CNRS), Génétique des Génomes Bactériens, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Génétique moléculaire, génomique, microbiologie (GMGM), Régulation de l'Expression Génétique (REG), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Compartimentation et dynamique cellulaires (CDC), Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC), Substances naturelles/chimie moléculaire, Université Louis Pasteur - Strasbourg I-Ecole européenne de chimie, polymères et matériaux [Strasbourg]-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de masse Bio-organique, UMR CNRS-ULP, Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Centre National de la Recherche Scientifique (CNRS)-Institut Curie-Université Pierre et Marie Curie - Paris 6 (UPMC), Institut Pluridisciplinaire Hubert Curien ( IPHC ), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), XLIM ( XLIM ), Université de Limoges ( UNILIM ) -Centre National de la Recherche Scientifique ( CNRS ), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Génétique moléculaire, génomique, microbiologie ( GMGM ), Régulation de l'Expression Génétique ( REG ), Sciences Analytiques et Interactions Ioniques et Biomoléculaires ( DSA-IPHC ), Compartimentation et dynamique cellulaires ( CDC ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -INSTITUT CURIE-Centre National de la Recherche Scientifique ( CNRS ), Université Louis Pasteur - Strasbourg I-Ecole européenne de chimie, polymères et matériaux [Strasbourg]-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), 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), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Curie [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH : Molecular Sequence Data, MESH : RNA, Messenger, Messenger, Drug Resistance, MESH: Amino Acid Sequence, MESH : Drug Resistance, Bacterial, MESH: Genome, Bacterial, Biochemistry, Genome, chemistry.chemical_compound, MESH : Bacterial Proteins, MESH: Betaproteobacteria, Peptide sequence, MESH: Bacterial Proteins, MESH : Betaproteobacteria, Arsenite, Genetics, 0303 health sciences, MESH : Amino Acid Sequence, MESH : Genes, Bacterial, Bacterial, Betaproteobacteria, General Medicine, MESH : Arsenic, Metals, MESH: Genes, Bacterial, MESH : Genome, Bacterial, Molecular Sequence Data, chemistry.chemical_element, Biology, Arsenic, 03 medical and health sciences, Bacterial Proteins, Drug Resistance, Bacterial, MESH: Arsenic, MESH: Drug Resistance, Bacterial, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, RNA, Messenger, Amino Acid Sequence, Gene, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, 030304 developmental biology, MESH: RNA, Messenger, Two-dimensional gel electrophoresis, MESH: Metals, MESH: Molecular Sequence Data, 030306 microbiology, MESH : Metals, Arsenate, RNA, chemistry, Genes, Genes, Bacterial, Genome, Bacterial
Abstract: International audience; The effect of high concentrations of arsenic has been investigated in Caenibacter arsenoxydans, a beta-proteobacterium isolated from an arsenic contaminated environment and able to oxidize arsenite to arsenate. As the genome of this bacterium has not yet been sequenced, the use of a specific proteomic approach based on nano-high performance liquid chromatography tandem mass spectrometry (nanoLC-MS/MS) studies and de novo sequencing to perform cross-species protein identifications was necessary. In addition, a random mutational analysis was performed. Twenty-two proteins and 16 genes were shown to be differentially accumulated and expressed, respectively, in cells grown in the presence of arsenite. Two genes involved in arsenite oxidation and one in arsenite efflux as well as two proteins responsible for arsenate reduction were identified. Moreover, numerous genes and proteins belonging to various functional classes including information and regulation pathways, intermediary metabolism, cell envelope and cellular processes were also up- or down-regulated, which demonstrates that bacterial response to arsenic is pleiotropic.
Published: 2006
Full Text: View/download PDF

30. Etude des biais de composition en acides aminés des protéines microbiennes

Author: Pascal, Géraldine, Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Génétique des Génomes Bactériens, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université d'Evry-Val d'Essonne, Claudine Médique(cmedigue@genoscope.cns.fr), and Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]
Subjects: photorabdus luminescens, psychrophile, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], correpondence analysis, analysis factorielle des correpondances, [SDV]Life Sciences [q-bio], prokaryote, aromaticity, procaryote, acide aminé, membran protein, aromaticité, protéine membranaire, amino acid
Abstract: Living organisms are subjected to diverse selection pressures not only on global phenotype but at each level of cellular organisation.We analysed the global amino acid composition of all proteins of each proteomes studied using multivariate analysis, Correspondence Analysis and a clustering method called dynamic clouds.We studied:(i) prokaryote models E. coli, B. subtilis and M. jannaschii,(ii) a representative sample of the prokaryote world including 28 organisms of with very diverse characteristics,(iii) the pathogenicity of P. luminescens,(iv) a psychrophile feature of the bacterium P. haloplanktis, for which life in the cold is characterised by proteins with ahigh asparagine bias, and(v) a perspective will be to apply these analyses to simple eukaryotes through preliminary analysis of codon usage by P.marneffei, a dimorphic pathogenic fungus.; Les organismes vivants sont soumis à diverses pressions de sélection qui n'agissent pas seulement au niveau du phénotype global mais à chaque niveau de l'organisation de la cellule.Nous avons analysé la composition globale en acides aminés de l'ensemble les protéines de chaque protéomes étudiés à l'aide, entres autres, de l'Analyse Factorielle des Correspondances et d'un outil de partitionnement, les nuées dynamiques.Ont été étudiés(i) les modèles microbiens les mieux connus E. coli, B. subtilis et M. jannaschii,(ii) un échantillon représentatif du monde procaryote de 28 organismes aux caractéristiques les plus diverses,(iii) la pathogénicité de P. luminescens,(iv) la qualité psychrophile de la bactérie P. haloplanktis, dont la vie à basse température est caractérisée par desprotéines fortement biaisées en asparagine et(v) une perspective d'application aux eucaryotes simples est évoquée au regard des travaux préliminaires sur l'usagedes codons de P. marneffei, un chamipgnon dimorphique et pathogène.
Published: 2005

