Search

Your search keyword '"Schenowitz, A"' showing total 9 results
Start Over Author "Schenowitz, A" Topic genetics
9 results on '"Schenowitz, A"'

2. Being pathogenic, plastic, and sexual while living with a nearly minimal bacterial genome.

Author

Pascal Sirand-Pugnet, Carole Lartigue, Marc Marenda, Daniel Jacob, Aurélien Barré, Valérie Barbe, Chantal Schenowitz, Sophie Mangenot, Arnaud Couloux, Beatrice Segurens, Antoine de Daruvar, Alain Blanchard, and Christine Citti

Subjects
Genetics, QH426-470
Abstract

Mycoplasmas are commonly described as the simplest self-replicating organisms, whose evolution was mainly characterized by genome downsizing with a proposed evolutionary scenario similar to that of obligate intracellular bacteria such as insect endosymbionts. Thus far, analysis of mycoplasma genomes indicates a low level of horizontal gene transfer (HGT) implying that DNA acquisition is strongly limited in these minimal bacteria. In this study, the genome of the ruminant pathogen Mycoplasma agalactiae was sequenced. Comparative genomic data and phylogenetic tree reconstruction revealed that approximately 18% of its small genome (877,438 bp) has undergone HGT with the phylogenetically distinct mycoides cluster, which is composed of significant ruminant pathogens. HGT involves genes often found as clusters, several of which encode lipoproteins that usually play an important role in mycoplasma-host interaction. A decayed form of a conjugative element also described in a member of the mycoides cluster was found in the M. agalactiae genome, suggesting that HGT may have occurred by mobilizing a related genetic element. The possibility of HGT events among other mycoplasmas was evaluated with the available sequenced genomes. Our data indicate marginal levels of HGT among Mycoplasma species except for those described above and, to a lesser extent, for those observed in between the two bird pathogens, M. gallisepticum and M. synoviae. This first description of large-scale HGT among mycoplasmas sharing the same ecological niche challenges the generally accepted evolutionary scenario in which gene loss is the main driving force of mycoplasma evolution. The latter clearly differs from that of other bacteria with small genomes, particularly obligate intracellular bacteria that are isolated within host cells. Consequently, mycoplasmas are not only able to subvert complex hosts but presumably have retained sexual competence, a trait that may prevent them from genome stasis and contribute to adaptation to new hosts.

Published
2007
Full Text
View/download PDF

3. Comparative genomic and proteomic analyses of two Mycoplasma agalactiae strains: clues to the macro- and micro-events that are shaping mycoplasma diversity

Author

Mangenot Sophie, Barbe Valérie, Sagné Eveline, Marenda Marc S, Sirand-Pugnet Pascal, Nouvel Laurent X, Schenowitz Chantal, Jacob Daniel, Barré Aurélien, Claverol Stéphane, Blanchard Alain, and Citti Christine

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background While the genomic era is accumulating a tremendous amount of data, the question of how genomics can describe a bacterial species remains to be fully addressed. The recent sequencing of the genome of the Mycoplasma agalactiae type strain has challenged our general view on mycoplasmas by suggesting that these simple bacteria are able to exchange significant amount of genetic material via horizontal gene transfer. Yet, events that are shaping mycoplasma genomes and that are underlining diversity within this species have to be fully evaluated. For this purpose, we compared two strains that are representative of the genetic spectrum encountered in this species: the type strain PG2 which genome is already available and a field strain, 5632, which was fully sequenced and annotated in this study. Results The two genomes differ by ca. 130 kbp with that of 5632 being the largest (1006 kbp). The make up of this additional genetic material mainly corresponds (i) to mobile genetic elements and (ii) to expanded repertoire of gene families that encode putative surface proteins and display features of highly-variable systems. More specifically, three entire copies of a previously described integrative conjugative element are found in 5632 that accounts for ca. 80 kbp. Other mobile genetic elements, found in 5632 but not in PG2, are the more classical insertion sequences which are related to those found in two other ruminant pathogens, M. bovis and M. mycoides subsp. mycoides SC. In 5632, repertoires of gene families encoding surface proteins are larger due to gene duplication. Comparative proteomic analyses of the two strains indicate that the additional coding capacity of 5632 affects the overall architecture of the surface and suggests the occurrence of new phase variable systems based on single nucleotide polymorphisms. Conclusion Overall, comparative analyses of two M. agalactiae strains revealed a very dynamic genome which structure has been shaped by gene flow among ruminant mycoplasmas and expansion-reduction of gene repertoires encoding surface proteins, the expression of which is driven by localized genetic micro-events.

