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51. Nocardia and Actinomyces

Author: Patrick Boiron, Petar Pujic, Blaine L. Beaman, Miora Ravalison, and Veronica Rodriguez-Nava
Subjects: biology, Physical Barrier, Intracellular parasite, Opportunistic infectious disease, Nocardiosis, medicine, Actinomycosis, Nocardia, medicine.disease, biology.organism_classification, Bacteria, Actinomyces, Microbiology
Abstract: Nocardiosis is an opportunistic infectious disease caused by a ubiquitous aerobic bacterium of the genus Nocardia that can be found in the environment. These intracellular bacteria are held responsible for many infections affecting the lungs, the brain or the skin, especially in immunocompromised patients. The taxonomy of this bacterium is complex and a multilocus sequence analysis may sometimes be necessary for a correct identification. Only three complete genomes of the genus Nocardia have so far been fully sequenced and referenced which constitutes an important stage in the study of this bacterium. Actinomyces belong to the normal indigenous microflora, so that they are considered as facultative pathogens. Actinomycosis is usually associated with the breakdown of normal physical barriers, such as disruption of mucosal membranes. Actinomycosis and nocardiosis are distinct diseases that respond to very different forms of therapy. Actinomyces can be readily distinguished from Nocardia by their distinct anaerobic versus aerobic patterns of growth after isolation from a clinical sample.
Published: 2015

52. List of Contributors

Author: Ernesto Abel-Santos, Soman N. Abraham, Shin-Ichi Aizawa, Michael J. Aldape, David C. Alexander, David G. Allison, Sebastian G.B. Amyes, Burt E. Anderson, Frank J. Anderson, Haike Antelmann, Frank W. Austin, Nieves Ayllón, Fang Bai, Angela Silva Barbosa, Michael R. Barer, Gregory S. Basarab, Blaine L. Beaman, Matthew Beard, Carolyn M. Black, Garry W. Blakely, Patrick Boiron, Hicham Bouabe, Joel A. Bozue, Cassandra L. Brinkman, Robert R. Brubaker, Amy E. Bryant, Robert J. Cain, Ana Cristina Calvo, Eneas Carvalho, Christian Capo, Santiago Castillo-Ramirez, John A. Chaddock, Robin R. Chamberland, Jill E. Clarridge, Christopher K. Cote, Sarah L. Cox, Sally J. Cutler, Donald J. Davidson, Nicholas P.J. Day, José de la Fuente, Magdia De Jesus, Julia R. Dorin, Charles J. Dorman, Ann E. Eakin, Paul G. Egland, Simon Ellis, Mark C. Enright, Benjamin A. Evans, Jake A. Everett, Joseph O. Falkinham, Feinan Fan, Huizhou Fan, Alexandra Faulds-Pain, Edward J. Feil, Cesar J. Figueroa, Åke Forsberg, Timothy J. Foster, Sandra M. Fox-Moon, Tatiana Rodrigues Fraga, David N. Fredricks, Nancy E. Freitag, María-Luisa García-López, Debora Garzetti, Curtis G. Gemmell, Joan A. Geoghegan, Thomas P. Gillis, Michael S. Gilmore, Robert J. Goldstone, Scott D. Gray-Owen, Nicole Guiso, Kelly N. Hallstrom, David R. Harper, Amanda T. Harrington, Jason B. Harris, John P. Hays, Yongqun He, Jared D. Heffron, Susan R. Heimer, Nicola J. High, Jan A. Hobot, Scott Hultgren, Tricia L. Humphreys, David A. Hunstad, Joseph U. Igietseme, Neil F. Inglis, Tim J.J. Inglis, Lourdes Isaac, Diane M. Janowicz, Shouguang Jin, Yongxin Jin, Anna-Lena Johansson, Randal N. Johnston, Jessica L. Jones, Sheryl S. Justice, Nadeem O. Kaakoush, Vasilios Kalas, Reeti Khare, I. King Jordan, Keiko Kobayashi, Katherine M. Kocan, Eija Könönen, Purnima S. Kumar, Peter A. Lambert, Richard J. Lamont, Ruiting Lan, Sue Lang, Didier Lereclus, Paul N. Levett, Xuefeng Li, Dongyou Liu, Shu-Lin Liu, Lin Ma, Steven D. Mahlen, Si Ming Man, Elisa Margolis, Thomas J. Marrie, Melissa J. Martin, Leonard W. Mayer, Malcolm McConville, Beth A. McCormick, Andrew McDowell, Brian J. McHugh, P. David McMullen, Gordon G. McSheffrey, Jean-Louis Mege, Adam J. Merritt, Michael F. Minnick, Hazel M. Mitchell, Donald Morrison, Kimberlee A. Musser, Masahiro Nagahama, Prescilla Emy Nagao, István Nagy, Emelie Näslund Salomonsson, Elizabeth J. Nazarian, Wright W. Nichols, Laila Noppa, Sophie Octavia, Masataka Oda, Itzhak Ofek, James D. Oliver, Patrick D. Olson, Yusuf Omosun, Edmund Ong, Rosario Osta, Andrés Otero, Petra C.F. Oyston, Daniel H. Paris, Robin Patel, Sheila Patrick, Joao H.F. Pedra, Brunella Posteraro, Patrizia Posteraro, Ian R. Poxton, Petar Pujic, Brittany J. Raffa, Alexander Rakin, Nalini Ramarao, Mario Ramirez, Miora Ravalison, Kurt D. Reed, Mark Reglinski, Allen L. Richards, Kristian Riesbeck, Thomas V. Riley, José-María Rodríguez-Calleja, Verónica Rodríguez-Nava, Kendra P. Rumbaugh, Kenneth E. Sanderson, Maurizio Sanguinetti, Jesús A. Santos, Renato L. Santos, Viveka Schaar, W. Michael Scheld, Jonathan E. Schmitz, Joseph D. Schwartzman, Maiara S. Severo, Nathan Sharon, Mark E. Shirtliff, Patricia J. Simner, David Šmajs, David G.E. Smith, Alexei Sorokin, Lisa D. Sprague, Shiranee Sriskandan, Dennis L. Stevens, Charles W. Stratton, Michal Strouhal, Yu Ching Su, Max Sussman, Elizabeth A. Talbot, Le Tang, Yi-Wei Tang, Ying Taur, Jeffrey M. Tessier, Julien Textoris, Nagaraja R. Thirumalapura, Hideaki Tsuge, Christine Y. Turenne, Miguel A. Valvano, José A. Vázquez-Boland, Suzanne J.C. Verhaegh, Ender Volkan, Waldemar Vollmer, William F. Wade, Ken B. Waites, Alan W. Walker, David H. Walker, Guiqing Wang, Qinning Wang, Xin Wang, Bruce Ward, Eleanor Watson, Ana A. Weil, Susan L. Welkos, Zhensong Wen, Nancy L. Wengenack, Lars F. Westblade, Hannah M. Wexler, Brendan W. Wren, Min Wu, Shangwei Wu, Weihui Wu, Li Xiao, Jing-Ren Zhang, Zuotao Zhao, and Guangming Zhong
Published: 2015

53. Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant

Author: Alberto Mendoza Herrera, Philippe Normand, María Antonia Cruz Hernández, Elizabeth G. Wilbanks, Alison M. Berry, Anna M O'Brien, Pascale Fournier, Katharina Pawlowski, Irina V. Demina, Petar Pujic, Theoden Vigil-Stenman, Kai Battenberg, Marc T. Facciotti, Claudine Médigue, Tomas Persson, Brian Vanden Heuvel, 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), Swedish Research Council [229-2005-679], Swedish Research Council VR [2007-17840-52674-16], CA Experiment Station project [PLS-2173-H], UC Davis Plant Sciences Graduate Fellowship, NSF GRFP [DGE-1148897], NSF [EF-0949453], ANR (BugsInACell) [ANR-13-BSV7-0013-03], ANR (Sesam) [ANR-10-BLAN-1708], UC Mexus-Conacyt [05-24], 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), and Börnke, Frederik
Subjects: General Science & Technology, Science, [SDV]Life Sciences [q-bio], Frankia, plante hôte, medicine.disease_cause, Rhizobium leguminosarum, Actinobacteria, Rhizobia, Bacterial Proteins, protéine bactérienne, Botany, Operon, medicine, Genetics, Datisca glomerata, Symbiosis, ComputingMilieux_MISCELLANEOUS, Phylogeny, régulation de l'expression génique, Multidisciplinary, Genome, biology, opéron, Bacterial, food and beverages, Rosales, Gene Expression Regulation, Bacterial, biology.organism_classification, Cucurbitaceae, Gene Expression Regulation, Candidatus, Medicine, curcubitaceae, Actinorhizal plant, symbiose, Genome, Bacterial, Research Article
Abstract: International audience; Frankia strains are nitrogen-fixing soil actinobacteria that can form root symbioses with actinorhizal plants. Phylogenetically, symbiotic frankiae can be divided into three clusters, and this division also corresponds to host specificity groups. The strains of cluster II which form symbioses with actinorhizal Rosales and Cucurbitales, thus displaying a broad host range, show suprisingly low genetic diversity and to date can not be cultured. The genome of the first representative of this cluster, Candidatus Frankia datiscae Dg1 (Dg1), a microsymbiont of Datisca glomerata, was recently sequenced. A phylogenetic analysis of 50 different housekeeping genes of Dg1 and three published Frankia genomes showed that cluster II is basal among the symbiotic Frankia clusters. Detailed analysis showed that nodules of Datisca glomerata, independent of the origin of the inoculum, contain several closely related cluster II Frankia operational taxonomic units. Actinorhizal plants and legumes both belong to the nitrogen-fixing plant clade, and bacterial signaling in both groups involves the common symbiotic pathway also used by arbuscular mycorrhizal fungi. However, so far, no molecules resembling rhizobial Nod factors could be isolated from Frankia cultures. Alone among Frankia genomes available to date, the genome of Dg1 contains the canonical nod genes nodA, nodB and nodC known from rhizobia, and these genes are arranged in two operons which are expressed in Datisca glomerata nodules. Furthermore, Frankia Dg1 nodC was able to partially complement a Rhizobium leguminosarum A34 nodC::Tn5 mutant. Phylogenetic analysis showed that Dg1 Nod proteins are positioned at the root of both alpha- and beta-rhizobial NodABC proteins. NodA-like acyl transferases were found across the phylum Actinobacteria, but among Proteobacteria only in nodulators. Taken together, our evidence indicates an Actinobacterial origin of rhizobial Nod factors.
Published: 2015

54. Immunological and chemical analysis of proteins fromEisenia foetidaearthworm

Author: Petar Pujic, José V. Torres, Ana Luisa Medina, Maria P. Carlos, José Angel Cova, and R. A. Vielma
Subjects: Two-dimensional gel electrophoresis, Lysis, Immunology, Earthworm, Biology, biology.organism_classification, Electrophoresis, Immune system, Biochemistry, Toxicity, biology.protein, Viability assay, Antibody, Agronomy and Crop Science, Food Science
Abstract: Previous studies have demonstrated the fibrinolitic and antibacterial activities of proteins from the earthworm Eisenia foetida (Ef) but their use as a food supplement for animals and humans is still being considered. We studied proteins from this worm in order to determine chemical composition (protein, fat and heavy metal levels), electrophoretic profile in SDS-PAGE and 2D gels, induction of humoral immune response in mice and toxicity in a human cell line. Chemical analysis revealed 61.8, 11.3 and 8.7 g% of proteins, fat and ash, respectively. Levels of heavy metals were low and similar to tunny fish. Sixteen bands were obtained by SDS-PAGE with a molecular weigh range of 6.9–205 kDa while twenty-three spots were observed following 2D gel electrophoresis. After three immunizations with Eisenia foetida lysate, high titer antibodies were produced without causing immediate hypersensitivity reactions. Good cell viability was observed when Ef proteins were added to a human cell line. These results suggest t...
Published: 2003

55. The kdgRKAT operon of Bacillus subtilis:detection of the transcript and regulation by the kdgR and ccpA genes

Author: Rozenn Dervyn, Alexei Sorokin, S. Dusko Ehrlich, and Petar Pujic
Subjects: Transcription, Genetic, Operon, Molecular Sequence Data, Bacillus subtilis, Biology, Microbiology, chemistry.chemical_compound, Bacterial Proteins, Transcription (biology), Gene expression, RNA, Messenger, Promoter Regions, Genetic, Gene, Regulator gene, Genetics, Base Sequence, Hexuronic Acids, Gene Expression Regulation, Bacterial, Blotting, Northern, biology.organism_classification, Culture Media, DNA-Binding Proteins, Repressor Proteins, RNA, Bacterial, Glucose, Terminator (genetics), Biochemistry, chemistry, CCPA, bacteria, Transcription Factors
Abstract: SUMMARY: Transcription of a new catabolic operon in Bacillus subtilis, involved in the late stages of galacturonic acid utilization, has been studied. The operon consists of four genes: kdgR, encoding the putative regulator protein; kdgK, encoding 2-keto-3-deoxyg I uconate kinase; kdgA, encoding 2-keto-3-deoxyg luconate-6-phosphate aldolase; and kdg, encoding a transporter. These four genes are organized in one transcriptional unit and map at 198" of the B. subtik chromosome. Primer extension experiments and Northern blot analysis show that an active σ-dependent promoter precedes kdgR and transcription is terminated at the putative pindependent terminator downstream of kdgr. The operon is negatively regulated by the kdgR and ccpA gene products, which belong t o the Lac1 family of transcription regulators. The expression of the genes in this operon can be induced by galacturonate and strongly repressed when glucose is present in the growth medium. Knockout mutations in genes kdgR and ccpA remove, respectively, the effects of galacturonate and glucose on the transcription of this operon.
Published: 1998

56. The Nocardia cyriacigeorgica GUH-2 genome shows ongoing adaptation of an environmental Actinobacteria to a pathogen's lifestyle

Author: Arnault Graindorge, Benoit Cournoyer, Veronica Rodriguez-Nava, Valérie Barbe, Philippe Normand, Sophie Mangenot, Yves Richard, Patrick Belli, Sébastien Ribun, Petar Pujic, Patrick Boiron, Anthony Zoropogui, David Roche, Didier Blaha, David Vallenet, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and 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)
Subjects: DNA, Bacterial, Evolution, [SDV]Life Sciences [q-bio], Biology, ENCODE, Genome, Synteny, Nocardia, Actinobacteria, Opportunistic pathogen, Evolution, Molecular, 03 medical and health sciences, Mice, Insertion sequences, Phylogenetics, COG, Genetics, Animals, Genome size, Phylogeny, 030304 developmental biology, Whole genome sequencing, 0303 health sciences, Comparative Genomic Hybridization, Mice, Inbred BALB C, Nocardia cyriacigeorgica, Virulence, 030306 microbiology, Ribosomal RNA, Regions of genomic plasticity, biology.organism_classification, Adaptation, Physiological, DNA Transposable Elements, Metabolome, Female, Genome, Bacterial, Biotechnology, Research Article
Abstract: BackgroundNocardia cyriacigeorgicais recognized as one of the most prevalent etiological agents of human nocardiosis. Human exposure to these Actinobacteria stems from direct contact with contaminated environmental matrices. The full genome sequence ofN. cyriacigeorgicastrain GUH-2 was studied to infer major trends in its evolution, including the acquisition of novel genetic elements that could explain its ability to thrive in multiple habitats.ResultsN. cyriacigeorgicastrain GUH-2 genome size is 6.19 Mb-long, 82.7% of its CDS have homologs in at least another actinobacterial genome, and 74.5% of these are found inN. farcinica. AmongN. cyriacigeorgicaspecific CDS, some are likely implicated in niche specialization such as those involved in denitrification and RuBisCO production, and are found in regions of genomic plasticity (RGP). Overall, 22 RGP were identified in this genome, representing 11.4% of its content. Some of these RGP encode a recombinase and IS elements which are indicative of genomic instability. CDS playing part in virulence were identified in this genome such as those involved in mammalian cell entry or encoding a superoxide dismutase. CDS encoding non ribosomal peptide synthetases (NRPS) and polyketide synthases (PKS) were identified, with some being likely involved in the synthesis of siderophores and toxins. COG analyses showed this genome to have an organization similar to environmental Actinobacteria.ConclusionN. cyriacigeorgicaGUH-2 genome shows features suggesting a diversification from an ancestral saprophytic state. GUH-2 ability at acquiring foreign DNA was found significant and to have led to functional changes likely beneficial for its environmental cycle and opportunistic colonization of a human host.
Published: 2013

