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1. Streptomyces cocklensis DSM 42063 and Actinacidiphila bryophytorum DSM 42138 Colonize Arabidopsis thaliana and Modulate Its Proteome

Author

Florence Arsène-Ploetze, Magali Rompais, Abdelmalek Alioua, Valérie Cognat, Mathieu Erhardt, Stefanie Graindorge, Sandrine Koechler, Jérôme Mutterer, Christine Carapito, and Hubert Schaller

Subjects
interactions, microbiota, plant metabolites, proteome modulation, Streptomycetaceae, Plant culture, SB1-1110, Botany, QK1-989
Abstract

Streptomycetaceae are found ubiquitously within plant microbiota. Several species belonging to this family are plant growth-promoting bacteria or may inhibit phytopathogens. Such bacteria therefore exert crucial functions in host development and resistance to stresses. Recent studies have shown that plants select beneficial bacteria into their microbiota. However, the selection process and the molecular mechanisms by which selected bacteria modulate the physiology of their host are not yet fully understood. Previous work revealed that the metabolic status of Arabidopsis thaliana was crucial for the selection of Streptomycetaceae into the microbiota, in particular bacteria phylogenetically related to Streptomyces cocklensis or Actinacidiphila bryophytorum (previously named Streptomyces bryophytorum). Here, the Arabidopsis-Streptomycetaceae interaction was further depicted by inoculating axenic A. thaliana with S. cocklensis DSM 42063 or A. bryophytorum DSM 42138. We showed that these two bacteria colonize A. thaliana ecotype Columbia-0 plants, but the colonization efficiency is reduced in a chs5 mutant of the same ecotype, being altered in isoprenoid, phenylpropanoid, and lipid profiles. We observed that A. bryophytorum inhibits growth of the chs5 mutant but not of the wild type, suggesting that the Arabidopsis-Actinacidiphila interaction depends on the metabolic status of the host. Using a mass spectrometry-based proteomic approach, we showed that S. cocklensis and A. bryophytorum modulate the A. thaliana proteome, in particular components involved in photosynthesis or phytohormone homeostasis. This study unveils specific aspects of the Arabidopsis-Streptomycetaceae interaction and highlights its complexity and diversity. [Figure: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Published
2024
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2. The TUTase URT1 connects decapping activators and prevents the accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis

Author

Hélène Scheer, Caroline de Almeida, Emilie Ferrier, Quentin Simonnot, Laure Poirier, David Pflieger, François M. Sement, Sandrine Koechler, Christina Piermaria, Paweł Krawczyk, Seweryn Mroczek, Johana Chicher, Lauriane Kuhn, Andrzej Dziembowski, Philippe Hammann, Hélène Zuber, and Dominique Gagliardi

Subjects
Science
Abstract

TUTase mediated uridylation of mRNA promotes degradation. Here, Scheer, de Almeida et al. show that Arabidopsis TUTase URT1 interacts directly with the translation inhibitor and decay factor DECAPPING5 and suppresses siRNA biogenesis by preventing accumulation of deadenylated mRNAs

Published
2021
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3. Sequence of the Mitochondrial Genome of Lactuca virosa Suggests an Unexpected Role in Lactuca sativa’s Evolution

Author

Arnaud Fertet, Stéfanie Graindorge, Sandrine Koechler, Gert-Jan de Boer, Emilie Guilloteau-Fonteny, and José M. Gualberto

Subjects
mitochondrial genome, genome evolution, lettuce, Lactuca virosa, Lactuca serriola, Lactuca saligna, Plant culture, SB1-1110
Abstract

The involvement of the different Lactuca species in the domestication and diversification of cultivated lettuce is not totally understood. Lactuca serriola is considered as the direct ancestor and the closest relative to Lactuca sativa, while the other wild species that can be crossed with L. sativa, Lactuca virosa, and Lactuca saligna, would have just contributed to the latter diversification of cultivated typologies. To contribute to the study of Lactuca evolution, we assembled the mtDNA genomes of nine Lactuca spp. accessions, among them three from L. virosa, whose mtDNA had not been studied so far. Our results unveiled little to no intraspecies variation among Lactuca species, with the exception of L. serriola where the accessions we sequenced diverge significantly from the mtDNA of a L. serriola accession already reported. Furthermore, we found a remarkable phylogenetic closeness between the mtDNA of L. sativa and the mtDNA of L. virosa, contrasting to the L. serriola origin of the nuclear and plastidial genomes. These results suggest that a cross between L. virosa and the ancestor of cultivated lettuce is at the origin of the actual mitochondrial genome of L. sativa.

Published
2021
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4. Phylogenomic Classification and Biosynthetic Potential of the Fossil Fuel-Biodesulfurizing Rhodococcus Strain IGTS8

Author

Dean Thompson, Valérie Cognat, Michael Goodfellow, Sandrine Koechler, Dimitri Heintz, Christine Carapito, Alain Van Dorsselaer, Huda Mahmoud, Vartul Sangal, and Wael Ismail

Subjects
biodesulfurization, Rhodococcus, 4S pathway, phylogenomics, dibenzothiophene, average nucleotide identity, Microbiology, QR1-502
Abstract

Rhodococcus strain IGTS8 is the most extensively studied model bacterium for biodesulfurization of fossil fuels via the non–destructive sulfur–specific 4S pathway. This strain was initially assigned to Rhodococcus rhodochrous and later to Rhodococcus erythropolis thus making its taxonomic status debatable and reflecting the limited resolution of methods available at the time. In this study, phylogenomic analyses of the whole genome sequences of strain IGTS8 and closely related rhodococci showed that R. erythropolis and Rhodococcus qingshengii are very closely related species, that Rhodococcus strain IGTS8 is a R. qingshengii strain and that several strains identified as R. erythropolis should be re-classified as R. qingshengii. The genomes of strains assigned to these species contain potentially novel biosynthetic gene clusters showing that members of these taxa should be given greater importance in the search for new antimicrobials and other industrially important biomolecules. The plasmid-borne dsz operon encoding fossil fuel desulfurization enzymes was present in R. qingshengii IGTS8 and R. erythropolis XP suggesting that it might be transferable between members of these species.

Published
2020
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5. Adaptation in Toxic Environments: Arsenic Genomic Islands in the Bacterial Genus Thiomonas.