Published
2010
Full Text
View/download PDF

4. Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography

Author

Ying Wang, Chantal Schenowitz, Jeffrey P. Tomkins, Claudine Médigue, Luis Gabriel Wall, Claudio Valverde, Benoit Cournoyer, Nadia Demange, Philippe Normand, Alison M. Berry, Louis S. Tisa, Juliana E. Mastronunzio, David Vallenet, David R. Benson, Pascal Lapierre, Emilie Bagnarol, Tania Rawnsley, Nathalie Choisne, Zoé Rouy, Johann Peter Gogarten, Céline Lavire, Alla Lapidus, Nicole Alloisio, Vincent Daubin, Arnaud Couloux, Stéphane Cruveiller, Ying Huang, Carla A. Bassi, James Niemann, Maria Pilar Francino, Derek M. Bickhart, J Maréchal, Laurent Labarre, Beth C. Mullin, Fernando Tavares, Olga R. Kopp, Michele Martinez, Eugene Goltsman, Anita Sellstedt, Pierre Pujic, 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), Department of Molecular and Cell Biology, University of Connecticut (UCONN), Department of Microbiology, University of New Hampshire (UNH), Department of Plant Sciences [Davis, CA], University of California [Davis] (UC Davis), University of California-University of California, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-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), 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), 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), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Department of Biochemistry & Cellular & Molecular Biology and the Genome Science & Technology Program, The University of Tennessee [Knoxville], Department of Biochemistry & Cellular 1 Molecular Biology and The Genome Science & Technology Program, Department of Plant Physiology, Umeå University, Genomics Institute, Clemson University, Departamento de Ciencia y Tecnología [Buenos Aires], Universidad Nacional de Quilmes (UNQ), 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 ), University of Connecticut ( UCONN ), University of New Hampshire ( UNH ), University of California [Davis] ( UC Davis ), Unité de recherche en génomique végétale ( URGV ), Institut National de la Recherche Agronomique ( INRA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Centre National de la Recherche Scientifique ( CNRS ), Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), 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 ), 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 ), Department of Energy / Joint Genome Institute ( DOE ), Los Alamos National Laboratory ( LANL ), Programa Interacciones Biologicas, Departamento de Cienca y Tecnologia, Universidad Nacional de Quilmes, 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 National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), 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), Department of Plant Sciences [Univ California Davis] (Plant - UC Davis), and University of California (UC)-University of California (UC)

Subjects
DNA, Bacterial, Root nodule, Prophages, [SDE.BE.ECOM]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.ecom, Molecular Sequence Data, Frankia, Plant Roots, Genome, Article, Actinobacteria, Evolution, Molecular, Magnoliopsida, 03 medical and health sciences, Symbiosis, Gene Duplication, Nitrogen Fixation, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Botany, Genetics, Phylogeny, Genetics (clinical), 030304 developmental biology, 2. Zero hunger, Frankia alni, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, 0303 health sciences, Facultative, Geography, biology, 030306 microbiology, fungi, food and beverages, Sequence Analysis, DNA, 15. Life on land, biology.organism_classification, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], DNA Transposable Elements, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Actinorhizal plant, [ SDE.BE.ECOM ] Environmental Sciences/Biodiversity and Ecology/domain_sde.be.ecom, Gene Deletion, Genome, Bacterial
Abstract