57. Regulators of aerobic and anaerobic respiration in Bacillus subtilis

Author: Petar Pujic, R. Chesnut, Guofu Sun, S. D. Ehrlich, Alexei Sorokin, S. M. Birkey, M. F. Duggan, F M Hulett, E. Sharkova, Unité de recherche Génétique Microbienne (UGM), Institut National de la Recherche Agronomique (INRA), and ProdInra, Migration
Subjects: Anaerobic respiration, Transcription, Genetic, Operon, Molecular Sequence Data, Mutant, Bacillus subtilis, Biology, Nitrate Reductase, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Bacterial Proteins, Nitrate Reductases, Respiratory function, Anaerobiosis, Promoter Regions, Genetic, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Molecular Biology, Gene, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Base Sequence, Models, Genetic, 030306 microbiology, Chromosome Mapping, Membrane Proteins, Cytochrome b Group, biology.organism_classification, Aerobiosis, Phenotype, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Heme A, Regulon, chemistry, Biochemistry, Genes, Bacterial, Enzyme Induction, Mutation, Genes, Lethal, Signal Transduction, Research Article
Abstract: Two Bacillus subtilis genes, designated resD and resE, encode proteins that are similar to those of two-component signal transduction systems and play a regulatory role in respiration. The overlapping resD-resE genes are transcribed during vegetative growth from a very weak promoter directly upstream of resD. They are also part of a larger operon that includes three upstream genes, resABC (formerly orfX14, -15, and -16), the expression of which is strongly induced postexponentially. ResD is required for the expression of the following genes: resA, ctaA (required for heme A synthesis), and the petCBD operon (encoding subunits of the cytochrome bf complex). The resABC genes are essential genes which encode products with similarity to cytochrome c biogenesis proteins. resD null mutations are more deleterious to the cell than those of resE. resD mutant phenotypes, directly related to respiratory function, include streptomycin resistance, lack of production of aa3 or caa3 terminal oxidases, acid accumulation when grown with glucose as a carbon source, and loss of ability to grow anaerobically on a medium containing nitrate. A resD mutation also affected sporulation, carbon source utilization, and Pho regulon regulation. The data presented here support an activation role for ResD, and to a lesser extent ResE, in global regulation of aerobic and anaerobic respiration i B.subtilis.
Published: 1996

58. Genome sequence of Micromonospora lupini Lupac 08, isolated from root nodules of Lupinus angustifolius

Author: David Vallenet, Aurélie Lajus, Martha E. Trujillo, Philippe Normand, Lorena Carro, Pedro M. Coll, Pablo Alonso-Vega, Petar Pujic, Rodrigo Bacigalupe, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and 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)
Subjects: DNA, Bacterial, Root nodule, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Biology, Microbiology, Micromonospora lupini, Micromonospora, 03 medical and health sciences, Lupinus, Botany, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Legume, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, 030306 microbiology, Nucleic acid sequence, Sequence Analysis, DNA, respiratory system, biology.organism_classification, Genome Announcements, Lupinus angustifolius, Micromonosporaceae, Root Nodules, Plant, human activities, Genome, Bacterial
Abstract: Micromonospora strains have been isolated from diverse niches, including soil, water, and marine sediments and root nodules of diverse symbiotic plants. In this work, we report the genome sequence of Micromonospora lupini Lupac 08 isolated from root nodules of the wild legume Lupinus angustifolious .
Published: 2012

59. Genome sequence of Blastococcus saxobsidens DD2, a stone-inhabiting bacterium

Author: Maher Gtari, Elena Crotti, Daniele Daffonchio, Valérie Barbe, Benoit Vacherie, Petar Pujic, Bessem Chouaia, Faten Ghodhbane-Gtari, Lorenzo Brusetti, Jérôme Gury, Imen Essoussi, Claudine Médigue, Imen Nouioui, Imed Sbissi, Philippe Normand, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and 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)
Subjects: Whole genome sequencing, 0303 health sciences, 030306 microbiology, Ecology, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Biology, biology.organism_classification, Settore BIO/19 - Microbiologia Generale, Genome, Blastococcus saxobsidens, Microbiology, Actinobacteria, Genome Announcements, Calcarenite, 03 medical and health sciences, Genus, Molecular Biology, Botany, Stone sample, Bacteria, Genome, Bacterial, 030304 developmental biology
Abstract: International audience; Members of the genus Blastococcus have been isolated from sandstone monuments, as well as from sea, soil, plant, and snow samples. We report here the genome sequence of a member of this genus, Blastococcus saxobsidens strain DD2, isolated from below the surface of a Sardinian wall calcarenite stone sample.
Published: 2012

60. Genome Sequence of Radiation-Resistant Modestobacter marinus Strain BC501, a Representative Actinobacterium That Thrives on Calcareous Stone Surfaces

Author: Maher Gtari, Jérôme Gury, Petar Pujic, Benoit Vacherie, Bessem Chouaia, Elena Crotti, Daniele Daffonchio, Imen Essoussi, Ines Abbassi-Ghozzi, Faten Ghodhbane-Gtari, Alexandra Calteau, Lorenzo Brusetti, Valérie Barbe, Claudine Médigue, Imen Nouioui, Philippe Normand, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and 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)
Subjects: DNA, Bacterial, Geologic Sediments, Operon, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Settore BIO/19 - Microbiologia Generale, Microbiology, 03 medical and health sciences, Molecular Biology, Actinomycetales, Gene, Soil Microbiology, 030304 developmental biology, Whole genome sequencing, Genetics, 0303 health sciences, Base Sequence, Strain (chemistry), biology, 030306 microbiology, Chromosome Mapping, Chromosome, Sequence Analysis, DNA, Ribosomal RNA, biology.organism_classification, Genome Announcements, Soil microbiology, Genome, Bacterial
Abstract: International audience; Here we report the full genome sequence of Modestobacter marinus strain BC501, an actinobacterial isolate that thrives on stone surfaces. The generated chromosome is circular, with a length of 5.57 Mb and a G+C content of 74.13%, containing 5,445 protein-coding genes, 48 tRNAs, and 3 ribosomal operons.
Published: 2012

61. Lectin genes in the Frankia alni genome

Author: Pascale Fournier, Stéphanie Anchisi, Anne-Emmanuelle Hay, J Maréchal, Petar Pujic, Nicole Alloisio, Philippe Normand, 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), 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), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS )
Subjects: Frankia, Bacterial genome size, Root hair, Nodulation, Alnus, Biochemistry, Microbiology, Streptomyces, Genome, 03 medical and health sciences, Lectins, Escherichia coli, Genetics, Cloning, Molecular, Symbiosis, Molecular Biology, Gene, Phylogeny, 030304 developmental biology, Frankia alni, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, 0303 health sciences, biology, 030306 microbiology, General Medicine, Binding, biology.organism_classification, Fusion protein, Genes, Bacterial, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Root Nodules, Plant, Lectin, Genome, Bacterial
Abstract: International audience; Frankia alni strain ACN14a's genome was scanned for the presence of determinants involved in interactions with its host plant, Alnus spp. One such determinant type is lectin, proteins that bind speciWcally to sugar motifs. The genome of F. alni was found to contain 7 such lectincoding genes, Wve of which were of the ricinB-type. The proteins coded by these genes contain either only the lectin domain, or also a heat shock protein or a serine-threonine kinase domain upstream. These lectins were found to have several homologs in Streptomyces spp., and a few in other bacterial genomes among which none in Frankia EAN1pec and CcI3 and two in strain EUN1f. One of these F. alni genes, FRAAL0616, was cloned in E. coli, fused with a reporter gene yielding a fusion protein that was found to bind to both root hairs and to bacterial hyphae. This protein was also found to modify the dynamics of nodule formation in A. glutinosa, resulting in a higher number of nodules per root. Its role could thus be to permit binding of microbial cells to root hairs and help symbiosis to occur under conditions of low Frankia cell counts such as in pioneer situations.
Published: 2012

