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Andres J, Arsène-Ploetze F, Barbe V, Brochier-Armanet C, Cleiss-Arnold J, Coppée JY, Dillies MA, Geist L, Joublin A, Koechler S, Lassalle F, Marchal M, Médigue C, Muller D, Nesme X, Plewniak F, Proux C, Ramírez-Bahena MH, Schenowitz C, Sismeiro O, Vallenet D, Santini JM, Bertin PN. Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium rhizobium sp. NT-26. Genome Biol Evol 2013; 5:934-53. [PMID: 23589360 PMCID: PMC3673622 DOI: 10.1093/gbe/evt061] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Arsenic is widespread in the environment and its presence is a result of natural or anthropogenic activities. Microbes have developed different mechanisms to deal with toxic compounds such as arsenic and this is to resist or metabolize the compound. Here, we present the first reference set of genomic, transcriptomic and proteomic data of an Alphaproteobacterium isolated from an arsenic-containing goldmine: Rhizobium sp. NT-26. Although phylogenetically related to the plant-associated bacteria, this organism has lost the major colonizing capabilities needed for symbiosis with legumes. In contrast, the genome of Rhizobium sp. NT-26 comprises a megaplasmid containing the various genes, which enable it to metabolize arsenite. Remarkably, although the genes required for arsenite oxidation and flagellar motility/biofilm formation are carried by the megaplasmid and the chromosome, respectively, a coordinate regulation of these two mechanisms was observed. Taken together, these processes illustrate the impact environmental pressure can have on the evolution of bacterial genomes, improving the fitness of bacterial strains by the acquisition of novel functions.
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Affiliation(s)
- Jérémy Andres
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS Université de Strasbourg, Strasbourg, France
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3
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Bertin PN, Heinrich-Salmeron A, Pelletier E, Goulhen-Chollet F, Arsène-Ploetze F, Gallien S, Lauga B, Casiot C, Calteau A, Vallenet D, Bonnefoy V, Bruneel O, Chane-Woon-Ming B, Cleiss-Arnold J, Duran R, Elbaz-Poulichet F, Fonknechten N, Giloteaux L, Halter D, Koechler S, Marchal M, Mornico D, Schaeffer C, Smith AAT, Van Dorsselaer A, Weissenbach J, Médigue C, Le Paslier D. Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta- and proteo-genomics. ISME J 2011; 5:1735-47. [PMID: 21562598 PMCID: PMC3197163 DOI: 10.1038/ismej.2011.51] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 02/17/2011] [Accepted: 03/29/2011] [Indexed: 01/07/2023]
Abstract
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.
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Affiliation(s)
- Philippe N Bertin
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and UdS, Strasbourg, France.
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4
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Cleiss-Arnold J, Koechler S, Proux C, Fardeau ML, Dillies MA, Coppee JY, Arsène-Ploetze F, Bertin PN. Temporal transcriptomic response during arsenic stress in Herminiimonas arsenicoxydans. BMC Genomics 2010; 11:709. [PMID: 21167028 PMCID: PMC3022917 DOI: 10.1186/1471-2164-11-709] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 12/17/2010] [Indexed: 02/02/2023] Open
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.
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Affiliation(s)
- Jessica Cleiss-Arnold
- Département Microorganismes, UMR7156 Université de Strasbourg/CNRS, Génétique Moléculaire, Génomique et Microbiologie, 28 rue Goethe, 67083 Strasbourg cedex, France
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Arsène-Ploetze F, Koechler S, Marchal M, Coppée JY, Chandler M, Bonnefoy V, Brochier-Armanet C, Barakat M, Barbe V, Battaglia-Brunet F, Bruneel O, Bryan CG, Cleiss-Arnold J, Cruveiller S, Erhardt M, Heinrich-Salmeron A, Hommais F, Joulian C, Krin E, Lieutaud A, Lièvremont D, Michel C, Muller D, Ortet P, Proux C, Siguier P, Roche D, Rouy Z, Salvignol G, Slyemi D, Talla E, Weiss S, Weissenbach J, Médigue C, Bertin PN. Structure, function, and evolution of the Thiomonas spp. genome. PLoS Genet 2010; 6:e1000859. [PMID: 20195515 PMCID: PMC2829063 DOI: 10.1371/journal.pgen.1000859] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Accepted: 01/25/2010] [Indexed: 11/19/2022] Open
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.