Author

Kelle C Freel, Martin C Krueger, Julien Farasin, Céline Brochier-Armanet, Valérie Barbe, Jeremy Andrès, Pierre-Etienne Cholley, Marie-Agnès Dillies, Bernd Jagla, Sandrine Koechler, Yann Leva, Ghislaine Magdelenat, Frédéric Plewniak, Caroline Proux, Jean-Yves Coppée, Philippe N Bertin, Hermann J Heipieper, and Florence Arsène-Ploetze

Subjects
Medicine, Science
Abstract

Acid mine drainage (AMD) is a highly toxic environment for most living organisms due to the presence of many lethal elements including arsenic (As). Thiomonas (Tm.) bacteria are found ubiquitously in AMD and can withstand these extreme conditions, in part because they are able to oxidize arsenite. In order to further improve our knowledge concerning the adaptive capacities of these bacteria, we sequenced and assembled the genome of six isolates derived from the Carnoulès AMD, and compared them to the genomes of Tm. arsenitoxydans 3As (isolated from the same site) and Tm. intermedia K12 (isolated from a sewage pipe). A detailed analysis of the Tm. sp. CB2 genome revealed various rearrangements had occurred in comparison to what was observed in 3As and K12 and over 20 genomic islands (GEIs) were found in each of these three genomes. We performed a detailed comparison of the two arsenic-related islands found in CB2, carrying the genes required for arsenite oxidation and As resistance, with those found in K12, 3As, and five other Thiomonas strains also isolated from Carnoulès (CB1, CB3, CB6, ACO3 and ACO7). Our results suggest that these arsenic-related islands have evolved differentially in these closely related Thiomonas strains, leading to divergent capacities to survive in As rich environments.

Published
2015
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7. Subinhibitory arsenite concentrations lead to population dispersal in Thiomonas sp.

Author

Marie Marchal, Romain Briandet, David Halter, Sandrine Koechler, Michael S DuBow, Marie-Claire Lett, and Philippe N Bertin

Subjects
Medicine, Science
Abstract

Biofilms represent the most common microbial lifestyle, allowing the survival of microbial populations exposed to harsh environmental conditions. Here, we show that the biofilm development of a bacterial species belonging to the Thiomonas genus, frequently found in arsenic polluted sites and playing a key role in arsenic natural remediation, is markedly modified when exposed to subinhibitory doses of this toxic element. Indeed, arsenite [As(III)] exposure led to a considerable impact on biofilm maturation by strongly increasing the extracellular matrix synthesis and by promoting significant cell death and lysis within microcolonies. These events were followed by the development of complex 3D-biofilm structures and subsequently by the dispersal of remobilized cells observed inside the previously formed hollow voids. Our results demonstrate that this biofilm community responds to arsenite stress in a multimodal way, enhancing both survival and dispersal. Addressing this complex bacterial response to As(III) stress, which might be used by other microorganisms under various adverse conditions, may be essential to understand how Thiomonas strains persist in extreme environments.

Published
2011
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8. Structure, function, and evolution of the Thiomonas spp. genome.

Author

Florence Arsène-Ploetze, Sandrine Koechler, Marie Marchal, Jean-Yves Coppée, Michael Chandler, Violaine Bonnefoy, Céline Brochier-Armanet, Mohamed Barakat, Valérie Barbe, Fabienne Battaglia-Brunet, Odile Bruneel, Christopher G Bryan, Jessica Cleiss-Arnold, Stéphane Cruveiller, Mathieu Erhardt, Audrey Heinrich-Salmeron, Florence Hommais, Catherine Joulian, Evelyne Krin, Aurélie Lieutaud, Didier Lièvremont, Caroline Michel, Daniel Muller, Philippe Ortet, Caroline Proux, Patricia Siguier, David Roche, Zoé Rouy, Grégory Salvignol, Djamila Slyemi, Emmanuel Talla, Stéphanie Weiss, Jean Weissenbach, Claudine Médigue, and Philippe N Bertin

Subjects
Genetics, QH426-470
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.

Published
2010
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9. A tale of two oxidation states: bacterial colonization of arsenic-rich environments.

Author

Daniel Muller, Claudine Médigue, Sandrine Koechler, Valérie Barbe, Mohamed Barakat, Emmanuel Talla, Violaine Bonnefoy, Evelyne Krin, Florence Arsène-Ploetze, Christine Carapito, Michael Chandler, Benoît Cournoyer, Stéphane Cruveiller, Caroline Dossat, Simon Duval, Michael Heymann, Emmanuelle Leize, Aurélie Lieutaud, Didier Lièvremont, Yuko Makita, Sophie Mangenot, Wolfgang Nitschke, Philippe Ortet, Nicolas Perdrial, Barbara Schoepp, Patricia Siguier, Diliana D Simeonova, Zoé Rouy, Béatrice Segurens, Evelyne Turlin, David Vallenet, Alain Van Dorsselaer, Stéphanie Weiss, Jean Weissenbach, Marie-Claire Lett, Antoine Danchin, and Philippe N Bertin

Subjects
Genetics, QH426-470
Abstract

Microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. Finding a means of preserving natural environments-including ground and surface waters-from arsenic constitutes a major challenge facing modern society. Although this metalloid is ubiquitous on Earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. In-depth exploration of the genome of the beta-proteobacterium Herminiimonas arsenicoxydans with regard to physiology, genetics, and proteomics, revealed that it possesses heretofore unsuspected mechanisms for coping with arsenic. Aside from multiple biochemical processes such as arsenic oxidation, reduction, and efflux, H. arsenicoxydans also exhibits positive chemotaxis and motility towards arsenic and metalloid scavenging by exopolysaccharides. These observations demonstrate the existence of a novel strategy to efficiently colonize arsenic-rich environments, which extends beyond oxidoreduction reactions. Such a microbial mechanism of detoxification, which is possibly exploitable for bioremediation applications of contaminated sites, may have played a crucial role in the occupation of ancient ecological niches on earth.

Published
2007
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10. The Arabidopsis thaliana–Streptomyces Interaction Is Controlled by the Metabolic Status of the Holobiont

Author

Stéfanie Graindorge, Claire Villette, Sandrine Koechler, Chloé Groh, Sophie Comtet-Marre, Pierre Mercier, Romaric Magerand, Pierre Peyret, Dimitri Heintz, Hubert Schaller, Florence Arsène-Ploetze, Institut de biologie moléculaire des plantes (IBMP), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Microbiologie Environnement Digestif Santé (MEDIS), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA)

Subjects
[SDV]Life Sciences [q-bio], Organic Chemistry, General Medicine, plant-bacteria interactions, Holobiont, metabolomics, Catalysis, holobiont, microbiota, plant–bacteria interactions, Computer Science Applications, Inorganic Chemistry, Physical and Theoretical Chemistry, Molecular Biology, Spectroscopy
Abstract

International audience; How specific interactions between plant and pathogenic, commensal, or mutualistic microorganisms are mediated and how bacteria are selected by a plant are important questions to address. Here, an Arabidopsis thaliana mutant called chs5 partially deficient in the biogenesis of isoprenoid precursors was shown to extend its metabolic remodeling to phenylpropanoids and lipids in addition to carotenoids, chlorophylls, and terpenoids. Such a metabolic profile was concomitant to increased colonization of the phyllosphere by the pathogenic strain Pseudomonas syringae pv. tomato DC3000. A thorough microbiome analysis by 16S sequencing revealed that Streptomyces had a reduced colonization potential in chs5. This study revealed that the bacteria–Arabidopsis interaction implies molecular processes impaired in the chs5 mutant. Interestingly, our results revealed that the metabolic status of A. thaliana was crucial for the specific recruitment of Streptomyces into the microbiota. More generally, this study highlights specific as well as complex molecular interactions that shape the plant microbiota.