62. Genome Sequence of the Human- and Animal-Pathogenic Strain Nocardia cyriacigeorgica GUH-2

Author: Blaine L. Beaman, Manuelle Neto, Céline Colinon, Arnault Graindorge, Yves Richard, L Beaman, S Petit, Anthony Zoropogui, Sophie Mangenot, Amélie Deredjian, David Vallenet, Petar Pujic, Sylvie Nazaret, Benoit Cournoyer, Valérie Barbe, Didier Blaha, Veronica Rodriguez-Nava, Philippe Normand, David Roche, Patrick Boiron, 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 Astrophysique de Toulouse-Tarbes (LATT), Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées
Subjects: [SDV]Life Sciences [q-bio], Molecular Sequence Data, Virulence, Nocardia Infections, Biology, Microbiology, Genome, Nocardia, 03 medical and health sciences, Plasmid, medicine, Animals, Humans, Molecular Biology, 030304 developmental biology, Whole genome sequencing, Genetics, 0303 health sciences, 030306 microbiology, Nocardiosis, Nucleic acid sequence, Gene Expression Regulation, Bacterial, biology.organism_classification, medicine.disease, 3. Good health, Genome Announcements, Genome, Bacterial
Abstract: The pathogenic strain Nocardia cyriacigeorgica GUH-2 was isolated from a fatal human nocardiosis case, and its genome was sequenced. The complete genomic sequence of this strain contains 6,194,645 bp, an average G+C content of 68.37%, and no plasmids. We also identified several protein-coding genes to which N. cyriacigeorgica 's virulence can potentially be attributed.
Published: 2012

63. Genome Sequence of 'Candidatus Frankia datiscae' Dg1, the Uncultured Microsymbiont from Nitrogen-Fixing Root Nodules of the Dicot Datisca glomerata

Author: Alison M. Berry, Natalia Ivanova, James Han, Amrita Pati, David Bruce, David R. Benson, Roxanne Tapia, Petar Pujic, Len A. Pennacchio, Chris Detter, Hazuki Teshima, Sam Pitluck, Shunsheng Han, Tomas Persson, Matt Nolan, Miriam Land, Olga Chertkov, Katharina Pawlowski, Tanja Woyke, Philippe Normand, Brian Vanden Heuvel, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and 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)
Subjects: Root nodule, [SDV]Life Sciences [q-bio], Frankia, Molecular Sequence Data, Microbiology, 03 medical and health sciences, Magnoliopsida, Nitrogen Fixation, Cucurbitales, Botany, Datisca glomerata, Symbiosis, Molecular Biology, 030304 developmental biology, 0303 health sciences, biology, Base Sequence, 030306 microbiology, Rosales, biology.organism_classification, Genome Announcements, Nitrogen fixation, Candidatus, Actinorhizal plant, Root Nodules, Plant, Genome, Bacterial
Abstract: Members of the noncultured clade of Frankia enter into root nodule symbioses with actinorhizal species from the orders Cucurbitales and Rosales. We report the genome sequence of a member of this clade originally from Pakistan but obtained from root nodules of the American plant Datisca glomerata without isolation in culture.
Published: 2011

64. Transcriptomics of Actinorhizal Symbioses Reveals Homologs of the Whole Common Symbiotic Signaling Cascade

Author: Patrick Wincker, Clothilde Queiroux, Pascale Fournier, Nicole Alloisio, Valérie Hocher, Philippe Normand, Corrinne Da Silva, Patrick Doumas, Didier Bogusz, Petar Pujic, Hassen Gherbi, Florence Auguy, UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), 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), Diversité et adaptation des plantes cultivées (UMR DIAPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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), 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 Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, UMR - Interactions Plantes Microorganismes Environnement ( UMR IPME ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Université de Montpellier ( UM ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ), 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 ), Diversité et adaptation des plantes cultivées ( DIAPC ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Institut National de la Recherche Agronomique ( INRA ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ), 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 ), Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud]), 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), Biochimie et Physiologie Moléculaire des Plantes (BPMP), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut de Génomique d'Evry (IG), Université Paris-Saclay-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-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université 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), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Biologie François JACOB (JACOB), Département Biologie Végétale (DPT BV), and Institut National de la Recherche Agronomique (INRA)
Subjects: Transcription, Genetic, Physiology, Frankia, Plant Science, Alnus, Plant Root Nodulation, Genome, Transcriptome, Gene Expression Regulation, Plant, Databases, Genetic, Génétique des plantes, alnus glutinosa, Clade, ComputingMilieux_MISCELLANEOUS, Oligonucleotide Array Sequence Analysis, Plant Proteins, 2. Zero hunger, Genetics, azote, 0303 health sciences, Vegetal Biology, biology, actinorhizal symbioses, Up-Regulation, Actinorhizal plant, Signal Transduction, Molecular Sequence Data, Down-Regulation, Plants genetics, Genes, Plant, Models, Biological, légumineuse, 03 medical and health sciences, Symbiosis, Betulaceae, Sequence Homology, Nucleic Acid, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Botany, Genetic predisposition, Plants Interacting with Other Organisms, Gene, 030304 developmental biology, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, 030306 microbiology, Gene Expression Profiling, gène, génome, fungi, Membrane Proteins, Reproducibility of Results, biology.organism_classification, carbone, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, transcriptome, Biologie végétale
Abstract: L'article original est publié par The American Society of Plant Biologists; International audience; Comparative transcriptomics of two actinorhizal symbiotic plants, Casuarina glauca and Alnus glutinosa, was used to gain insight into their symbiotic programs triggered following contact with the nitrogen-fixing actinobacterium Frankia. Approximately 14,000 unigenes were recovered in roots and 3-week-old nodules of each of the two species. A transcriptomic array was designed to monitor changes in expression levels between roots and nodules, enabling the identification of up- and downregulated genes as well as root- and nodule-specific genes. The expression levels of several genes emblematic of symbiosis were confirmed by quantitative polymerase chain reaction. As expected, several genes related to carbon and nitrogen exchange, defense against pathogens, or stress resistance were strongly regulated. Furthermore, homolog genes of the common and nodule-specific signaling pathways known in legumes were identified in the two actinorhizal symbiotic plants. The conservation of the host plant signaling pathway is all the more surprising in light of the lack of canonical nod genes in the genomes of its bacterial symbiont, Frankia. The evolutionary pattern emerging from these studies reinforces the hypothesis of a common genetic ancestor of the Fabid (Eurosid I) nodulating clade with a genetic predisposition for nodulation.
Published: 2011

65. The Frankia alni symbiotic transcriptome

Author: Claudine Médigue, Masatoshi Yamaura, Petar Pujic, Philippe Normand, David Vallenet, Pascale Fournier, Ken-ichi Kucho, Kentaro Kakoi, Nicole Alloisio, Clothilde Queiroux, 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), 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), Graduate School of Science and Engineering, Kagoshima University, 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), 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 ), 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 ), and 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)
Subjects: Physiology, Computational biology, Biology, Alnus, Genes, Plant, Transcriptome, 03 medical and health sciences, Species Specificity, Gene Expression Regulation, Plant, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Nitrogen Fixation, Databases, Genetic, Symbiosis, 030304 developmental biology, Oligonucleotide Array Sequence Analysis, 0303 health sciences, 030306 microbiology, Gene Expression Profiling, Reproducibility of Results, Biological Transport, General Medicine, Gene Expression Regulation, Bacterial, Quaternary Ammonium Compounds, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genes, Bacterial, Frankia, Root Nodules, Plant, Agronomy and Crop Science, Rhizobium
Abstract: International audience; The actinobacteria Frankia spp. are able to induce the formation of nodules on the roots of a large spectrum of actinorhizal plants, where they convert dinitrogen to ammonia in exchange for plant photosynthates. In the present study, transcriptional analyses were performed on nitrogen-replete free-living Frankia alni cells and on Alnus glutinosa nodule bacteria, using whole-genome microarrays. Distribution of nodule-induced genes on the genome was found to be mostly over regions with high synteny between three Frankia spp. genomes, while nodule-repressed genes, which were mostly hypothetical and not conserved, were spread around the genome. Genes known to be related to nitrogen fixation were highly induced, nif (nitrogenase), hup2 (hydrogenase uptake), suf (sulfur-iron cluster), and shc (hopanoids synthesis). The expression of genes involved in ammonium assimilation and transport was strongly modified, suggesting that bacteria ammonium assimilation was limited. Genes involved in particular in transcriptional regulation, signaling processes, protein drug export, protein secretion, lipopolysaccharide, and peptidoglycan biosynthesis that may play a role in symbiosis were also identified. We also showed that this Frankia symbiotic transcriptome was highly similar among phylogenetically distant plant families Betulaceae and Myricaceae. Finally, comparison with rhizobia transcriptome suggested that F. alni is metabolically more active in symbiosis than rhizobia.
Published: 2010

66. Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations

Author: David Bruce, William S. Adney, Ravi D. Barabote, Gary Xie, Rebecca E. Parales, Philippe Normand, Thomas Brettin, Anamaria Necsulea, David H. Leu, Alison M. Berry, Céline Lavire, Vincent Daubin, Jean F. Challacombe, Petar Pujic, Xin Clare Xu, Chris Detter, Claudine Médigue, Alla Lapidus, Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Department of Plant Sciences [Univ California Davis] (Plant - UC Davis), University of California [Davis] (UC Davis), University of California (UC)-University of California (UC), 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-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), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), 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)-Université Claude Bernard Lyon 1 (UCBL), 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)-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), 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), National Renewable Energy Laboratory, Golden, Department of Microbiology, Department of Energy / Joint Genome Institute ( DOE ), Los Alamos National Laboratory ( LANL ), Department of Plant Sciences [Davis, CA], University of California [Davis] ( UC Davis ), 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 ), Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ), 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 ), University of California-University of California, 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), 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), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), and 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)
Subjects: DNA, Bacterial, Letter, Hot Temperature, Pseudogene, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, Genome, Evolution, Molecular, 03 medical and health sciences, Bacterial Proteins, Actinomycetales, Genetics, Gene, Genetics (clinical), 030304 developmental biology, [ SDV.BID ] Life Sciences [q-bio]/Biodiversity, 2. Zero hunger, Base Composition, Principal Component Analysis, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, 0303 health sciences, Ecology, 030306 microbiology, Thermophile, Prokaryote, Sequence Analysis, DNA, Chromosomes, Bacterial, 15. Life on land, Ribosomal RNA, biology.organism_classification, Adaptation, Physiological, Flagella, Proteome, Mobile genetic elements, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Genome, Bacterial
Abstract: We present here the complete 2.4 Mb genome of the cellulolytic actinobacterial thermophile, Acidothermus cellulolyticus 11B. New secreted glycoside hydrolases and carbohydrate esterases were identified in the genome, revealing a diverse biomass-degrading enzyme repertoire far greater than previously characterized, and significantly elevating the industrial value of this organism. A sizable fraction of these hydrolytic enzymes break down plant cell walls and the remaining either degrade components in fungal cell walls or metabolize storage carbohydrates such as glycogen and trehalose, implicating the relative importance of these different carbon sources. A novel feature of the A. cellulolyticus secreted cellulolytic and xylanolytic enzymes is that they are fused to multiple tandemly arranged carbohydrate binding modules (CBM), from families 2 and 3. Interestingly, CBM3 was found to be always N-terminal to CBM2, suggesting a functional constraint driving this organization. While the catalytic domains of these modular enzymes are either diverse or unrelated, the CBMs were found to be highly conserved in sequence and may suggest selective substrate-binding interactions. For the most part, thermophilic patterns in the genome and proteome of A. cellulolyticus were weak, which may be reflective of the recent evolutionary history of A. cellulolyticus since its divergence from its closest phylogenetic neighbor Frankia, a mesophilic plant endosymbiont and soil dweller. However, ribosomal proteins and non-coding RNAs (rRNA and tRNAs) in A. cellulolyticus showed thermophilic traits suggesting the importance of adaptation of cellular translational machinery to environmental temperature. Elevated occurrence of IVYWREL amino acids in A. cellulolyticus orthologs compared to mesophiles, and inverse preferences for G and A at the first and third codon positions also point to its ongoing thermoadaptation. Additional interesting features in the genome of this cellulolytic, hot-springs dwelling prokaryote include a low occurrence of pseudogenes or mobile genetic elements, an unexpected complement of flagellar genes, and presence of three laterally-acquired genomic islands of likely ecophysiological value.
Published: 2009

67. Differential Frankia protein patterns induced by phenolic extracts from Myricaceae seeds

Author: Maria P. Fernandez, J Maréchal, Petar Pujic, Jean Popovici, Emilie Bagnarol, Nicole Alloisio, Philippe Normand, 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 ), 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), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), and 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)
Subjects: Physiology, Frankia, Plant Science, Myricaceae, 03 medical and health sciences, chemistry.chemical_compound, Biosynthesis, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Protein biosynthesis, 030304 developmental biology, Gel electrophoresis, 0303 health sciences, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, biology, 030306 microbiology, Cell Biology, General Medicine, Metabolism, biology.organism_classification, chemistry, Biochemistry, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Actinorhizal plant, Bacteria
Abstract: Two-dimensional gel electrophoresis was used to identify differentially displayed proteins expressed during the early symbiotic interactions between the bacterium Frankia and actinorhizal plants. Myricaceae, the most primitive actinorhizal family, was used as an experimental model to study specificity mechanisms because it includes species with either narrow or large specificity. Seed phenolic extracts from two Myricaceae species, Myrica gale, a narrow specificity host and Morella cerifera considered as a promiscuous host, were used to induce three Frankia strains ACN14a, M16467 and Ea112. The global protein pattern was altered by exposure to the plant extracts. The addition of 30 mg I -1 of seed phenolic extracts provoked the inhibition of many protein biosynthesis whereas 1 and 10 mg I -1 induced a global reprogramming of Frankia protein pattern. Changes in intensity of 11 5 spots in response to seed extracts were detected and analyzed by matrix-assisted laser desorption/ ionization time of flight mass spectrometry. Fifty proteins were efficiently identified with Frankia protein data banks deduced from the sequences of Frankia strains ACN14a and EaN1pec genomes. Differential proteins were involved in different metabolism pathways such as glycolysis and gluconeo-genesis, transcription, fatty acids, carbohydrates, coenzymes and purines metabolisms. Chaperones biosynthesis and iron transport regulation, essential for nitrogen fixation, seem to be strain dependant. Several proteins possibly involved in the regulation of nodulation were also differentially expressed. The most obvious response was the upregulation of oxidative stress proteins such as FeSOD and Tellurium resistance proteins, suggesting a reorganization of Frankia metabolism to protect against host plant defense.
Published: 2007

68. Frankia alni proteome under nitrogen-fixing and nitrogen-replete conditions

Author: Servane Félix, David Vallenet, Philippe Normand, J Maréchal, Zoé Rouy, Petar Pujic, Nicole Alloisio, Claudine Médigue, 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-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), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-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 ), Structure et évolution des génomes ( SEG ), CNS-Université d'Évry-Val-d'Essonne ( UEVE ) -Centre National de la Recherche Scientifique ( CNRS ), 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), and 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)
Subjects: Cell signaling, Physiology, Frankia, Plant Science, 03 medical and health sciences, chemistry.chemical_compound, Biosynthesis, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Extracellular, Secretion, 030304 developmental biology, Frankia alni, 0303 health sciences, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, biology, 030306 microbiology, Nitrogenase, Cell Biology, General Medicine, biology.organism_classification, chemistry, Biochemistry, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Proteome, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Frankia alni induces root nodules on Alnus, in which the bacterium differentiates into nitrogen (N)-fixing cells called vesicles. In culture, F. alni also undergoes major morphological changes as it alternates between N-replete and N-fixing conditions. Lack of biologically available N induces the synthesis of vesicles in which nitrogenase is protected from molecular oxygen by a thick lipid hopanoid envelope. Very little is known about the molecular basis of Frankia–host interaction as well as Frankia cell differentiation. The recent determination of the complete genome sequence of F. alni strain ACN14a has permitted us to characterize its proteome, particularly in the extracellular compartment, which could be involved in Frankia–host interaction, and in the switch from N-replete to N-fixing conditions. To that end, 126 bacterial proteins were analyzed by two-dimensional protein gel electrophoresis and identified by matrix-assisted laser desorption/ionization time of flight fingerprinting using a F. alni proteome database. Interestingly, the extracellular fraction contains some glycolytic enzymes lacking secretion signals, already reported to be extracellularly localized in some streptococci, as well as some abundant stress-resistance proteins. As expected, several proteins involved in N assimilation and oxidative defense system were upregulated in F. alni grown under N-fixing vs N-replete conditions. Furthermore, two Raf kinase inhibitor protein homologs that could play a role in cellular signaling, and a hemoglobin-like protein HbN that could be involved in detoxification of nitric oxide were also upregulated. More surprising, a succinate dehydrogenase was strongly downregulated, which could be linked to the need of pyruvate for the biosynthesis of hopanoids or to reduced oxygen diffusion in vesicles.
Published: 2007