31. Effects of a mosquitocidal toxin on a mammalian epithelial cell line expressing its target receptor

Author: Yannick, Pauchet, Frédéric, Luton, Claude, Castella, Jean-François, Charles, Georges, Romey, David, Pauron, Réponse des Organismes aux Stress Environnementaux (ROSE), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Institut de pharmacologie moléculaire et cellulaire (IPMC), Université Nice Sophia Antipolis (1965 - 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), Génétique des Génomes Bactériens, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Nice Sophia Antipolis (... - 2019) (UNS), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: Cell Membrane Permeability, Mosquito Control, CULEX, Glycosylphosphatidylinositols, [SDV]Life Sciences [q-bio], Bacterial Toxins, fungi, Epithelial Cells, alpha-Glucosidases, TARGET PROTEIN, CPM1, BINARY TOXIN, BIOINSECTICIDE, Recombinant Proteins, Cell Line, Radioligand Assay, Dogs, Membrane Microdomains, CRYSTAL TOXIN, MDCK CELLS, Vacuoles, parasitic diseases, Animals, BACILLUS SPHAERICUS
Abstract: The spread of diseases transmitted by Anopheles and Culex mosquitoes, such as malaria and West Nile fever, is a growing concern for human health. Bacillus sphaericus binary toxin (Bin) is one of the few available bioinsecticides able to control populations of these mosquitoes efficiently. We previously showed that Bin binds to Cpm1, an alpha-glucosidase located on the apical side of Culex larval midgut epithelium. We analysed the effects of Bin by expressing a construct encoding Cpm1 in the mammalian epithelial MDCK cell line. Cpm1 is targeted to the apical side of polarized MDCK, where it is anchored by glycosylphosphatidylinositol (GPI) and displays alpha-glucosidase activity. Bin bound to transfected cells and induced a non-specific current presumably related to the opening of pores. The formation of these pores may be related to the location of the toxin/receptor complex in lipid raft microdomains. Finally, Bin promoted the time-dependent appearance of intracytoplasmic vacuoles but did not drive cell lysis. Thus, the dual functionality (enzyme/toxin receptor) of Cpm1 is fully conserved in MDCK cells and Cpm1 is an essential target protein for Bin cytotoxicity in Culex mosquitoes.
Published: 2005
Full Text: View/download PDF

32. Regulation of the Bacillus subtilis ytmI operon, involved in sulfur metabolism

Author: Sandrine Auger, Isabelle Guillouard, Antoine Danchin, Pierre Burguière, Isabelle Martin-Verstraete, Juliette Fert, Génétique des Génomes Bactériens, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), This research was supported by grants from the 'Ministère de l'Education Nationale de la Recherche et de la Technologie,' the 'Centre National de la Recherche Scientifique' (URA 2171), the 'Institut Pasteur,' the 'Université Paris 7,' the 'Fondation pour la recherche médicale,' and the European Biotech Program (contract QLG2 CT9901455)., and Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]
Subjects: Genotype, Transcription, Genetic, Operon, Molecular Sequence Data, Restriction Mapping, Repressor, Genetics and Molecular Biology, Bacillus subtilis, Biology, Microbiology, trp operon, 03 medical and health sciences, Bacterial Proteins, gal operon, Molecular Biology, Gene, 030304 developmental biology, Regulator gene, 0303 health sciences, Base Sequence, 030306 microbiology, GENE EXPRESSION REGULATION, ABC TRANSPORTER, Promoter, biology.organism_classification, SEQUENCE ANALYSIS, Phosphotransferases (Alcohol Group Acceptor), SULFUR METABOLISM, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Biochemistry, Mutagenesis, Site-Directed, Cystine, ATP-Binding Cassette Transporters, Sulfur
Abstract: The YtlI regulator of Bacillus subtilis activates the transcription of the ytmI operon encoding an l -cystine ABC transporter, a riboflavin kinase, and proteins of unknown function. The expression of the ytlI gene and the ytmI operon was high with methionine and reduced with sulfate. Using deletions and site-directed mutagenesis, a cis -acting DNA sequence important for YtlI-dependent regulation was identified upstream from the −35 box of ytmI . Gel mobility shift assays confirmed that YtlI specifically interacted with this sequence. The replacement of the sulfur-regulated ytlI promoter by the xylA promoter led to constitutive expression of a ytmI ′ -lacZ fusion in a ytlI mutant, suggesting that the repression of ytmI expression by sulfate was mainly at the level of YtlI synthesis. We further showed that the YrzC regulator negatively controlled ytlI expression while this repressor also acted on ytmI expression via YtlI. The cascade of regulation observed in B. subtilis is conserved in Listeria spp. Both a YtlI-like regulator and a ytmI -type operon are present in Listeria spp. Indeed, the Lmo2352 protein from Listeria monocytogenes was able to replace YtlI for the activation of ytmI expression and a lmo2352′ -lacZ fusion was repressed in the presence of sulfate via YrzC in B. subtilis . A common motif, AT(A/T)ATTCCTAT, was found in the promoter region of the ytlI and lmo2352 genes. Deletion of part of this motif or the introduction of point mutations in this sequence confirmed its involvement in ytlI regulation.
Published: 2005
Full Text: View/download PDF

33. The PatB protein of Bacillus subtilis is a C-S-lyase

Author: Antoine Danchin, M.P. Gomez, Sandrine Auger, Isabelle Martin-Verstraete, Génétique des Génomes Bactériens, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], This research was supported by grants from the Ministère de l’Education Nationale de la Recherche et de la Technologie, the Centre National de la Recherche Scientifique (URA 2171), the Institut Pasteur, the Université Paris 7 and the European Biotech Program (contract QLG2 CT9901455)., and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Mutant, Sulfur metabolism, Cystine, Lyases, Bacillus subtilis, Biochemistry, 03 medical and health sciences, chemistry.chemical_compound, Methionine, Bacterial Proteins, CYSTATHIONINE BETA-LYASE, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, METHIONINE BIOSYNTHESIS, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Cysteine Synthase, CYSTEINE DESULFHYDRASE, biology, 030306 microbiology, Cystathionine gamma-Lyase, General Medicine, biology.organism_classification, Lyase, Cystathionine beta synthase, Carbon-Sulfur Lyases, Enzyme, SULFUR METABOLISM, chemistry, biology.protein
Abstract: International audience; The PatB protein of Bacillus subtilis had both cystathionine beta-lyase and cysteine desulfhydrase activities in vitro. The apparent K(m) value of the PatB protein for cystathionine was threefold higher than that of the MetC protein, the previously characterized cystathionine beta-lyase of B. subtilis. In the presence of cystathionine as sole sulfur source, the patB gene present on a multicopy plasmid restored the growth of a metC mutant. In addition, the patB metC double mutant was unable to grow in the presence of sulfate or cystine while the patB or metC single mutants grew similarly to the wild-type strains in the presence of the same sulfur sources. In a metC mutant, the PatB protein can replace the MetC enzyme in the methionine biosynthetic pathway.
Published: 2005
Full Text: View/download PDF

