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5 results on '"MESH: Genes, Bacterial"'

1. Regulation of PI-2b Pilus Expression in Hypervirulent Streptococcus agalactiae ST-17 BM110

Author

Périchon, Bruno, Szili, Noémi, du Merle, Laurence, Rosinski-Chupin, Isabelle, Gominet, Myriam, Bellais, Samuel, Poyart, Claire, Trieu-Cuot, Patrick, Dramsi, Shaynoor, Bidault, Floran, Biologie des Bactéries pathogènes à Gram-positif, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Ecologie et Evolution de la Résistance aux Antibiotiques / Ecology and Evolution of Antibiotics Resistance (EERA), Institut Pasteur [Paris] (IP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Sud Orsay-Centre National de la Recherche Scientifique (CNRS), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), This work was supported by the DIM Malinf from the Conseil Régional d'Ile-de-France (Grant DIM130065) to CP and SD. NS was recipient of a doctoral fellowship from the DIM Malinf. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript., Université Paris-Sud - Paris 11 (UP11)-Institut Pasteur [Paris] (IP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Sud Orsay-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] - Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11) - Institut Pasteur [Paris] - Assistance publique - Hôpitaux de Paris (AP-HP) - Centre National de la Recherche Scientifique (CNRS), Institut Cochin (UM3 (UMR 8104 / U1016)), and Université Paris Descartes - Paris 5 (UPD5) - Institut National de la Santé et de la Recherche Médicale (INSERM) - Centre National de la Recherche Scientifique (CNRS)

Subjects
Transcription, Genetic, MESH: Codon, Initiator, [SDV]Life Sciences [q-bio], Codon, Initiator, lcsh:Medicine, MESH: Virulence, Biochemistry, Nucleic Acids, Lactococcus, lcsh:Science, Pathology and laboratory medicine, Virulence, Genomics, Medical microbiology, [SDV] Life Sciences [q-bio], Group B streptococci, Fimbriae Proteins, Pathogens, Cellular Structures and Organelles, MESH: Genes, Bacterial, Lactococcus Lactis, Research Article, Pathogen Motility, MESH: Operon, Virulence Factors, DNA transcription, Microbiology, Streptococcus agalactiae, MESH: Fimbriae, Bacterial, Operon, Genetics, Operons, Gene Prediction, Medicine and health sciences, Bacteria, MESH: Transcription, Genetic, lcsh:R, Organisms, Biology and Life Sciences, Streptococcus, Computational Biology, Cell Biology, DNA, Genome Analysis, MESH: Fimbriae Proteins, MESH: Streptococcus agalactiae, Microbial pathogens, Pili and Fimbriae, Genetic Loci, Genes, Bacterial, MESH: Gene Deletion, Fimbriae, Bacterial, Bacterial pathogens, lcsh:Q, Gene expression, Gene Deletion
Abstract

International audience; The widely spread Streptococcus agalactiae (also known as Group B Streptococcus, GBS) "hypervirulent" ST17 clone is strongly associated with neonatal meningitis. The PI-2b locus is mainly found in ST17 strains but is also present in a few non ST17 human isolates such as the ST-7 prototype strain A909. Here, we analysed the expression of the PI-2b pilus in the ST17 strain BM110 as compared to the non ST17 A909. Comparative genome analyses revealed the presence of a 43-base pair (bp) hairpin-like structure in the upstream region of PI-2b operon in all 26 ST17 genomes, which was absent in the 8 non-ST17 strains carrying the PI-2b locus. Deletion of this 43-bp sequence in strain BM110 resulted in a 3-to 5-fold increased transcription of PI-2b. Characterization of PI-2b promoter region in A909 and BM110 strains was carried out by RNAseq, primer extension, qRT-PCR and transcriptional fusions with gfpas reporter gene. Our results indicate the presence of a single promoter (Ppi2b) with a transcriptional start site (TSS) mapped 37 bases upstream of the start codon of the first PI-2b gene. The large operon of 16 genes located upstream of PI-2b codes for the group B carbohydrate (also known as antigen B), a major constituent of the bacterial cell wall. We showed that the hairpin sequence located between antigen B and PI-2b operons is a transcriptional terminator. In A909, increased expression of PI-2b probably results from read-through transcription from antigen B operon. In addition, we showed that an extended 5′ promoter region is required for maximal transcription of gfpas a reporter gene in S. agalactiae from Ppi2b promoter. Gene reporter assays performed in Lactococcus lactis strain NZ9000, a related non-pathogenic Gram-positive species, revealed that GBS-specific regulatory factors are required to drive PI-2b transcription. PI-2b expression is up-regulated in the BM110AcovR mutant as compared to the parental BM110 strain, but this effect is probably indirect. Collectively, our results indicate that PI-2b expression is regulated in GBS ST17 strains, which may confer a selective advantage in the human host either by reducing host immune responses and/or increasing their dissemination potential.