Soil bacteria that also form mutualistic symbioses in plants encounter two major levels of selection. One occurs during adaptation to and survival in soil, and the other occurs in concert with host plant speciation and adaptation. Actinobacteria from the genus Frankia are facultative symbionts that form N2-fixing root nodules on diverse and globally distributed angiosperms in the “actinorhizal” symbioses. Three closely related clades of Frankia sp. strains are recognized; members of each clade infect a subset of plants from among eight angiosperm families. We sequenced the genomes from three strains; their sizes varied from 5.43 Mbp for a narrow host range strain (Frankia sp. strain HFPCcI3) to 7.50 Mbp for a medium host range strain (Frankia alni strain ACN14a) to 9.04 Mbp for a broad host range strain (Frankia sp. strain EAN1pec.) This size divergence is the largest yet reported for such closely related soil bacteria (97.8%–98.9% identity of 16S rRNA genes). The extent of gene deletion, duplication, and acquisition is in concert with the biogeographic history of the symbioses and host plant speciation. Host plant isolation favored genome contraction, whereas host plant diversification favored genome expansion. The results support the idea that major genome expansions as well as reductions can occur in facultative symbiotic soil bacteria as they respond to new environments in the context of their symbioses.

Published
2006

5. [Untitled]

Author

Dominique Jacques, Hagay Sobol, Claire Julian-Reynier, Hubert Allemand, François Eisinger, Alain Brigand, Gerard Schenowitz, Jean-Pierre Giordanella, Remi Didelot, Jean Faivre, and Jean-François Seitz

Subjects
Cancer Research, medicine.medical_specialty, education.field_of_study, medicine.diagnostic_test, business.industry, Colorectal cancer, Population, Colonoscopy, medicine.disease, law.invention, Clinical trial, Oncology, Randomized controlled trial, law, Relative risk, Family medicine, Epidemiology, Genetics, Physical therapy, Medicine, business, education, Genetics (clinical), Mass screening
Abstract

Objective: Evidence-based counseling and prevention are not available so far for hereditary cancer prone persons, since we lack data based on clinical trials. There are very few high-risk persons in the population as a whole. Based on a familial history analysis, only 1.2% of all healthy volunteers attending screening centers reached the arbitrary high-risk level defined as a Relative Risk of more than 4. We describe a randomized trial based on colonoscopic screening for colorectal cancer on a sub-group of high-risk group persons. Materials and methods:Among the 77 members of the French Institutional Preventive Center Network, 37 took part in this protocol. During the first 3 years, 850,000 persons were interviewed at these 37 Health centers. The enrolment process was particularly time-consuming, since a large amount of information had to be delivered to the participants. Results: The mean rate of recruitment of eligible candidates was far lower than predicted, averaging only 1.4 per 1,000 persons interviewed instead of the 9/1,000 expected. This mean figure was based, however, on inclusion rates ranging from 0.06/1,000 to 7/1,000 among the different centers. The low rates of recruitment were mainly due to the inter-center heterogeneity (differences in commitment and in the resources), and to the fact that the acceptability of undergoing a colonoscopy turned out to be lower than predicted. Conclusion: Population trials on cancer prone persons are feasible, but vast numbers have to be pre-screened to identify the few people with a high hereditary risk and willing to accept screening within a controlled trial.

Published
2001

6. Genome sequence of the -rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia

Author

Claudine Médigue, Delphine Capela, Chantal Schenowitz, Catherine Masson-Boivin, Sébastien Carrère, Valérie Barbe, Marta Marchetti, Zoé Rouy, Claire Amadou, Bertrand Servin, Aurélie Lajus, Jacques Batut, Carole Dossat, Maged M. Saad, Géraldine Pascal, Sophie Mangenot, Véréna Poinsot, Stéphane Cruveiller, Michelle D. Glew, Cyril Bontemps, Departement /u563 : Immunologie et Maladies infectieuses, Centre de Physiopathologie Toulouse Purpan (CPTP), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), Génétique moléculaire, génomique, microbiologie (GMGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Dynamique des Génomes et Adaptation Microbienne (DynAMic), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Département d'Astrophysique, de physique des Particules, de physique Nucléaire et de l'Instrumentation Associée (DAPNIA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre d'études techniques de l'équipement Est (CETE Est), Avant création Cerema, Interactions moléculaires et réactivité chimique et photochimique (IMRCP), Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Fluides, Energie, Réacteurs, Matériaux et Transferts (FERMAT), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie moléculaire des relations plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-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), Centre de Physiopathologie Toulouse Purpan ex IFR 30 et IFR 150 (CPTP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Laboratoire de Biologie Moléculaire des Relations Plantes-Microorganismes, Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and 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)