34. The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens

Author: Antoine Danchin, Elie Dassa, Rachel Vincent, Caroline Boursaux-Eude, Carmen Buchrieser, Sophie Gaudriault, Patricia Siguier, Eric Duchaud, Kerrie Powell, Michael Chandler, Christophe Rusniok, Stéphanie Bocs, Alain Givaudan, Vincent Paul Mary Wingate, Richard Derose, Noël Boemare, Mohamed Zouine, Sylviane Derzelle, Philippe Glaser, Frank Kunst, Anne Lanois, Georges Freyssinet, Lionel Frangeul, Claudine Médigue, Jean-François Charles, Sead Taourit, Génomique des Microorganismes Pathogènes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Intégration et Analyse Génomique (Plate-Forme 4) (PF4), Institut Pasteur [Paris] (IP), Ecologie microbienne des insectes et interactions hôte-pathogène (EMIP), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), Génomique métabolique (UMR 8030), 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)-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), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Génétique des Génomes Bactériens, Programmation Moléculaire et Toxicologie Génétique, Bayer Cropscience, This work received financial support from the Institut Pasteur, the Centre National de la Recherche Scientifique, the Institut National de la Recherche Agronomique and the Ministère de l'Industrie et des Finances (Après séquençage des Génomes)., Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris], 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 Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Proteome, Sequence analysis, Bacterial Toxins, Molecular Sequence Data, Biomedical Engineering, Virulence, Bioengineering, Xenorhabdus, Biology, Applied Microbiology and Biotechnology, Genome, Microbiology, 03 medical and health sciences, Sequence Analysis, Protein, Photorhabdus luminescens, Animals, Amino Acid Sequence, Symbiosis, Pathogen, 030304 developmental biology, 0303 health sciences, Sequence Homology, Amino Acid, 030306 microbiology, fungi, Gene Expression Regulation, Bacterial, biology.organism_classification, Horizontal gene transfer, Molecular Medicine, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Photorhabdus, Rhabditoidea, Sequence Alignment, Genome, Bacterial, Biotechnology
Abstract: 50 ref.; International audience; Photorhabdus luminescens is a symbiont of nematodes and a broad-spectrum insect pathogen. The complete genome sequence of strain TT01 is 5,688,987 base pairs (bp) long and contains 4,839 predicted protein-coding genes. Strikingly, it encodes a large number of adhesins, toxins, hemolysins, proteases and lipases, and contains a wide array of antibiotic synthesizing genes. These proteins are likely to play a role in the elimination of competitors, host colonization, invasion and bioconversion of the insect cadaver, making P. luminescens a promising model for the study of symbiosis and host-pathogen interactions. Comparison with the genomes of related bacteria reveals the acquisition of virulence factors by extensive horizontal transfer and provides clues about the evolution of an insect pathogen. Moreover, newly identified insecticidal proteins may be effective alternatives for the control of insect pests.
Published: 2003
Full Text: View/download PDF

35. A double epidemic model for the SARS propagation

Author: Tuen-Wai Ng, Gabriel Turinici, Antoine Danchin, Department of Mathematics, The University of Hong Kong (HKU), Centre d'Enseignement et de Recherche en Mathématiques et Calcul Scientifique (CERMICS), École des Ponts ParisTech (ENPC), Methods and engineering of multiscale computing from atom to continuum (MICMAC), Inria Paris-Rocquencourt, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-École des Ponts ParisTech (ENPC), Génétique des Génomes Bactériens, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]
Subjects: China, Severe Acute Respiratory Syndrome - epidemiology, Hong Kong - epidemiology, Disease, medicine.disease_cause, Severe Acute Respiratory Syndrome, Models, Biological, Disease Outbreaks, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, 0302 clinical medicine, Sars virus, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, medicine, Humans, lcsh:RC109-216, 030212 general & internal medicine, 030304 developmental biology, Coronavirus, 0303 health sciences, business.industry, Outbreak, Monitoring system, SARS Virus, Virology, 3. Good health, Infectious Diseases, Severe acute respiratory syndrome-related coronavirus, Hong Kong, Epidemic model, business, Demography, Research Article
Abstract: Background: An epidemic of a Severe Acute Respiratory Syndrome (SARS) caused by a new coronavirus has spread from the Guangdong province to the rest of China and to the world, with a puzzling contagion behavior. It is important both for predicting the future of the present outbreak and for implementing effective prophylactic measures, to identify the causes of this behavior. Results: In this report, we show first that the standard Susceptible-Infected-Removed (SIR) model cannot account for the patterns observed in various regions where the disease spread. We develop a model involving two superimposed epidemics to study the recent spread of the SARS in Hong Kong and in the region. We explore the situation where these epidemics may be caused either by a virus and one or several mutants that changed its tropism, or by two unrelated viruses. This has important consequences for the future: the innocuous epidemic might still be there and generate, from time to time, variants that would have properties similar to those of SARS. Conclusion: We find that, in order to reconcile the existing data and the spread of the disease, it is convenient to suggest that a first milder outbreak protected against the SARS. Regions that had not seen the first epidemic, or that were affected simultaneously with the SARS suffered much more, with a very high percentage of persons affected. We also find regions where the data appear to be inconsistent, suggesting that they are incomplete or do not reflect an appropriate identification of SARS patients. Finally, we could, within the framework of the model, fix limits to the future development of the epidemic, allowing us to identify landmarks that may be useful to set up a monitoring system to follow the evolution of the epidemic. The model also suggests that there might exist a SARS precursor in a large reservoir, prompting for implementation of precautionary measures when the weather cools down. © 2003 Ng et al; licensee BioMed Central Ltd., published_or_final_version
Published: 2003
Full Text: View/download PDF

36. The metNPQ operon of Bacillus subtilis encodes an ABC permease transporting methionine sulfoxide, D- and L-methionine

Author: Antoine Danchin, Isabelle Martin-Verstraete, Marie-Françoise Hullo, Sandrine Auger, Elie Dassa, Génétique des Génomes Bactériens, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Programmation Moléculaire et Toxicologie Génétique, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]
Subjects: Amino Acid Transport Systems, Operon, [SDV]Life Sciences [q-bio], Sulfur metabolism, ATP-binding cassette transporter, Bacillus subtilis, Biology, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Methionine, Molecular Biology, 030304 developmental biology, Adenosine Triphosphatases, 0303 health sciences, 030306 microbiology, Methionine sulfoxide, Permease, Escherichia coli Proteins, Wild type, General Medicine, biology.organism_classification, chemistry, Biochemistry, ATP-Binding Cassette Transporters, Carrier Proteins
Abstract: The Bacillus subtilis yusCBAoperon, which encodes an ABC-type transporter, contains an S-box motif in its promoter region. We showed that the expression of these genes is repressed via the S-box system when methionine is available. The YusCB proteins are involved in the transport of both D -a ndL-methionine but also methionine sulfoxide. A yusCB mutant is unable to grow in the presence of 5 µM L-methionine or 100 µM methionine sulfoxide, while it grows similarly to the wild type with 100 µM L-methionine and 1 mM methionine sulfoxide. Other uptake systems are therefore present for these two compounds. In contrast, the Yus ABC transporter corresponds to the sole D-methionine uptake system. We propose to rename yusC, yusB and yusA as metN, metP and metQ, respectively.  2003 Elsevier SAS. All rights reserved.
Published: 2003
Full Text: View/download PDF