Published
2022
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11. Phylogenomic Classification and Biosynthetic Potential of the Fossil Fuel-Biodesulfurizing Rhodococcus Strain IGTS8

Author

Christine Carapito, Wael Ismail, Sandrine Koechler, Alain Van Dorsselaer, Michael Goodfellow, Dimitri Heintz, Valérie Cognat, Vartul Sangal, Dean Thompson, Huda Mahmoud, Institut de biologie moléculaire des plantes (IBMP), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), and Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Microbiology (medical), Operon, lcsh:QR1-502, digital DNA-DNA hybridization, Microbiology, Genome, lcsh:Microbiology, 03 medical and health sciences, Phylogenomics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Rhodococcus, Sciences du Vivant [q-bio]/Biologie végétale, dibenzothiophene, biodesulfurization, Gene, 030304 developmental biology, Genetics, 0303 health sciences, biology, 030306 microbiology, Strain (biology), average nucleotide identity, phylogenomics, Rhodococcus rhodochrous, C500, biology.organism_classification, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 4S pathway, Bacteria
Abstract

International audience; Rhodococcus strain IGTS8 is the most extensively studied model bacterium for biodesulfurization of fossil fuels via the non-destructive sulfur-specific 4S pathway. This strain was initially assigned to Rhodococcus rhodochrous and later to Rhodococcus erythropolis thus making its taxonomic status debatable and reflecting the limited resolution of methods available at the time. In this study, phylogenomic analyses of the whole genome sequences of strain IGTS8 and closely related rhodococci showed that R. erythropolis and Rhodococcus qingshengii are very closely related species, that Rhodococcus strain IGTS8 is a R. qingshengii strain and that several strains identified as R. erythropolis should be reclassified as R. qingshengii. The genomes of strains assigned to these species contain potentially novel biosynthetic gene clusters showing that members of these taxa should be given greater importance in the search for new antimicrobials and other industrially important biomolecules. The plasmid-borne dsz operon encoding fossil fuel desulfurization enzymes was present in R. qingshengii IGTS8 and R. erythropolis XP suggesting that it might be transferable between members of these species.

Published
2020
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12. High-Resolution Mapping of 3' Extremities of RNA Exosome Substrates by 3' RACE-Seq

Author

Sandrine Koechler, Hélène Zuber, Natalia Sikorska, Hélène Scheer, Caroline de Almeida, Dominique Gagliardi, Institut de biologie moléculaire des plantes (IBMP), and Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)

Subjects
chemistry.chemical_classification, 0303 health sciences, Exosome complex, RNA, RNA-binding protein, Computational biology, Biology, Nucleotidyltransferase, RNA Helicase A, Exosome, 03 medical and health sciences, 0302 clinical medicine, chemistry, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Nucleotide, 030217 neurology & neurosurgery, Illumina dye sequencing, 030304 developmental biology
Abstract

International audience; The main 3'-5' exoribonucleolytic activity of eukaryotic cells is provided by the RNA exosome. The exosome is constituted by a core complex of nine subunits (Exo9), which coordinates the recruitment and the activities of distinct types of cofactors. The RNA exosome cofactors confer distributive and processive 3'-5' exoribonucleolytic, endoribonucleolytic, and RNA helicase activities. In addition, several RNA binding proteins and terminal nucleotidyltransferases also participate in the recognition of exosome RNA substrates.To fully understand the biological roles of the exosome, the respective functions of its cofactors must be deciphered. This entails the high-resolution analysis of 3' extremities of degradation or processing intermediates in different mutant backgrounds or growth conditions. Here, we describe a detailed 3' RACE-seq procedure for targeted mapping of exosome substrate 3' ends. This procedure combines a 3' RACE protocol with Illumina sequencing to enable the high-resolution mapping of 3' extremities and the identification of untemplated nucleotides for selected RNA targets.

Published
2020
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13. Organization of the TC and TE cellular T-DNA regions in Nicotiana otophora and functional analysis of three diverged TE-6b genes

Author

Sandrine Koechler, Léon Otten, François Dorlhac de Borne, Nicolas Sierro, Ke Chen, Malek Alouia, Nikolai V. Ivanov, Institut de biologie moléculaire des plantes (IBMP), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), and Shanghai Jiao Tong University [Shanghai]

Subjects
DNA, Bacterial, 0106 biological sciences, 0301 basic medicine, Agrobacterium vitis, 6b oncogene, DNA, Plant, Agrobacterium, Inverted repeat, Nicotiana tabacum, Flowers, Plant Science, Genes, Plant, 01 natural sciences, natural transformant, Evolution, Molecular, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Gene Expression Regulation, Plant, Tobacco, Genetics, Gene, Nicotiana otophora, Nicotiana, biology, vivipary, plast genes, fungi, Chromosome Mapping, food and beverages, Cell Biology, Agrobacterium tumefaciens, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, Molecular biology, Agrobacterium rhizogenes, Otophora, 030104 developmental biology, Seeds, cT-DNA, 010606 plant biology & botany
Abstract

Nicotiana otophora contains Agrobacterium-derived T-DNA sequences introduced by horizontal gene transfer (Chen et al., 2014). Sixty-nine contigs were assembled into four different cellular T-DNAs (cT-DNAs) totalling 83 kb. TC and TE result from two successive transformation events, each followed by duplication, yielding two TC and two TE inserts. TC is also found in other Nicotiana species, whereas TE is unique to N. otophora. Both cT-DNA regions are partially duplicated inverted repeats. Analysis of the cT-DNA divergence patterns allowed reconstruction of the evolution of the TC and TE regions. TC and TE carry 10 intact open reading frames. Three of these are TE-6b genes, derived from a single 6b gene carried by the Agrobacterium strain which inserted TE in the N. otophora ancestor. 6b genes have so far only been found in Agrobacterium tumefaciens or Agrobacterium vitis T-DNAs and strongly modify plant growth (Chen and Otten, 2016). The TE-6b genes were expressed in Nicotiana tabacum under the constitutive 2 × 35S promoter. TE-1-6b-R and TE-2-6b led to shorter plants, dark-green leaves, a strong increase in leaf vein development and modified petiole wings. TE-1-6b-L expression led to a similar phenotype, but in addition leaves show outgrowths at the margins, flowers were modified and plants became viviparous, i.e. embryos germinated in the capsules at an early stage of their development. Embryos could be rescued by culture in vitro. The TE-6b phenotypes are very different from the earlier described 6b phenotypes and could provide new insight into the mode of action of the 6b genes.