Subjects
Letter, Molecular Sequence Data, Genomics, Genome, Rhizobia, 03 medical and health sciences, Nitrogen Fixation, Proteobacteria, Botany, Genetics, RHIZOBIUM, Phylogeny, Genetics (clinical), 030304 developmental biology, Synteny, Comparative genomics, 0303 health sciences, Sinorhizobium meliloti, [SDV.GEN]Life Sciences [q-bio]/Genetics, Base Sequence, biology, 030306 microbiology, Cupriavidus taiwanensis, Cupriavidus, SYMBIOSIS, food and beverages, Fabaceae, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, SYMBIOSE RHIZOBIUM-LEGUMINEUSE, CUPRIAVIDUS TAIWANENSIS, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Genes, Bacterial, bacteria, Rhizobium, GENOMICS, Genome, Bacterial
Abstract

We report the first complete genome sequence of a β-proteobacterial nitrogen-fixing symbiont of legumes, Cupriavidus taiwanensis LMG19424. The genome consists of two chromosomes of size 3.42 Mb and 2.50 Mb, and a large symbiotic plasmid of 0.56 Mb. The C. taiwanensis genome displays an unexpected high similarity with the genome of the saprophytic bacterium C. eutrophus H16, despite being 0.94 Mb smaller. Both organisms harbor two chromosomes with large regions of synteny interspersed by specific regions. In contrast, the two species host highly divergent plasmids, with the consequence that C. taiwanensis is symbiotically proficient and less metabolically versatile. Altogether, specific regions in C. taiwanensis compared with C. eutrophus cover 1.02 Mb and are enriched in genes associated with symbiosis or virulence in other bacteria. C. taiwanensis reveals characteristics of a minimal rhizobium, including the most compact (35-kb) symbiotic island (nod and nif) identified so far in any rhizobium. The atypical phylogenetic position of C. taiwanensis allowed insightful comparative genomics of all available rhizobium genomes. We did not find any gene that was both common and specific to all rhizobia, thus suggesting that a unique shared genetic strategy does not support symbiosis of rhizobia with legumes. Instead, phylodistribution analysis of more than 200 Sinorhizobium meliloti known symbiotic genes indicated large and complex variations of their occurrence in rhizobia and non-rhizobia. This led us to devise an in silico method to extract genes preferentially associated with rhizobia. We discuss how the novel genes we have identified may contribute to symbiotic adaptation.

Published
2008

7. Deciphering the evolution and metabolism of an anammox bacterium from a community genome

Author

Jean Weissenbach, Nuria Fonknechten, Delphine Bartol-Mavel, Bas E. Dutilh, Patrick Wincker, Béatrice Ségurens, Denis Le Paslier, Chris van der Drift, Huub J. M. Op den Camp, Mike S. M. Jetten, Berend Snel, Irina Cirpus, Harry R. Harhangi, Holger Daims, Martijn A. Huynen, Hans-Werner Mewes, Sophie Mangenot, Astrid Collingro, Chantal Schenowitz-Truong, Harald Meier, Michael Wagner, Claudine Médigue, Jan T. Keltjens, Laura van Niftrik, Valérie Barbe, Marc Strous, Dmitrij Frishman, Matthias Horn, Boran Kartal, Markus Schmid, Michael W. Taylor, Angelika Lehner, Katinka T. van de Pas-Schoonen, David Vallenet, Thomas Rattei, Jack van de Vossenberg, and Eric Pelletier