Published
2017

2. Transcriptional Analysis and Subcellular Protein Localization Reveal Specific Features of the Essential WalKR System in Staphylococcus aureus

Author

Olivier Poupel, Tarek Msadek, Simonetta Gribaldo, Sarah Dubrac, Mati Moyat, Luisa C. S. Antunes, Julie Groizeleau, Biologie des Bactéries pathogènes à Gram-positif, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], Support was provided by Institut Pasteur Transversal Research Program No. 336, Agence Nationale de la Recherche, Grant ANR-08-ALIA-0011 NABAB, and Agence Nationale de la Recherche, Grant ANR-09-MIEN-0010 GRABIRON., We are grateful to Dr. Stephen Leppla and Dr. Inka Sastalla for providing plasmid pTetONGFPopt. We thank Ons Ben Aïssa and Dr. Michel Débarbouillé for constructing walR and walJ transcriptional lacZ fusions, Dr. Gouzel Karimova for the kind gift of E. coli strain DHT1 and plasmids pKTop, pKT25 and pUT18c, Dr. Pascale Romby for RNA folding predictions and Adeline Mallet (Ultrapole, Institut Pasteur) for transmission electron micrographs., ANR-08-ALIA-0011,NABAB,Stratégie Non AntiBiotique Anti-Bactéries pathogènes : exploration des capacités inhibitrices des écosystèmes naturels contre les contaminations à S. aureus en contexte laitier(2008), ANR-09-MIEN-0010,Grablron,' Nouveaux systèmes d'acquisition du fer chez les pathogènes Gram+ extracellulaires '(2009), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)

Subjects
0301 basic medicine, Transcription, Genetic, Operon, Staphylococcus, [SDV]Life Sciences [q-bio], Oligonucleotides, lcsh:Medicine, Bacillus, MESH: Base Sequence, Pathology and Laboratory Medicine, Biochemistry, MESH: Bacterial Proteins/metabolism, MESH: Staphylococcus aureus/genetics, Nucleic Acids, Gene cluster, Medicine and Health Sciences, Staphylococcus Aureus, MESH: Staphylococcus aureus/cytology, Promoter Regions, Genetic, MESH: Phylogeny, lcsh:Science, Phylogeny, MESH: Transcription, Genetic, MESH: Biofilms/growth & development, Regulation of gene expression, Genetics, MESH: Operon/genetics, Multidisciplinary, Nucleotides, Sequence analysis, Protein subcellular localization prediction, Bacterial Pathogens, Protein Transport, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Medical Microbiology, Prokaryotic Models, MESH: Cell Division, Pathogens, MESH: Genes, Bacterial, MESH: Bacterial Proteins/genetics, Cell Division, Protein Binding, Subcellular Fractions, Research Article, Bacillus subtilis, MESH: Gene Expression Regulation, Bacterial, MESH: Protein Transport, taphylococcus aureus, Genetic loci, Molecular Sequence Data, 030106 microbiology, DNA transcription, MESH: Cell Membrane/metabolism, Biology, Plasmid construction, Research and Analysis Methods, Microbiology, MESH: Genetic Loci, 03 medical and health sciences, Model Organisms, Bacterial Proteins, MESH: Mutation/genetics, MESH: Protein Binding, MESH: Subcellular Fractions/metabolism, Molecular Biology Techniques, Sequencing Techniques, Operons, Microbial Pathogens, Molecular Biology, Gene, MESH: Staphylococcus aureus/metabolism, MESH: Molecular Sequence Data, Base Sequence, Bacteria, Cell Membrane, lcsh:R, Organisms, Biology and Life Sciences, Promoter, Gene Expression Regulation, Bacterial, DNA, Regulon, Genes, Bacterial, MESH: Promoter Regions, Genetic/genetics, Biofilms, Mutation, lcsh:Q, Gene expression, Cloning
Abstract