Published
2018
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14. Comparison of biofilm formation and motility processes in arsenic-resistant Thiomonas spp. strains revealed divergent response to arsenite

Author

Sandrine Koechler, Caroline Proux, Bernd Jagla, Aline Huber, Mathieu Erhardt, Hugo Varet, Marie-Agnès Dillies, Julien Farasin, Jean-Yves Coppée, Florence Arsène-Ploetze, Romain Briandet, Julien Deschamps, Géosciences Rennes (GR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Transcriptome et Epigénome (PF2), Institut Pasteur [Paris] (IP), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut de biologie moléculaire des plantes (IBMP), This work was supported by the Université de Strasbourg (UdS), the Centre National de la Recherche Scientifique (CNRS) and the Region Alsace to J.F. This study was financed by the THIOFILM (ANR-12-ADAP-0013) projects. Julien Farasin was supported by the Agence Nationale de la Recherche, ANR THIOFILM (ANR-12-ADAP-0013), ANR-12-ADAP-0013,THIOFILM,Rôle des biofilms dans l'adaptation et la variabilité génomique des bactéries du genre Thiomonas, impliqués dans les processus de remédiation naturelle dans les drainages miniers :(2012), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris], Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), and Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]

Subjects
0301 basic medicine, Arsenites, [SDV]Life Sciences [q-bio], 030106 microbiology, chemistry.chemical_element, Bioengineering, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Applied Microbiology and Biotechnology, Biochemistry, biofilm, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Bioremediation, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Drug Resistance, Bacterial, Extreme environment, Arsenic, ComputingMilieux_MISCELLANEOUS, Research Articles, Burkholderiales, Arsenite, biology, Gene Expression Profiling, Biofilm, Thiomonas, Special Issue Article, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, chemistry, Biofilms, Environmental Pollutants, Bacteria, Locomotion, Biotechnology
Abstract

Bacteria of the genus Thiomonas are found ubiquitously in arsenic contaminated waters such as acid mine drainage (AMD), where they contribute to the precipitation and the natural bioremediation of arsenic. In these environments, these bacteria have developed a large range of resistance strategies among which the capacity to form particular biofilm structures. The biofilm formation is one of the most ubiquitous adaptive response observed in prokaryotes to various stresses, such as those induced in the presence of toxic compounds. This study focused on the process of biofilm formation in three Thiomonas strains (CB1, CB2 and CB3) isolated from the same AMD. The results obtained here show that these bacteria are all capable of forming biofilms, but the architecture and the kinetics of formation of these biofilms differ depending on whether arsenite is present in the environment and from one strain to another. Indeed, two strains favoured biofilm formation, whereas one favoured motility in the presence of arsenite. To identify the underlying mechanisms, the patterns of expression of some genes possibly involved in the process of biofilm formation were investigated in Thiomonas sp. CB2 in the presence and absence of arsenite, using a transcriptomic approach (RNA-seq). The findings obtained here shed interesting light on how the formation of biofilms, and the motility processes contribute to the adaptation of Thiomonas strains to extreme environments.

Published
2017
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15. Erratum to: Multiple controls affect arsenite oxidase gene expression in Herminiimonas arsenicoxydans

Author

Odile Sismeiro, Florence Goulhen-Chollet, Philippe N. Bertin, Caroline Proux, Florence Hommais, Sandrine Koechler, Florence Arsène-Ploetze, Jean-Yves Coppé, Didier Lièvremont, Marie-Agnès Dillies, Jessica Cleiss-Arnold, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Microbiologie, adaptation et pathogénie (MAP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Chromatine et Régulation de la Pathogénie bactérienne (CRP), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Dynamique, évolution et expression de génomes de microorganismes (DEEGM), and Rodrigue, Agnès

Subjects
0301 basic medicine, Microbiology (medical), Transcription, Genetic, Arsenites, [SDV]Life Sciences [q-bio], 030106 microbiology, Arsenite oxidase, Molecular Sequence Data, lcsh:QR1-502, Microbiology, lcsh:Microbiology, 03 medical and health sciences, Bacterial Proteins, Oxalobacteraceae, Gene expression, Operon, Amino Acid Sequence, Herminiimonas arsenicoxydans, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Conserved Sequence, ComputingMilieux_MISCELLANEOUS, biology, Base Sequence, Gene Expression Profiling, Quorum Sensing, [SDV.EE.IEO] Life Sciences [q-bio]/Ecology, environment/Symbiosis, Gene Expression Regulation, Bacterial, biology.organism_classification, [SDV] Life Sciences [q-bio], [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Parasitology, Genes, Bacterial, Mutation, Erratum, Oxidoreductases, Sequence Alignment, Metabolic Networks and Pathways, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Both the speciation and toxicity of arsenic are affected by bacterial transformations, i.e. oxidation, reduction or methylation. These transformations have a major impact on environmental contamination and more particularly on arsenic contamination of drinking water. Herminiimonas arsenicoxydans has been isolated from an arsenic- contaminated environment and has developed various mechanisms for coping with arsenic, including the oxidation of As(III) to As(V) as a detoxification mechanism.In the present study, a differential transcriptome analysis was used to identify genes, including arsenite oxidase encoding genes, involved in the response of H. arsenicoxydans to As(III). To get insight into the molecular mechanisms of this enzyme activity, a Tn5 transposon mutagenesis was performed. Transposon insertions resulting in a lack of arsenite oxidase activity disrupted aoxR and aoxS genes, showing that the aox operon transcription is regulated by the AoxRS two-component system. Remarkably, transposon insertions were also identified in rpoN coding for the alternative N sigma factor (sigma54) of RNA polymerase and in dnaJ coding for the Hsp70 co-chaperone. Western blotting with anti-AoxB antibodies and quantitative RT-PCR experiments allowed us to demonstrate that the rpoN and dnaJ gene products are involved in the control of arsenite oxidase gene expression. Finally, the transcriptional start site of the aoxAB operon was determined using rapid amplification of cDNA ends (RACE) and a putative -12/-24 sigma54-dependent promoter motif was identified upstream of aoxAB coding sequences.These results reveal the existence of novel molecular regulatory processes governing arsenite oxidase expression in H. arsenicoxydans. These data are summarized in a model that functionally integrates arsenite oxidation in the adaptive response to As(III) in this microorganism.

Published
2017

16. Metagenomic insights into microbial metabolism affecting arsenic dispersion in Mediterranean marine sediments

Author

Fabienne Battaglia-Brunet, Frédéric Plewniak, Benjamin Navet, Olivier Bouchez, Sandrine Koechler, Pierre Peyret, Philippe N. Bertin, Fabienne Séby, Eric Dugat-Bony, Génétique moléculaire, génomique, microbiologie (GMGM), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Laboratoire de Génétique Cellulaire (LGC), 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-Institut National de la Recherche Agronomique (INRA), Ultra Traces Analyses Aquitaine (UT2A), Ultra Traces Analyses Aquitaine, Bureau de Recherches Géologiques et Minières (BRGM) (BRGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), This work was supported by the Agence Nationale de la Recherche (ANR-2008-CESA-003), the Centre National de la Recherche Scientifique (CNRS) in the frame of the ‘Groupement de Recherche—Métabolisme de l'Arsenic chez les Microorganismes (GDR2909-CNRS)’ (http://gdr2909.alsace.cnrs.fr/) and the Université de Strasbourg (UdS)., and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
Geologic Sediments, Biogeochemical cycle, Microorganism, Microbial metabolism, arsenic pollution, chemistry.chemical_element, Biology, Arsenic, 03 medical and health sciences, chemistry.chemical_compound, Proteobacteria, Mediterranean Sea, Genetics, Water Pollutants, 14. Life underwater, metagenomic, Water pollution, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Sulfur-Reducing Bacteria, Sulfates, 030306 microbiology, Ecology, Arsenate, marine sediment, Sequence Analysis, DNA, 6. Clean water, microbial metabolism, Gene Ontology, chemistry, Microbial population biology, Genes, Bacterial, 13. Climate action, Metagenomics, Metagenome, France
Abstract