37. Identification of Bacillus subtilis CysL, a regulator of the cysJI Operon, which encodes sulfite reductase

Author: Farid Chetouani, Isabelle Martin-Verstraete, Isabelle Guillouard, Marie-Françoise Hullo, Antoine Danchin, Sandrine Auger, Génétique des Génomes Bactériens, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Génomique des Microorganismes Pathogènes, This research was supported by grants from the Ministère de l'Education Nationale de la Recherche et de la Technologie, the Centre National de la Recherche Scientifique (URA 2171), the Institut Pasteur, the Université Paris 7, and the European Biotech Program (contract QLG2 CT9901455)., Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: Operon, [SDV]Life Sciences [q-bio], Mutant, Molecular Sequence Data, Sulfite Reductase (Ferredoxin), Bacillus subtilis, Biology, Microbiology, Sulfite reductase, 03 medical and health sciences, Transcription (biology), Transcriptional regulation, Oxidoreductases Acting on Sulfur Group Donors, Gene Regulation, Amino Acid Sequence, Cysteine, Promoter Regions, Genetic, Molecular Biology, Gene, 030304 developmental biology, 0303 health sciences, Base Sequence, 030306 microbiology, Arabidopsis Proteins, Gene Expression Regulation, Bacterial, biology.organism_classification, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Biochemistry, Trans-Activators, Sulfur
Abstract: The way in which the genes involved in cysteine biosynthesis are regulated is poorly characterized in Bacillus subtilis . We showed that CysL (formerly YwfK), a LysR-type transcriptional regulator, activates the transcription of the cysJI operon, which encodes sulfite reductase. We demonstrated that a cysL mutant and a cysJI mutant have similar phenotypes. Both are unable to grow using sulfate or sulfite as the sulfur source. The level of expression of the cysJI operon is higher in the presence of sulfate, sulfite, or thiosulfate than in the presence of cysteine. Conversely, the transcription of the cysH and cysK genes is not regulated by these sulfur sources. In the presence of thiosulfate, the expression of the cysJI operon was reduced 11-fold, whereas the expression of the cysH and cysK genes was increased, in a cysL mutant. A cis -acting DNA sequence located upstream of the transcriptional start site of the cysJI operon (positions −76 to −70) was shown to be necessary for sulfur source- and CysL-dependent regulation. CysL also negatively regulates its own transcription, a common characteristic of the LysR-type regulators. Gel mobility shift assays and DNase I footprint experiments showed that the CysL protein specifically binds to cysJ and cysL promoter regions. This is the first report of a regulator of some of the genes involved in cysteine biosynthesis in B. subtilis .
Published: 2002
Full Text: View/download PDF

38. Extracting biological information from dna arrays : an unexpected link between arginine and methionine metabolism in bacillus subtilis

Author: Sekowska, Agnieszka, Robin, Stephane, Daudin, Jean-Jacques, Hénaut, Alain, Danchin, Antoine, Centre de recherche Université de Hong-Kong-Pasteur, Réseau International des Instituts Pasteur (RIIP), Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Génome et Informatique, Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Génétique des Génomes Bactériens, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), This work benefited from the support of the BACELL European Union program, European Project: 26873,BACELL HEALTH, Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Mathématiques et Modélisation d'Evry, and Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]
Subjects: methionine, DNA arrays, Gene Expression Profiling, Research, [SDV]Life Sciences [q-bio], Genetic Variation, Membrane Transport Proteins, arginine, Gene Expression Regulation, Bacterial, RNA, Bacterial, bacillus subtilis, Genes, Bacterial, Thioglycosides, Mutation, Operon, Sulfur, Oligonucleotide Array Sequence Analysis
Abstract: Background: In global gene expression profiling experiments, variation in the expression of genes of interest can often be hidden by general noise. To determine how biologically significant variation can be distinguished under such conditions we have analyzed the differences in gene expression when Bacillus subtilis is grown either on methionine or on methylthioribose as sulfur source. Results: An unexpected link between arginine metabolism and sulfur metabolism was discovered, enabling us to identify a high-affinity arginine transport system encoded by the yqiXYZ genes. In addition, we tentatively identified a methionine/methionine sulfoxide transport system which is encoded by the operon ytmIJKLMhisP and is presumably used in the degradation of methionine sulfoxide to methane sulfonate for sulfur recycling. Experimental parameters resulting in systematic biases in gene expression were also uncovered. In particular, we found that the late competence operons comE, comF and comG were associated with subtle variations in growth conditions. Conclusions: Using variance analysis it is possible to distinguish between systematic biases and relevant gene-expression variation in transcriptome experiments. Co-variation of metabolic gene expression pathways was thus uncovered linking nitrogen and sulfur metabolism in B. subtilis.
Published: 2001
Full Text: View/download PDF

39. Antagonistic effects of dual PTS-catalysed phosphorylation on the Bacillus subtilis transcriptional activator LevR

Author: Bernhard Erni, Josef Deutscher, Véronique Charrier, Isabelle Martin-Verstraete, Georges Rapoport, Anne Galinier, Jörg Stülke, Biochimie Microbienne, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie et Chimie des Protéines, Centre National de la Recherche Scientifique (CNRS), Department für Chemie und Biochemie [Bern], Universität Bern [Bern] (UNIBE), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Universität Bern [Bern], Génétique des Génomes Bactériens, Department of General Microbiology Georg-Augus, Georg-August-Universität Göttingen, Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biochimie Microbienne, Institut Pasteur de Madagascar, and Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)
Subjects: Transcriptional Activation, Operon, [SDV]Life Sciences [q-bio], Mutant, Molecular Sequence Data, Catabolite repression, Bacillus subtilis, macromolecular substances, Microbiology, 03 medical and health sciences, Bacterial Proteins, Escherichia coli, Amino Acid Sequence, Phosphorylation, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Alanine, 0303 health sciences, biology, 030306 microbiology, Phosphotransferases, PEP group translocation, biology.organism_classification, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Biochemistry, Genes, Bacterial, Mutation, bacteria, Electrophoresis, Polyacrylamide Gel, Phosphoenolpyruvate carboxykinase, Sequence Alignment, Transcription Factors
Abstract: International audience; LevR, which controls the expression of the lev operon of Bacillus subtilis, is a regulatory protein containing an N‐terminal domain similar to the NifA/NtrC transcriptional activator family and a C‐terminal domain similar to the regulatory part of bacterial anti‐terminators, such as BglG and LicT. Here, we demonstrate that the activity of LevR is regulated by two phosphoenolpyruvate (PEP)‐dependent phosphorylation reactions catalysed by the phosphotransferase system (PTS), a transport system for sugars, polyols and other sugar derivatives. The two general components of the PTS, enzyme I and HPr, and the two soluble, sugar‐specific proteins of the lev‐PTS, LevD and LevE, form a signal transduction chain allowing the PEP‐dependent phosphorylation of LevR, presumably at His‐869. This phosphorylation seems to inhibit LevR activity and probably regulates the induction of the lev operon. Mutants in which His‐869 of LevR has been replaced with a non‐phosphorylatable alanine residue exhibited constitutive expression from the lev promoter, as do levD or levE mutants. In contrast, PEP‐dependent phosphorylation of LevR in the presence of only the general components of the PTS, enzyme I and HPr, regulates LevR activity positively. This phosphorylation most probably occurs at His‐585. Mutants in which His‐585 has been replaced with an alanine had lost stimulation of LevR activity and PEP‐dependent phosphorylation by enzyme I and HPr. This second phosphorylation of LevR at His‐585 is presumed to play a role in carbon catabolite repression.
Published: 1998
Full Text: View/download PDF