International audience; The WalKR two-component system, controlling cell wall metabolism, is highly conserved among Bacilli and essential for cell viability. In Staphylococcus aureus, walR and walK are followed by three genes of unknown function: walH, walI and walJ. Sequence analysis and transcript mapping revealed a unique genetic structure for this locus in S. aureus: the last gene of the locus, walJ, is transcribed independently, whereas transcription of the tetra-cis-tronic walRKHI operon occurred from two independent promoters located upstream from walR. Protein topology analysis and protein-protein interactions in E. coli as well as subcel-lular localization in S. aureus allowed us to show that WalH and WalI are membrane-bound proteins, which associate with WalK to form a complex at the cell division septum. While these interactions suggest that WalH and WalI play a role in activity of the WalKR regulatory pathway, deletion of walH and/or walI did not have a major effect on genes whose expression is strongly dependent on WalKR or on associated phenotypes. No effect of WalH or WalI was seen on tightly controlled WalKR regulon genes such as sle1 or saouhsc_00773, which encodes a CHAP-domain amidase. Of the genes encoding the two major S. aureus autolysins, AtlA and Sle1, only transcription of atlA was increased in the ΔwalH or ΔwalI mutants. Likewise, bacterial autolysis was not increased in the absence of WalH and/or WalI and biofilm formation was lowered rather than increased. Our results suggest that contrary to their major role as WalK inhibitors in B. subtilis, the WalH and WalI proteins have evolved a different function in S. aureus, where they are more accessory. A phylogenomic analysis shows a striking conservation of the 5 gene wal cluster along the evolutionary history of Bacilli, supporting the key importance of this signal transduction system, and indicating that the walH and walI genes were lost in the ancestor of Streptococcaceae, leading to their atypical 3 wal gene cluster, walRKJ.

Published
2016

3. Reduced set of virulence genes allows high accuracy prediction of bacterial pathogenicity in humans

Author

Gregorio Iraola, Gustavo Vazquez, Lucía Spangenberg, Hugo Naya, Institut Pasteur de Montevideo, Réseau International des Instituts Pasteur (RIIP), Seccion Genetica Evolutiva, Facultad de Ciencias, Universidad de la República [Montevideo] (UCUR), Departamento de Ciencias e Ingeniería de la Computación [Bahía Blanca], Universidad Nacional del Sur [Argentina] (UNS), Departamento de Produccion Animal y Pasturas, Facultad de Agronomıa, and The authors acknowledge the financial support provided by Agencia Nacional de Investigacion e Innovacion - Uruguay (PhD. grant to LS), Comision Sectorial de Investigacion Cientıfica - Uruguay (MSc grant to GI) and Consejo Nacional de Investigacion Cientıfica y Tecnica - Argentina (research grant to GV).

Subjects
[SDV]Life Sciences [q-bio], Gene Expression, Human pathogen, Pathogenesis, MESH: Virulence, Genome, Molecular Cell Biology, Genome Evolution, 0303 health sciences, Multidisciplinary, Virulence, biology, Bacterial taxonomy, Genomics, Phenotype, Bacterial Pathogens, Host-Pathogen Interaction, Medicine, MESH: Genes, Bacterial, MESH: Diabetes Mellitus, Type 1, Research Article, MESH: Diabetes Mellitus, Type 2, MESH: Diabetes Mellitus, MESH: Clinical Trials as Topic, Science, Computational biology, Bacterial genome size, MESH: Periodontics, Microbiology, Molecular Genetics, 03 medical and health sciences, Gammaproteobacteria, Genetics, Humans, Biology, Microbial Pathogens, Gene, 030304 developmental biology, MESH: Humans, Bacteria, 030306 microbiology, Computational Biology, Bacteriology, biology.organism_classification, MESH: Male, MESH: Bacteria, Genes, Bacterial, MESH: Blood Glucose, MESH: Female
Abstract

International audience; Although there have been great advances in understanding bacterial pathogenesis, there is still a lack of integrative information about what makes a bacterium a human pathogen. The advent of high-throughput sequencing technologies has dramatically increased the amount of completed bacterial genomes, for both known human pathogenic and non-pathogenic strains; this information is now available to investigate genetic features that determine pathogenic phenotypes in bacteria. In this work we determined presence/absence patterns of 814 different virulence-related genes among more than 600 finished bacterial genomes from both human pathogenic and non-pathogenic strains, belonging to different taxonomic groups (i.e: Actinobacteria, Gammaproteobacteria, Firmicutes, etc.). An accuracy of 95% using a cross-fold validation scheme with in-fold feature selection is obtained when classifying human pathogens and non-pathogens. A reduced subset of highly informative genes (120) is presented and applied to an external validation set. The statistical model was implemented in the BacFier v1.0 software (freely available at http : ==bacfier:googlecode:com=files=Bacfier v1 0:zip), that displays not only the prediction (pathogen/non-pathogen) and an associated probability for pathogenicity, but also the presence/absence vector for the analyzed genes, so it is possible to decipher the subset of virulence genes responsible for the classification on the analyzed genome. Furthermore, we discuss the biological relevance for bacterial pathogenesis of the core set of genes, corresponding to eight functional categories, all with evident and documented association with the phenotypes of interest. Also, we analyze which functional categories of virulence genes were more distinctive for pathogenicity in each taxonomic group, which seems to be a completely new kind of information and could lead to important evolutionary conclusions.