Chantier qualité GA; International audience; Microorganisms dwelling in sediments have a crucial role in biogeochemical cycles and are expected to have a strong influence on the cycle of arsenic, a metalloid responsible for severe water pollution and presenting major health risks for human populations. We present here a metagenomic study of the sediment from two harbours on the Mediterranean French coast, l'Estaque and St Mandrier. The first site is highly polluted with arsenic and heavy metals, while the arsenic concentration in the second site is below toxicity levels. The goal of this study was to elucidate the potential impact of the microbial community on the chemical parameters observed in complementary geochemical studies performed on the same sites. The metagenomic sequences, along with those from four publicly available metagenomes used as control data sets, were analysed with the RAMMCAP workflow. The resulting functional profiles were compared to determine the over-represented Gene Ontology categories in the metagenomes of interest. Categories related to arsenic resistance and dissimilatory sulphate reduction were over-represented in l'Estaque. More importantly, despite very similar profiles, the identification of specific sequence markers for sulphate-reducing bacteria and sulphur-oxidizing bacteria showed that sulphate reduction was significantly more associated with l'Estaque than with St Mandrier. We propose that biotic sulphate reduction, arsenate reduction and fermentation may together explain the higher mobility of arsenic observed in l'Estaque in previous physico-chemical studies of this site. This study also demonstrates that it is possible to draw sound conclusions from comparing complex and similar unassembled metagenomes at the functional level, even with very low sequence coverage

Published
2013
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17. Subinhibitory Arsenite Concentrations Lead to Population Dispersal in Thiomonas sp

Author

Romain Briandet, Philippe N. Bertin, Marie Marchal, David Halter, Michael Dubow, Marie-Claire Lett, Sandrine Koechler, Institut de génétique et microbiologie [Orsay] (IGM), and Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Microorganism, Applied Microbiology, Microbial metabolism, Colony Count, Microbial, lcsh:Medicine, biofilm, chemistry.chemical_compound, stress, viabilité, Nucleic Acids, Molecular Cell Biology, souche, Extreme environment, lcsh:Science, Arsenite, Cellular Stress Responses, 0303 health sciences, education.field_of_study, Multidisciplinary, tolerance, biology, Polysaccharides, Bacterial, Microbial Growth and Development, Thiomonas, Betaproteobacteria, Extracellular Matrix, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, bioremediation, metabolism, viability, strains, oxidation, cell, Research Article, Arsenites, Movement, Population, Microbiology, Microbial Ecology, 03 medical and health sciences, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, education, métabolisme, Biology, 030304 developmental biology, 030306 microbiology, tolérance, lcsh:R, Biofilm, oxydation, biology.organism_classification, bioremédiation, chemistry, 13. Climate action, Biofilms, Biological dispersal, lcsh:Q, cellule
Abstract

International audience; Biofilms represent the most common microbial lifestyle, allowing the survival of microbial populations exposed to harsh environmental conditions. Here, we show that the biofilm development of a bacterial species belonging to the Thiomonas genus, frequently found in arsenic polluted sites and playing a key role in arsenic natural remediation, is markedly modified when exposed to subinhibitory doses of this toxic element. Indeed, arsenite [As(III)] exposure led to a considerable impact on biofilm maturation by strongly increasing the extracellular matrix synthesis and by promoting significant cell death and lysis within microcolonies. These events were followed by the development of complex 3D-biofilm structures and subsequently by the dispersal of remobilized cells observed inside the previously formed hollow voids. Our results demonstrate that this biofilm community responds to arsenite stress in a multimodal way, enhancing both survival and dispersal. Addressing this complex bacterial response to As(III) stress, which might be used by other microorganisms under various adverse conditions, may be essential to understand how Thiomonas strains persist in extreme environments.

Published
2011
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18. Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta-and proteo-genomics

Author

Odile Bruneel, Denis Le Paslier, Damien Mornico, Eric Pelletier, Adam Alexander T. Smith, Béatrice Chane-Woon-Ming, Philippe N. Bertin, Sandrine Koechler, Robert Duran, Florence Goulhen-Chollet, Sebastien Gallien, Marie Marchal, Florence Arsène-Ploetze, David Vallenet, Corinne Casiot, Alexandra Calteau, Jean Weissenbach, Nuria Fonknechten, Jessica Cleiss-Arnold, Christine Schaeffer, Béatrice Lauga, Violaine Bonnefoy, Ludovic Giloteaux, Claudine Médigue, Alain Van Dorsselaer, David Halter, Audrey Heinrich-Salmeron, Françoise Elbaz-Poulichet, Génétique moléculaire, génomique, microbiologie (GMGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), Hydrosciences Montpellier (HSM), 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), 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)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale et microbiologie (IBSM), Université de la Méditerranée - Aix-Marseille 2-Université Paul Cézanne - Aix-Marseille 3-Université de Provence - Aix-Marseille 1-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux (IPREM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), UMR 7156 Génétique Moléculaire, Génomique et Microbiologie, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA), Laboratoire de spectrométrie de masse bioorganique, Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de Masse BioOrganique, Département des Sciences Analytiques, Institut Pluridisciplinaire Hubert Curien, Strasbourg, France (LSMBO-DSA-IPHC), 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), Université de Strasbourg (UNISTRA)-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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), 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), Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), 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), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), and Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Proteomics, Iron, Microorganism, Microbial metabolism, Genomics, functional ecology, Microbiology, Mining, Arsenic, 03 medical and health sciences, uncultured microorganism, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, bacterial phylum, Phylogenetics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], extreme environment, Herminiimonas arsenicoxydans, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), Ecosystem, Phylogeny, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, synecology, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, 0303 health sciences, Bacteria, biology, Reverse Transcriptase Polymerase Chain Reaction, 030306 microbiology, Phylum, Ecology, microbial genomics, 15. Life on land, biology.organism_classification, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 13. Climate action, Metagenomics, Candidatus, Original Article, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Sulfur
Abstract

International audience; By their metabolic activities, microorganisms have a crucial role in the biogeochemical cycles of elements. The complete understanding of these processes requires, however, the deciphering of both the structure and the function, including synecologic interactions, of microbial communities. Using a metagenomic approach, we demonstrated here that an acid mine drainage highly contaminated with arsenic is dominated by seven bacterial strains whose genomes were reconstructed. Five of them represent yet uncultivated bacteria and include two strains belonging to a novel bacterial phylum present in some similar ecosystems, and which was named 'Candidatus Fodinabacter communificans.' Metaproteomic data unravelled several microbial capabilities expressed in situ, such as iron, sulfur and arsenic oxidation that are key mechanisms in biomineralization, or organic nutrient, amino acid and vitamin metabolism involved in synthrophic associations. A statistical analysis of genomic and proteomic data and reverse transcriptase-PCR experiments allowed us to build an integrated model of the metabolic interactions that may be of prime importance in the natural attenuation of such anthropized ecosystems.