69. Phylogenetic analysis of polyketide synthase I domains from soil metagenomic libraries allows selection of promising clones

Author: Petar Pujic, Cyrille Jarrin, Guy Perrière, Patrick Robe, Aurélien Ginolhac, Timothy M. Vogel, Hélène Bertrand, Karine Tuphile, Pascal Simonet, Benjamin Gillet, Renaud Nalin, 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), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), 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)-Université Claude Bernard Lyon 1 (UCBL), 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)-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), and 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)
Subjects: 0106 biological sciences, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Molecular Sequence Data, 01 natural sciences, Applied Microbiology and Biotechnology, Genome, Polymerase Chain Reaction, Conserved sequence, Substrate Specificity, Microbial Ecology, 03 medical and health sciences, Polyketide, Phylogenetics, 010608 biotechnology, Polyketide synthase, Genomic library, Amino Acid Sequence, Cloning, Molecular, Conserved Sequence, Phylogeny, Soil Microbiology, Gene Library, Genetics, 0303 health sciences, Ecology, Phylogenetic tree, biology, 030306 microbiology, Kinetics, Metagenomics, biology.protein, Food Science, Biotechnology
Abstract: The metagenomic approach provides direct access to diverse unexplored genomes, especially from uncultivated bacteria in a given environment. This diversity can conceal many new biosynthetic pathways. Type I polyketide synthases (PKSI) are modular enzymes involved in the biosynthesis of many natural products of industrial interest. Among the PKSI domains, the ketosynthase domain (KS) was used to screen a large soil metagenomic library containing more than 100,000 clones to detect those containing PKS genes. Over 60,000 clones were screened, and 139 clones containing KS domains were detected. A 700-bp fragment of the KS domain was sequenced for 40 of 139 randomly chosen clones. None of the 40 protein sequences were identical to those found in public databases, and nucleic sequences were not redundant. Phylogenetic analyses were performed on the protein sequences of three metagenomic clones to select the clones which one can predict to produce new compounds. Two PKS-positive clones do not belong to any of the 23 published PKSI included in the analysis, encouraging further analyses on these two clones identified by the selection process.
Published: 2004

70. Actinomyces and Nocardia

Author: Blaine L. Beaman and Petar Pujic
Subjects: biology, Lower respiratory tract infection, Nocardiosis, medicine, Nocardia, Actinomycosis, Actinomycetales, biology.organism_classification, medicine.disease, Actinomycetoma, Actinomyces, Bacteria, Microbiology
Abstract: Publisher Summary Actinomyces are Gram-positive, pleiomorphic, often filamentous, rod-shaped bacteria belonging to the family Actinomycetales. Morphologically, many species resemble nocardioform actinomycetes whereas others are more coryneform. Most Actinomyces species are parasitic and represent part of the normal flora on the mucous membranes, especially of the oral and gastro intestinal tract of mammals and humans. Two broad categories of disease caused by various species of Actinomyces arc recognized in humans. These include: (1) actinomvcosis found anywhere in the body and (2) plaque formation on the teeth with subsequent periodontal disease. The genus Nocardia consists of partially acid-fast, Gram-positive, strictly aerobic, and non-motile bacteria that produce branching filamentous cells during the growth phase. A wide variety, of animals, and some plants, may become infected by Nocardia species. The most prevalent form is nocardiosis, although the most apparent disease visually is nocardially-induced actinomycetoma. In humans, nocardiosis often starts as a lower respiratory tract infection that may begin with flu-like symptoms. The infection may be self-limited or it may progress with a varied pulmonary presentation.
Published: 2002

71. The kdgRKAT operon of Bacillus subtilis: Detection of the transcript and regulation by the kdgR and ccpA genes

Author: Petar Pujic, Rozenn Dervyn, Sorokin, A., Ehrlich, S. D., Unité de recherche Génétique Microbienne (UGM), Institut National de la Recherche Agronomique (INRA), and ProdInra, Migration
Subjects: [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology
Abstract: 1 tables 4 graph.; International audience
Published: 1998

72. The complete genome sequence of the gram-positive bacterium Bacillus subtilis

Author: Daniel Portetelle, Angelo Tognoni, Vladimir Lazarevic, Hiroshi Yoshikawa, Carlo V. Bruschi, A. Düsterhöft, H. Wedler, J.-J. Codani, S. C. Brignell, Masaya Fujita, B. Roche, Motoki Mizuno, Junichi Sekiguchi, P. Koetter, Miyuki Kumano, K. Yoshida, Richard A. Daniel, Alain Brans, Y. Kobayashi, Jeff Errington, B.-S. Shin, BJ Guy, Simone J. Séror, Peter Terpstra, S. Fuma, Y. Kasahara, Mary O'Reilly, F Scoffone, Claudine Médigue, R. Wambutt, Matthias Rose, G. Koningstein, Nathalie Galleron, M. G. Bertero, M. Klaerr-Blanchard, Bernard Joris, B. Oudega, Michael A. Rieger, G. Alloni, Mitsuhiro Itaya, Simon Ming-Yuen Lee, Bénédicte Purnelle, Steffen Porwollik, Marie-Françoise Hullo, Alla Lapidus, Valentina Tosato, Colin R. Harwood, N. Medina, Catherine Mauël, Kevin M. Devine, Kanako Kurita, Ken-Ichi Takemaru, Nicola J. Cummings, Susanne Krogh, Louis M. Jones, Micheline Vandenbol, Rainer Borriss, K. Ogawa, Alain Levine, E. Presecan, Bolotin Ap, E. Scanlan, Hisashi Yoshikawa, Michio Takeuchi, G. Guiseppi, J. Lauber, Stanislav Dusko Ehrlich, Ivan Moszer, D. Moestl, K. Yasumoto, S. Schleich, S. Hosono, E. Tacconi, E. Wedler, Georges Rapoport, E. J. Golightly, Sierd Bron, T. Takagi, Shigeki Uchiyama, C. Fabret, Kazuko Haga, Alexei Sorokin, L. Boursier, Pascale Serror, Vasco Azevedo, Guido Grandi, Petar Pujic, A. M. Prescott, Sa Youl Ghim, A. Ogiwara, François Denizot, Hiroki Yamamoto, Blazenka Soldo, R. Schroeter, S. Masuda, S. Brouillet, André Goffeau, Agnieszka Sekowska, A. Tamakoshi, Naotake Ogasawara, Alain Viari, Eugenio Ferrari, V. Capuano, Eduardo P. C. Rocha, Dimitri Karamata, S. Lardinois, D. Foulger, Michiel A. Noback, Ian F. Connerton, Katsunori Yata, Victor Parro, Alessandra M. Albertini, Alain Hénaut, Carsten Klein, C. Fritz, Toshitada Sato, P. Winters, Alessandro Galizzi, Yoshito Sadaie, Stacey Reynolds, H. Liu, Hideyuki Takahashi, Tetsu Tanaka, David Noone, S. Borchert, S. Nakai, T. Weitzenegger, Kunio Yamane, F. Kunst, S.-H. Park, P. T. Emmerson, M. Braun, Emmanuelle Zumstein, Yasutaro Fujita, Philippe Bessières, Noel Carter, Antoine Danchin, A. Vassarotti, B. Caldwell, M. Rey, Françoise Vannier, Carlo Rivolta, Thomas Pohl, Rafael P. Mellado, H. Hilbert, K. D. Entian, Jacques Haiech, Siger Holsappel, Soo Keun Choi, Philippe Glaser, and Anil Wipat
Subjects: DNA, Bacterial, Cloning, Organism, Molecular Sequence Data, Bacillus subtilis, Biology, TERMINATORS, Genome, REGION, Microbiology, Bacterial Proteins, STRANDS, Gene density, Gene family, YEAST ARTIFICIAL CHROMOSOMES, Gene, Prophage, Genetics, Multidisciplinary, COMPETENCE, ACIDS, biology.organism_classification, DNA-SEQUENCES, REPLICATION, Horizontal gene transfer, Minimal genome, PROJECT, Genome, Bacterial
Abstract: Bacillus subtilis is the best-characterized member of the Gram-positive bacteria. Its genome of 4,214,810 base pairs comprises 4,100 protein-coding genes. Of these protein-coding genes, 53% are represented once, while a quarter of the genome corresponds to several gene families that have been greatly expanded by gene duplication, the largest family containing 77 putative ATP-binding transport proteins. In addition, a large proportion of the genetic capacity is devoted to the utilization of a variety of carbon sources, including many plant-derived molecules. The identification of five signal peptidase genes, as well as several genes for components of the secretion apparatus, is important given the capacity of Bacillus strains to secrete large amounts of industrially important enzymes. Many of the genes are involved in the synthesis of secondary metabolites, including antibiotics, that are more typically associated with Streptomyces species. The genome contains at least ten prophages or remnants of prophages, indicating that bacteriophage infection has played an important evolutionary role in horizontal gene transfer, in particular in the propagation of bacterial pathogenesis.
Published: 1997