Published
2012

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

Author

Sarah Dubrac, Tarek Msadek, Olivier Poupel, Isabelle Martin-Verstraete, Olga Soutourina, Génétique des Génomes Bactériens, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Biologie des Bactéries Pathogènes à Gram-positif, I. M-V. and O. S. are full and assistant professors at the Université Paris 7, respectively. Research was supported by grants from the Centre National de la Recherche Scientifique (CNRS URA 2171 and 2172), the Institut Pasteur (Grand Programme Horizontal N°9 and PTR N°256) and the European Commission for the group of T. M. (Grants StaphDynamics, LHSM-CT-2006-019064, and BaSysBio, LSHG-CT-2006-037469)., We are grateful to S. Foster for providing us with S. aureus strains and valuable discussions. We thank O. Sismeiro, C. Lacroix and J.-Y. Coppee for macroarray preparation, S. Rousseau and P. Vantadour for loading transcriptome data onto the Genoscript database and P. Courtin for metabolite analysis., European Project: 35105,STAPHDYNAMICS, European Project: 38901,BASYSBIO, and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV]Life Sciences [q-bio], Mutant, MESH: Virulence, medicine.disease_cause, Mice, chemistry.chemical_compound, MESH: Oxidants, MESH: Staphylococcus aureus, MESH: Up-Regulation, Homeostasis, MESH: Animals, Disulfides, lcsh:QH301-705.5, Pathogen, Regulation of gene expression, Mice, Inbred BALB C, 0303 health sciences, MESH: Oxidative Stress, Virulence, Staphylococcal Infections, Oxidants, Up-Regulation, MESH: Copper, MESH: Tellurium, MESH: Homeostasis, Staphylococcus aureus, Cystine, MESH: Hydrogen Peroxide, Microbiology/Microbial Physiology and Metabolism, Female, Tellurium, MESH: Genes, Bacterial, Microbiology/Cellular Microbiology and Pathogenesis, Intracellular, Research Article, lcsh:Immunologic diseases. Allergy, Immunology, MESH: Mice, Inbred BALB C, MESH: Staphylococcal Infections, Biology, Microbiology, Cell Line, 03 medical and health sciences, Virology, Genetics, medicine, Animals, MESH: Disulfides, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Mice, Molecular Biology, Cysteine metabolism, 030304 developmental biology, Metal ion homeostasis, 030306 microbiology, Macrophages, MESH: Macrophages, MESH: Cystine, Hydrogen Peroxide, MESH: Cell Line, Oxidative Stress, lcsh:Biology (General), chemistry, Genes, Bacterial, MESH: Gene Deletion, Parasitology, lcsh:RC581-607, MESH: Female, Copper, Gene Deletion
Abstract

We have characterized a novel pleiotropic role for CymR, the master regulator of cysteine metabolism. We show here that CymR plays an important role both in stress response and virulence of Staphylococcus aureus. Genes involved in detoxification processes, including oxidative stress response and metal ion homeostasis, were differentially expressed in a ΔcymR mutant. Deletion of cymR resulted in increased sensitivity to hydrogen peroxide-, disulfide-, tellurite- and copper-induced stresses. Estimation of metabolite pools suggests that this heightened sensitivity could be the result of profound metabolic changes in the ΔcymR mutant, with an increase in the intracellular cysteine pool and hydrogen sulfide formation. Since resistance to oxidative stress within the host organism is important for pathogen survival, we investigated the role of CymR during the infectious process. Our results indicate that the deletion of cymR promotes survival of S. aureus inside macrophages, whereas virulence of the ΔcymR mutant is highly impaired in mice. These data indicate that CymR plays a major role in virulence and adaptation of S. aureus for survival within the host., Author Summary Staphylococcus aureus is a very harmful human pathogen that is a major cause of nosocomial infections. Humans have developed sophisticated defense strategies against invading bacteria, including the innate immune response, with the generation of an oxidative burst inside phagocytic cells. Staphylococcal infections are extremely difficult to eradicate due to the remarkable capacity of these bacteria to adapt to different environmental conditions both inside and outside the host organism. Sulfur metabolism is essential for all living organisms and is tightly controlled by regulatory proteins. In this paper, we revealed an important role for CymR, a major regulator of sulfur metabolism, in adaptation of S. aureus to the host environment. Inactivation of the gene encoding this regulator in S. aureus leads to a mutant bacterium with increased vulnerability to stress conditions including oxidative stress encountered inside the host. More importantly, the deletion of the cymR gene strongly affected the interaction of S. aureus with its host, leading to impaired virulence in mice. Our results place CymR among the potential targets for attenuation of S. aureus infections.