Subjects
Energy and redox metabolism [NCMLS 4], Hydrolases, Brocadia fulgida, Bioinformatics, ved/biology.organism_classification_rank.species, Genomics, Biology, Genome, Evolution, Molecular, Bioreactors, Operon, Anaerobiosis, Ladderane, Phylogeny, Genetics, Multidisciplinary, Bacteria, ved/biology, Fatty Acids, biology.organism_classification, Biological Evolution, Quaternary Ammonium Compounds, Anammoxosome, Hydrazines, Mitochondrial medicine [IGMD 8], Genes, Bacterial, Metagenomics, Anammox, Ecological Microbiology, Thermodynamics, Scalindua, Oxidoreductases, Cellular energy metabolism [UMCN 5.3], Genome, Bacterial
Abstract

Ten years ago a fortuitous discovery led to the identification of oceanic bacteria capable of anaerobic ammonium oxidation (anammox). It was soon recognized that the anammox reaction has great ecological significance, as it is responsible for removing up to 50% of fixed nitrogen from the oceans. The genome of the anammox bacterium Kuenenia stuttgartiensis has now been sequenced in a remarkable feat of what is called environmental genomics. Anammox bacteria grow very slowly and are not available in pure culture. For genome analysis an inoculum of wastewater sludge was grown in a bioreactor for one year, clocking up 10–15 generations. The DNA of the whole microbial community was sequenced and the genome of this one anammox bacterium was deduced from the results. With the genome sequence known, it will be possible to gain insight into the metabolism and evolution of these important bacteria. The genome of Kuenenia stuttgartiensis has been sequenced to learn more about anaerobic ammonium oxidation. Anaerobic ammonium oxidation (anammox) has become a main focus in oceanography and wastewater treatment1,2. It is also the nitrogen cycle's major remaining biochemical enigma. Among its features, the occurrence of hydrazine as a free intermediate of catabolism3,4, the biosynthesis of ladderane lipids5,6 and the role of cytoplasm differentiation7 are unique in biology. Here we use environmental genomics8,9—the reconstruction of genomic data directly from the environment—to assemble the genome of the uncultured anammox bacterium Kuenenia stuttgartiensis10 from a complex bioreactor community. The genome data illuminate the evolutionary history of the Planctomycetes and allow us to expose the genetic blueprint of the organism's special properties. Most significantly, we identified candidate genes responsible for ladderane biosynthesis and biological hydrazine metabolism, and discovered unexpected metabolic versatility.

Published
2006

8. Being Pathogenic, Plastic, and Sexual while Living with a Nearly Minimal Bacterial Genome

Author

Chantal Schenowitz, Aurélien Barré, Christine Citti, Béatrice Segurens, Alain Blanchard, Carole Lartigue, Marc S. Marenda, Valérie Barbe, Daniel J. Jacob, Sophie Mangenot, Pascal Sirand-Pugnet, Arnaud Couloux, Antoine de Daruvar, Génomique, développement et pouvoir pathogène (GD2P), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Centre de Bioinformatique de Bordeaux (CBIB), CGFB, Bayer Cropscience, Laboratoire Bordelais de Recherche en Informatique (LaBRI), and Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)

Subjects
Cancer Research, Mycoplasma agalactiae, ved/biology.organism_classification_rank.species, [INFO.INFO-OH]Computer Science [cs]/Other [cs.OH], ruminant, Regulatory Sequences, Nucleic Acid, Genome, Phylogeny, Genetics (clinical), ComputingMilieux_MISCELLANEOUS, bactérie, Genetics, 0303 health sciences, Phylogenetic tree, biology, santé animale, Mycoplasma mycoides, Ruminants, Infectious Diseases, Horizontal gene transfer, DNA, Circular, bactérie pathogène, Research Article, Gene Transfer, Horizontal, lcsh:QH426-470, Lipoproteins, Molecular Sequence Data, Bacterial genome size, DNA, Ribosomal, Microbiology, 03 medical and health sciences, Bacterial Proteins, Phylogenetics, Animals, DNA Restriction-Modification Enzymes, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Comparative genomics, Evolutionary Biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, 030306 microbiology, ved/biology, génome, Genetic Variation, Genetics and Genomics, biology.organism_classification, Eubacteria, lcsh:Genetics, Genes, Bacterial, Genome, Bacterial
Abstract