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Affiliation(s)
- Florence Arsène-Ploetze
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université de Strasbourg, Strasbourg, France
| | - Sandrine Koechler
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université de Strasbourg, Strasbourg, France
| | - Marie Marchal
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université de Strasbourg, Strasbourg, France
| | - Jean-Yves Coppée
- Genopole, Plate-forme puces à ADN, Institut Pasteur, Paris, France
| | - Michael Chandler
- Laboratoire de Microbiologie et Génétique Moléculaire, UMR5100, Toulouse, France
| | - Violaine Bonnefoy
- Laboratoire de Chimie Bactérienne, UPR9043 CNRS, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Céline Brochier-Armanet
- Laboratoire de Chimie Bactérienne, UPR9043 CNRS, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Mohamed Barakat
- Institut de Biologie Environnementale et de Biotechnologie, CEA-CNRS-Université Aix-Marseille II, Saint-Paul-lez-Durance, France
| | - Valérie Barbe
- Institut de Génomique, CEA-DSV, Génoscope, Evry, France
| | | | - Odile Bruneel
- Laboratoire Hydrosciences Montpellier, UMR 5569 CNRS, IRD and Universités Montpellier I and II, Montpellier, France
| | - Christopher G. Bryan
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université de Strasbourg, Strasbourg, France
| | - Jessica Cleiss-Arnold
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université de Strasbourg, Strasbourg, France
| | - Stéphane Cruveiller
- Institut de Génomique, CEA-DSV, Génoscope, Evry, France
- Génomique Métabolique, Laboratoire de Génomique Comparative, CNRS UMR8030, Evry, France
| | - Mathieu Erhardt
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Audrey Heinrich-Salmeron
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université de Strasbourg, Strasbourg, France
| | - Florence Hommais
- Unité Microbiologie, Adaptation, Pathogénie, CNRS-INSA-UCB UMR 5240, Université Lyon 1, Villeurbanne, France
| | | | - Evelyne Krin
- Génétique des Génomes Bactériens, URA2171, Institut Pasteur, Paris, France
| | - Aurélie Lieutaud
- Laboratoire de Chimie Bactérienne, UPR9043 CNRS, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Didier Lièvremont
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université de Strasbourg, Strasbourg, France
| | - Caroline Michel
- Environnement et Procédés, Ecotechnologie, BRGM, Orléans, France
| | - Daniel Muller
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université de Strasbourg, Strasbourg, France
| | - Philippe Ortet
- Institut de Biologie Environnementale et de Biotechnologie, CEA-CNRS-Université Aix-Marseille II, Saint-Paul-lez-Durance, France
| | - Caroline Proux
- Genopole, Plate-forme puces à ADN, Institut Pasteur, Paris, France
| | - Patricia Siguier
- Laboratoire de Microbiologie et Génétique Moléculaire, UMR5100, Toulouse, France
| | - David Roche
- Institut de Génomique, CEA-DSV, Génoscope, Evry, France
- Génomique Métabolique, Laboratoire de Génomique Comparative, CNRS UMR8030, Evry, France
| | - Zoé Rouy
- Institut de Génomique, CEA-DSV, Génoscope, Evry, France
| | - Grégory Salvignol
- Génomique Métabolique, Laboratoire de Génomique Comparative, CNRS UMR8030, Evry, France
| | - Djamila Slyemi
- Laboratoire de Chimie Bactérienne, UPR9043 CNRS, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Emmanuel Talla
- Laboratoire de Chimie Bactérienne, UPR9043 CNRS, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Stéphanie Weiss
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université de Strasbourg, Strasbourg, France
| | - Jean Weissenbach
- Institut de Génomique, CEA-DSV, Génoscope, Evry, France
- Génomique Métabolique, Laboratoire de Génomique Comparative, CNRS UMR8030, Evry, France
| | - Claudine Médigue
- Institut de Génomique, CEA-DSV, Génoscope, Evry, France
- Génomique Métabolique, Laboratoire de Génomique Comparative, CNRS UMR8030, Evry, France
| | - Philippe N. Bertin
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université de Strasbourg, Strasbourg, France
- * E-mail:
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6
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Koechler S, Cleiss-Arnold J, Proux C, Sismeiro O, Dillies MA, Goulhen-Chollet F, Hommais F, Lièvremont D, Arsène-Ploetze F, Coppée JY, Bertin PN. Multiple controls affect arsenite oxidase gene expression in Herminiimonas arsenicoxydans. BMC Microbiol 2010; 10:53. [PMID: 20167112 PMCID: PMC2848651 DOI: 10.1186/1471-2180-10-53] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Accepted: 02/18/2010] [Indexed: 11/10/2022] Open
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 (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. 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.
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Affiliation(s)
- Sandrine Koechler
- UMR7156 Génétique Moléculaire, Génomique et Microbiologie, CNRS Université de Strasbourg, 28 rue Goethe, 67000 Strasbourg, France
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