Published
2011
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19. Effect of arsenite on swimming motility delays surface colonization in Herminiimonas arsenicoxydans

Author

Sandrine Koechler, Marie Marchal, B. Kammerer, Philippe N. Bertin, Romain Briandet, UMR 7156 Génétique Moléculaire, Génomique et Microbiologie, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, ANR COBIAS project, Groupement de Recherche - Metabolisme de l'Arsenic chez les Microorganismes GDR2909-CNRS, Génétique moléculaire, génomique, microbiologie (GMGM), and Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Arsenites, [SDV]Life Sciences [q-bio], Mutant, chemistry.chemical_element, Motility, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Oxalobacteraceae, Herminiimonas arsenicoxydans, Arsenic, 030304 developmental biology, Arsenite, 0303 health sciences, Microscopy, Confocal, biology, 030306 microbiology, Biofilm, Arsenate, biology.organism_classification, Cell biology, chemistry, Biofilms, Oxidoreductases, Oxidation-Reduction, Bacteria
Abstract

Herminiimonas arsenicoxydans is a Gram-negative bacterium able to detoxify arsenic-contaminated environments by oxidizing arsenite [As(III)] to arsenate [As(V)] and by scavenging arsenic ions in an extracellular matrix. Its motility and colonization behaviour have been previously suggested to be influenced by arsenite. Using time-course confocal laser scanning microscopy, we investigated its biofilm development in the absence and presence of arsenite. Arsenite was shown to delay biofilm initiation in the wild-type strain; this was partly explained by its toxicity, which caused an increased growth lag time. However, this delayed adhesion step in the presence of arsenite was not observed in either a swimming motility defective fliL mutant or an arsenite oxidase defective aoxB mutant; both strains displayed the wild-type surface properties and growth capacities. We propose that during the biofilm formation process arsenite acts on swimming motility as a result of the arsenite oxidase activity, preventing the switch between planktonic and sessile lifestyles. Our study therefore highlights the existence, under arsenite exposure, of a competition between swimming motility, resulting from arsenite oxidation, and biofilm initiation.

Published
2010
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20. Temporal transcriptomic response during arsenic stress in Herminiimonas arsenicoxydans

Author

Jean-Yves Coppée, Marie-Laure Fardeau, Marie-Agnès Dillies, Jessica Cleiss-Arnold, Philippe N. Bertin, Caroline Proux, Florence Arsène-Ploetze, Sandrine Koechler, 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] (IP), Laboratoire de Microbiologie IRD, JCA was supported by a grant from the French Ministry of Education and Research. Financial support came from the Centre National de la Recherche Scientifique, the Agence Nationale de la Recherche (ANR 07-BLAN-0118 project) and the Université de Strasbourg. This work was done in the frame of the Groupement de Recherche (GDR2909-CNRS): ' Métabolisme de l'Arsenic chez les Micro-organismes'., ANR-07-BLAN-0118,RARE,Reactivity of an arsenic-rich ecosystem: an integrated genomics approach(2007), and Institut Pasteur [Paris]

Subjects
inorganic chemicals, Time Factors, Transcription, Genetic, lcsh:QH426-470, Movement, lcsh:Biotechnology, Sulfur metabolism, chemistry.chemical_element, medicine.disease_cause, Arsenic, Transcriptome, 03 medical and health sciences, Bacterial Proteins, Stress, Physiological, Oxalobacteraceae, lcsh:TP248.13-248.65, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Gene expression, medicine, Genetics, Cluster Analysis, Herminiimonas arsenicoxydans, 030304 developmental biology, 0303 health sciences, biology, 030306 microbiology, Gene Expression Profiling, Gene Expression Regulation, Bacterial, Metabolism, biology.organism_classification, Molecular biology, Kinetics, lcsh:Genetics, chemistry, Biochemistry, Oxidation-Reduction, Oxidative stress, Bacteria, Research Article, Biotechnology
Abstract

Background Arsenic is present in numerous ecosystems and microorganisms have developed various mechanisms to live in such hostile environments. Herminiimonas arsenicoxydans, a bacterium isolated from arsenic contaminated sludge, has acquired remarkable capabilities to cope with arsenic. In particular our previous studies have suggested the existence of a temporal induction of arsenite oxidase, a key enzyme in arsenic metabolism, in the presence of As(III). Results Microarrays were designed to compare gene transcription profiles under a temporal As(III) exposure. Transcriptome kinetic analysis demonstrated the existence of two phases in arsenic response. The expression of approximatively 14% of the whole genome was significantly affected by an As(III) early stress and 4% by an As(III) late exposure. The early response was characterized by arsenic resistance, oxidative stress, chaperone synthesis and sulfur metabolism. The late response was characterized by arsenic metabolism and associated mechanisms such as phosphate transport and motility. The major metabolic changes were confirmed by chemical, transcriptional, physiological and biochemical experiments. These early and late responses were defined as general stress response and specific response to As(III), respectively. Conclusion Gene expression patterns suggest that the exposure to As(III) induces an acute response to rapidly minimize the immediate effects of As(III). Upon a longer arsenic exposure, a broad metabolic response was induced. These data allowed to propose for the first time a kinetic model of the As(III) response in bacteria.

Published
2010
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21. Multiple controls affect arsenite oxidase gene expression in Herminiimonas arsenicoxydans

Author

Didier Lièvremont, Jessica Cleiss-Arnold, Philippe N. Bertin, Florence Arsène-Ploetze, Odile Sismeiro, Sandrine Koechler, Jean-Yves Coppée, Florence Hommais, Caroline Proux, Marie-Agnès Dillies, Florence Goulhen-Chollet, 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], 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), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Financial support came from the Centre National de la Recherche Scientifique, the Agence Nationale de la Recherche (ANR 07-BLAN-0118 project) and the Université de Strasbourg., ANR-07-BLAN-0118,RARE,Reactivity of an arsenic-rich ecosystem: an integrated genomics approach(2007), and Institut Pasteur [Paris] (IP)

Subjects
Microbiology (medical), MESH: Operon, MESH: Mutation, Operon, MESH: Oxalobacteraceae, lcsh:QR1-502, MESH: Sequence Alignment, MESH: Amino Acid Sequence, MESH: Base Sequence, Microbiology, MESH: Quorum Sensing, lcsh:Microbiology, 03 medical and health sciences, chemistry.chemical_compound, MESH: Gene Expression Profiling, Sigma factor, Gene expression, Research article, MESH: Oxidoreductases, Herminiimonas arsenicoxydans, Gene, MESH: Bacterial Proteins, 030304 developmental biology, Arsenite, Genetics, 0303 health sciences, MESH: Gene Expression Regulation, Bacterial, MESH: Conserved Sequence, MESH: Molecular Sequence Data, biology, 030306 microbiology, MESH: Transcription, Genetic, biology.organism_classification, 3. Good health, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, MESH: Metabolic Networks and Pathways, rpoN, Transposon mutagenesis, MESH: Arsenites, MESH: Genes, Bacterial
Abstract