40. Protein Phosphorylation Chain of a Bacillus subtilis Fructose-Specific Phosphotransferase System and Its Participation in Regulation of the Expression of the lev Operon †

Author: and Anne Galinier, Isabelle Martin-Verstraete, Véronique Charrier, Josef Deutscher, Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Génétique des Génomes Bactériens, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut de biologie et chimie des protéines [Lyon] (IBCP), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, and Galinier, Anne
Subjects: Genotype, Operon, Recombinant Fusion Proteins, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Mutant, lac operon, Fructose, Bacillus subtilis, Biochemistry, Gene Expression Regulation, Enzymologic, 03 medical and health sciences, Escherichia coli, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Protein phosphorylation, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Cloning, Molecular, Phosphoenolpyruvate Sugar Phosphotransferase System, Integral membrane protein, Conserved Sequence, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Base Sequence, Sequence Homology, Amino Acid, biology, 030306 microbiology, Gene Expression Regulation, Bacterial, PEP group translocation, biology.organism_classification, Molecular biology, Amino acid, [SDV] Life Sciences [q-bio], Kinetics, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Oligodeoxyribonucleotides, chemistry, Mutagenesis, Site-Directed, bacteria
Abstract: The proteins encoded by the fructose-inducible lev operon of Bacillus subtilis are components of a phosphotransferase system. They transport fructose by a mechanism which couples sugar uptake and phosphoenolpyruvate-dependent sugar phosphorylation. The complex transport system consists of two integral membrane proteins (LevF and LevG) and two soluble, hydrophilic proteins (LevD and LevE). The two soluble proteins from together with the general proteins of the phosphotransferase system, enzyme I and HPr, a protein phosphorylation chain which serves to phosphorylate fructose transported by LevF and LevG. We have synthesized modified LevD and LevE by fusing a His-tag to the N-terminus of each protein allowing rapid and efficient purification of the proteins. We determined His-9 in LevD and His-15 in LevE as the sites of PEP-dependent phosphorylation by isolating single, labeled peptides derived from 32P-labeled LevD, LevD(His)6, and LevE(His)6. The labeled peptides were subsequently analyzed by amino acid sequencing and mass spectroscopy. Mutations replacing the phosphorylatable histidyl residue in LevD with an alanyl residue and in LevE with a glutamate or aspartate were introduced in the levD and levE genes. These mutations caused strongly reduced fructose uptake via the lev-PTS. The mutant proteins were synthesized with a N-terminal His-tag and purified. Mutant LevD(His)6 was very slowly phosphorylated, whereas mutant LevE(His)6 was not phosphorylated at all. The corresponding levD and levE alleles were incorporated into the chromosome of a B. subtilis strain expressing the lacZ gene under control of the lev promoter. The mutations affecting the site of phosphorylation in either LevD or LevE were found to cause constitutive expression from the lev promoter of B. subtilis.
Published: 1997
Full Text: View/download PDF

41. The Pleiotropic CymR Regulator of Staphylococcus aureus Plays an Important Role in Virulence and Stress Response

Author: Sarah Dubrac, Tarek Msadek, Olivier Poupel, Isabelle Martin-Verstraete, Olga Soutourina, Génétique des Génomes Bactériens, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Biologie des Bactéries Pathogènes à Gram-positif, I. M-V. and O. S. are full and assistant professors at the Université Paris 7, respectively. Research was supported by grants from the Centre National de la Recherche Scientifique (CNRS URA 2171 and 2172), the Institut Pasteur (Grand Programme Horizontal N°9 and PTR N°256) and the European Commission for the group of T. M. (Grants StaphDynamics, LHSM-CT-2006-019064, and BaSysBio, LSHG-CT-2006-037469)., We are grateful to S. Foster for providing us with S. aureus strains and valuable discussions. We thank O. Sismeiro, C. Lacroix and J.-Y. Coppee for macroarray preparation, S. Rousseau and P. Vantadour for loading transcriptome data onto the Genoscript database and P. Courtin for metabolite analysis., European Project: 35105,STAPHDYNAMICS, European Project: 38901,BASYSBIO, and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV]Life Sciences [q-bio], Mutant, MESH: Virulence, medicine.disease_cause, Mice, chemistry.chemical_compound, MESH: Oxidants, MESH: Staphylococcus aureus, MESH: Up-Regulation, Homeostasis, MESH: Animals, Disulfides, lcsh:QH301-705.5, Pathogen, Regulation of gene expression, Mice, Inbred BALB C, 0303 health sciences, MESH: Oxidative Stress, Virulence, Staphylococcal Infections, Oxidants, Up-Regulation, MESH: Copper, MESH: Tellurium, MESH: Homeostasis, Staphylococcus aureus, Cystine, MESH: Hydrogen Peroxide, Microbiology/Microbial Physiology and Metabolism, Female, Tellurium, MESH: Genes, Bacterial, Microbiology/Cellular Microbiology and Pathogenesis, Intracellular, Research Article, lcsh:Immunologic diseases. Allergy, Immunology, MESH: Mice, Inbred BALB C, MESH: Staphylococcal Infections, Biology, Microbiology, Cell Line, 03 medical and health sciences, Virology, Genetics, medicine, Animals, MESH: Disulfides, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Mice, Molecular Biology, Cysteine metabolism, 030304 developmental biology, Metal ion homeostasis, 030306 microbiology, Macrophages, MESH: Macrophages, MESH: Cystine, Hydrogen Peroxide, MESH: Cell Line, Oxidative Stress, lcsh:Biology (General), chemistry, Genes, Bacterial, MESH: Gene Deletion, Parasitology, lcsh:RC581-607, MESH: Female, Copper, Gene Deletion
Abstract: We have characterized a novel pleiotropic role for CymR, the master regulator of cysteine metabolism. We show here that CymR plays an important role both in stress response and virulence of Staphylococcus aureus. Genes involved in detoxification processes, including oxidative stress response and metal ion homeostasis, were differentially expressed in a ΔcymR mutant. Deletion of cymR resulted in increased sensitivity to hydrogen peroxide-, disulfide-, tellurite- and copper-induced stresses. Estimation of metabolite pools suggests that this heightened sensitivity could be the result of profound metabolic changes in the ΔcymR mutant, with an increase in the intracellular cysteine pool and hydrogen sulfide formation. Since resistance to oxidative stress within the host organism is important for pathogen survival, we investigated the role of CymR during the infectious process. Our results indicate that the deletion of cymR promotes survival of S. aureus inside macrophages, whereas virulence of the ΔcymR mutant is highly impaired in mice. These data indicate that CymR plays a major role in virulence and adaptation of S. aureus for survival within the host., Author Summary Staphylococcus aureus is a very harmful human pathogen that is a major cause of nosocomial infections. Humans have developed sophisticated defense strategies against invading bacteria, including the innate immune response, with the generation of an oxidative burst inside phagocytic cells. Staphylococcal infections are extremely difficult to eradicate due to the remarkable capacity of these bacteria to adapt to different environmental conditions both inside and outside the host organism. Sulfur metabolism is essential for all living organisms and is tightly controlled by regulatory proteins. In this paper, we revealed an important role for CymR, a major regulator of sulfur metabolism, in adaptation of S. aureus to the host environment. Inactivation of the gene encoding this regulator in S. aureus leads to a mutant bacterium with increased vulnerability to stress conditions including oxidative stress encountered inside the host. More importantly, the deletion of the cymR gene strongly affected the interaction of S. aureus with its host, leading to impaired virulence in mice. Our results place CymR among the potential targets for attenuation of S. aureus infections.
Published: 2010
Full Text: View/download PDF