73. Organization of the Bacillus subtilis 168 chromosome between kdg and the attachment site of the SP beta prophage: use of Long Accurate PCR and yeast artificial chromosomes for sequencing

Author: Stanislav Dusko Ehrlich, Petar Pujic, Alexei Sorokin, Nathalie Galleron, and V. Capuano
Subjects: Yeast artificial chromosome, Genetics, Contig, Sequence Homology, Amino Acid, Molecular Sequence Data, Nucleic acid sequence, Chromosome Mapping, Promoter, Biology, Chromosomes, Bacterial, Microbiology, Genome, Polymerase Chain Reaction, DNA sequencing, Bacterial Proteins, Genes, Bacterial, Attachment Sites, Microbiological, Amino Acid Sequence, Gene, Chromosomes, Artificial, Yeast, Lysogeny, Prophage, Genome, Bacterial, Bacillus subtilis
Abstract: Within the Bacillus subtilis genome sequencing project, the region between lysA and ilvA was assigned to our laboratory. In this report we present the sequence of the last 36 kb of this region, between the kdg operon and the attachment site of the SP beta prophage. A two-step strategy was used for the sequencing. In the first step, total chromosomal DNA was cloned in phage M13-based vectors and the clones carrying inserts from the target region were identified by hybridization with a cognate yeast artificial chromosome (YAC) from our collection. Sequencing of the clones allowed us to establish a number of contigs. In the second step the contigs were mapped by Long Accurate (LA) PCR and the remaining gaps closed by sequencing of the PCR products. The level of sequence inaccuracy due to LA PCR errors appeared to be about 1 in 10,000, which does not affect significantly the final sequence quality. This two-step strategy is efficient and we suggest that it can be applied to sequencing of longer chromosomal regions. The 36 kb sequence contains 38 coding sequences (CDSs), 19 of which encode unknown proteins. Seven genetic loci already mapped in this region, xpt, metB, ilvA, ilvD, thyB, dfrA and degR were identified. Eleven CDSs were found to display significant similarities to known proteins from the data banks, suggesting possible functions for some of the novel genes: cspD may encode a cold shock protein; bcsA, the first bacterial homologue of chalcone synthase; exol, a 5' to 3' exonuclease, similar to that of DNA polymerase I of Escherichia coli; and bsaA, a stress-response-associated protein. The protein encoded by yplP has homology with the transcriptional NifA-like regulators. The arrangement of the genes relative to possible promoters and terminators suggests 19 potential transcription units.
Published: 1996

74. A new approach using multiplex long accurate PCR and yeast artificial chromosomes for bacterial chromosome mapping and sequencing

Author: Nathalie Galleron, Alla Lapidus, V. Capuano, Stanislav Dusko Ehrlich, Alexei Sorokin, Petar Pujic, Unité de recherche Génétique Microbienne (UGM), Institut National de la Recherche Agronomique (INRA), and ProdInra, Migration
Subjects: DNA, Bacterial, clone (Java method), Yeast artificial chromosome, Sequence analysis, [SDV]Life Sciences [q-bio], Molecular Sequence Data, AMPLIFICATION CHAINE POLYMERASE, Bacillus subtilis, Polymerase Chain Reaction, 03 medical and health sciences, Bacterial Proteins, Genetics, Multiplex, rRNA Operon, Chromosomes, Artificial, Yeast, Genetics (clinical), ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Bacterial artificial chromosome, Base Sequence, biology, 030306 microbiology, Circular bacterial chromosome, DNA Helicases, Chromosome Mapping, Sequence Analysis, DNA, Chromosomes, Bacterial, biology.organism_classification, Electrophoresis, Gel, Pulsed-Field, [SDV] Life Sciences [q-bio], RRNA Operon, DnaB Helicases
Abstract: An efficient approach for structural studies on bacterial chromosomes is presented. It is based on high-resolution PCR map construction by using a multiplex long accurate PCR (MLA PCR) protocol and a YAC clone carrying the region to be mapped as indicator. The high-resolution PCR map of the bacillus subtilis rrnB-dnaB region is presented as an example. Data are also presented on the use of DNA generated by LA PCR for sequencing; they are relevant to LA PCR induced mutations and justify the application of such mapping for sequencing long stretches of bacterial chromosomes.
Published: 1996

75. Ribosomal RNA Operons inStreptomyces rimosus:Sequence of therrnF and Comparative Analysis of rrn Promoter Regions

Author: Petar Pujic, Sonja Durajlija, Suada Panda, Andreja Mikoc, Miroslav Plohl, Vera Gamulin, 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), and Pujic, Petar
Subjects: [SDE] Environmental Sciences, rRNA operon, streptomycetes, [SDE]Environmental Sciences, bacteria, multiple promoters, X62884
Abstract: International audience; One of the six Streptomyces rimosus ribosomal RNA operons, rrnF, was completely sequenced. rRNA genes, arranged in the order 16S-23S-5S, encode 1529, 3121 and 120 nucleotides long rRNAs, respectively. tRNA genes were not found in the 16S-23S spacer region, or at the 3' end of the operon. Only one putative promoter of the rrnF operon (P4) was identified by sequence similarity. Open reading frames, located on both sides of the rrnF, are conserved at the same positions in some other Streptomyces rRNA operons. According to the conserved EcoRI sites, two more types of promoter regions exist in the five remaining S. rimosus rRNA operons. Three operons have type I promoter region and a sequenced representative contained four putative promoters (P1-P4). Type II promoter region, present in two operons, is most likely deletion derivative of the type I and misses P2 and P3 promoters. Only the most proximal promoter, P4, and downstream DNA sequences are highly conserved in all three analysed promoter regions of S. rimosus rRNA operons.