Background Both the speciation and toxicity of arsenic are affected by bacterial transformations, i.e. oxidation, reduction or methylation. These transformations have a major impact on environmental contamination and more particularly on arsenic contamination of drinking water. Herminiimonas arsenicoxydans has been isolated from an arsenic- contaminated environment and has developed various mechanisms for coping with arsenic, including the oxidation of As(III) to As(V) as a detoxification mechanism. Results In the present study, a differential transcriptome analysis was used to identify genes, including arsenite oxidase encoding genes, involved in the response of H. arsenicoxydans to As(III). To get insight into the molecular mechanisms of this enzyme activity, a Tn5 transposon mutagenesis was performed. Transposon insertions resulting in a lack of arsenite oxidase activity disrupted aoxR and aoxS genes, showing that the aox operon transcription is regulated by the AoxRS two-component system. Remarkably, transposon insertions were also identified in rpoN coding for the alternative N sigma factor (σ54) of RNA polymerase and in dnaJ coding for the Hsp70 co-chaperone. Western blotting with anti-AoxB antibodies and quantitative RT-PCR experiments allowed us to demonstrate that the rpoN and dnaJ gene products are involved in the control of arsenite oxidase gene expression. Finally, the transcriptional start site of the aoxAB operon was determined using rapid amplification of cDNA ends (RACE) and a putative -12/-24 σ54-dependent promoter motif was identified upstream of aoxAB coding sequences. Conclusion These results reveal the existence of novel molecular regulatory processes governing arsenite oxidase expression in H. arsenicoxydans. These data are summarized in a model that functionally integrates arsenite oxidation in the adaptive response to As(III) in this microorganism.

Published
2010
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22. Enhanced structural and functional genome elucidation of the arsenite-oxidizing strain Herminiimonas arsenicoxydans by proteomics data

Author

Christine Carapito, Michaël Heymann, Sandrine Koechler, Philippe N. Bertin, Evelyne Turlin, Claudine Médigue, Alain Van Dorsselaer, Valérie Kugler, Florence Arsène-Ploetze, Stéphanie Weiss, Stéphane Cruveiller, Magalie Stauffert, Jessica Cleiss, Jean-Yves Coppée, Génétique moléculaire, génomique, microbiologie (GMGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Génétique des Génomes Bactériens, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Puces à ADN (Plate-Forme 2) (PF2), Institut Pasteur [Paris] (IP), Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut Gilbert-Laustriat : Biomolécules, Biotechnologie, Innovation Thérapeutique, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Compartimentation et dynamique cellulaires (CDC), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Curie [Paris]-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Institut Pasteur [Paris], Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC), Laboratoire de Spectrométrie de masse Bio-organique, UMR CNRS-ULP, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), and Centre National de la Recherche Scientifique (CNRS)-Institut Curie-Université Pierre et Marie Curie - Paris 6 (UPMC)

Subjects
Proteomics, Proteome, Arsenites, Biology, Tandem mass spectrometry, Models, Biological, Biochemistry, Transcriptome, 03 medical and health sciences, chemistry.chemical_compound, Oxalobacteraceae, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Herminiimonas arsenicoxydans, 030304 developmental biology, Arsenite, Genetics, Gel electrophoresis, 0303 health sciences, 030306 microbiology, General Medicine, Genome project, biology.organism_classification, chemistry, Oxidation-Reduction, Genome, Bacterial
Abstract

International audience; The arsenite-oxidizing strain Herminiimonas arsenicoxydans proteome was investigated with gel electrophoresis and tandem mass spectrometry analyses. The comparison of experimental and theoretical M(r) and pI, as well as that of peptide sequences identified by MS and predicted protein sequences, allowed the correction of five protein annotations. More importantly, the functional analysis of SDS- and 2D-PAGE proteome maps obtained in the presence of arsenic, combined with partial transcriptomic results indicate that H. arsenicoxydans expressed genes and proteins required not only for arsenic detoxification or stress response but also involved in motility, exopolysaccharide synthesis, phosphate import or energetic metabolism. This study provides therefore new insights into the adaptation processes of H. arsenicoxydans in response to arsenic.

Published
2009
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23. A tale of two oxidation states: bacterial colonization of arsenic-rich environments

Author

Caroline Dossat, Barbara Schoepp, Jean Weissenbach, Yuko Makita, Valérie Barbe, Patricia Siguier, Béatrice Segurens, Michael Chandler, Wolfgang Nitschke, Sophie Mangenot, Zoé Rouy, Stéphanie Weiss, David Vallenet, Benoit Cournoyer, Diliana D. Simeonova, Philippe Ortet, Antoine Danchin, Florence Arsène-Ploetze, Sandrine Koechler, Christine Carapito, Mohamed Barakat, Evelyne Krin, Didier Lièvremont, Daniel Muller, Emmanuelle Leize, Simon Duval, Philippe N. Bertin, Marie-Claire Lett, Nicolas Perdrial, Michaël Heymann, Stéphane Cruveiller, Aurélie Lieutaud, Violaine Bonnefoy, Evelyne Turlin, Claudine Médigue, Emmanuel Talla, Alain Van Dorsselaer, Génétique moléculaire, génomique, microbiologie (GMGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes (LEMIRE), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Génétique des Génomes Bactériens, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pluridisciplinaire Hubert Curien (IPHC), Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Centre de géochimie de la surface (CGS), Centre National de la Recherche Scientifique (CNRS)-Université Louis Pasteur - Strasbourg I-Institut national des sciences de l'Univers (INSU - CNRS), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Génétique moléculaire, génomique, microbiologie ( GMGM ), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique ( CNRS ), Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes ( LEMIRE ), Université de la Méditerranée - Aix-Marseille 2-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de chimie bactérienne ( LCB ), Aix Marseille Université ( AMU ) -Centre National de la Recherche Scientifique ( CNRS ), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Institut Pluridisciplinaire Hubert Curien ( IPHC ), Laboratoire de microbiologie et génétique moléculaires ( LMGM ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Centre de géochimie de la surface ( CGS ), Institut national des sciences de l'Univers ( INSU - CNRS ) -Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique ( CNRS ), Structure et évolution des génomes ( SEG ), and CNS-Université d'Évry-Val-d'Essonne ( UEVE ) -Centre National de la Recherche Scientifique ( CNRS )