42. Structure, Function, and Evolution of the Thiomonas spp. Genome

Author: Florence Hommais, Jean Weissenbach, Odile Bruneel, Emmanuel Talla, Philippe N. Bertin, Patricia Siguier, Daniel Muller, Jean-Yves Coppée, Caroline Proux, Stéphanie Weiss, Valérie Barbe, Florence Arsène-Ploetze, Marie Marchal, Gregory Salvignol, Audrey Heinrich-Salmeron, Zoé Rouy, Fabienne Battaglia-Brunet, Didier Lièvremont, Christopher G. Bryan, Caroline Michel, Philippe Ortet, Sandrine Koechler, Céline Brochier-Armanet, Jessica Cleiss-Arnold, Mohamed Barakat, Michael Chandler, Stéphane Cruveiller, Djamila Slyemi, Aurélie Lieutaud, Catherine Joulian, Evelyne Krin, Violaine Bonnefoy, David Roche, Claudine Médigue, Mathieu Erhardt, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Puces à ADN (Plate-Forme 2) (PF2), Institut Pasteur [Paris], Laboratoire de microbiologie et génétique moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), 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)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), 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 Paris-Saclay, Bureau de Recherches Géologiques et Minières (BRGM) (BRGM), Hydrosciences Montpellier (HSM), Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie moléculaire des plantes (IBMP), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Génétique des Génomes Bactériens, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Dynamique, évolution et expression de génomes de microorganismes (DEEGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Génomique métabolique (UMR 8030), 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)-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), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-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 de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut Pasteur [Paris] (IP), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Cancer Research, Prophages, MESH: Genome, Bacterial, Genome, MESH: Prophages, MESH: Genomic Islands, MESH: Genetic Variation, MESH: Betaproteobacteria, MESH: Evolution, Molecular, Genetics (clinical), Genetics, Comparative Genomic Hybridization, 0303 health sciences, biology, MESH: Energy Metabolism, Betaproteobacteria, Thiomonas, Genetics and Genomics/Microbial Evolution and Genomics, Adaptation, Physiological, Horizontal gene transfer, MESH: Genes, Bacterial, Metabolic Networks and Pathways, Research Article, Plasmids, Genome evolution, lcsh:QH426-470, Gene Transfer, Horizontal, Genomic Islands, MESH: Carbon, Genomics, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Environment, Arsenic, Evolution, Molecular, 03 medical and health sciences, Genes, Duplicate, MESH: Plasmids, MESH: Arsenic, Microbiology/Environmental Microbiology, MESH: Environment, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Prophage, 030304 developmental biology, Comparative genomics, MESH: Genes, Duplicate, 030306 microbiology, Human evolutionary genetics, Genetic Variation, biology.organism_classification, MESH: Adaptation, Physiological, Carbon, MESH: Gene Transfer, Horizontal, MESH: Comparative Genomic Hybridization, lcsh:Genetics, Genes, Bacterial, MESH: Metabolic Networks and Pathways, Energy Metabolism, Genome, Bacterial
Abstract: Bacteria of the Thiomonas genus are ubiquitous in extreme environments, such as arsenic-rich acid mine drainage (AMD). The genome of one of these strains, Thiomonas sp. 3As, was sequenced, annotated, and examined, revealing specific adaptations allowing this bacterium to survive and grow in its highly toxic environment. In order to explore genomic diversity as well as genetic evolution in Thiomonas spp., a comparative genomic hybridization (CGH) approach was used on eight different strains of the Thiomonas genus, including five strains of the same species. Our results suggest that the Thiomonas genome has evolved through the gain or loss of genomic islands and that this evolution is influenced by the specific environmental conditions in which the strains live., Author Summary Recent advances in the field of arsenic microbial metabolism have revealed that bacteria colonize a large panel of highly contaminated environments. Belonging to the order of Burkholderiales, Thiomonas strains are ubiquitous in arsenic-contaminated environments. The genome of one of them, i.e. Thiomonas sp. 3As, was deciphered and compared to the genome of several other Thiomonas strains. We found that their flexible gene pool evolved to allow both the surviving and growth in their peculiar environment. In particular, the acquisition by strains of the same species of different genomic islands conferred heavy metal resistance and metabolic idiosyncrasies. Our comparative genomic analyses suggest that the natural environment influences the genomic evolution of these bacteria. Importantly, these results highlight the genomic variability that may exist inside a taxonomic group, enlarging the concept of bacterial species.
Published: 2010
Full Text: View/download PDF

43. Genome analysis : recombination, repair and recombinational hotspots

Author: Eduardo Rocha, Pascal SIRAND-PUGNET, Alain Blanchard, Génétique des Génomes Bactériens, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Génomique, développement et pouvoir pathogène (GD2P), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Alain Blanchard (Editeur), Glenn Browning (Editeur), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Inconnu, A Blanchard, G Browning, and ProdInra, Migration
Subjects: [SDV] Life Sciences [q-bio], MALADIE, [SDV]Life Sciences [q-bio], ANALYSE DU GENOME, GENETIQUE, BIOLOGIE MOLECULAIRE, ComputingMilieux_MISCELLANEOUS, MYCOPLASME
Abstract: Nombre de pages de l'ouvrage: XII-604 p.; International audience