Mycoplasmas are commonly described as the simplest self-replicating organisms, whose evolution was mainly characterized by genome downsizing with a proposed evolutionary scenario similar to that of obligate intracellular bacteria such as insect endosymbionts. Thus far, analysis of mycoplasma genomes indicates a low level of horizontal gene transfer (HGT) implying that DNA acquisition is strongly limited in these minimal bacteria. In this study, the genome of the ruminant pathogen Mycoplasma agalactiae was sequenced. Comparative genomic data and phylogenetic tree reconstruction revealed that ∼18% of its small genome (877,438 bp) has undergone HGT with the phylogenetically distinct mycoides cluster, which is composed of significant ruminant pathogens. HGT involves genes often found as clusters, several of which encode lipoproteins that usually play an important role in mycoplasma–host interaction. A decayed form of a conjugative element also described in a member of the mycoides cluster was found in the M. agalactiae genome, suggesting that HGT may have occurred by mobilizing a related genetic element. The possibility of HGT events among other mycoplasmas was evaluated with the available sequenced genomes. Our data indicate marginal levels of HGT among Mycoplasma species except for those described above and, to a lesser extent, for those observed in between the two bird pathogens, M. gallisepticum and M. synoviae. This first description of large-scale HGT among mycoplasmas sharing the same ecological niche challenges the generally accepted evolutionary scenario in which gene loss is the main driving force of mycoplasma evolution. The latter clearly differs from that of other bacteria with small genomes, particularly obligate intracellular bacteria that are isolated within host cells. Consequently, mycoplasmas are not only able to subvert complex hosts but presumably have retained sexual competence, a trait that may prevent them from genome stasis and contribute to adaptation to new hosts., Author Summary Mycoplasmas are cell wall–lacking prokaryotes that evolved from ancestors common to Gram-positive bacteria by way of massive losses of genetic material. With their minimal genome, mycoplasmas are considered to be the simplest free-living organisms, yet several species are successful pathogens of man and animal. In this study, we challenged the commonly accepted view in which mycoplasma evolution is driven only by genome down-sizing. Indeed, we showed that a significant amount of genes underwent horizontal transfer among different mycoplasma species that share the same ruminant hosts. In these species, the occurrence of a genetic element that can promote DNA transfer via cell-to-cell contact suggests that some mycoplasmas may have retained or acquired sexual competence. Transferred genes were found to encode proteins that are likely to be associated with mycoplasma–host interactions. Sharing genetic resources via horizontal gene transfer may provide mycoplasmas with a means for adapting to new niches or to new hosts and for avoiding irreversible genome erosion.

9. Comparative genomic and proteomic analyses of two Mycoplasma agalactiae strains: clues to the macro- and micro-events that are shaping mycoplasma diversity