Subjects
MESH: Oxidation-Reduction, Cancer Research, Drug Resistance, MESH : Models, Biological, QH426-470, MESH : Carbon, MESH : Drug Resistance, Bacterial, MESH: Genome, Bacterial, Arsenic, Bacteria, Biodegradation, Environmental, Carbon, Bacterial, Energy Metabolism, Genome, Metals, Models, Biological, Oxidation-Reduction, Phylogeny, MESH: Biodegradation, Environmental, 0302 clinical medicine, Herminiimonas arsenicoxydans, MESH: Phylogeny, ComputingMilieux_MISCELLANEOUS, Genetics (clinical), 0303 health sciences, Ecology, MESH: Energy Metabolism, MESH : Arsenic, 6. Clean water, Biodegradation, Environmental, Research Article, inorganic chemicals, MESH : Biodegradation, Environmental, MESH : Genome, Bacterial, Energy metabolism, chemistry.chemical_element, MESH: Carbon, Biology, Genomic databases, Microbiology, Models, Biological, 03 medical and health sciences, Bacterial colonization, Bioremediation, Drug Resistance, Bacterial, MESH: Arsenic, MESH: Drug Resistance, Bacterial, SDV:BBM, Genetics, MESH : Bacteria, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, MESH : Oxidation-Reduction, MESH: Metals, 030306 microbiology, MESH : Metals, MESH: Models, Biological, MESH : Phylogeny, Computational Biology, Oxidation reduction, Genetics and Genomics, biology.organism_classification, Archaea, MESH : Energy Metabolism, Eubacteria, MESH: Bacteria, Positive chemotaxis, chemistry, 13. Climate action, Genome, Bacterial, 030217 neurology & neurosurgery
Abstract

Microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. Finding a means of preserving natural environments—including ground and surface waters—from arsenic constitutes a major challenge facing modern society. Although this metalloid is ubiquitous on Earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. In-depth exploration of the genome of the β-proteobacterium Herminiimonas arsenicoxydans with regard to physiology, genetics, and proteomics, revealed that it possesses heretofore unsuspected mechanisms for coping with arsenic. Aside from multiple biochemical processes such as arsenic oxidation, reduction, and efflux, H. arsenicoxydans also exhibits positive chemotaxis and motility towards arsenic and metalloid scavenging by exopolysaccharides. These observations demonstrate the existence of a novel strategy to efficiently colonize arsenic-rich environments, which extends beyond oxidoreduction reactions. Such a microbial mechanism of detoxification, which is possibly exploitable for bioremediation applications of contaminated sites, may have played a crucial role in the occupation of ancient ecological niches on earth., Author Summary Microorganisms play a crucial role in nutrient biogeochemical cycles. Arsenic is found throughout the environment from both natural and anthropogenic sources. Its inorganic forms are highly toxic and impair the physiology of most higher organisms. Arsenic contamination of groundwater supplies is giving rise to increasingly severe human health problems in both developing and industrial countries. In the present work, we investigated the metabolism of this metalloid in Herminiimonas arsenicoxydans, a representative organism of a novel bacterial genus widespread in aquatic environments. Examination of the genome sequence and experimental evidence revealed that it is remarkably capable of coping with arsenic. Our observations support the existence of multiple strategies allowing arsenic-metabolizing microbes to efficiently colonize toxic environments. In particular, arsenic oxidation and scavenging may have played a crucial role in the development of early stages of life on Earth. Such mechanisms may one day be exploited as part of a potential bioremediation strategy in toxic environments.

Published
2007
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24. Identification of genes and proteins involved in the pleiotropic response to arsenic stress in Caenibacter arsenoxydans, a metalloresistant beta-proteobacterium with an unsequenced genome

Author

Emmanuelle Leize-Wagner, Sandrine Koechler, Evelyne Turlin, Christine Carapito, Philippe N. Bertin, Alain Van Dorsselaer, Antoine Danchin, Marie-Claire Lett, Daniel Muller, Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Laboratoire de Biologie Tumorale, CRLCC Paul Strauss, XLIM (XLIM), Université de Limoges (UNILIM)-Centre National de la Recherche Scientifique (CNRS), Génétique des Génomes Bactériens, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Génétique moléculaire, génomique, microbiologie (GMGM), Régulation de l'Expression Génétique (REG), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Compartimentation et dynamique cellulaires (CDC), Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC), Substances naturelles/chimie moléculaire, Université Louis Pasteur - Strasbourg I-Ecole européenne de chimie, polymères et matériaux [Strasbourg]-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de masse Bio-organique, UMR CNRS-ULP, Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Centre National de la Recherche Scientifique (CNRS)-Institut Curie-Université Pierre et Marie Curie - Paris 6 (UPMC), Institut Pluridisciplinaire Hubert Curien ( IPHC ), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), XLIM ( XLIM ), Université de Limoges ( UNILIM ) -Centre National de la Recherche Scientifique ( CNRS ), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Génétique moléculaire, génomique, microbiologie ( GMGM ), Régulation de l'Expression Génétique ( REG ), Sciences Analytiques et Interactions Ioniques et Biomoléculaires ( DSA-IPHC ), Compartimentation et dynamique cellulaires ( CDC ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -INSTITUT CURIE-Centre National de la Recherche Scientifique ( CNRS ), Université Louis Pasteur - Strasbourg I-Ecole européenne de chimie, polymères et matériaux [Strasbourg]-Centre National de la Recherche Scientifique ( CNRS ), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Curie [Paris]-Centre National de la Recherche Scientifique (CNRS)

Subjects
MESH : Molecular Sequence Data, MESH : RNA, Messenger, Messenger, Drug Resistance, MESH: Amino Acid Sequence, MESH : Drug Resistance, Bacterial, MESH: Genome, Bacterial, Biochemistry, Genome, chemistry.chemical_compound, MESH : Bacterial Proteins, MESH: Betaproteobacteria, Peptide sequence, MESH: Bacterial Proteins, MESH : Betaproteobacteria, Arsenite, Genetics, 0303 health sciences, MESH : Amino Acid Sequence, MESH : Genes, Bacterial, Bacterial, Betaproteobacteria, General Medicine, MESH : Arsenic, Metals, MESH: Genes, Bacterial, MESH : Genome, Bacterial, Molecular Sequence Data, chemistry.chemical_element, Biology, Arsenic, 03 medical and health sciences, Bacterial Proteins, Drug Resistance, Bacterial, MESH: Arsenic, MESH: Drug Resistance, Bacterial, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, RNA, Messenger, Amino Acid Sequence, Gene, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, 030304 developmental biology, MESH: RNA, Messenger, Two-dimensional gel electrophoresis, MESH: Metals, MESH: Molecular Sequence Data, 030306 microbiology, MESH : Metals, Arsenate, RNA, chemistry, Genes, Genes, Bacterial, Genome, Bacterial
Abstract

International audience; The effect of high concentrations of arsenic has been investigated in Caenibacter arsenoxydans, a beta-proteobacterium isolated from an arsenic contaminated environment and able to oxidize arsenite to arsenate. As the genome of this bacterium has not yet been sequenced, the use of a specific proteomic approach based on nano-high performance liquid chromatography tandem mass spectrometry (nanoLC-MS/MS) studies and de novo sequencing to perform cross-species protein identifications was necessary. In addition, a random mutational analysis was performed. Twenty-two proteins and 16 genes were shown to be differentially accumulated and expressed, respectively, in cells grown in the presence of arsenite. Two genes involved in arsenite oxidation and one in arsenite efflux as well as two proteins responsible for arsenate reduction were identified. Moreover, numerous genes and proteins belonging to various functional classes including information and regulation pathways, intermediary metabolism, cell envelope and cellular processes were also up- or down-regulated, which demonstrates that bacterial response to arsenic is pleiotropic.

Published
2006
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