Published
2010

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

Author

Florence Hommais, Jean Weissenbach, Odile Bruneel, Emmanuel Talla, Philippe N. Bertin, Patricia Siguier, Daniel Muller, Jean-Yves Coppée, Caroline Proux, Stéphanie Weiss, Valérie Barbe, Florence Arsène-Ploetze, Marie Marchal, Gregory Salvignol, Audrey Heinrich-Salmeron, Zoé Rouy, Fabienne Battaglia-Brunet, Didier Lièvremont, Christopher G. Bryan, Caroline Michel, Philippe Ortet, Sandrine Koechler, Céline Brochier-Armanet, Jessica Cleiss-Arnold, Mohamed Barakat, Michael Chandler, Stéphane Cruveiller, Djamila Slyemi, Aurélie Lieutaud, Catherine Joulian, Evelyne Krin, Violaine Bonnefoy, David Roche, Claudine Médigue, Mathieu Erhardt, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Puces à ADN (Plate-Forme 2) (PF2), Institut Pasteur [Paris], Laboratoire de microbiologie et génétique moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Bureau de Recherches Géologiques et Minières (BRGM) (BRGM), Hydrosciences Montpellier (HSM), Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie moléculaire des plantes (IBMP), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Génétique des Génomes Bactériens, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Dynamique, évolution et expression de génomes de microorganismes (DEEGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut Pasteur [Paris] (IP), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Cancer Research, Prophages, MESH: Genome, Bacterial, Genome, MESH: Prophages, MESH: Genomic Islands, MESH: Genetic Variation, MESH: Betaproteobacteria, MESH: Evolution, Molecular, Genetics (clinical), Genetics, Comparative Genomic Hybridization, 0303 health sciences, biology, MESH: Energy Metabolism, Betaproteobacteria, Thiomonas, Genetics and Genomics/Microbial Evolution and Genomics, Adaptation, Physiological, Horizontal gene transfer, MESH: Genes, Bacterial, Metabolic Networks and Pathways, Research Article, Plasmids, Genome evolution, lcsh:QH426-470, Gene Transfer, Horizontal, Genomic Islands, MESH: Carbon, Genomics, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Environment, Arsenic, Evolution, Molecular, 03 medical and health sciences, Genes, Duplicate, MESH: Plasmids, MESH: Arsenic, Microbiology/Environmental Microbiology, MESH: Environment, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Prophage, 030304 developmental biology, Comparative genomics, MESH: Genes, Duplicate, 030306 microbiology, Human evolutionary genetics, Genetic Variation, biology.organism_classification, MESH: Adaptation, Physiological, Carbon, MESH: Gene Transfer, Horizontal, MESH: Comparative Genomic Hybridization, lcsh:Genetics, Genes, Bacterial, MESH: Metabolic Networks and Pathways, Energy Metabolism, Genome, Bacterial
Abstract

Bacteria of the Thiomonas genus are ubiquitous in extreme environments, such as arsenic-rich acid mine drainage (AMD). The genome of one of these strains, Thiomonas sp. 3As, was sequenced, annotated, and examined, revealing specific adaptations allowing this bacterium to survive and grow in its highly toxic environment. In order to explore genomic diversity as well as genetic evolution in Thiomonas spp., a comparative genomic hybridization (CGH) approach was used on eight different strains of the Thiomonas genus, including five strains of the same species. Our results suggest that the Thiomonas genome has evolved through the gain or loss of genomic islands and that this evolution is influenced by the specific environmental conditions in which the strains live., Author Summary Recent advances in the field of arsenic microbial metabolism have revealed that bacteria colonize a large panel of highly contaminated environments. Belonging to the order of Burkholderiales, Thiomonas strains are ubiquitous in arsenic-contaminated environments. The genome of one of them, i.e. Thiomonas sp. 3As, was deciphered and compared to the genome of several other Thiomonas strains. We found that their flexible gene pool evolved to allow both the surviving and growth in their peculiar environment. In particular, the acquisition by strains of the same species of different genomic islands conferred heavy metal resistance and metabolic idiosyncrasies. Our comparative genomic analyses suggest that the natural environment influences the genomic evolution of these bacteria. Importantly, these results highlight the genomic variability that may exist inside a taxonomic group, enlarging the concept of bacterial species.

Published
2010

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