Author

Daniel J. Jacob, Alain Blanchard, Laurent-Xavier Nouvel, Marc S. Marenda, Christine Citti, Sophie Mangenot, Valérie Barbe, Pascal Sirand-Pugnet, Eveline Sagné, Stéphane Claverol, Chantal Schenowitz, Aurélien Barré, Ecole Nationale Vétérinaire de Toulouse - ENVT (FRANCE), Centre National de la Recherche Scientifique - CNRS (FRANCE), Université de Bordeaux 2 - Victor Segalen (FRANCE), Institut National de la Recherche Agronomique - INRA (FRANCE), Institut National de la Santé et de la Recherche Médicale - INSERM (FRANCE), Institut Bergonié (FRANCE), Commissariat à l'Energie Atomique et aux énergies alternatives - CEA (FRANCE), Université d'Évry-Val-d'Essonne - UEVE (FRANCE), Université de Bordeaux 1 (FRANCE), Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), Génomique, développement et pouvoir pathogène (GD2P), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre de Bioinformatique de Bordeaux (CBIB), CGFB, Centre Génomique Fonctionnelle Bordeaux [Bordeaux] (CGFB), Institut Polytechnique de Bordeaux-Université de Bordeaux Ségalen [Bordeaux 2], This research was supported by grants from the Institute National de la Recherche Agronomique (AgroBI, INRA), the University Victor Segalen Bordeaux 2, and the Ecole Nationale Veterinaire de Toulouse., Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut de Biologie François JACOB (JACOB), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay

Subjects
Proteomics, AGALACTIE CONTAGIEUSE, Horizontal gene transfert, Mycoplasma agalactiae, ved/biology.organism_classification_rank.species, ruminant, Genome, Gene duplication, protéomique, protéome, génomique comparée, Genetics, bactérie, 0303 health sciences, Comparative Genomic Hybridization, Integrative conjugative element, santé animale, Gene Pool, GENOMIQUE, Multigene Family, Horizontal gene transfer, TRANSFERT HORIZONTAL, bactérie pathogène, Research Article, Biotechnology, DNA, Bacterial, Gene Flow, Gene Transfer, Horizontal, lcsh:QH426-470, lcsh:Biotechnology, Molecular Sequence Data, élément mobile, Genomics, Biology, Polymorphism, Single Nucleotide, Evolution, Molecular, 03 medical and health sciences, lcsh:TP248.13-248.65, Comparative genomic, mycoplasme, Amino Acid Sequence, mollicute, pathologie animale, Gene, Surface protein, mycoplasma agalactiae, 030304 developmental biology, diversité, Genetic diversity, [SDV.GEN]Life Sciences [q-bio]/Genetics, Base Sequence, 030306 microbiology, ved/biology, Insertion sequence, génome, Proteomic, Sequence Analysis, DNA, GENETIQUE, Mutagenesis, Insertional, lcsh:Genetics, Médecine vétérinaire et santé animal, Mobile genetic elements, Genome, Bacterial
Abstract

Background While the genomic era is accumulating a tremendous amount of data, the question of how genomics can describe a bacterial species remains to be fully addressed. The recent sequencing of the genome of the Mycoplasma agalactiae type strain has challenged our general view on mycoplasmas by suggesting that these simple bacteria are able to exchange significant amount of genetic material via horizontal gene transfer. Yet, events that are shaping mycoplasma genomes and that are underlining diversity within this species have to be fully evaluated. For this purpose, we compared two strains that are representative of the genetic spectrum encountered in this species: the type strain PG2 which genome is already available and a field strain, 5632, which was fully sequenced and annotated in this study. Results The two genomes differ by ca. 130 kbp with that of 5632 being the largest (1006 kbp). The make up of this additional genetic material mainly corresponds (i) to mobile genetic elements and (ii) to expanded repertoire of gene families that encode putative surface proteins and display features of highly-variable systems. More specifically, three entire copies of a previously described integrative conjugative element are found in 5632 that accounts for ca. 80 kbp. Other mobile genetic elements, found in 5632 but not in PG2, are the more classical insertion sequences which are related to those found in two other ruminant pathogens, M. bovis and M. mycoides subsp. mycoides SC. In 5632, repertoires of gene families encoding surface proteins are larger due to gene duplication. Comparative proteomic analyses of the two strains indicate that the additional coding capacity of 5632 affects the overall architecture of the surface and suggests the occurrence of new phase variable systems based on single nucleotide polymorphisms. Conclusion Overall, comparative analyses of two M. agalactiae strains revealed a very dynamic genome which structure has been shaped by gene flow among ruminant mycoplasmas and expansion-reduction of gene repertoires encoding surface proteins, the expression of which is driven by localized genetic micro-events.

Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results