44. Characterization of NrnA homologs from Mycobacterium tuberculosis and Mycoplasma pneumoniae.

Author: Postic G, Danchin A, and Mechold U
Subjects: Escherichia coli genetics, Exoribonucleases genetics, Genetic Complementation Test, MicroRNAs chemistry, Mutation, Phosphoric Monoester Hydrolases genetics, Recombinant Proteins chemistry, Recombinant Proteins genetics, Streptococcus mutans enzymology, Streptococcus mutans genetics, Exoribonucleases chemistry, Mycobacterium tuberculosis enzymology, Mycoplasma pneumoniae enzymology
Abstract: Processive RNases are unable to degrade efficiently very short oligonucleotides, and they are complemented by specific enzymes, nanoRNases, that assist in this process. We previously identified NrnA (YtqI) from Bacillus subtilis as a bifunctional protein with the ability to degrade nanoRNA (RNA oligos ≤5 nucleotides) and to dephosphorylate 3'-phosphoadenosine 5'-phosphate (pAp) to AMP. While the former activity is analogous to that of oligoribonuclease (Orn) from Escherichia coli, the latter corresponds to CysQ. NrnA homologs are widely present in bacterial and archaeal genomes. They are found preferably in genomes that lack Orn or CysQ homologs. Here, we characterize NrnA homologs from important human pathogens, Mpn140 from Mycoplasma pneumoniae, and Rv2837c from Mycobacterium tuberculosis. Like NrnA, these enzymes degrade nanoRNA and dephosphorylate pAp in vitro. However, they show dissimilar preferences for specific nanoRNA substrate lengths. Whereas NrnA prefers RNA 3-mers with a 10-fold higher specific activity compared to 5-mers, Rv2837c shows a preference for nanoRNA of a different length, namely, 2-mers. Mpn140 degrades Cy5-labeled nanoRNA substrates in vitro with activities varying within one order of magnitude as follows: 5-mer>4-mer>3-mer>2-mer. In agreement with these in vitro activities, both Rv2837c and Mpn140 can complement the lack of their functional counterparts in E. coli: CysQ and Orn. The NrnA homolog from Streptococcus mutans, SMU.1297, was previously shown to hydrolyze pAp and to complement an E. coli cysQ mutant. Here, we show that SMU.1297 can complement an E. coli orn(-) mutant, suggesting that having both pAp-phosphatase and nanoRNase activity is a common feature of NrnA homologs.
Published: 2012
Full Text: View/download PDF

45. Global regulation of gene expression in response to cysteine availability in Clostridium perfringens.

Author: André G, Haudecoeur E, Monot M, Ohtani K, Shimizu T, Dupuy B, and Martin-Verstraete I
Subjects: Amino Acid Sequence, Bacterial Proteins chemistry, Bacterial Proteins metabolism, Clostridium perfringens chemistry, Clostridium perfringens genetics, Molecular Sequence Data, Sequence Alignment, Sulfur metabolism, Bacterial Proteins genetics, Clostridium perfringens metabolism, Cysteine metabolism, Gene Expression Regulation, Bacterial
Abstract: Background: Cysteine has a crucial role in cellular physiology and its synthesis is tightly controlled due to its reactivity. However, little is known about the sulfur metabolism and its regulation in clostridia compared with other firmicutes. In Clostridium perfringens, the two-component system, VirR/VirS, controls the expression of the ubiG operon involved in methionine to cysteine conversion in addition to the expression of several toxin genes. The existence of links between the C. perfringens virulence regulon and sulfur metabolism prompted us to analyze this metabolism in more detail., Results: We first performed a tentative reconstruction of sulfur metabolism in C. perfringens and correlated these data with the growth of strain 13 in the presence of various sulfur sources. Surprisingly, C. perfringens can convert cysteine to methionine by an atypical still uncharacterized pathway. We further compared the expression profiles of strain 13 after growth in the presence of cystine or homocysteine that corresponds to conditions of cysteine depletion. Among the 177 genes differentially expressed, we found genes involved in sulfur metabolism and controlled by premature termination of transcription via a cysteine specific T-box system (cysK-cysE, cysP1 and cysP2) or an S-box riboswitch (metK and metT). We also showed that the ubiG operon was submitted to a triple regulation by cysteine availability via a T-box system, by the VirR/VirS system via the VR-RNA and by the VirX regulatory RNA.In addition, we found that expression of pfoA (theta-toxin), nagL (one of the five genes encoding hyaluronidases) and genes involved in the maintenance of cell redox status was differentially expressed in response to cysteine availability. Finally, we showed that the expression of genes involved in [Fe-S] clusters biogenesis and of the ldh gene encoding the lactate dehydrogenase was induced during cysteine limitation., Conclusion: Several key functions for the cellular physiology of this anaerobic bacterium were controlled in response to cysteine availability. While most of the genes involved in sulfur metabolism are regulated by premature termination of transcription, other still uncharacterized mechanisms of regulation participated in the induction of gene expression during cysteine starvation.
Published: 2010
Full Text: View/download PDF

46. Complex phenotypes of a mutant inactivated for CymR, the global regulator of cysteine metabolism in Bacillus subtilis.

Author: Hullo MF, Martin-Verstraete I, and Soutourina O
Subjects: Bacillus subtilis growth & development, Bacterial Proteins metabolism, Gene Expression Regulation, Bacterial, Phenotype, Bacillus subtilis genetics, Bacillus subtilis metabolism, Bacterial Proteins genetics, Cysteine metabolism, Gene Silencing, Genes, Regulator, Mutation
Abstract: We characterized various phenotypes of a mutant inactivated for CymR, the master regulator of cysteine metabolism in Bacillus subtilis. The deletion of cymR resulted in impaired growth in the presence of cystine and increased sensitivity to hydrogen peroxide-, disulfide-, paraquat- and tellurite-induced stresses. Estimation of metabolite pools suggested that these phenotypes could be the result of profound metabolic changes in the DeltacymR mutant including an increase of the intracellular cysteine pool and hydrogen sulfide formation, as well as a depletion of branched-chain amino acids.
Published: 2010
Full Text: View/download PDF

47. RcsB plays a central role in H-NS-dependent regulation of motility and acid stress resistance in Escherichia coli.

Author: Krin E, Danchin A, and Soutourina O
Subjects: Escherichia coli genetics, Escherichia coli metabolism, Escherichia coli Proteins genetics, Fimbriae Proteins genetics, Flagella metabolism, Hydrogen-Ion Concentration, Molecular Sequence Data, Movement, Operon, Phosphorylation, Phosphotransferases genetics, Regulatory Elements, Transcriptional, Suppression, Genetic, Trans-Activators genetics, Trans-Activators metabolism, Transcription Factors genetics, Escherichia coli physiology, Escherichia coli Proteins metabolism, Fimbriae Proteins metabolism, Flagella genetics, Gene Expression Regulation, Bacterial, Phosphotransferases metabolism, Stress, Physiological, Transcription Factors metabolism
Abstract: In Escherichia coli, hns mutants lack flagellar motility and display an increase in acid stress resistance. Spontaneous phenotypic revertants showed reversion of both H-NS-controlled phenotypes. In the present study, suppressor mutations were identified in the rcsB gene. In addition to RcsA, our experiments establish that H-NS indirectly controlled the RcsB regulator via repression of RcsD. We also show that RcsB(D56E), mimicking phosphorylated RcsB, interacts with GadE to form a RcsB-P/GadE complex, a general direct regulator of glutamate-, arginine- and lysine-dependent acid resistance pathways. In addition, we showed that H-NS positively affects motility via the flhDC master operon repression by RcsB. This substantiates the central role of RcsB in H-NS-mediated control of motility and acid stress resistance., (2010 Elsevier Masson SAS. All rights reserved.)
Published: 2010
Full Text: View/download PDF