76. The Bacillus subtilis chromosome region encoding homologues of the Escherichia coli mssA and rpsA gene products

Author: Petar Pujic, Stanislav Dusko Ehrlich, Pascale Serror, Alexei Sorokin, Vasco Azevedo, ProdInra, Migration, Unité de recherche Génétique Microbienne (UGM), and Institut National de la Recherche Agronomique (INRA)
Subjects: Ribosomal Proteins, Molecular Sequence Data, Bacillus subtilis, Biology, Gram-Positive Bacteria, medicine.disease_cause, Microbiology, Homology (biology), Gene product, Open Reading Frames, 03 medical and health sciences, Bacterial Proteins, Ribosomal protein, Gene expression, Escherichia coli, medicine, Amino Acid Sequence, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Gene, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, 0303 health sciences, Reporter gene, Base Sequence, Sequence Homology, Amino Acid, 030306 microbiology, Escherichia coli Proteins, Phosphotransferases, Sequence Analysis, DNA, Chromosomes, Bacterial, biology.organism_classification, Molecular biology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Genes, Bacterial
Abstract: SUMMARY: A gene was found in Bacillus subtilis which encodes a protein highly homologous to the Escherichia coli rpsA gene product, the S1 ribosomal protein. The B. subtilis protein contains the domain responsible for binding to ribosomes and two S1 motifs, instead of four as found in the E. coli protein. The B. subtilis protein is similar in this way to the equivalent protein of plant chloroplast ribosomes, supposed to be the counterpart of E. coli S1. The gene is expressed during vegetative growth in B. subtilis at the transcriptional and translational levels, as judged by Northern hybridization and expression in a translational fusion with a reporter gene. In contrast to the E. coli situation, it can be inactivated without dramatic effects on cell viability. Southern hybridization of the B. subtilis DNA fragment encoding this gene revealed specific homologous fragments in all other Gram-positive bacteria tested. The hybridization pattern with B. stearothermophilus suggests the presence of at least two homologous genes in this bacterium. We show that in B. subtilis the ORF preceding the rpsA homologue encodes a protein which is highly similar to the product of the E. coli mssA gene which is located upstream of rpsA. Again, in contrast to the E. coli situation, where these genes are co-transcribed, in B. subtilis they are separated by a transcription terminator and the mssA homologue is transcribed during sporulation. We suggest that during the evolution very similar structures and genetic organization of these two genes were conserved but acquired different functions in Gram-negative and Gram-positive bacteria.

77. Ribosomal RNA Operons in Streptomyces rimosus: Sequence of the rrnF and Comparative Analysis of rrn Promoter Regions

Author: Petar Pujic, Durajlija-Žinić, S., Pandža, S., Mikoč, A., Plohl, M., and Gamulin, V.

78. Chitinolytic actinobacteria isolated from an Algerian semi-arid soil: development of an antifungal chitinase-dependent assay and GH18 chitinase gene identification

Author: Hasna Boubakri, Petar Pujic, Meriem Gasmi, Philippe Normand, Lorena Carro, M. Kitouni, Laboratoire de Biologie Appliquée et Santé, Université des Frères Mentouri (Constantine 1), Laboratoire de Génie Microbiologie et Application, 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), Ministry of Higher Education and Scientific Research, Algeria, Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and 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)
Subjects: 0106 biological sciences, Catabolic repression, [SDV]Life Sciences [q-bio], Microorganism, Micromonospora, 01 natural sciences, Applied Microbiology and Biotechnology, Streptomyces, Microbiology, Actinobacteria, Gene capture, 03 medical and health sciences, chemistry.chemical_compound, Chitin, Microbial ecology, 010608 biotechnology, antifungal agent, Antifungal activity, genes, BOX-PCR, 0303 health sciences, GH18, biology, 030306 microbiology, gène, Chitinase, Ribosomal RNA, biology.organism_classification, chemistry, biology.protein, antifongique
Abstract: The purpose of this study was to explore the microbial potential of a semi-arid sandy soil from south-central Algeria in order to isolate new chitinolytic actinobacteria. This soil is subjected to high temperatures (up to 43 degrees C) and has low nutrient content. Strains were isolated by plating soil suspensions on Bennett and Colloidal Chitin (CCM) medium. An initial clustering of isolates was made through BOX-PCR genetic profiling. Next, a 16S rRNA gene sequencing of representative isolates was realized. We also identified optimum physicochemical conditions for chitinolytic activity. A rapid in vitro assay based on glucose catabolic repression was developed to select isolates having a chitinase-dependent antifungal activity against two phytopathogenic fungi. Gene identification of glycosyl hydrolase family 18 (GH18) permitted us to assess the divergence of chitinase genes. Forty isolates were obtained from the semi-arid sandy soil. The molecular identification permitted us to assign them to Streptomyces or Micromonospora genera with seven possibly new bacterial species. For chitinolytic activity, 100% of isolates were able to grow and degrade colloidal chitin at pH 7 and at a temperature ranging from 30 to 40 degrees C. We also observed that Micromonospora strains had atypical activity patterns, with a strong chitinase activity maintained at high temperature. Finally, three strains presented an interesting chitinolytic potential to reduce fungal growth with new GH18 sequences. This study presents a new rapid method to detect antifungal chitinase-dependent activity that allowed to identify potentially new species of actinobacteria and new GH18 gene sequences.

79. Organization of the Bacillus subtilis 168 chromosome between kdg and the attachment site of the SPbeta prophage : use of long accurate PCR and yeast artificial chromosomes for sequencing

Author: Capuano, V., Nathalie Galleron, Petar Pujic, Sorokin, A., Ehrlich, S. D., ProdInra, Migration, Unité de recherche Génétique Microbienne (UGM), and Institut National de la Recherche Agronomique (INRA)
Subjects: [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, AMPLIFICATION CHAINE POLYMERASE, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, ComputingMilieux_MISCELLANEOUS
Abstract: International audience

80. The root symbiosis between Frankia bacterium and actinorhizal plants | La symbiose racinaire entre la bactérie frankia et les plantes actinorhiziennes

Author: Petar Pujic and Normand, P.

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80 results on '"Petar Pujic"'

51. Nocardia and Actinomyces

52. List of Contributors

53. Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant

54. Immunological and chemical analysis of proteins fromEisenia foetidaearthworm

55. The kdgRKAT operon of Bacillus subtilis:detection of the transcript and regulation by the kdgR and ccpA genes

56. The Nocardia cyriacigeorgica GUH-2 genome shows ongoing adaptation of an environmental Actinobacteria to a pathogen's lifestyle

57. Regulators of aerobic and anaerobic respiration in Bacillus subtilis

58. Genome sequence of Micromonospora lupini Lupac 08, isolated from root nodules of Lupinus angustifolius

59. Genome sequence of Blastococcus saxobsidens DD2, a stone-inhabiting bacterium

60. Genome Sequence of Radiation-Resistant Modestobacter marinus Strain BC501, a Representative Actinobacterium That Thrives on Calcareous Stone Surfaces

61. Lectin genes in the Frankia alni genome

62. Genome Sequence of the Human- and Animal-Pathogenic Strain Nocardia cyriacigeorgica GUH-2

63. Genome Sequence of 'Candidatus Frankia datiscae' Dg1, the Uncultured Microsymbiont from Nitrogen-Fixing Root Nodules of the Dicot Datisca glomerata

64. Transcriptomics of Actinorhizal Symbioses Reveals Homologs of the Whole Common Symbiotic Signaling Cascade

65. The Frankia alni symbiotic transcriptome

66. Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations

67. Differential Frankia protein patterns induced by phenolic extracts from Myricaceae seeds

68. Frankia alni proteome under nitrogen-fixing and nitrogen-replete conditions

69. Phylogenetic analysis of polyketide synthase I domains from soil metagenomic libraries allows selection of promising clones

70. Actinomyces and Nocardia

71. The kdgRKAT operon of Bacillus subtilis: Detection of the transcript and regulation by the kdgR and ccpA genes

72. The complete genome sequence of the gram-positive bacterium Bacillus subtilis

73. Organization of the Bacillus subtilis 168 chromosome between kdg and the attachment site of the SP beta prophage: use of Long Accurate PCR and yeast artificial chromosomes for sequencing

74. A new approach using multiplex long accurate PCR and yeast artificial chromosomes for bacterial chromosome mapping and sequencing

75. Ribosomal RNA Operons inStreptomyces rimosus:Sequence of therrnF and Comparative Analysis of rrn Promoter Regions

76. The Bacillus subtilis chromosome region encoding homologues of the Escherichia coli mssA and rpsA gene products

77. Ribosomal RNA Operons in Streptomyces rimosus: Sequence of the rrnF and Comparative Analysis of rrn Promoter Regions

78. Chitinolytic actinobacteria isolated from an Algerian semi-arid soil: development of an antifungal chitinase-dependent assay and GH18 chitinase gene identification

79. Organization of the Bacillus subtilis 168 chromosome between kdg and the attachment site of the SPbeta prophage : use of long accurate PCR and yeast artificial chromosomes for sequencing

80. The root symbiosis between Frankia bacterium and actinorhizal plants | La symbiose racinaire entre la bactérie frankia et les plantes actinorhiziennes

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