48. The pleiotropic CymR regulator of Staphylococcus aureus plays an important role in virulence and stress response.

Author: Soutourina O, Dubrac S, Poupel O, Msadek T, and Martin-Verstraete I
Subjects: Animals, Cell Line, Copper pharmacology, Cystine pharmacology, Disulfides pharmacology, Female, Gene Deletion, Homeostasis physiology, Hydrogen Peroxide pharmacology, Macrophages cytology, Mice, Mice, Inbred BALB C, Oxidants pharmacology, Oxidative Stress drug effects, Oxidative Stress physiology, Staphylococcus aureus pathogenicity, Tellurium pharmacology, Up-Regulation physiology, Virulence, Cystine metabolism, Genes, Bacterial physiology, Macrophages microbiology, Staphylococcal Infections microbiology, Staphylococcus aureus genetics, Staphylococcus aureus metabolism
Abstract: We have characterized a novel pleiotropic role for CymR, the master regulator of cysteine metabolism. We show here that CymR plays an important role both in stress response and virulence of Staphylococcus aureus. Genes involved in detoxification processes, including oxidative stress response and metal ion homeostasis, were differentially expressed in a DeltacymR mutant. Deletion of cymR resulted in increased sensitivity to hydrogen peroxide-, disulfide-, tellurite- and copper-induced stresses. Estimation of metabolite pools suggests that this heightened sensitivity could be the result of profound metabolic changes in the DeltacymR mutant, with an increase in the intracellular cysteine pool and hydrogen sulfide formation. Since resistance to oxidative stress within the host organism is important for pathogen survival, we investigated the role of CymR during the infectious process. Our results indicate that the deletion of cymR promotes survival of S. aureus inside macrophages, whereas virulence of the DeltacymR mutant is highly impaired in mice. These data indicate that CymR plays a major role in virulence and adaptation of S. aureus for survival within the host.
Published: 2010
Full Text: View/download PDF

49. PssA is required for alpha-amylase secretion in Antarctic Pseudoalteromonas haloplanktis.

Author: Parrilli E, Giuliani M, Pezzella C, Danchin A, Marino G, and Tutino ML
Subjects: Bacterial Outer Membrane Proteins genetics, Cold Temperature, Cosmids, Gene Deletion, Gene Expression Regulation, Bacterial, Glycosyltransferases genetics, Pseudoalteromonas genetics, Bacterial Outer Membrane Proteins metabolism, Glycosyltransferases metabolism, Pseudoalteromonas enzymology, alpha-Amylases metabolism
Abstract: Extracellular protein secretion is an essential feature in bacterial physiology. The ability to efficiently secrete diverse hydrolytic enzymes represents a key nutritional strategy for all bacteria, including micro-organisms living in extreme and hostile habitats, such as cold environments. However, little is known about protein secretion mechanisms in psychrophilic bacteria. In this study, the recombinant secretion of a cold-adapted alpha-amylase in the Antarctic Gram-negative Pseudoalteromonas haloplanktis TAC125 was investigated. By a combination of several molecular techniques, the function of the pssA gene was related to alpha-amylase secretion in this psychrophilic bacterium. Deletion of the pssA gene completely abolished amylase secretion without affecting the extracellular targeting of other substrates mediated by canonical secretion systems. The pssA gene product, PssA, is a multidomain lipoprotein, predicted to be localized in the bacterial outer membrane, and displaying three TPR (tetratricopeptide repeat) domains and two LysM modules. Based on functional annotation of these domains, combined with the experimental results reported herein, we suggest a role for PssA as a molecular adaptor, in charge of recruiting other cellular components required for specific alpha-amylase secretion. To the best of our knowledge, no proteins exhibiting the same domain organization have previously been linked to protein secretion.
Published: 2010
Full Text: View/download PDF

50. Degradation of nanoRNA is performed by multiple redundant RNases in Bacillus subtilis.

Author: Fang M, Zeisberg WM, Condon C, Ogryzko V, Danchin A, and Mechold U
Subjects: Bacillus subtilis genetics, DNA metabolism, Genetic Complementation Test, Mutation, Oligoribonucleotides chemistry, Phylogeny, RNA chemistry, RNA metabolism, Ribonucleases classification, Ribonucleases genetics, Bacillus subtilis enzymology, Oligoribonucleotides metabolism, Ribonucleases metabolism
Abstract: Escherichia coli possesses only one essential oligoribonuclease (Orn), an enzyme that can degrade oligoribonucleotides of five residues and shorter in length (nanoRNA). Firmicutes including Bacillus subtilis do not have an Orn homolog. We had previously identified YtqI (NrnA) as functional analog of Orn in B. subtilis. Screening a genomic library from B. subtilis for genes that can complement a conditional orn mutant, we identify here YngD (NrnB) as a second nanoRNase in B. subtilis. Like NrnA, NrnB is a member of the DHH/DHHA1 protein family of phosphoesterases. NrnB degrades nanoRNA 5-mers in vitro similarily to Orn. Low expression levels of NrnB are sufficient for orn complementation. YhaM, a known RNase present in B. subtilis, degrades nanoRNA efficiently in vitro but requires high levels of expression for only partial complementation of the orn(-) strain. A triple mutant (nrnA(-), nrnB(-), yhaM(-)) in B. subtilis is viable and shows almost no impairment in growth. Lastly, RNase J1 seems also to have some 5'-to-3' exoribonuclease activity on nanoRNA and thus can potentially finish degradation of RNA. We conclude that, unlike in E. coli, degradation of nanoRNA is performed in a redundant fashion in B. subtilis.
Published: 2009
Full Text: View/download PDF

Catalog

Books, media, physical & digital resources

See catalog results

Searchworks

Select search scope, currently: Articles Catalog books, media & more in Jio Institute collections Articles journal articles & other e-resources

Search

Search Constraints

Refine your results

Search Limiters

Topic

Publication Year Range

Language

Publication Type

Journal

Region

Database

Publisher

104 results on '"Génétique des Génomes Bactériens"'

Search Results

Catalog

Select search scope, currently: Articles

Catalog

books, media & more in Jio Institute collections

Articles

journal articles & other e-resources